PT	AU	BA	BE	GP	AF	BF	CA	TI	SO	SE	BS	LA	DT	CT	CY	CL	SP	HO	DE	ID	AB	C1	RP	EM	RI	OI	FU	FX	CR	NR	TC	Z9	U1	U2	PU	PI	PA	SN	EI	BN	J9	JI	PD	PY	VL	IS	PN	SU	SI	MA	BP	EP	AR	DI	D2	EA	EY	PG	WC	SC	GA	UT	PM	OA	HC	HP	DA
J	Mallott, EK; Malhi, RS; Garber, PA				Mallott, E. K.; Malhi, R. S.; Garber, P. A.			Brief Communication: High-Throughput Sequencing of Fecal DNA to Identify Insects Consumed by Wild Weddell's Saddleback Tamarins (Saguinus weddelli, Cebidae, Primates) in Bolivia	AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY			English	Article						pyrosequencing; metagenomics; faunivory; primates; feeding ecology	PREY DNA; MITOCHONDRIAL-DNA; ARTHROPOD PREY; FUSCICOLLIS; DIET; MYSTAX; FECES; MONKEYS; CHIMPANZEES; PREDATION	The genus Saguinus represents a successful radiation of over 20 species of small-bodied New World monkeys. Studies of the tamarin diet indicate that insects and small vertebrates account for approximate to 16-45% of total feeding and foraging time, and represent an important source of lipids, protein, and metabolizable energy. Although tamarins are reported to commonly consume large-bodied insects such as grasshoppers and walking sticks (Orthoptera), little is known concerning the degree to which smaller or less easily identifiable arthropod prey comprises an important component of their diet. To better understand tamarin arthropod feeding behavior, fecal samples from 20 wild Bolivian saddleback tamarins (members of five groups) were collected over a 3 week period in June 2012, and analyzed for the presence of arthropod DNA. DNA was extracted using a Qiagen stool extraction kit, and universal insect primers were created and used to amplify a approximate to 280 bp section of the COI mitochondrial gene. Amplicons were sequenced on the Roche 454 sequencing platform using high-throughput sequencing techniques. An analysis of these samples indicated the presence of 43 taxa of arthropods including 10 orders, 15 families, and 12 identified genera. Many of these taxa had not been previously identified in the tamarin diet. These results highlight molecular analysis of fecal DNA as an important research tool for identifying anthropod feeding patterns in primates, and reveal broad diversity in the taxa, foraging microhabitats, and size of arthropods consumed by tamarin monkeys. Am J Phys Anthropol 156:474-481, 2015. (c) 2014 Wiley Periodicals, Inc.	[Mallott, E. K.; Malhi, R. S.; Garber, P. A.] Univ Illinois, Dept Anthropol, Urbana, IL 61801 USA; [Malhi, R. S.] Univ Illinois, Inst Genom Biol, Urbana, IL 61801 USA	Mallott, EK (reprint author), Univ Illinois, Dept Anthropol, 109 Davenport Hall,607 S Mathews Ave, Urbana, IL 61801 USA.	mallott2@illinois.edu		Malhi, Ripan/0000-0002-1484-0292; Mallott, Elizabeth/0000-0001-5446-8563				61	11	11	2	33	WILEY-BLACKWELL	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0002-9483	1096-8644		AM J PHYS ANTHROPOL	Am. J. Phys. Anthropol.	MAR	2015	156	3					474	481		10.1002/ajpa.22654				8	Anthropology; Evolutionary Biology	Anthropology; Evolutionary Biology	CC3VE	WOS:000350277800013	25369770				22-11-18
J	Wallinger, C; Staudacher, K; Sint, D; Thalinger, B; Oehm, J; Juen, A; Traugott, M				Wallinger, Corinna; Staudacher, Karin; Sint, Daniela; Thalinger, Bettina; Oehm, Johannes; Juen, Anita; Traugott, Michael			Evaluation of an automated protocol for efficient and reliable DNA extraction of dietary samples	ECOLOGY AND EVOLUTION			English	Article						BioSprint; cetyltrimethylammonium bromide; DNA isolation; molecular gut content analysis; molecular scatology; trophic interactions	GUT-CONTENT-ANALYSIS; FOOD-WEB; MOLECULAR-DETECTION; SOIL INSECT; PCR ASSAYS; PREY; PREDATION; LINKS; PURIFICATION; SELECTION	Molecular techniques have become an important tool to empirically assess feeding interactions. The increased usage of next-generation sequencing approaches has stressed the need of fast DNA extraction that does not compromise DNA quality. Dietary samples here pose a particular challenge, as these demand high-quality DNA extraction procedures for obtaining the minute quantities of short-fragmented food DNA. Automatic high-throughput procedures significantly decrease time and costs and allow for standardization of extracting total DNA. However, these approaches have not yet been evaluated for dietary samples. We tested the efficiency of an automatic DNA extraction platform and a traditional CTAB protocol, employing a variety of dietary samples including invertebrate whole-body extracts as well as invertebrate and vertebrate gut content samples and feces. Extraction efficacy was quantified using the proportions of successful PCR amplifications of both total and prey DNA, and cost was estimated in terms of time and material expense. For extraction of total DNA, the automated platform performed better for both invertebrate and vertebrate samples. This was also true for prey detection in vertebrate samples. For the dietary analysis in invertebrates, there is still room for improvement when using the high-throughput system for optimal DNA yields. Overall, the automated DNA extraction system turned out as a promising alternative to labor-intensive, low-throughput manual extraction methods such as CTAB. It is opening up the opportunity for an extensive use of this cost-efficient and innovative methodology at low contamination risk also in trophic ecology.	[Wallinger, Corinna; Staudacher, Karin; Sint, Daniela; Thalinger, Bettina; Oehm, Johannes; Juen, Anita; Traugott, Michael] Univ Innsbruck, Inst Ecol, Mt Agr Res Unit, Innsbruck, Austria	Wallinger, C (reprint author), Univ Innsbruck, Inst Ecol, Mt Agr Res Unit, Innsbruck, Austria.	corinna.wallinger@uibk.ac.at		Sint, Daniela/0000-0003-3387-4284; Wallinger, Corinna/0000-0002-7153-9690; Traugott, Michael/0000-0001-9719-5059; Thalinger, Bettina/0000-0001-9315-8648	ERA-Net BiodivERsA; FORMAS; Austrian Science Fund [I786]	ERA-Net BiodivERsA; FORMAS; Austrian Science Fund, Grant/Award Number: I786		45	2	2	2	19	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	2045-7758			ECOL EVOL	Ecol. Evol.	AUG	2017	7	16					6382	6389		10.1002/ece3.3197				8	Ecology; Evolutionary Biology	Environmental Sciences & Ecology; Evolutionary Biology	FG1BQ	WOS:000409528000029	28861241	DOAJ Gold, Green Published			22-11-18
J	Wood, JR; Holdaway, RJ; Orwin, KH; Morse, C; Bonner, KI; Davis, C; Bolstridge, N; Dickie, IA				Wood, Jamie R.; Holdaway, Robert J.; Orwin, Kate H.; Morse, Chris; Bonner, Karen I.; Davis, Carina; Bolstridge, Nicola; Dickie, Ian A.			No single driver of biodiversity: divergent responses of multiple taxa across land use types	ECOSPHERE			English	Article						animals; bacteria; biodiversity; community structure; DNA metabarcoding; fungi; intensification; land use; plants; soil	AGRICULTURAL INTENSIFICATION; SPECIES RICHNESS; MICROBIAL COMMUNITIES; CONSISTENT RESPONSES; GLOBAL BIODIVERSITY; FUNGAL COMMUNITIES; PLANT DIVERSITY; SOIL-PH; CONSERVATION; ABUNDANCE	Understanding the responses of biodiversity to different land use regimes is critical for managing biodiversity in the face of future land use change. However, there is still significant uncertainty around how consistent the responses of different taxonomic groups to land use change are. Here, we use a combination of high-throughput environmental DNA sequencing and traditional field-based survey methods to examine how patterns of richness and community composition correlate among four domains/kingdoms (bacteria, fungi, plants, and metazoans) and the four most-abundant animal taxonomic groups (arachnids, Collembola, insects, and nematodes) across five different land use types (natural forest, planted forest, unimproved grassland, improved grassland, and vineyards). Richness for each taxonomic group varied between land use types, yet different taxa showed inconsistent responses to land use, and their richness was rarely correlated. This contrasted with community composition of taxonomic groups, for which there was relatively good discrimination of land use types and there was strong correlation between group responses. We found little evidence for consistent drivers of taxonomic richness, yet identified several significant drivers of community composition that were shared across many groups. Drivers of composition were not the same as the drivers of diversity, suggesting diversity and composition are independently controlled. While land use intensification has been viewed as having generally negative effects on biodiversity, our results provide evidence that different taxa respond divergently across different land uses. Further, our study demonstrates the power of high-throughput sequencing of environmental DNA as a tool for addressing broad ecological patterns relating to landscape biodiversity.	[Wood, Jamie R.; Holdaway, Robert J.; Orwin, Kate H.; Morse, Chris; Bonner, Karen I.; Davis, Carina; Bolstridge, Nicola] Landcare Res, POB 69040, Lincoln 7640, New Zealand; [Dickie, Ian A.] Univ Canterbury, Sch Biol Sci, Bioprotect Res Ctr, Private Bag 4800, Christchurch 8140, New Zealand	Wood, JR (reprint author), Landcare Res, POB 69040, Lincoln 7640, New Zealand.	woodj@landcareresearch.co.nz			New Zealand Ministry of Business, Innovation and Employment [PROP-29430-ESI-LCR]	This research was funded by the New Zealand Ministry of Business, Innovation and Employment (PROP-29430-ESI-LCR). K. Drew, E. Hayman, S. Kruis, H. Maule, and G. Walls provided field assistance, and D. Park assisted with DNA analyses. We thank the landowners of the study sites. P. Bellingham provided helpful comments on the manuscript. JRW, RJH, and IAD designed the study; RJH, CM, KIB, and IAD undertook fieldwork and sample collection; KHO, KIB, CD, and NB subsampled soil samples and performed function measurements; JRW, CD, and NB performed molecular analyses; RJH and IAD performed bioinformatic and statistical analyses; JRW, RJH, KHO, and IAD wrote the manuscript.		61	0	0	14	27	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	2150-8925			ECOSPHERE	Ecosphere	NOV	2017	8	11							e01997	10.1002/ecs2.1997				17	Ecology	Environmental Sciences & Ecology	FP0WV	WOS:000417330000013		DOAJ Gold			22-11-18
J	Blanckenhorn, WU; Rohner, PT; Bernasconi, MV; Haugstetter, J; Buser, A				Blanckenhorn, Wolf U.; Rohner, Patrick T.; Bernasconi, Marco V.; Haugstetter, Johannes; Buser, Andres			Is qualitative and quantitative metabarcoding of dung fauna biodiversity feasible?	ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY			English	Article						Biodiversity assessment; Barcode; Species detection; Survival; Taxonomic resolution	MITOCHONDRIAL-DNA SEQUENCES; INTERNATIONAL RING TEST; CHAIN-REACTION PRIMERS; VETERINARY PARASITICIDES; SCATHOPHAGIDAE DIPTERA; MOLECULAR SYSTEMATICS; IVERMECTIN RESIDUES; SPECIES-DIVERSITY; SEPSID FLIES; CATTLE DUNG	In biodiversity assessments, especially of small-bodied organisms for which taxonomic expertise is lacking, identification by genetic barcoding may be a cost-effective and efficient alternative to traditional identification of species by morphology, ecology, and behavior. The authors tested the feasibility and accuracy of such an approach using dung insects of practical relevance in ecotoxicological assessments of veterinary pharmaceutical residues in the environment. They produced 8 known mixtures that varied in absolute and relative composition of small-bodied and large-bodied species to see whether mitochondrial cytochrome c oxidase subunit 1 barcoding picks up all species qualitatively and quantitatively. As demonstrated before in other contexts, such metabarcoding of large numbers of dung insect specimens is principally possible using next-generation sequencing. The authors recovered most species in a sample (low type I error), at minimum permitting analysis of species richness. They obtained even quantitative responses reflecting the body size of the species, although the number of specimens was not well detected. The latter is problematic when calculating diversity indices. Nevertheless, the method yielded too many closely related false positives (type II error), thus generally overestimating species diversity and richness. These errors can be reduced by refining methods and data filtering, although this requires bioinformatics expertise often unavailable where such research is carried out. Identification by barcoding foremost hinges on a good reference database, which does not yet exist for dung organisms but would be worth developing for practical applications. Environ Toxicol Chem 2016;35:1970-1977. (c) 2015 SETAC	[Blanckenhorn, Wolf U.; Rohner, Patrick T.; Bernasconi, Marco V.] Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland; [Bernasconi, Marco V.] Nat Museum Luzern, Luzern, Switzerland; [Haugstetter, Johannes; Buser, Andres] Ecogen GmbH, Schlieren, Switzerland	Blanckenhorn, WU (reprint author), Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland.	wolf.blanckenhorn@ieu.uzh.ch		Rohner, Patrick T./0000-0002-9840-1050	SwissBOL; German Umweltbundesamt (UBA); University of Zurich	We thank SwissBOL for funding the present study and the German Umweltbundesamt (UBA) and the University of Zurich for additional funding and continuing support.		59	7	7	1	32	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0730-7268	1552-8618		ENVIRON TOXICOL CHEM	Environ. Toxicol. Chem.	AUG	2016	35	8					1970	1977		10.1002/etc.3275				8	Environmental Sciences; Toxicology	Environmental Sciences & Ecology; Toxicology	DR7CH	WOS:000380057100011	26450644				22-11-18
J	Zhang, F; Sun, XX; Zhang, XC; Zhang, S; Lu, J; Xia, YM; Huang, YH; Wang, XJ				Zhang, Fan; Sun, Xiao X.; Zhang, Xian C.; Zhang, Shuo; Lu, Jie; Xia, Yong M.; Huang, Yan H.; Wang, Xue J.			The interactions between gut microbiota and entomopathogenic fungi: a potential approach for biological control of Blattella germanica (L.)	PEST MANAGEMENT SCIENCE			English	Article						Blattella germanica; anti-entomopathogenic fungi assay; interactions; gut microbiota; biological control	FREE DESERT LOCUSTS; METARHIZIUM-ANISOPLIAE; BEAUVERIA-BASSIANA; SCHISTOCERCA-GREGARIA; DELPHACODES-KUSCHELI; INTESTINAL FLORA; GENOMIC ANALYSIS; DALBULUS-MAIDIS; BACTERIA; COCKROACH	BACKGROUNDMetarhizium anisopliae and Beauveria bassiana mainly infect insects through the cuticle; gut infection occasionally occurs. Micro-organisms existing in the gut may play a crucial role in the evolution and ecology of host defenses against fungal pathogens. To evaluate whether the gut bacteria participate in antifungal activity, and to determine their role in host protection, the interactions between gut bacteria and M. anisopliae and the diversity of gut microbiota in cockroaches were studied. RESULTSAn oral feeding test showed that the mortality of conventional cockroaches was significantly lower than that of germ-free cockroaches; both gut homogenates and aqueous fecal extracts showed antifungal activity, but the samples from germ-free cockroaches did not. Twenty-two bacterial strains with antifungal activity and siderophore-producing ability were isolated from the gut and feces of cockroaches. Using high-throughput sequencing techniques, a total of 23 different phyla and 212 genera were detected. The composition of the microbiota of the hindgut was vastly different from those of the foregut and midgut; higher diversity and abundance of Bacteroides and Pseudomonas were found in the hindgut. CONCLUSIONThe gut microbiota of German cockroaches may play a critical role in protecting cockroaches from fungal invasion and colonization. Removing certain bacteria from the B. germanica microbiota may facilitate microbial control using fungal pathogens. (c) 2017 Society of Chemical Industry	[Wang, Xue J.] Shandong Ctr Control & Prevent, 16992 Jingshi Rd, Jinan 250014, Shandong, Peoples R China; [Zhang, Fan; Sun, Xiao X.; Zhang, Xian C.; Zhang, Shuo; Lu, Jie; Xia, Yong M.] Shandong Normal Univ, Coll Life Sci, Key Lab Anim Resistance Biol Shandong Prov, Jinan, Shandong, Peoples R China; [Huang, Yan H.] Food & Fermentat Engn Key Lab Shandong Prov, Jinan, Shandong, Peoples R China	Wang, XJ (reprint author), Shandong Ctr Control & Prevent, 16992 Jingshi Rd, Jinan 250014, Shandong, Peoples R China.	zhangfan0531@163.com		Zhang, fan/0000-0002-3281-6325	National Natural Science Foundation of China [81572027]; Shandong Province Medical and Health Science and Technology Development Program [2009HW055]; Shandong Provincial Natural Science Foundation [ZR2012CQ040]	This study was supported by the National Natural Science Foundation of China (81572027), Shandong Province Medical and Health Science and Technology Development Program (2009HW055) and Shandong Provincial Natural Science Foundation (ZR2012CQ040).		60	1	1	19	47	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1526-498X	1526-4998		PEST MANAG SCI	Pest Manag. Sci.	FEB	2018	74	2					438	447		10.1002/ps.4726				10	Agronomy; Entomology	Agriculture; Entomology	FR9PX	WOS:000419406700022	28888066				22-11-18
J	Malacrino, A; Schena, L; Campolo, O; Laudani, F; Mosca, S; Giunti, G; Strano, CP; Palmeri, V				Malacrino, Antonino; Schena, Leonardo; Campolo, Orlando; Laudani, Francesca; Mosca, Saveria; Giunti, Giulia; Strano, Cinzia Patricia; Palmeri, Vincenzo			A Metabarcoding Survey on the Fungal Microbiota Associated to the Olive Fruit Fly	MICROBIAL ECOLOGY			English	Article						454 Pyrosequencing; High-throughput sequencing; Bactrocera oleae; Cladosporium; Colletotrichum; Pseudocercospora	PARASITOID PSYTTALIA-CONCOLOR; BIOLOGICAL-CONTROL; BACTROCERA-OLEAE; ABUNDANCE DISTRIBUTIONS; MOLECULAR ANALYSIS; HIGH-THROUGHPUT; ANTHRACNOSE; COMMUNITIES; TREE; DIVERSITY	The occurrence of interaction between insects and fungi is interesting from an ecological point of view, particularly when these interactions involve insect pests and plant pathogens within an agroecosystem. In this study, we aimed to perform an accurate analysis on the fungal microbiota associated to Bactrocera oleae (Rossi) through a metabarcoding approach based on 454 pyrosequencing. From this analysis, we retrieved 43,549 reads that clustered into 128 operational taxonomic units (OTUs), of which 29 resulted in the "core" associate fungi of B. oleae. This fungal communitywasmainly represented by sooty mould fungi, such as Cladosporium spp., Alternaria spp. and Aureobasidium spp., by plant pathogens like Colletotrichum spp. and Pseudocercospora spp., along with several other less abundant taxa whose ecology is unclear in most of the cases. Our findings lead to new insights into the microbial ecology of this specific ecological niche, enabling the understanding of a complex network of interactions within the olive agroecosystem.	[Malacrino, Antonino; Schena, Leonardo; Campolo, Orlando; Laudani, Francesca; Mosca, Saveria; Giunti, Giulia; Strano, Cinzia Patricia; Palmeri, Vincenzo] Univ Mediterranea Reggio Calabria, Dipartimento Agr, Reggio Di Calabria, Italy; [Malacrino, Antonino] Univ Palermo, Dipartimento Sci Agr & Forestali, Palermo, Italy	Schena, L (reprint author), Univ Mediterranea Reggio Calabria, Dipartimento Agr, Reggio Di Calabria, Italy.	lschena@unirc.it	Schena, Leonardo/A-7492-2018; Malacrino, Antonino/J-3652-2012	Schena, Leonardo/0000-0002-9737-2593; Malacrino, Antonino/0000-0002-0811-1229; GIUNTI, GIULIA/0000-0003-0258-6183	SAF@MED [PON a3_00016, PON PON03PE_00090_2]	This work was partially funded by SAF@MED (PON a3_00016)-PON Ricerca e competitivita 2007-2013 and PON PON03PE_00090_2 "Modelli sostenibili e nuove tecnologie per la valorizzazione delle olive e dell'olio extravergine di oliva prodotto in Calabria"-PON Ricerca e competitivita 2007-2013.		48	13	13	2	24	SPRINGER	NEW YORK	233 SPRING ST, NEW YORK, NY 10013 USA	0095-3628	1432-184X		MICROB ECOL	Microb. Ecol.	APR	2017	73	3					677	684		10.1007/s00248-016-0864-z				8	Ecology; Marine & Freshwater Biology; Microbiology	Environmental Sciences & Ecology; Marine & Freshwater Biology; Microbiology	EQ2ZG	WOS:000397940000016	27687872				22-11-18
J	Fromont, C; Riegler, M; Cook, JM				Fromont, Caroline; Riegler, Markus; Cook, James M.			Relative Abundance and Strain Diversity in the Bacterial Endosymbiont Community of a Sap-Feeding Insect Across Its Native and Introduced Geographic Range	MICROBIAL ECOLOGY			English	Article						Endosymbiont; Geography; Carsonella; Wolbachia; Psyllid	BAYESIAN PHYLOGENETIC INFERENCE; INFECTION DENSITY; WOLBACHIA DENSITY; ACYRTHOSIPHON-PISUM; RHAGOLETIS-CERASI; HOST GENOTYPE; SEQUENCE DATA; PEA APHID; 16S RDNA; POPULATIONS	Most insects are associated with bacterial symbionts. The bacterial diversity and community composition within hosts may play an important role in shaping insect population biology, ecology and evolution. We focussed on the bacterial microbiome of the Australian fig homotomid Mycopsylla fici (Hemiptera: Psylloidea), which can cause defoliation of its only host tree, Ficus macrophylla. This sap-feeding insect is native to mainland Australia and Lord Howe Island (LHI) but also occurs where its host has been planted, notably in New Zealand. By using a high-throughput 16S rDNA amplicon sequencing approach, we compared the bacterial diversity and community composition in individual adult males of four host populations, Sydney, Brisbane, LHI and Auckland. We also compared males, females and nymphs of the Sydney population. The microbiome of M. fici was simple and consisted mostly of the following three maternally inherited endosymbiont species: the primary endosymbiont Carsonella, a secondary (S-) endosymbiont and Wolbachia. However, the relative abundance of their sequence reads varied between host populations, except for similarities between Sydney and Auckland. In addition, insects from Sydney and Auckland had identical bacterial strains supporting the hypothesis that Sydney is the source population for Auckland. In contrast, mainland and LHI populations harboured the same S-endosymbiont, co-diverged Carsonella but different Wolbachia strains. Besides detecting endosymbiont-specific patterns of either co-evolution or horizontal acquisition, our study highlights that relative abundance of maternally inherited endosymbionts should also be taken into account when studying bacterial communities across host populations, as variations in bacterial density may impact host biology and ecology.	[Fromont, Caroline; Riegler, Markus; Cook, James M.] Western Sydney Univ, Hawkesbury Inst Environm, Locked Bag 1797, Penrith, NSW 2751, Australia	Fromont, C (reprint author), Western Sydney Univ, Hawkesbury Inst Environm, Locked Bag 1797, Penrith, NSW 2751, Australia.	c.fromont@westernsydney.edu.au			Hawkesbury Institute for the Environment Postgraduate Research Award; Hermon Slade Foundation [HSF 12/10]	CF was supported by a Hawkesbury Institute for the Environment Postgraduate Research Award. This research was also supported by a research grant of the Hermon Slade Foundation (HSF 12/10) to MR and JMC. We want to thank Tim Sutton, Desi Quintans, Aidan Hall, Jane DeGabriel, Courtney Campany and John Early for helping with the field collections as well as the Lord Howe Island Board and NSW Office of Environment and Heritage for the permission to collect specimens. We also want to thank Caroline Janitz, Emma Hackett and Jocelyn King from the Next-Generation Sequencing Facility at Western Sydney University for the 16S metagenomic sequencing services and advices.		85	2	2	8	39	SPRINGER	NEW YORK	233 SPRING ST, NEW YORK, NY 10013 USA	0095-3628	1432-184X		MICROB ECOL	Microb. Ecol.	OCT	2017	74	3					722	734		10.1007/s00248-017-0971-5				13	Ecology; Marine & Freshwater Biology; Microbiology	Environmental Sciences & Ecology; Marine & Freshwater Biology; Microbiology	FF4YH	WOS:000408969500019	28386769				22-11-18
J	Receveur, JP; Pechal, JL; Benbow, ME; Donato, G; Rainey, T; Wallace, JR				Receveur, Joseph P.; Pechal, Jennifer L.; Benbow, M. Eric; Donato, Gary; Rainey, Tadhgh; Wallace, John R.			Changes in Larval Mosquito Microbiota Reveal Non-target Effects of Insecticide Treatments in Hurricane-Created Habitats	MICROBIAL ECOLOGY			English	Article						Microbial ecology; Microbe; Higher organism interactions; Community genomics; Non-target effects	AEDES-AEGYPTI; BACTERIAL COMMUNITIES; VECTOR COMPETENCE; METHOPRENE; DIVERSITY; ECOSYSTEM; PATTERNS; DECOMPOSITION; REPRODUCTION; ISRAELENSIS	Ephemeral aquatic habitats and their associated microbial communities (microbiomes) play important roles in the growth and development of numerous aquatic insects, including mosquitoes (Diptera). Biological control agents, such as Bacillus thuringiensis israelensis (Biz) or insect growth regulators (e.g., methoprene), are commonly used to control mosquitoes in these habitats. However, it is unknown how commonly used control compounds affect the mosquito internal microbiome and potentially alter their life history traits. The objectives of this study were threefold: characterize the internal microbiota of Aedes larvae (Culicidae) in ephemeral forested mosquito habitat using high-throughput amplicon based sequencing, assess how mosquito control treatments affect the internal microbial communities of larval mosquitoes, and determine if changes to the microbiome resulted from direct or indirect treatment effects. The larval microbiome varied in community composition and diversity with development stage and treatment, suggesting potential effects of control compounds on insect microbial ecology. While microbial community differences due to Bti treatment were a result of indirect effects on larval development, methoprene had significant impacts on bacterial and algal taxa that could not be explained by indirect treatment effects. These results provide new information on the interactions between pesticide treatments and insect microbial communities.	[Receveur, Joseph P.; Wallace, John R.] Millersville Univ Pennsylvania, Dept Biol, Millersville, PA 17551 USA; [Receveur, Joseph P.; Pechal, Jennifer L.; Benbow, M. Eric] Michigan State Univ, Dept Entomol, E Lansing, MI 48824 USA; [Benbow, M. Eric] Michigan State Univ, Dept Osteopath Med Specialties, E Lansing, MI 48824 USA; [Benbow, M. Eric] Michigan State Univ, Ecol Evolutionary Biol & Behav Program, E Lansing, MI 48824 USA; [Donato, Gary; Rainey, Tadhgh] Hunterdon Cty Div Hlth, Flemington, NJ USA	Wallace, JR (reprint author), Millersville Univ Pennsylvania, Dept Biol, Millersville, PA 17551 USA.	john.wallace@millersville.edu		Pechal, Jennifer/0000-0002-2588-2519	Hunterdon County Vector Control Program (HCVCP) black fly grant [6032305751]; Commonwealth of Pennsylvania University Biologists (CPUB) Student Research Grant; Neimeyer-Hodgson Student Research Grant; Noonan Endowment award; William Yurkiewicz Fellowship; College of Agriculture and Natural Resources (Department of Entomology); College of Osteopathic Medicine (Department of Osteopathic Medical Specialties)	We would like to thank Matthew Silva, Greg Vaccarino, Frank Herr, Ryan Walker, and Jon Rutt for assistance in the field; Courtney Weatherbee for assistance with DNA extraction; and Chris Hardy, Brent Horton, and Sepi Yalda, who served on JRs thesis committee. Funding support for this project was provided by Hunterdon County Vector Control Program (HCVCP) black fly grant no. 6032305751, Commonwealth of Pennsylvania University Biologists (CPUB) Student Research Grant, Neimeyer-Hodgson Student Research Grant, Noonan Endowment award, and William Yurkiewicz Fellowship. We also thank the College of Agriculture and Natural Resources (Department of Entomology) and the College of Osteopathic Medicine (Department of Osteopathic Medical Specialties) for funding this work (MEB).		64	0	0	7	9	SPRINGER	NEW YORK	233 SPRING ST, NEW YORK, NY 10013 USA	0095-3628	1432-184X		MICROB ECOL	Microb. Ecol.	OCT	2018	76	3					719	728		10.1007/s00248-018-1175-3				10	Ecology; Marine & Freshwater Biology; Microbiology	Environmental Sciences & Ecology; Marine & Freshwater Biology; Microbiology	GS3ZE	WOS:000443567600014	29549385				22-11-18
J	Albrectsen, BR; Siddique, AB; Decker, VHG; Unterseher, M; Robinson, KM				Albrectsen, Benedicte Riber; Siddique, Abu Bakar; Decker, Vicki Huizu Guo; Unterseher, Martin; Robinson, Kathryn M.			Both plant genotype and herbivory shape aspen endophyte communities	OECOLOGIA			English	Article						Herbivory; Arboreal endophytes; Salicinoid; Bipartite graphics; Competition	POPULUS TREMULA LEAVES; FUNGAL ENDOPHYTES; INSECT HERBIVORES; CONDENSED TANNINS; CHEMICAL DEFENSE; MELAMPSORA-RUST; HOST-PLANT; DIVERSITY; MUTUALISM; TREES	Salicinoid phenolic glycosides are common defence substances in salicaceous trees and specialist leaf beetles use these compounds for their own defence against predators. Salicinoids vary qualitatively and qualitatively in aspen (Populus tremula) and this variation has a genetic basis. The foliar endophyte mycobiome is plentiful and we hypothesised that it is related to plant genotype, potentially mediated by salicinoid composition, and that interactions with the leaf beetle Chrysomela tremula may alter this relationship. We studied these three-way interactions in controlled greenhouse experiments. Endophytic fungi were isolated from sterilised leaf tissues with and without beetle damage, and from beetles. We confirmed that endophyte composition was influenced by host genotype. Beetle activity added generalist morphs to the mycobiome that overrode the initial host association. Yeast-like genera (Cryptococcus and Rhodotorula) were isolated only from beetle-damaged tissues and from beetles, whereas fast-growing filamentous fungi dominated beetle-free control plants. Competition experiments between filamentous fungi of plant origin and beetle-related yeasts suggested interaction of both stimulating and inhibiting modes of action amongst the fungi. As a result, we detected examples of amensalism, commensalism, parasitism and competition between the morphs tested, but we found no evidence of mutualism, and consequently no co-evolutionary relationship could be demonstrated, between yeasts carried by beetles, host genotype and associated filamentous morphs. Endophyte studies are method-dependent and high-throughput sequencing technology best define the fungal mycobiome, culturing however continues to be a cheap way to provide fundamental ecological insights and it is also required for experimental studies.	[Albrectsen, Benedicte Riber; Decker, Vicki Huizu Guo; Robinson, Kathryn M.] Umea Univ, Dept Plant Physiol, Umea Plant Sci Ctr, Umea, Sweden; [Siddique, Abu Bakar; Unterseher, Martin] Ernst Moritz Arndt Univ Greifswald, Inst Bot & Landschaftsokol, Soldmannstr 15, D-17487 Greifswald, Germany; [Unterseher, Martin] Evangel Schulzentrum Martinschule, Max Planck Str 7, D-17491 Greifswald, Germany	Albrectsen, BR (reprint author), Umea Univ, Dept Plant Physiol, Umea Plant Sci Ctr, Umea, Sweden.	Benedicte.albrectsen@umu.se	Siddique, Abu Bakar/R-1776-2018	Siddique, Abu Bakar/0000-0002-3178-523X	Swedish Foundation for Strategic Research [RBb08-0003]; European COoperation in Science and Technology through the COST action [FA1405]	This work was supported by funds from the Swedish Foundation for Strategic Research (Project no. RBb08-0003) awarded to BRA, VHGD and KMR. The European COoperation in Science and Technology is acknowledged for its support through the COST action: FA1405 to BRA, VHGD and ABS.		71	1	1	6	6	SPRINGER	NEW YORK	233 SPRING ST, NEW YORK, NY 10013 USA	0029-8549	1432-1939		OECOLOGIA	Oecologia	JUN	2018	187	2					535	545		10.1007/s00442-018-4097-3				11	Ecology	Environmental Sciences & Ecology	GJ2OW	WOS:000435111800016	29492690	Green Published, Other Gold			22-11-18
J	Briem, F; Zeisler, C; Guenay, Y; Staudacher, K; Vogt, H; Traugott, M				Briem, Felix; Zeisler, Christiane; Guenay, Yasemin; Staudacher, Karin; Vogt, Heidrun; Traugott, Michael			Identifying plant DNA in the sponging-feeding insect pest Drosophila suzukii	JOURNAL OF PEST SCIENCE			English	Article						Chloroplast DNA; Diet metabarcoding; Feeding experiment; Molecular gut content analysis; Spotted Wing Drosophila; High-throughput sequencing; NGS	SPOTTED WING DROSOPHILA; GUT-CONTENT-ANALYSIS; DIPTERA DROSOPHILIDAE; PREY DNA; PREDATORS; HOST; PCR; IDENTIFICATION; PREFERENCES; MATSUMURA	Drosophila suzukii (Diptera: Drosophilidae) is a highly polyphagous invasive pest threatening fruit production in the Americas and Europe. The current knowledge of its host plants is mainly based on oviposition and larval development in fruits, while little is known on the diet of the adult flies. This information is important for developing effective control strategies. Here, we examine DNA-based techniques to determine food plants of D. suzukii. Adult flies were fed with raspberries (Rubus idaeus) and allowed to digest up to 72 h after feeding. Raspberry DNA was detected by diagnostic PCR for up to 48 h post-feeding with a significant negative effect of time on DNA detection success but no significant differences between male and female flies in detection probabilities. As D. suzukii walks on plants, its body surface can get contaminated with DNA. With a bleaching experiment, we succeeded to remove contaminating external plant DNA, while the DNA in the gut content stayed unaffected. Finally, field-collected flies were subjected to a next-generation sequencing approach, demonstrating that plant DNA from different host plants can be efficiently detected in both bleached and non-bleached specimens. In order to safeguard against erroneous host plant detections, we recommend bleaching flies before they are subjected to DNA extraction. The current findings encourage the use of DNA-based gut content analysis in D. suzukii to obtain a better understanding of its feeding ecology which is a prerequisite for developing successful control strategies.	[Briem, Felix; Vogt, Heidrun] JKI, Inst Plant Protect Fruit Crops & Viticulture, Fed Res Ctr Cultivated Plants, Lab Entomol, Schwabenheimer Str 101, D-69221 Dossenheim, Germany; [Zeisler, Christiane; Guenay, Yasemin; Staudacher, Karin; Traugott, Michael] Univ Innsbruck, Mt Agr Res Unit, Inst Ecol, Technikerstr 25, A-6020 Innsbruck, Austria; [Guenay, Yasemin] Austrian Acad Sci, Inst Interdisciplinary Mt Res, IGF, Technikerstr 21a, A-6020 Innsbruck, Austria	Briem, F (reprint author), JKI, Inst Plant Protect Fruit Crops & Viticulture, Fed Res Ctr Cultivated Plants, Lab Entomol, Schwabenheimer Str 101, D-69221 Dossenheim, Germany.	Felix.Briem@julius-kuehn.de		Briem, Felix/0000-0003-3873-8812	Federal Ministry for Food and Agriculture (BMEL) of Germany; Mountain Agriculture Research Unit	We thank the Federal Ministry for Food and Agriculture (BMEL) of Germany for financial funding. We also acknowledge financial support through the Mountain Agriculture Research Unit ("Call for Projects 2016") for KS, D. Swarovski KG (Aktion D. Swarovski KG 2016) and a PhD scholarship (University of Innsbruck) for CZ. We thank Michael Fink for providing access to the high-performance computing (HPC) cluster systems as the computational (bioinformatics) results presented have been achieved (in part) using the HPC infrastructure LEO of the University of Innsbruck. Finally, we thank Anto Dominic Raja and Doreen Gabriel for statistical support and Juergen Just and Anja Frank (all JKI) for laboratory assistance and rearing D. suzukii.		53	0	0	15	15	SPRINGER HEIDELBERG	HEIDELBERG	TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY	1612-4758	1612-4766		J PEST SCI	J. Pest Sci.	JUN	2018	91	3					985	994		10.1007/s10340-018-0963-3				10	Entomology	Entomology	GG9NA	WOS:000433026600005					22-11-18
J	Kelley, ST; Dobler, S				Kelley, Scott T.; Dobler, Susanne			Comparative analysis of microbial diversity in Longitarsus flea beetles (Coleoptera: Chrysomelidae)	GENETICA			English	Article						16S rRNA; Bacteria; Biodiversity; Herbivory; Metagenomics; Microbial ecology; Phylogeny	CULTURE-INDEPENDENT METHODS; FLY CERATITIS-CAPITATA; BACTERIAL DIVERSITY; BARK BEETLES; HOST PLANTS; HERBIVOROUS INSECTS; SERRATIA-MARCESCENS; GUT MICROBES; EVOLUTION; COMMUNITY	Herbivorous beetles comprise a significant fraction of eukaryotic biodiversity and their plant-feeding adaptations make them notorious agricultural pests. Despite more than a century of research on their ecology and evolution, we know little about the diversity and function of their symbiotic microbial communities. Recent culture-independent molecular studies have shown that insects possess diverse gut microbial communities that appear critical for their survival. In this study, we combined culture-independent methods and high-throughput sequencing strategies to perform a comparative analysis of Longitarsus flea-beetles microbial community diversity (MCD). This genus of beetle herbivores contains host plant specialists and generalists that feed on a diverse array of toxic plants. Using a deep-sequencing approach, we characterized the MCD of eleven Longitarsus species across the genus, several of which represented independent shifts to the same host plant families. Database comparisons found that Longitarsus-associated microbes came from two habitat types: insect guts and the soil rhizosphere. Statistical clustering of the Longitarsus microbial communities found little correlation with the beetle phylogeny, and uncovered discrepancies between bacterial communities extracted directly from beetles and those from frass. A Principal Coordinates Analysis also found some correspondence between beetle MCD and host plant family. Collectively, our data suggest that environmental factors play a dominant role in shaping Longitarsus MCD and that the root-feeding beetle larvae of these insects are inoculated by soil rhizosphere microbes. Future studies will investigate MCD of select Longitarsus species across their geographic ranges and explore the connection between the soil rhizosphere and the beetle MCD.	[Kelley, Scott T.] San Diego State Univ, Dept Biol, San Diego, CA 92182 USA; [Dobler, Susanne] Univ Hamburg, Inst Zool, D-20146 Hamburg, Germany	Kelley, ST (reprint author), San Diego State Univ, Dept Biol, 5500 Campanile Dr, San Diego, CA 92182 USA.	skelley@sciences.sdsu.edu; susanne.dobler@uni-hamburg.de		Dobler, Susanne/0000-0002-0635-7719	Alexander von Humboldt Foundation	We wish to thank all the members of the Dobler lab who helped make this study possible, especially K. Meyer, S. Marzez and C. Baden. We thank V. Thackray, the editor B. Normark, and two anonymous reviewers for their many helpful suggestions. This study was funded by a grant from the Alexander von Humboldt Foundation. Finally, as first author, I would like to extend a very special thank you to Professor Richard G. Harrison. Rick's lectures on evolutionary biology were wonderful and inspired me during a very difficult period of my undergraduate education at Cornell University. After taking Rick's class, I knew for certain that I would become an evolutionary biologist. I also thank Rick for taking a chance and hiring me as a research technician in his lab after my difficult stint as an elementary school teacher in Houston, Texas. Once again, this experience with Rick proved to be tremendously inspirational and guided me towards my eventual career as a biology professor. During my time in Rick's lab I learned molecular biology skills from the world's best (Steven Bogdanowicz), uncovered my passion for phylogenetics, discovered the joys of working with insects, came to know my future Ph.D. advisor, and met some of the best graduate students and scientists in evolutionary biology. Thus, I credit much of my career success, and indeed happiness, to Rick's kindness and generosity.		67	15	15	1	32	SPRINGER	DORDRECHT	VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS	0016-6707			GENETICA	Genetica	MAY	2011	139	5					541	550		10.1007/s10709-010-9498-0				10	Genetics & Heredity	Genetics & Heredity	760JK	WOS:000290320400002	20844936				22-11-18
J	Galliot, JN; Brunel, D; Berard, A; Chauveau, A; Blanchetete, A; Lanore, L; Farruggia, A				Galliot, Jean-Noel; Brunel, Dominique; Berard, Aurelie; Chauveau, Aurelie; Blanchetete, Andre; Lanore, Laurent; Farruggia, Anne			Investigating a flower-insect forager network in a mountain grassland community using pollen DNA barcoding	JOURNAL OF INSECT CONSERVATION			English	Article						Flower-foraging insects; Semi-natural grasslands; Plant-pollinator interactions; DNA barcoding; Pollen loads	CROP POLLINATION; AGRICULTURAL INTENSIFICATION; BEES; FLIES; BIODIVERSITY; DIVERSITY; PLANTS; SPECIALIZATION; IDENTIFICATION; LANDSCAPES	Faced with the decline of pollinators, it is relevant to strengthen our understanding of the whole plant-pollinator web in semi-natural grasslands that serve as refuges for pollinator populations. The aim of this study was to explore the diversity of flower-foraging insects involved in pollen transfer in mountain semi-natural grasslands. Insects actively collecting pollen and/or nectar were caught in spring in six mountain semi-natural grasslands displaying a floristic richness gradient. Individual determinations of insects were made at the finest possible taxonomic scale and pollen loads were removed from the insect body. Using next-generation DNA sequencing, pollens were identified through the ribosomal DNA cistron using the ITS2 database and the ITS plant rDNA cistron sequences from Genbank. A total of 236 flower-foraging insects were collected. Diptera represented 82% of the total catches distantly followed by Hymenoptera (15%) and Apoidea (bees) (11%). Visual observations revealed that Diptera foraged on 16 of the 21 flower species visited by insects. DNA metabarcoding showed that 82% (191) of all of the collected insects were carrying pollen and 44% (104) were carrying two genera of plants or more. Our results demonstrate that Diptera are potential key-pollinators in mountain semi-natural grasslands that cannot be overlooked by the scientific community. However difficulties of taxonomic determination due to severe shortage of experts for Diptera have to be urgently overcome. Further studies on the link between pollen transfer and actual pollination in a global change context are also required. Moreover, our results support the idea that DNA metabarcoding provides accurate information about the plants-insects networks but it also pointed out sensitive issues, especially the necessity to build reliable national barcode databases.	[Galliot, Jean-Noel; Brunel, Dominique; Berard, Aurelie; Chauveau, Aurelie] Univ Paris Saclay, EPGV US 1279, INRA, CEA,IG CNG, F-91000 Evry, France; [Blanchetete, Andre] INRA, Herbipole UE1414, F-63820 Laqueuille, France; [Lanore, Laurent; Farruggia, Anne] Clermont Univ, VetAgro Sup, INRA, Herbivores UMR1213, F-63122 St Genes Champanelle, France	Galliot, JN (reprint author), Univ Paris Saclay, EPGV US 1279, INRA, CEA,IG CNG, F-91000 Evry, France.	jean-noel.galliot@inra.fr						66	1	1	11	32	SPRINGER	DORDRECHT	VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS	1366-638X	1572-9753		J INSECT CONSERV	J. Insect Conserv.	DEC	2017	21	05-Jun					827	837		10.1007/s10841-017-0022-z				11	Biodiversity Conservation; Entomology	Biodiversity & Conservation; Entomology	FP4TD	WOS:000417608400008					22-11-18
J	Douglas, AE				Douglas, Angela E.			Microbial Brokers of Insect-Plant Interactions Revisited	JOURNAL OF CHEMICAL ECOLOGY			English	Review						Insect-plant interactions; Microbial brokers; Microbiota; Symbiosis	ENDOSYMBIOTIC BACTERIA; MEDIATED INTERACTIONS; CELLULOSE DIGESTION; NITROGEN-FIXATION; ESCHERICHIA-COLI; HIGH-THROUGHPUT; GUT MICROBIOTA; CELL; SYMBIONTS; EVOLUTION	Recent advances in sequencing methods have transformed the field of microbial ecology, making it possible to determine the composition and functional capabilities of uncultured microorganisms. These technologies have been instrumental in the recognition that resident microorganisms can have profound effects on the phenotype and fitness of their animal hosts by modulating the animal signaling networks that regulate growth, development, behavior, etc. Against this backdrop, this review assesses the impact of microorganisms on insect-plant interactions, in the context of the hypothesis that microorganisms are biochemical brokers of plant utilization by insects. There is now overwhelming evidence for a microbial role in insect utilization of certain plant diets with an extremely low or unbalanced nutrient content. Specifically, microorganisms enable insect utilization of plant sap by synthesizing essential amino acids. They also can broker insect utilization of plant products of extremely high lignocellulose content, by enzymatic breakdown of complex plant polysaccharides, nitrogen fixation, and sterol synthesis. However, the experimental evidence for microbial-mediated detoxification of plant allelochemicals is limited. The significance of microorganisms as brokers of plant utilization by insects is predicted to vary, possibly widely, as a result of potentially complex interactions between the composition of the microbiota and the diet and insect developmental age or genotype. For every insect species feeding on plant material, the role of resident microbiota as biochemical brokers of plant utilization is a testable hypothesis.	[Douglas, Angela E.] Cornell Univ, Dept Entomol, Ithaca, NY 13853 USA; [Douglas, Angela E.] Cornell Univ, Dept Mol Biol & Genet, Ithaca, NY 13853 USA	Douglas, AE (reprint author), Cornell Univ, Dept Entomol, Ithaca, NY 13853 USA.	aes326@cornell.edu			NSF [BIO 1241099]; AFRI [NYW-2011-04650]; Sarkaria Institute for Insect Physiology and Toxicology	This work was supported by NSF grant BIO 1241099, AFRI grant NYW-2011-04650 and the Sarkaria Institute for Insect Physiology and Toxicology.		88	48	48	4	123	SPRINGER	DORDRECHT	VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS	0098-0331	1573-1561		J CHEM ECOL	J. Chem. Ecol.	JUL	2013	39	7			SI		952	961		10.1007/s10886-013-0308-x				10	Biochemistry & Molecular Biology; Ecology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology	200NW	WOS:000323076800014	23793897	Green Accepted			22-11-18
J	Andrew, DR				Andrew, David R.			A new view of insect-crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics	ARTHROPOD STRUCTURE & DEVELOPMENT			English	Article						Expressed sequence tag; Phylogeny; Arthropoda; Tetraconata; Pancrustacea; Branchiopoda; Hexapoda; Nervous system evolution	RNA GENE-SEQUENCES; ARTHROPOD RELATIONSHIPS; PHYLOGENETIC ANALYSES; NERVOUS-SYSTEM; TERRESTRIAL CRUSTACEANS; MITOCHONDRIAL GENOME; HIGH-THROUGHPUT; ANIMAL KINGDOM; COMPLETE 28S; EVOLUTION	The enormous diversity of Arthropoda has complicated attempts by systematists to deduce the history of this group in terms of phylogenetic relationships and phenotypic change. Traditional hypotheses regarding the relationships of the major arthropod groups (Chelicerata, Myriapoda, Crustacea, and Hexapoda) focus on suites of morphological characters, whereas phylogenomics relies on large amounts of molecular sequence data to infer evolutionary relationships. The present discussion is based on expressed sequence tags (ESTs) that provide large numbers of short molecular sequences and so provide an abundant source of sequence data for phylogenetic inference. This study presents well-supported phylogenies of diverse arthropod and metazoan outgroup taxa obtained from publicly-available databases. An in-house bioinformatics pipeline has been used to compile and align conserved orthologs from each taxon for maximum likelihood inferences. This approach resolves many currently accepted hypotheses regarding internal relationships between the major groups of Arthropoda, including monophyletic Hexapoda, Tetraconata (Crustacea + Hexapoda), Myriapoda, and Chelicerata sensu lato (Pycnogonida + Euchelicerata). "Crustacea" is a paraphyletic group with some taxa more closely related to the monophyletic Hexapoda. These results support studies that have utilized more restricted EST data for phylogenetic inference, yet they differ in important regards from recently published phylogenies employing nuclear protein-coding sequences. The present results do not, however, depart from other phylogenies that resolve Branchiopoda as the crustacean sister group of Hexapoda. Like other molecular phylogenies, EST-derived phylogenies alone are unable to resolve morphological convergences or evolved reversals and thus omit what may be crucial events in the history of life. For example, molecular data are unable to resolve whether a Hexapod-Branchiopod sister relationship infers a branchiopod-like ancestry of the Hexapoda, or whether this assemblage originates from a malacostracan-like ancestor, with the morphologically simpler Branchiopoda being highly derived. Whereas this study supports many internal arthropod relationships obtained by other sources of molecular data, other approaches are required to resolve such evolutionary scenarios. The approach presented here turns out to be essential: integrating results of molecular phylogenetics and neural cladistics to infer that Branchiopoda evolved simplification from a more elaborate ancestor. Whereas the phenomenon of evolved simplification may be widespread, it is largely invisible to molecular techniques unless these are performed in conjunction with morphology-based strategies. (C) 2011 Elsevier Ltd. All rights reserved.	Univ Arizona, Dept Neurosci, Tucson, AZ 85721 USA	Andrew, DR (reprint author), Univ Arizona, Dept Neurosci, 1040 E 4th St,Gould Simpson Bldg 611, Tucson, AZ 85721 USA.	dandrew@email.arizona.edu			IGERT	I thank Ingo Ebersberger (at the Center for Integrative Bioinformatics in Vienna) for building and providing a custom core ortholog set for this study with the latest version of InParanoid. I would also like to acknowledge Travis Wheeler and the IGERT program in comparative genomics at the University of Arizona for help in conceiving and scripting the phylogenetic analysis pipeline, as well as the support at the High Performance Computing center at the University of Arizona for help in executing analyses. Nicholas Strausfeld provided insightful and indispensable comments during the drafting of this manuscript. This study was supported by an IGERT training fellowship in Comparative Genomics through the University of Arizona. Two anonymous reviewers provided valuable and appreciated comments to this manuscript.		85	42	44	0	39	ELSEVIER SCI LTD	OXFORD	THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND	1467-8039	1873-5495		ARTHROPOD STRUCT DEV	Arthropod Struct. Dev.	MAY	2011	40	3			SI		289	302		10.1016/j.asd.2011.02.001				14	Entomology	Entomology	788GP	WOS:000292433700008	21315832				22-11-18
J	Wang, QQ; Tang, GH				Wang, Qiqi; Tang, Guanghui			Genomic and phylogenetic analysis of the complete mitochondrial DNA sequence of walnut leaf pest Paleosepharia posticata (Coleoptera: Chrysomeloidea)	JOURNAL OF ASIA-PACIFIC ENTOMOLOGY			English	Article						Coleoptera; Paleosepharia posticata; Mitochondrial genome; Phylogenetic analysis	GENE ORGANIZATION; ORTHOPTERA; EVOLUTION; HEMIPTERA; SELECTION; SOFTWARE; PROGRAM; INSECTA; MODEL	Mitochondrial DNA (mitogenome) has been widely used in species identification and comparison among closely related species and is valuable for phylogenetic studies. However, considering the large amount and high biodiversity of coleopteran insects, only about 100 complete or nearly complete mitogenome sequences of coleopterans were found in GenBank, largely limiting the research of biological evolution among coleopteran insects. In this study, the complete mitochondrial sequence of Paleosepharia posticata, an important walnut leaf pest, was determined by the next-generation sequencing technology and verified using Sanger sequencing method. The mitogenome of P. posticata was 15,729 bp with an A + T content of 79.8%, and was very similar with other reported coleopteran insects in genome complement, gene order and nucleotide composition. All of the protein-coding genes started with the typical ATN initiation codons except for nad1 (TTG). The ancestral gene order with trnI-trnQ-trnM located between the A + T-rich region and nad2 and the formerly identified conserved elements of coleopteran mitogenomes, such as the motif 'TAGTA' between trnS(UCN) and nad2, the overlap 'ATGATAA' between atp8 and atp6 genes and poly-T stretch in the A + T-rich region, were also present in the P. posticata mitogenome. A special 'ATGATAA' between nad41 and nad4, which was 'ATGTTAA' in many insect mitogenomes, was observed in the mitogenome of P. posticata and coleopteran species used in this study. Phylogenetic trees inferred from the amino acid and nucleotide sequence data for the 13 protein-coding genes strongly supported the monopoly of Elateriformia, the paraphyly of Staphyliniformia, and the sister relationship of Scarabaeoidea and Staphylinoidea.	[Wang, Qiqi; Tang, Guanghui] Northwest Agr & Forestry Univ, Coll Forestry, Yangling 712100, Shaanxi, Peoples R China	Tang, GH (reprint author), Northwest Agr & Forestry Univ, Coll Forestry, Yangling 712100, Shaanxi, Peoples R China.	tanggh@nwsuaf.edu.cn			National Natural Science Foundation of China [31270690]	This project was supported by the National Natural Science Foundation of China (No. 31270690).		62	2	3	6	12	KOREAN SOC APPLIED ENTOMOLOGY	SUWON	NATL INST AGRICULTURAL SCIENCE & TECHNOLOGY, DIVISION ENTOMOLOGY, RDA, 249 SEODUN-DONG, SUWON, 441-707, SOUTH KOREA	1226-8615	1876-7990		J ASIA-PAC ENTOMOL	J. Asia-Pac. Entomol.	SEP	2017	20	3					840	853		10.1016/j.aspcn.2017.05.010				14	Entomology	Entomology	FS4HH	WOS:000419749200015					22-11-18
J	Haran, J; Delvare, G; Vayssieres, JF; Benoit, L; Cruaud, P; Rasplus, JY; Cruaud, A				Haran, Julien; Delvare, Gerard; Vayssieres, Jean-Francois; Benoit, Laure; Cruaud, Perrine; Rasplus, Jean-Yves; Cruaud, Astrid			Increasing the utility of barcode databases through high-throughput sequencing of amplicons from dried museum specimens, an example on parasitic hymenoptera (Braconidae)	BIOLOGICAL CONTROL			English	Article						Braconidae; Biological control; Gut content; Dry insect collections; Sub-Saharan Africa	SPECIES COMPLEX HYMENOPTERA; BIOLOGICAL-CONTROL; DIPTERA TEPHRITIDAE; WASPS HYMENOPTERA; DNA; COLLECTIONS; TAXONOMY; POPULATION; CERATITIS; PLATFORM	Parasitic hymenoptera are natural enemies of a wide range of crop pests. However, the complex taxonomy of this group and the scarcity of taxonomic expertise make difficult the accurate identification of species, which limits their use in biological control programs. In this study, we explored the potential of a two-step PCR approach combined with Illumina sequencing to recover mitochondrial protein coding genes (COI and Cytb) from dry specimens from a reference collection, whose DNA was extracted non-destructively. We studied 18 species of afrotropical Braconidae (Microgastrinae, Opiinae and Braconinae) collected 10 to 35 years ago. Depending on the target region, sequences were obtained from 61 to 90% of the specimens. The full barcode was reconstructed in ca 90% of the species. A customized analysis pipeline allowed us to manage the high rate of contamination and to identify co-amplified sequences of hosts of parasitoids. As a result, in a single analysis, we were able to 1) generate new barcodes for poorly known species, 2) obtain a preliminary overview of intra specific variability, 3) generate a few data on host-parasitoid associations based on remains of hosts in adult wasps. This cost-effective approach should allow to improve the quality of reference molecular databases by capitalizing on museum specimens identified by expert taxonomists, in order to set up more efficient biological control programs.	[Haran, Julien; Delvare, Gerard; Benoit, Laure] Univ Montpellier, IRD, INRA, CBGP,Cirad,Montpellier SupAgro, Montpellier, France; [Vayssieres, Jean-Francois] Cirad, UR Hortsys, CI Baillarguet, Montpellier, France; [Cruaud, Perrine; Rasplus, Jean-Yves; Cruaud, Astrid] Univ Montpellier, Montpellier SupAgro, IRD, CBGP,INRA,Cirad, Montpellier, France	Haran, J (reprint author), Univ Montpellier, IRD, INRA, CBGP,Cirad,Montpellier SupAgro, Montpellier, France.	julien.haran@cirad.fr		HARAN, Julien/0000-0001-9458-3785	INRA	We acknowledge Emmanuelle Artige (Collection plateform CBGP) for her help with sampling specimens in collections. We also thank Audrey Weber (INRA, AGAP) for the sequencing of the library. The project was supported by the recurring funding of the INRA to AC & JYR.		56	0	0	12	12	ACADEMIC PRESS INC ELSEVIER SCIENCE	SAN DIEGO	525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA	1049-9644	1090-2112		BIOL CONTROL	Biol. Control	JUL	2018	122						93	100		10.1016/j.biocontrol.2018.04.001				8	Biotechnology & Applied Microbiology; Entomology	Biotechnology & Applied Microbiology; Entomology	GG2JN	WOS:000432518000012					22-11-18
J	Poelchau, MF; Coates, BS; Childers, CP; de Leon, AAP; Evans, JD; Hackett, K; Shoemaker, D				Poelchau, Monica F.; Coates, Brad S.; Childers, Christopher P.; de Leon, Adalberto A. Perez; Evans, Jay D.; Hackett, Kevin; Shoemaker, DeWayne			Agricultural applications of insect ecological genomics	CURRENT OPINION IN INSECT SCIENCE			English	Article							RHIPICEPHALUS BOOPHILUS MICROPLUS; FIELD-EVOLVED RESISTANCE; HORIZONTAL GENE-TRANSFER; TERMITE RETICULITERMES FLAVIPES; POTENTIAL ECONOMIC-IMPACT; DOUBLE-STRANDED-RNA; CATTLE TICK; TETRANYCHUS-URTICAE; LUCILIA-CUPRINA; HONEY-BEE	Agricultural entomology is poised to benefit from the application of ecological genomics, particularly the fields of biofuels generation and pest control. Metagenomic methods can characterize microbial communities of termites, woodboring beetles and livestock pests, and transcriptomic approaches reveal molecular bases behind wood-digesting capabilities of these insects, leading to potential mechanisms for biofuel generation. Genome sequences are being exploited to develop new pest control methods, identify candidate antigens to vaccinate livestock, and discover RNAi target sequences and potential non-target effects in other insects. Gene content analyses of pest genome sequences and their endosymbionts suggest metabolic interdependencies between organisms, exposing potential gene targets for insect control. Finally, genome-wide association studies and genotyping by high-throughput sequencing promise to improve management of pesticide resistance.	[Poelchau, Monica F.; Childers, Christopher P.] USDA ARS, Natl Agr Lib, Beltsville, MD 20705 USA; [Coates, Brad S.] USDA ARS, Corn Insects & Crop Genet Res Unit, Ames, IA 50011 USA; [de Leon, Adalberto A. Perez] USDA ARS, Knipling Bushland US Livestock Insects Res Lab, Kerrville, TX 78028 USA; [de Leon, Adalberto A. Perez] Vet Pest Genom Ctr, Kerrville, TX 78028 USA; [Evans, Jay D.] USDA ARS, Bee Res Lab, Beltsville, MD 20705 USA; [Hackett, Kevin] USDA ARS, Off Natl Programs, Crop Prod & Protect, Beltsville, MD 20705 USA; [Shoemaker, DeWayne] USDA ARS, Imported Fire Ant & Household Insects Res Unit, Gainesville, FL 32608 USA	Poelchau, MF (reprint author), USDA ARS, Natl Agr Lib, Beltsville, MD 20705 USA.; Shoemaker, D (reprint author), USDA ARS, Imported Fire Ant & Household Insects Res Unit, Gainesville, FL 32608 USA.	Monica.poelchau@ars.usda.gov; dewayne.shoemaker@ars.usda.gov		Coates, Brad/0000-0001-8908-1529; Childers, Chris/0000-0002-1253-5550; Evans, Jay/0000-0002-0036-4651; Poelchau, Monica/0000-0002-4584-6056				122	4	4	3	35	ELSEVIER SCIENCE BV	AMSTERDAM	PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS	2214-5745	2214-5753		CURR OPIN INSECT SCI	Curr. Opin. Insect Sci.	FEB	2016	13						61	69		10.1016/j.cois.2015.12.002				9	Biology; Ecology; Entomology	Life Sciences & Biomedicine - Other Topics; Environmental Sciences & Ecology; Entomology	DM4FL	WOS:000376301800010	27436554				22-11-18
J	Garofalo, C; Osimani, A; Milanovic, V; Taccari, M; Cardinali, F; Aquilanti, L; Riolo, P; Ruschioni, S; Isidoro, N; Clementi, F				Garofalo, Cristiana; Osimani, Andrea; Milanovic, Vesna; Taccari, Manuela; Cardinali, Federica; Aquilanti, Lucia; Riolo, Paola; Ruschioni, Sara; Isidoro, Nunzio; Clementi, Francesca			The microbiota of marketed processed edible insects as revealed by high-throughput sequencing	FOOD MICROBIOLOGY			English	Article						Microbial community; Next-generation sequencing; Entomophagy; Acheta domesticus; Locusta migratoria; Tenebrio molitor	LACTIC-ACID BACTERIA; NUTRITIONAL COMPOSITION; IMBRASIA-BELINA; EMPEROR MOTH; FOOD; DIVERSITY; GUT; SAFETY; CATERPILLAR; COMMUNITIES	Entomophagy has been linked to nutritional, economic, social and ecological benefits. However, scientific studies on the potential safety risks in eating edible insects need to be carried out for legislators, markets and consumers. In this context, the microbiota of edible insects deserves to be deeply investigated. The aim of this study was to elucidate the microbial species occurring in some processed marketed edible insects, namely powdered small crickets, whole dried small crickets (Acheta domesticus), whole dried locusts (Locusta migratoria), and whole dried mealworm larvae (Tenebrio molitor), through culture dependent (classical microbiological analyses) and -independent methods (pyrosequencing). A great bacterial diversity and variation among insects was seen. Relatively low counts of total mesophilic aerobes, Enterobacteriaceae, lactic acid bacteria, Clostridium perfringens spores, yeasts and moulds in all of the studied insect batches were found. Furthermore, the presence of several gut-associated bacteria, some of which may act as opportunistic pathogens in humans, were found through pyrosequencing. Food spoilage bacteria were also identified, as well as Spiroplasma spp. in mealworm larvae, which has been found to be related to neurodegenerative diseases in animals and humans. Although viable pathogens such as Salmonella spp. and Listeria monocytogenes were not detected, the presence of Listeria spp., Staphylococcus spp., Clostridium spp. and Bacillus spp. (with low abundance) was also found through pyrosequencing. The results of this study contribute to the elucidation of the microbiota associated with edible insects and encourage further studies aimed to evaluate the influence of rearing and processing conditions on that microbiota. (C) 2016 Elsevier Ltd. All rights reserved.	[Garofalo, Cristiana; Osimani, Andrea; Milanovic, Vesna; Taccari, Manuela; Cardinali, Federica; Aquilanti, Lucia; Riolo, Paola; Ruschioni, Sara; Isidoro, Nunzio; Clementi, Francesca] Univ Politecn Marche, Dipartimento Sci Agr Alimentari & Ambientali, Via Brecce Bianche, I-60131 Ancona, Italy	Osimani, A (reprint author), Univ Politecn Marche, Dipartimento Sci Agr Alimentari & Ambientali, Via Brecce Bianche, I-60131 Ancona, Italy.	a.osimani@univpm.it		OSIMANI, ANDREA/0000-0003-4095-6181; AQUILANTI, Lucia/0000-0001-8898-2886; Garofalo, Cristiana/0000-0001-8235-8935				56	25	25	12	172	ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD	LONDON	24-28 OVAL RD, LONDON NW1 7DX, ENGLAND	0740-0020	1095-9998		FOOD MICROBIOL	Food Microbiol.	APR	2017	62						15	22		10.1016/j.fm.2016.09.012				8	Biotechnology & Applied Microbiology; Food Science & Technology; Microbiology	Biotechnology & Applied Microbiology; Food Science & Technology; Microbiology	EF7HE	WOS:000390499900003	27889142		Y	N	22-11-18
J	Jacobsen, RM; Kauserud, H; Sverdrup-Thygeson, A; Bjorbwkmo, MM; Birkemoe, T				Jacobsen, Rannveig M.; Kauserud, Havard; Sverdrup-Thygeson, Anne; Bjorbwkmo, Marit Markussen; Birkemoe, Tone			Wood-inhabiting insects can function as targeted vectors for decomposer fungi	FUNGAL ECOLOGY			English	Article						Animal-mediated dispersal; Dead wood; Decomposition; DNA barcoding; High-throughput sequencing; Insect-vectored dispersal; Polypores; Saproxylic insects; Scanning electron microscopy; Wood-decay fungi	BASIDIOCARP-FEEDING BEETLES; LONG-DISTANCE DISPERSAL; SEED DISPERSAL; FOREST FRAGMENTATION; COMMUNITY COMPOSITION; POPULATION-STRUCTURE; FOMITOPSIS-PINICOLA; SPORE DISPERSAL; CLIMATE-CHANGE; NORWAY SPRUCE	Most wood-inhabiting fungi are assumed to be dispersed primarily by wind, with the exception of a few species involved in mutualistic relationships with insects. In this study we tested whether several species of wood-inhabiting insects can function as dispersal vectors for non-mutualistic fungi, which would indicate that wood-inhabiting fungi can benefit from targeted animal-mediated dispersal. We sampled wood-inhabiting beetles (Coleoptera) from freshly felled wood experimentally added to forests and used DNA metabarcoding to investigate the fungal DNA carried by these insects. Staphylinid beetles rarely contained fungal DNA, while Endomychus coccineus, Glischrochilus hortensis and Glischrochilus quadripunctatus frequently carried fungal DNA with a composition specific to the insect taxon. A large proportion of the obtained fungal sequences (34%) represented decomposer fungi, including well-known wood-decay fungi such as Fomitopsis pinicola, Fames fomentarius, Trichaptum abietinum and Trametes versicolor. Scanning electron microscopy further showed that some of the fungal material was carried as spores or yeast cells on the insect exoskeletons. Our results suggest that insect vectored dispersal is of broader importance to wood-inhabiting fungi than previously assumed. (C) 2017 The Authors. Published by Elsevier Ltd.	[Jacobsen, Rannveig M.; Sverdrup-Thygeson, Anne; Birkemoe, Tone] Norwegian Univ Life Sci, Fac Environm Sci & Nat Resource Management, Hogskoleveien 12, N-1433 As, Norway; [Kauserud, Havard; Bjorbwkmo, Marit Markussen] Univ Oslo, Sect Genet & Evolutionary Biol EVOGENE, Blindernveien 31, N-0316 Oslo, Norway	Jacobsen, RM (reprint author), Norwegian Univ Life Sci, Fac Environm Sci & Nat Resource Management, Hogskoleveien 12, N-1433 As, Norway.	rannveig.jacobsen@nmbu.no		Jacobsen, Rannveig Margrete/0000-0003-4055-1096				109	4	4	3	21	ELSEVIER SCI LTD	OXFORD	THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND	1754-5048	1878-0083		FUNGAL ECOL	Fungal Ecol.	OCT	2017	29						76	84		10.1016/j.funeco.2017.06.006				9	Ecology; Mycology	Environmental Sciences & Ecology; Mycology	FH6RW	WOS:000411305400010		Other Gold			22-11-18
J	Osimani, A; Milanovic, V; Garofalo, C; Cardinali, F; Roncolini, A; Sabbatini, R; De Filippis, F; Ercolini, D; Gabucci, C; Petruzzelli, A; Tonucci, F; Clementi, F; Aquilanti, L				Osimani, Andrea; Milanovic, Vesna; Garofalo, Cristiana; Cardinali, Federica; Roncolini, Andrea; Sabbatini, Riccardo; De Filippis, Francesca; Ercolini, Danilo; Gabucci, Claudia; Petruzzelli, Annalisa; Tonucci, Franco; Clementi, Francesca; Aquilanti, Lucia			Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR	INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY			English	Article						Novel foods; Spore-forming bacteria; Risk analysis; Food safety; Edible insects	LARVAE TENEBRIO-MOLITOR; TRANSFERABLE ANTIBIOTIC RESISTANCES; LOCUSTA-MIGRATORIA-MIGRATORIOIDES; LACTIC-ACID BACTERIA; COXIELLA-BURNETII; ESCHERICHIA-COLI; FATTY-ACIDS; STENOTROPHOMONAS-MALTOPHILIA; ALPHITOBIUS-DIAPERINUS; INDEPENDENT METHODS	The present study aimed to identify the microbiota present in six species of processed edible insects produced in Thailand and marketed worldwide via the internet, namely, giant water bugs (Belostoma lutarium), black ants (Polyrhachis), winged termites (alates, Termitoidae), rhino beetles (Hyboschema contractum), mole crickets (Gryllotalpidae), and silkworm pupae (Bombyx mori). For each species, two samples of boiled, dried and salted insects were purchased. The microbial DNA was extracted from the insect samples and subjected to polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), high-throughput sequencing and qualitative real-time PCR assays. The microbiota of the analyzed samples were widely characterized by the presence of spore-forming bacteria mainly represented by the genera Bacillus and Clostridium. Moreover, the genera Anaerobacillus, Paenibacillus, Geobacillus, Pseudomonas, Stenotrophomonas, Massilia, Delftia, Lactobacillus, Staphylococcus, Streptococcus, Vagococcus, and Vibrio were also detected. Real-time PCR allowed for ascertainment of the absence of Coxiella burnetii, Shiga toxin-producing E. coli (STEC), and Pseudomonas aeruginosa in all samples. The results of this study confirm the importance of combining different molecular techniques to characterize the biodiversity of complex ecosystems such as edible insects. The presence of potential human pathogens suggests the need for a careful application of good manufacturing practices during insect processing. This study provides further data that will be useful in risk analyses of edible insects as a novel food source.	[Osimani, Andrea; Milanovic, Vesna; Garofalo, Cristiana; Cardinali, Federica; Roncolini, Andrea; Sabbatini, Riccardo; Clementi, Francesca; Aquilanti, Lucia] Univ Politecn Marche, Dipartimento Sci Agr Alimentari & Ambientali, Via Brecce Bianche, I-60131 Ancona, Italy; [De Filippis, Francesca; Ercolini, Danilo] Univ Naples Federico II, Dept Agr Sci, Div Microbiol, Portici, Italy; [De Filippis, Francesca; Ercolini, Danilo] Univ Naples Federico II, Task Force Microbiome Studies, Naples, Italy; [Gabucci, Claudia; Petruzzelli, Annalisa; Tonucci, Franco] Ctr Riferimento Reg Autocontrollo, Ist Zooprofilatt Sperimentale Umbria & Marche, Via Canonici 140, I-61100 Pesaro, Italy	Garofalo, C (reprint author), Univ Politecn Marche, Dipartimento Sci Agr Alimentari & Ambientali, Via Brecce Bianche, I-60131 Ancona, Italy.	c.garofalo@univpm.it		De Filippis, Francesca/0000-0002-3474-2884; OSIMANI, ANDREA/0000-0003-4095-6181; Ercolini, Danilo/0000-0003-3061-9560				84	2	2	26	31	ELSEVIER SCIENCE BV	AMSTERDAM	PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS	0168-1605	1879-3460		INT J FOOD MICROBIOL	Int. J. Food Microbiol.	Jul-02	2018	276						54	62		10.1016/j.ijfoodmicro.2018.04.013				9	Food Science & Technology; Microbiology	Food Science & Technology; Microbiology	GG2HN	WOS:000432510900008	29665523				22-11-18
J	Doxey, AC; Mansfield, MJ; Montecucco, C				Doxey, Andrew C.; Mansfield, Michael J.; Montecucco, Cesare			Discovery of novel bacterial toxins by genomics and computational biology	TOXICON			English	Article; Proceedings Paper	10th Conference on Basic Science and Clinical Aspects of Botulinum and Other Toxins (TOXINS)	JAN 18-21, 2017	Madrid, SPAIN	Int Neurotoxin Assoc		Bacterial toxins; Botulinum; Diphtheria; Genomics; Bioinformatics; Metagenomics; BoNT; Toxin discovery	NEUROTOXIN GENE CLUSTERS; BOTULINUM NEUROTOXIN; DIPHTHERIA-TOXIN; PROTEIN TOXINS; UNCULTURED MICROORGANISMS; NEUROTRANSMITTER RELEASE; VIRULENCE FACTORS; CELL BIOLOGY; WEB SERVER; SEQUENCE	Hundreds and hundreds of bacterial protein toxins are presently known. Traditionally, toxin identification begins with pathological studies of bacterial infectious disease. Following identification and cultivation of a bacterial pathogen, the protein toxin is purified from the culture medium and its pathogenic activity is studied using the methods of biochemistry and structural biology, cell biology, tissue and organ biology, and appropriate animal models, supplemented by bioimaging techniques. The ongoing and explosive development of high-throughput DNA sequencing and bioinformatic approaches have set in motion a revolution in many fields of biology, including microbiology. One consequence is that genes encoding novel bacterial toxins can be identified by bioinformatic and computational methods based on previous knowledge accumulated from studies of the biology and pathology of thousands of known bacterial protein toxins. Starting from the paradigmatic cases of diphtheria toxin, tetanus and botulinum neurotoxins, this review discusses traditional experimental approaches as well as bioinformatics and genomics-driven approaches that facilitate the discovery of novel bacterial toxins. We discuss recent work on the identification of novel botulinum-like toxins from genera such as Weissella, Chryseobacterium, and Enteroccocus, and the implications of these computationally identified toxins in the field. Finally, we discuss the promise of metagenomics in the discovery of novel toxins and their ecological niches, and present data suggesting the existence of uncharacterized, botulinum-like toxin genes in insect gut metagenomes. (C) 2018 Published by Elsevier Ltd.	[Doxey, Andrew C.; Mansfield, Michael J.] Univ Waterloo, Dept Biol, Waterloo, ON, Canada; [Montecucco, Cesare] Univ Padua, Dept Biomed Sci, Padua, Italy	Doxey, AC (reprint author), Univ Waterloo, Dept Biol, Waterloo, ON, Canada.; Montecucco, C (reprint author), Univ Padua, Dept Biomed Sci, Padua, Italy.	acdoxey@uwaterloo.ca		Doxey, Andrew/0000-0003-2015-099X	Natural Sciences and Engineering Research Council of Canada; Ministry of Defence of Italy; University of Padova	This work was supported by the Natural Sciences and Engineering Research Council of Canada, through a Discovery Grant to A.C.D, as well as an Ontario Early Researcher Award (A.C.D.). This work was also supported by the Ministry of Defence of Italy and by the University of Padova (C.M.).		87	7	7	4	6	PERGAMON-ELSEVIER SCIENCE LTD	OXFORD	THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND	0041-0101			TOXICON	Toxicon	Jun-01	2018	147				SI		2	12		10.1016/j.toxicon.2018.02.002				11	Pharmacology & Pharmacy; Toxicology	Pharmacology & Pharmacy; Toxicology	GG9IV	WOS:000433015100002	29438679		Y	Y	22-11-18
J	Cameron, SL; Lo, N; Bourguignon, T; Svenson, GJ; Evans, TA				Cameron, Stephen L.; Lo, Nathan; Bourguignon, Thomas; Svenson, Gavin J.; Evans, Theodore A.			A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae): Robust support for interfamilial relationships and molecular synapomorphies define major clades	MOLECULAR PHYLOGENETICS AND EVOLUTION			English	Article						Termites; Phylogeny; Mitochondrial genomics; Rare genomic changes	INSECTA HEMIPTERA HETEROPTERA; TRANSFER-RNA GENES; COMPOSITIONAL HETEROGENEITY; HIGH-THROUGHPUT; SEQUENCE DATA; ISOPTERA; DICTYOPTERA; COCKROACH; RHINOTERMITIDAE; REARRANGEMENTS	Despite their ecological significance as decomposers and their evolutionary significance as the most speciose eusocial insect group outside the Hymenoptera, termite (Blattodea: Termitoidae or Isoptera) evolutionary relationships have yet to be well resolved. Previous morphological and molecular analyses strongly conflict at the family level and are marked by poor support for backbone nodes. A mitochondrial (mt) genome phylogeny of termites was produced to test relationships between the recognised termite families, improve nodal support and test the phylogenetic utility of rare genomic changes found in the termite mt genome. Complete mt genomes were sequenced for 7 of the 9 extant termite families with additional representatives of each of the two most speciose families Rhinotermitidae (3 of 7 subfamilies) and Termitidae (3 of 8 subfamilies). The mt genome of the well supported sister-group of termites, the subsocial cockroach Cryptocercus, was also sequenced. A highly supported tree of termite relationships was produced by all analytical methods and data treatment approaches, however the relationship of the termites + Cryptocercus clade to other cockroach lineages was highly affected by the strong nucleotide compositional bias found in termites relative to other dictyopterans. The phylogeny supports previously proposed suprafamilial termite lineages, the Euisoptera and Neoisoptera, a later derived Kalotermitidae as sister group of the Neoisoptera and a monophyletic clade of dampwood (Stolotermitidae, Archotermopsidae) and harvester termites (Hodotermitidae). In contrast to previous termite phylogenetic studies, nodal supports were very high for family-level relationships within termites. Two rare genomic changes in the mt genome control region were found to be molecular synapomorphies for major clades. An elongated stem-loop structure defined the clade Polyphagidae + (Cryptocercus + termites), and a further series of compensatory base changes in this stem-loop is synapomorphic for the Neoisoptera. The complicated repeat structures first identified in Reticulitermes, composed of short (A-type) and long (B-type repeats) defines the clade Heterotermitinae + Termitidae, while the secondary loss of A-type repeats is synapomorphic for the non-macrotermitine Termitidae. (C) 2012 Elsevier Inc. All rights reserved.	[Cameron, Stephen L.] Queensland Univ Technol, Fac Sci & Engn, Earth Environm & Biol Sci Sch, Brisbane, Qld 4001, Australia; [Lo, Nathan] Univ Sydney, Sch Biol Sci, Sydney, NSW 2006, Australia; [Bourguignon, Thomas] Hokkaido Univ, Grad Sch Environm Sci, Sapporo, Hokkaido 0600810, Japan; [Svenson, Gavin J.] Cleveland Museum Nat Hist, Dept Invertebrate Zool, Cleveland, OH 44106 USA; [Evans, Theodore A.] Natl Univ Singapore, Dept Biol Sci, Singapore 117543, Singapore	Cameron, SL (reprint author), Queensland Univ Technol, Fac Sci & Engn, Earth Environm & Biol Sci Sch, GPO Box 2434, Brisbane, Qld 4001, Australia.	sl.cameron@qut.edu.au	Evans, Theodore/A-6020-2008; Cameron, Stephen/A-3742-2008	Evans, Theodore/0000-0002-0558-3036; Cameron, Stephen/0000-0002-6694-4130; Bourguignon, Thomas/0000-0002-4035-8977	US National Science Foundation [DEB0444972, DEB1050569]; Australian Research Council [DP1097265]; Taxonomy Research & Information Network (TRIM); Atlas of Living Australia	The authors would like to thank David Yeates (Australian National Insect Collection) for advice and support of this research, Cate Smith (CSIRO Plant Industry) for assistance with sequencing, and Jessica Ware (Rutgers University) and Michael Whiting (Brigham Young University) for donating specimens. This study was supported US National Science Foundation grants DEB0444972 (SLC), DEB1050569 (GJS), Australian Research Council grant DP1097265 (NL), the Taxonomy Research & Information Network (TRIM) and the Atlas of Living Australia. SLC, NL and TAE would like to acknowledge the more than 80 years of continuous research into termites at the CSIRO, which comprised the lion's share of termite research in Australia, and mourn the end of this research at CSIRO in 2011.		88	68	73	3	99	ACADEMIC PRESS INC ELSEVIER SCIENCE	SAN DIEGO	525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA	1055-7903	1095-9513		MOL PHYLOGENET EVOL	Mol. Phylogenet. Evol.	OCT	2012	65	1					163	173		10.1016/j.ympev.2012.05.034				11	Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & Heredity	Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & Heredity	996CG	WOS:000308061000015	22683563				22-11-18
J	Dupuis, JR; Brunet, BMT; Bird, HM; Lumley, LM; Fagua, G; Boyle, B; Levesque, R; Cusson, M; Powell, JA; Sperling, FAH				Dupuis, J. R.; Brunet, B. M. T.; Bird, H. M.; Lumley, L. M.; Fagua, G.; Boyle, B.; Levesque, R.; Cusson, M.; Powell, J. A.; Sperling, F. A. H.			Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex	MOLECULAR PHYLOGENETICS AND EVOLUTION			English	Article						Phylogenomics; Systematics; Genotyping-by-sequencing; RAD-seq; Population genetics; Species relationships	MAXIMUM-LIKELIHOOD PHYLOGENIES; MULTILOCUS GENOTYPE DATA; MITOCHONDRIAL-DNA; GENE TREES; LEPIDOPTERA-TORTRICIDAE; EVOLUTIONARY HISTORY; POPULATION-STRUCTURE; RAD MARKERS; DE-NOVO; INFERENCE	High throughput sequencing technologies have revolutionized the potential to reconcile incongruence between gene and species trees, and numerous approaches have been developed to take advantage of these advances. Genotyping-by-sequencing is becoming a regular tool for gathering phylogenetic data, yet comprehensive evaluations of phylogenetic methods using these data are sparse. Here we use multiple phylogenetic and population genetic methods for genotyping-by-sequencing data to assess species relationships in a group of forest insect pests, the spruce budworm (Choristoneura fumiferana) species complex. With few exceptions, all methods agree on the same relationships, most notably placing C. pinus as basal to the remainder of the group, rather than C fumiferana as previously suggested. We found strong support for the monophyly of C pinus, C fumiferana, and C retiniana, but more ambiguous relationships and signatures of introgression in a Glade of western lineages, including C carnana, C lambertiana, C occidentalis occidentalis, C. occidentalis biennis, and C orae. This represents the most taxonomically comprehensive genomic treatment of the spruce budworm species group, which is further supported by the broad agreement among multiple methodologies. (C) 2017 Elsevier Inc. All rights reserved.	[Dupuis, J. R.; Brunet, B. M. T.; Bird, H. M.; Lumley, L. M.; Fagua, G.; Sperling, F. A. H.] Univ Alberta, Dept Biol Sci, CW 405 Biosci Ctr, Edmonton, AB T6G 2E9, Canada; [Lumley, L. M.; Cusson, M.] Nat Resources Canada, Canadian Forest Serv, Laurentian Forestry Ctr, 1055 PEPS,POB 10380, Quebec City, PQ, Canada; [Fagua, G.] Pontificia Univ Javeriana, Dept Biol, Carrera 7 40-62, Bogota, DC, Colombia; [Boyle, B.; Levesque, R.] Univ Laval, IBIS, Quebec City, PQ, Canada; [Powell, J. A.] Univ Calif Berkeley, Dept Environm Sci Policy & Management, 130 Mulford Hall 3114, Berkeley, CA 94720 USA	Dupuis, JR (reprint author), USDA ARS, DKI PBARC, 64 Nowelo St, Hilo, HI 96720 USA.	jrdupuis@hawaii.edu	Sperling, Felix/H-8376-2012	Sperling, Felix/0000-0001-5148-4226; Brunet, Bryan/0000-0001-5083-9662; Lumley, Lisa/0000-0002-8925-8803	Alberta Innovates Bio Solutions grant [VCS-11-034]; National Science and Engineering Research Council [217174]; Genomics Research and Development Initiative (GRDI) grant; Genome Quebec grant (GreenSNPs project); Academic Vice rectory of the "Pontificia Universidad Javeriana-Bogota"-Administrative Department of Science, Technology and Innovation of Colombia (COLCIENCIAS) [DJE-012-2011, APCC-80-134]; WestGrid; Compute Canada Calcul Canada	We thank Alberta Environment and Sustainable Resource Development, G. Anweiler, S. Brunet, Canadian Forest Service, J. De Benedictis, J. Dombroskie, J. Doucette, A. Hundsdoerfer, J.F. Landry, L. Nolan, B. Proshek, A. Roe, D. Rubinoff, Saskatchewan Environment, and C. Whitehouse for assistance in specimen collection and two anonymous reviewers for comments. Funding was provided by an Alberta Innovates Bio Solutions grant (# VCS-11-034) and National Science and Engineering Research Council Discovery grant (# 217174) to FAHS, a Genomics Research and Development Initiative (GRDI) grant to M. Cusson, a Genome Quebec grant (GreenSNPs project) to R. Levesque, and a scholarship from the Academic Vice rectory of the "Pontificia Universidad Javeriana-Bogota" (Agreement DJE-012-2011)-Administrative Department of Science, Technology and Innovation of Colombia (COLCIENCIAS, APCC-80-134) to G. Fagua. This research was enabled in part by support provided by WestGrid (www.westgrid.ca) and Compute Canada Calcul Canada (www.computecanada.ca).		109	6	6	4	51	ACADEMIC PRESS INC ELSEVIER SCIENCE	SAN DIEGO	525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA	1055-7903	1095-9513		MOL PHYLOGENET EVOL	Mol. Phylogenet. Evol.	JUN	2017	111						158	168		10.1016/j.ympev.2017.04.001				11	Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & Heredity	Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & Heredity	EU0QA	WOS:000400715100013	28390910				22-11-18
J	Reineke, A; Assaf, HA; Kulanek, D; Mori, N; Pozzebon, A; Duso, C				Reineke, A.; Assaf, H. A.; Kulanek, D.; Mori, N.; Pozzebon, A.; Duso, C.			A novel set of microsatellite markers for the European Grapevine Moth Lobesia botrana isolated using next-generation sequencing and their utility for genetic characterization of populations from Europe and the Middle East	BULLETIN OF ENTOMOLOGICAL RESEARCH			English	Article						microsatellites; SSR markers; Lobesia botrana; 454 pyrosequencing; population genetics	CYDIA-POMONELLA L.; MULTILOCUS GENOTYPE DATA; CODLING MOTH; LEPIDOPTERA-TORTRICIDAE; EUPHYDRYAS-AURINIA; LOCI; DIFFERENTIATION; VARIABILITY; INSECT; NOCTUIDAE	Using a high-throughput 454 pyrosequencing approach a novel set of microsatellite markers was developed for one of the key grapevine insect pests, the European grapevine moth Lobesia botrana (Lepidoptera: Tortricidae). 20 primer pairs flanking a microsatellite motif were designed based on the sequences obtained and were subsequently evaluated in a sample of 14 L. botrana populations from Europe and the Middle East. 11 markers showed stable and reproducible amplification patterns; however, one of the 11 markers was monomorphic in all L. botrana populations analysed. Estimated frequencies of null alleles of more than 20% were evident for two of the markers tested, but varied substantially depending on the respective L. botrana population. In 12 of the 14 L. botrana populations observed heterozygosities were lower to those expected under Hardy-Weinberg equilibrium, indicating a deficiency of heterozygotes in the respective populations. The overall FST value of 0.075 suggested a moderate but significant genetic differentiation between the L. botrana populations included in this study. In addition, a clear geographic structure was detected in the set of samples, evident through a significant isolation by distance and through results from structure analysis. In structure analysis, L. botrana populations were grouped in two clearly separated clusters according to their European (Spain, Italy, Germany) or Middle Eastern (Israel, Syria, Turkey) origin. This novel set of microsatellite markers can now be applied to study the evolutionary ecology of this species including host shifts and host adaptation as well as spread of individuals across worldwide viticulture.	[Reineke, A.; Kulanek, D.] Geisenheim Univ, Dept Phytomed, D-65366 Geisenheim, Germany; [Assaf, H. A.; Mori, N.; Pozzebon, A.; Duso, C.] Univ Padua, Dept Agron Food Nat Resources Anim & Environm, I-35020 Padua, Italy	Reineke, A (reprint author), Geisenheim Univ, Dept Phytomed, D-65366 Geisenheim, Germany.	annette.reineke@hs-gm.de	Pozzebon, Alberto/B-7328-2009	Pozzebon, Alberto/0000-0002-2445-7211; Duso, Carlo/0000-0002-2600-2536	Cariparo (Padova)	We sincerely thank our colleagues in Europe for help in collecting L. botrana specimens, in particular Berthold Fuchs (D_LOR), Gertrud Wegener-Kiss (D_KAI), Karl-Josef Schirra and Ursula Hetterling (D_NW), Ozlem Altindisli (T_MAL, T_MCA, T_MLA, T_MMA), Tirtza Zahavi (IL_MG), Bruno Bagnoli and Andrea Lucchi (E_YEL). Thanks to Mirjam Hauck for help in the laboratory and Cariparo (Padova) for supporting PhD studies of Haya Abou-Assaf.		47	2	2	2	36	CAMBRIDGE UNIV PRESS	CAMBRIDGE	EDINBURGH BLDG, SHAFTESBURY RD, CB2 8RU CAMBRIDGE, ENGLAND	0007-4853	1475-2670		B ENTOMOL RES	Bull. Entomol. Res.	AUG	2015	105	4					408	416		10.1017/S0007485315000267				9	Entomology	Entomology	CQ0LE	WOS:000360286600004	25850369				22-11-18
J	Brandon-Mong, GJ; Gan, HM; Sing, KW; Lee, PS; Lim, PE; Wilson, JJ				Brandon-Mong, G. -J.; Gan, H. -M.; Sing, K. -W.; Lee, P. -S.; Lim, P. -E.; Wilson, J. -J.			DNA metabarcoding of insects and allies: an evaluation of primers and pipelines	BULLETIN OF ENTOMOLOGICAL RESEARCH			English	Article						Arthropoda; biodiversity; COI; high-throughput sequencing; Illumina MiSeq; Malaise trap	BIODIVERSITY ASSESSMENT; ANNEALING TEMPERATURE; PCR; GENERATION; DIVERSITY; BARCODE; SAMPLES; RECOMBINATION; COMMUNITIES; ARTHROPODS	Metabarcoding, the coupling of DNA-based species identification and high-throughput sequencing, offers enormous promise for arthropod biodiversity studies but factors such as cost, speed and ease-of-use of bioinformatic pipelines, crucial for making the leapt from demonstration studies to a real-world application, have not yet been adequately addressed. Here, four published and one newly designed primer sets were tested across a diverse set of 80 arthropod species, representing 11 orders, to establish optimal protocols for Illumina-based metabarcoding of tropical Malaise trap samples. Two primer sets which showed the highest amplification success with individual specimen polymerase chain reaction (PCR, 98%) were used for bulk PCR and Illumina MiSeq sequencing. The sequencing outputs were subjected to both manual and simple metagenomics quality control and filtering pipelines. We obtained acceptable detection rates after bulk PCR and high-throughput sequencing (80-90% of input species) but analyses were complicated by putative heteroplasmic sequences and contamination. The manual pipeline produced similar or better outputs to the simple metagenomics pipeline (1.4 compared with 0.5 expected:unexpected Operational Taxonomic Units). Our study suggests that metabarcoding is slowly becoming as cheap, fast and easy as conventional DNA barcoding, and that Malaise trap metabarcoding may soon fulfill its potential, providing a thermometer for biodiversity.	[Brandon-Mong, G. -J.; Sing, K. -W.; Lee, P. -S.; Wilson, J. -J.] Univ Malaya, Inst Biol Sci, Museum Zool, Fac Sci, Kuala Lumpur 50603, Malaysia; [Brandon-Mong, G. -J.; Sing, K. -W.; Lee, P. -S.; Wilson, J. -J.] Univ Malaya, Inst Biol Sci, Ecol & Biodivers Program, Fac Sci, Kuala Lumpur 50603, Malaysia; [Gan, H. -M.] Monash Univ Malaysia, Sch Sci, Petaling Jaya 47500, Selangor, Malaysia; [Gan, H. -M.] Monash Univ Malaysia, Genom Facil, Petaling Jaya 47500, Selangor, Malaysia; [Lim, P. -E.] Univ Malaya, IOES, Kuala Lumpur 50603, Malaysia	Wilson, JJ (reprint author), Univ Malaya, Inst Biol Sci, Museum Zool, Fac Sci, Kuala Lumpur 50603, Malaysia.	johnwilson@um.edu.my	LIM, PHAIK EEM/B-5331-2010; Wilson, John James/C-4656-2012	LIM, PHAIK EEM/0000-0001-9186-1487; Wilson, John James/0000-0002-3583-3550; Gan, Han Ming/0000-0001-7987-738X	High Impact Research Grant (Chancellery) from the University of Malaya; University of Malaya; Monash University Malaysia Tropical Medicine and Biology Platform	This study was supported by a High Impact Research Grant (Chancellery) from the University of Malaya to J. J. W. and P. E. L.; K. W. S. and P. S. L. are supported by postgraduate scholarships from the University of Malaya. Yee Yoke Pei (Ecology and Biodiversity Program, UM) and Narong Jaturas (Department of Parasitology, UM) assisted in sample collection and laboratory work. M. Sugumaran (coordinator of Rimba Ilmu Botanic Garden) provided permission to deploy the Malaise trap. H. M. G. is grateful to the Monash University Malaysia Tropical Medicine and Biology Platform for financial and infrastructure support.		77	35	36	7	90	CAMBRIDGE UNIV PRESS	CAMBRIDGE	EDINBURGH BLDG, SHAFTESBURY RD, CB2 8RU CAMBRIDGE, ENGLAND	0007-4853	1475-2670		B ENTOMOL RES	Bull. Entomol. Res.	DEC	2015	105	6					717	727		10.1017/S0007485315000681				11	Entomology	Entomology	CW7GL	WOS:000365166000008	26344799				22-11-18
J	Lucas, JA				Lucas, J. A.			Advances in plant disease and pest management	JOURNAL OF AGRICULTURAL SCIENCE			English	Article							SYSTEMIC ACQUIRED-RESISTANCE; WHEAT BLOSSOM MIDGE; DEFENSE RESPONSES; SITODIPLOSIS-MOSELLANA; FUNCTIONAL GENOMICS; NEMATODE RESISTANCE; DIFFERENT BIOTYPES; EFFECTOR PROTEINS; FOOD SECURITY; INSECT PESTS	Pests and diseases impact on crop yield and quality, and also reduce resource-use efficiency. Improved crop protection strategies to prevent such damage and loss can increase production and make a substantial contribution to food security. DNA-based technologies are likely to greatly increase the speed, sensitivity and accuracy of pest and pathogen detection and diagnosis. Rapid sequencing of nucleic acids from infected plants will aid identification of novel disease agents. Biomarkers of disease or crop damage such as volatile chemicals or blends may also be used to detect pest outbreaks. Biosensors coupled to information networks will provide real-time monitoring and surveillance of crops or stored produce and hence early warning of emerging problems and new invasive species. Challenges remain in the dissemination of new technologies and information to resource poor farmers in developing countries, although the rapid extension of the internet, mobile phones and other communication networks will provide new opportunities. Defining the genetic and molecular basis of innate plant immunity has been a major advance in plant biology with the potential to identify new targets for intervention via novel chemistry or genetic modification (GM). Identification of regulatory genes, signal molecules, pathways and networks controlling induced plant defence should lead to the development of a new generation of defence modulators, delivered either as crop protection products, or via biological agents on seeds or in the root zone. There should also be opportunities to select more responsive crop genotypes, or to develop transgenic crops tailored to respond to specific chemical cues or molecular patterns diagnostic for particular biotic threats. Sequencing of the genomes of the major crop species and their wild relatives will expand enormously the known gene pool and diversity of genetic resources available for plant breeders to access. It should be possible to identify genomic regions and genes conferring more durable, quantitative resistance to pathogens. The breeding cycle will be accelerated by high-throughput phenotyping and more efficient selection of resistance traits using within-gene markers. GM approaches will facilitate pyramiding (combining) resistance genes with different specificities and modes of action, thereby reducing the risk of directional selection for virulence. Analysis of the genomes of plant pathogens and invertebrate pests is already providing new information on genes, gene families and processes involved in host colonization and pathogenicity. Comparative genomics of species with diverse host ranges, contrasting feeding habits and different pathogenic lifestyles will identify new targets for inhibiting pest attack and aid the development of novel antimicrobial drugs and pesticides. Understanding the natural ecology of pests and pathogens, such as the factors determining host location, resource exploitation and interactions with other organisms, will improve our ability to manipulate behaviour, or exploit natural enemies or other antagonists of pest species. Volatile signals, either from natural plant sources, or engineered in transgenic crops, will be more widely used to modify pest behaviour. It may also be possible to manipulate microbial communities regulating pathogen populations and activity, and thereby recruit and retain more effective biocontrol agents. Insights into the natural diversity and activity of soil and microbial populations in the zones surrounding roots and seeds will provide new information on mechanism of suppression regulating pest species. Fully effective interventions are unlikely, due to the complexity and diversity of the soil system, but there should be progress towards integrated control regimes combining more resistant crop genotypes (either selected or GM) with targeted management of natural suppressive processes. Harnessing new technologies and knowledge to create more durable resistant crops and sustainable disease and pest management systems will require improved understanding of the factors driving pest and pathogen adaptation and evolution. There must also be an increased emphasis on translational research and delivery, and developing strategies appropriate for lower-input production systems, if the second 'green revolution' is to become a reality.	Rothamsted Res, Ctr Sustainable Pest & Dis Management, Dept Plant Pathol & Microbiol, Harpenden AL5 3BQ, Herts, England	Lucas, JA (reprint author), Rothamsted Res, Ctr Sustainable Pest & Dis Management, Dept Plant Pathol & Microbiol, Harpenden AL5 3BQ, Herts, England.	john.lucas@bbsrc.ac.uk	Emchi, Karma/Q-1952-2016; Lucas, John/D-9699-2013					137	32	33	8	250	CAMBRIDGE UNIV PRESS	NEW YORK	32 AVENUE OF THE AMERICAS, NEW YORK, NY 10013-2473 USA	0021-8596			J AGR SCI	J. Agric. Sci.		2011	149			1			91	114		10.1017/S0021859610000997				24	Agriculture, Multidisciplinary	Agriculture	729WY	WOS:000287986100010					22-11-18
J	Jubeaux, G; Audouard-Combe, F; Simon, R; Tutundjian, R; Salvador, A; Geffard, O; Chaumot, A				Jubeaux, Guillaume; Audouard-Combe, Fabien; Simon, Romain; Tutundjian, Renaud; Salvador, Arnaud; Geffard, Olivier; Chaumot, Arnaud			Vitellogenin-like Proteins among Invertebrate Species Diversity: Potential of Proteomic Mass Spectrometry for Biomarker Development	ENVIRONMENTAL SCIENCE & TECHNOLOGY			English	Article							ENDOCRINE DISRUPTION; MYTILUS-EDULIS; SIGNATURE PEPTIDE; MOLECULAR CLOCK; YOLK PROTEINS; EVOLUTION; CONSERVATION; EXPOSURE; ESTROGEN; MUSSELS	Cost-effective methodologies along with cross-species applicability constitute key points for biomarker development in ecotoxicology. With the advent of cheaper affordable genomic techniques and high throughput sequencing, omics tools could facilitate the assessment of effects of environmental contaminants for all taxa biodiversity. We assessed the potential of absolute quantification of proteins using mass spectrometry to develop vitellogenin(Vg)-like protein assays for invertebrates. We used available sequences in public databases to rapidly identify Vg-proteotypic peptides in seven species from different main taxa of protostome invertebrates (mollusk bivalves, crustacean amphipods, branchiopods, copepods and isopods, and insect diptera). Functional validation was performed by comparing proteomic signals from reproductive female tissue samples and negative controls (male or juvenile tissues). In a second part, we demonstrate in gammarids, daphnids, drosophilids, and gastropods that the assay validated in Vg-sequenced species can be applied to Vg-unsequenced species thanks to the evolutionary conservation of Vg-proteotypic peptide motifs. Finally, we discuss the relevance of mass spectrometry for biomarker development (specific measurement, rapid development, transferability across species). Our study supplies an illustration of the promising strategy to address the challenge of biodiversity in ecotoxicology, which consists in employing omics tools from comparative and evolutionary perspectives.	[Jubeaux, Guillaume; Audouard-Combe, Fabien; Tutundjian, Renaud; Geffard, Olivier; Chaumot, Arnaud] Irstea, UR MALY, F-69336 Lyon, France; [Simon, Romain; Salvador, Arnaud] Univ Lyon 1, Inst Sci Analyt, UMR 5280, F-69622 Villeurbanne, France	Chaumot, A (reprint author), Irstea, UR MALY, 3 Bis Quai Chauveau,CP 220, F-69336 Lyon, France.	arnaud.chaumot@irstea.fr		Salvador, Arnaud/0000-0002-5981-3028; chaumot, arnaud/0000-0001-9132-3419	French national research program PNRPE [Convention n_CV05000088, Convention n_0006942]	This research was funded by the French national research program PNRPE (Convention n_CV05000088 and Convention n_0006942). We thank R. Allemand for kindly providing samples of Drosophila melanogaster, D. subobscura, and D. immigrans, F. Bonneton for Tribolium castaneum, K. Glover and R. Skern for Lepeophtheirus salmonis, B. Gourbal for Biomphalaria glabrata, S. Huchette for Haliotis tuberculata, C. Souty for Armadillidium vulgare, and B. Xuereb for Mytilus edulis. We are grateful to H. Queau for technical assistance, and we thank M. Coquery and P. Bados for experimental facilities at Irstea, Laboratoire d'analyses physicochimiques des milieux aquatiques.		44	6	6	1	38	AMER CHEMICAL SOC	WASHINGTON	1155 16TH ST, NW, WASHINGTON, DC 20036 USA	0013-936X			ENVIRON SCI TECHNOL	Environ. Sci. Technol.	Jun-05	2012	46	11					6315	6323		10.1021/es300550h				9	Engineering, Environmental; Environmental Sciences	Engineering; Environmental Sciences & Ecology	952HJ	WOS:000304783000087	22578134				22-11-18
J	Tay, WT; Elfekih, S; Polaszek, A; Court, LN; Evans, GA; Gordon, KHJ; De Barro, PJ				Tay, W. T.; Elfekih, S.; Polaszek, A.; Court, L. N.; Evans, G. A.; Gordon, K. H. J.; De Barro, P. J.			Novel molecular approach to define pest species status and tritrophic interactions from historical Bemisia specimens	SCIENTIFIC REPORTS			English	Article							TABACI HEMIPTERA ALEYRODIDAE; MITOCHONDRIAL GENOMES; HYMENOPTERA; APHELINIDAE; COMPLEX; PARASITOIDS; POPULATIONS; WHITEFLIES; EVOLUTION; SEQUENCE	Museum specimens represent valuable genomic resources for understanding host-endosymbiont/parasitoid evolutionary relationships, resolving species complexes and nomenclatural problems. However, museum collections suffer DNA degradation, making them challenging for molecular-based studies. Here, the mitogenomes of a single 1912 Sri Lankan Bemisia emiliae cotype puparium, and of a 1942 Japanese Bemisia puparium are characterised using a Next-Generation Sequencing approach. Whiteflies are small sap-sucking insects including B. tabaci pest species complex. Bemisia emiliae's draft mitogenome showed a high degree of homology with published B. tabaci mitogenomes, and exhibited 98-100% partial mitochondrial DNA Cytochrome Oxidase I (mtCOI) gene identity with the B. tabaci species known as Asia II-7. The partial mtCOI gene of the Japanese specimen shared 99% sequence identity with the Bemisia 'JpL' genetic group. Metagenomic analysis identified bacterial sequences in both Bemisia specimens, while hymenopteran sequences were also identified in the Japanese Bemisia puparium, including complete mtCOI and rRNA genes, and various partial mtDNA genes. At 88-90% mtCOI sequence identity to Aphelinidae wasps, we concluded that the 1942 Bemisia nymph was parasitized by an Eretmocerus parasitoid wasp. Our approach enables the characterisation of genomes and associated metagenomic communities of museum specimens using 1.5 ng gDNA, and to infer historical tritrophic relationships in Bemisia whiteflies.	[Tay, W. T.; Elfekih, S.; Court, L. N.; Gordon, K. H. J.] CSIRO, Black Mt Labs, Clunies Ross St, Canberra, ACT 2601, Australia; [Polaszek, A.] Nat Hist Museum, London, England; [Evans, G. A.] USDA APHIS NIS, BARC West, Beltsville, MD 20705 USA; [De Barro, P. J.] CSIRO, Brisbane, Qld 4001, Australia	Tay, WT (reprint author), CSIRO, Black Mt Labs, Clunies Ross St, Canberra, ACT 2601, Australia.	weetek.tay@csiro.au	Court, Leon/J-7138-2013; Tay, Wee Tek/C-1818-2008; De Barro, Paul/C-1724-2008; Elfekih, Samia/J-6706-2013	Tay, Wee Tek/0000-0002-8451-0811; 	CSIRO OCE Postdoctoral Fellowship	S.E. was supported by a CSIRO OCE Postdoctoral Fellowship. We thank Tom Walsh and Matthew Morgan for input to improve an earlier version of the manuscript.		66	4	4	0	9	NATURE PUBLISHING GROUP	LONDON	MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND	2045-2322			SCI REP-UK	Sci Rep	Mar-27	2017	7								429	10.1038/s41598-017-00528-7				13	Multidisciplinary Sciences	Science & Technology - Other Topics	EP5AJ	WOS:000397391000005	28348369	DOAJ Gold, Green Published			22-11-18
J	Xiao, GH; Ying, SH; Zheng, P; Wang, ZL; Zhang, SW; Xie, XQ; Shang, YF; St Leger, RJ; Zhao, GP; Wang, CS; Feng, MG				Xiao, Guohua; Ying, Sheng-Hua; Zheng, Peng; Wang, Zheng-Liang; Zhang, Siwei; Xie, Xue-Qin; Shang, Yanfang; St Leger, Raymond J.; Zhao, Guo-Ping; Wang, Chengshu; Feng, Ming-Guang			Genomic perspectives on the evolution of fungal entomopathogenicity in Beauveria bassiana	SCIENTIFIC REPORTS			English	Article							METARHIZIUM-ANISOPLIAE; GENE-EXPRESSION; BIOLOGICAL-CONTROL; FILAMENTOUS FUNGI; VIRULENCE FACTOR; INSECT PESTS; BIOSYNTHESIS; ASPERGILLUS; METABOLISM; PROTEINS	The ascomycete fungus Beauveria bassiana is a pathogen of hundreds of insect species and is commercially produced as an environmentally friendly mycoinsecticide. We sequenced the genome of B. bassiana and a phylogenomic analysis confirmed that ascomycete entomopathogenicity is polyphyletic, but also revealed convergent evolution to insect pathogenicity. We also found many species-specific virulence genes and gene family expansions and contractions that correlate with host ranges and pathogenic strategies. These include B. bassiana having many more bacterial-like toxins (suggesting an unsuspected potential for oral toxicity) and effector-type proteins. The genome also revealed that B. bassiana resembles the closely related Cordyceps militaris in being heterothallic, although its sexual stage is rarely observed. A high throughput RNA-seq transcriptomic analysis revealed that B. bassiana could sense and adapt to different environmental niches by activating well-defined gene sets. The information from this study will facilitate further development of B. bassiana as a cost-effective mycoinsecticide.	[Xiao, Guohua; Zheng, Peng; Zhang, Siwei; Shang, Yanfang; Wang, Chengshu] Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Plant Physiol & Ecol, Key Lab Insect Dev & Evolutionary Biol, Shanghai 200032, Peoples R China; [Ying, Sheng-Hua; Wang, Zheng-Liang; Xie, Xue-Qin; Feng, Ming-Guang] Zhejiang Univ, Coll Life Sci, Hangzhou 310058, Peoples R China; [St Leger, Raymond J.] Univ Maryland, Dept Entomol, College Pk, MD 20742 USA; [Zhao, Guo-Ping; Wang, Chengshu] Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Plant Physiol & Ecol, Key Lab Synthet Biol, Shanghai, Peoples R China	Wang, CS (reprint author), Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Plant Physiol & Ecol, Key Lab Insect Dev & Evolutionary Biol, Shanghai 200032, Peoples R China.	cswang@sibs.ac.cn; mgfeng@zju.edu.cn	Xiao, Guohua/G-3083-2013; St. Leger, Raymond/N-3219-2013; Wang, Chengshu/A-1656-2011	Xiao, Guohua/0000-0003-3407-2734; Wang, Chengshu/0000-0003-1477-1466	Ministry of Science and Technology of China [2009CB118904, 2011AA10A204]; Natural Science Foundation of China [30930018]; Chinese Academy of Sciences [KSCX2-EW-N-06]	This study was supported by the Ministry of Science and Technology of China (Grant No. 2009CB118904 and 2011AA10A204), the Natural Science Foundation of China (Grant No. 30930018) and the Chinese Academy of Sciences (Grant No. KSCX2-EW-N-06).		80	230	254	14	157	NATURE PUBLISHING GROUP	LONDON	MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND	2045-2322			SCI REP-UK	Sci Rep	Jul-02	2012	2								483	10.1038/srep00483				10	Multidisciplinary Sciences	Science & Technology - Other Topics	969SY	WOS:000306080000001	22761991	DOAJ Gold, Green Published	Y	N	22-11-18
J	Zhao, Y; Zhang, S; Luo, JY; Wang, CY; Lv, LM; Cui, JJ				Zhao, Yao; Zhang, Shuai; Luo, Jun-Yu; Wang, Chun-Yi; Lv, Li-Min; Cui, Jin-Jie			Bacterial communities of the cotton aphid Aphis gossypii associated with Bt cotton in northern China	SCIENTIFIC REPORTS			English	Article							SAP-FEEDING INSECTS; FACULTATIVE SYMBIONTS; ACYRTHOSIPHON-PISUM; SECONDARY SYMBIONTS; HORIZONTAL TRANSFER; HIGH-THROUGHPUT; HOST GENOTYPE; PEA APHIDS; ENDOSYMBIONT; DIVERSITY	Aphids are infected with a wide variety of endosymbionts that can confer ecologically relevant traits. However, the bacterial communities of most aphid species are still poorly characterized. This study investigated the bacterial diversity of the cotton aphid Aphis gossypii associated with Bt cotton in northern China by targeting the V4 region of the 16S rDNA using the Illumina MiSeq platform. Our sequencing data revealed that bacterial communities of A. gossypii were generally dominated by the primary symbiont Buchnera, together with the facultative symbionts Arsenophonus and Hamiltonella. To our knowledge, this is the first report documenting the facultative symbiont Hamiltonella in A. gossypii. Moreover, the bacterial community structure was similar within aphids from the same province, but distinct among those from different provinces. The taxonomic diversity of the bacterial community is greater in Hebei Province compared with in samples from Henan and Shandong Provinces. The selection pressure exerted by the different geographical locations could explain the differences found among the various provinces. These findings broaden our understanding of the interactions among aphids, endosymbionts and their environments, and provide clues to develop potential biocontrol techniques against this cotton aphid.	[Zhao, Yao; Zhang, Shuai; Luo, Jun-Yu; Wang, Chun-Yi; Lv, Li-Min; Cui, Jin-Jie] CAAS, Inst Cotton Res, State Key Lab Cotton Biol, Anyang 455000, Peoples R China; [Zhao, Yao] Huazhong Agr Univ, Hubei Insect Resources Utilizat & Sustainable Pes, Wuhan 430070, Peoples R China	Cui, JJ (reprint author), CAAS, Inst Cotton Res, State Key Lab Cotton Biol, Anyang 455000, Peoples R China.	cuijinjie@126.com			National Special Transgenic Project of China [2014ZX08011-002]	We acknowledge Bo Chu, Si-Bao Wang and Li Wang for aphid sample collection. This research was supported by the National Special Transgenic Project of China (2014ZX08011-002).		57	2	2	3	32	NATURE PUBLISHING GROUP	LONDON	MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND	2045-2322			SCI REP-UK	Sci Rep	Apr-15	2016	6								22958	10.1038/srep22958				8	Multidisciplinary Sciences	Science & Technology - Other Topics	DJ4FO	WOS:000374161000001	27079679	DOAJ Gold, Green Published			22-11-18
J	Pornon, A; Escaravage, N; Burrus, M; Holota, H; Khimoun, A; Mariette, J; Pellizzari, C; Iribar, A; Etienne, R; Taberlet, P; Vidal, M; Winterton, P; Zinger, L; Andalo, C				Pornon, Andre; Escaravage, Nathalie; Burrus, Monique; Holota, Helene; Khimoun, Aurelie; Mariette, Jerome; Pellizzari, Charlene; Iribar, Amaia; Etienne, Roselyne; Taberlet, Pierre; Vidal, Marie; Winterton, Peter; Zinger, Lucie; Andalo, Christophe			Using metabarcoding to reveal and quantify plant-pollinator interactions	SCIENTIFIC REPORTS			English	Article							ANIMAL MUTUALISTIC NETWORKS; ENVIRONMENTAL DNA; RHODODENDRON-FERRUGINEUM; POLLEN MORPHOLOGY; BIODIVERSITY; COMMUNITIES; POPULATION; BEES; IDENTIFICATION; CONSERVATION	Given the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number of trnL and ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number of trnL and ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 and trnL sequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole.	[Pornon, Andre; Escaravage, Nathalie; Burrus, Monique; Holota, Helene; Pellizzari, Charlene; Iribar, Amaia; Etienne, Roselyne; Zinger, Lucie; Andalo, Christophe] Univ Toulouse 3, Lab Evolut & Diversite Biol EDB, F-31062 Toulouse, France; [Pornon, Andre; Escaravage, Nathalie; Burrus, Monique; Holota, Helene; Pellizzari, Charlene; Iribar, Amaia; Etienne, Roselyne; Zinger, Lucie; Andalo, Christophe] CNRS, EDB, UMR 5174, F-31062 Toulouse, France; [Khimoun, Aurelie] Univ Bourgogne, Lab Biogeosci, 6 Bld Gabriel, F-21000 Dijon, France; [Mariette, Jerome] INRA, Toulouse UR875, Plate Forme Bioinformat Genotoul, Math & Informat Appl, F-31320 Castanet Tolosan, France; [Taberlet, Pierre] Univ Grenoble 1, CNRS UMR 5553, Lab Ecol Alpine, BP 43, F-38041 Grenoble, France; [Vidal, Marie] INRA UAR1209, Genotoul, GeT PlaGe, F-31320 Castanet Tolosan, France; [Winterton, Peter] Univ Toulouse 3, Dept Langues & Gest, F-31062 Toulouse, France	Pornon, A (reprint author), Univ Toulouse 3, Lab Evolut & Diversite Biol EDB, F-31062 Toulouse, France.; Pornon, A (reprint author), CNRS, EDB, UMR 5174, F-31062 Toulouse, France.	andre.pornon@univ-tlse3.fr	Zinger, Lucie/D-2527-2010	Zinger, Lucie/0000-0002-3400-5825	French Laboratory of Excellence project "TULIP" [ANR-10-LABX-41, ANR-11-IDEX-0002-02]; Centre National de la Recherche Scientifique-INEE (ERESA program) [DJ/ST/IP/2013/D-112]	This work was supported by the French Laboratory of Excellence project "TULIP" (ANR-10-LABX-41; ANR-11-IDEX-0002-02) and by the Centre National de la Recherche Scientifique-INEE (ERESA program: DJ/ST/IP/2013/D-112).		60	18	21	9	93	NATURE PUBLISHING GROUP	LONDON	MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND	2045-2322			SCI REP-UK	Sci Rep	Jun-03	2016	6								27282	10.1038/srep27282				12	Multidisciplinary Sciences	Science & Technology - Other Topics	DN4AD	WOS:000377004500001	27255732	DOAJ Gold, Green Published			22-11-18
J	Gibson, J; Shokralla, S; Porter, TM; King, I; van Konynenburg, S; Janzen, DH; Hallwachs, W; Hajibabaei, M				Gibson, Joel; Shokralla, Shadi; Porter, Teresita M.; King, Ian; van Konynenburg, Steven; Janzen, Daniel H.; Hallwachs, Winnie; Hajibabaei, Mehrdad			Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics	PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA			English	Article						cytochrome c oxidase subunit I; Costa Rica; insect; Malaise trap; NGS	GUT CONTENTS; BIODIVERSITY; DIVERSITY; BARCODE; AMPLIFICATION; REGION; PCR; SEQUENCES; RECOVERY; BACTERIA	Conventional assessments of ecosystem sample composition are based on morphology-based or DNA barcode identification of individuals. Both approaches are costly and time-consuming, especially when applied to the large number of specimens and taxa commonly included in ecological investigations. Next-generation sequencing approaches can overcome the bottleneck of individual specimen isolation and identification by simultaneously sequencing specimens of all taxa in a bulk mixture. Here we apply multiple parallel amplification primers, multiple DNA barcode markers, 454-pyrosequencing, and Illumina MiSeq sequencing to the same sample to maximize recovery of the arthropod macrobiome and the bacterial and other microbial microbiome of a bulk arthropod sample. We validate this method with a complex sample containing 1,066 morphologically distinguishable arthropods from a tropical terrestrial ecosystem with high taxonomic diversity. Multiamplicon next-generation DNA barcoding was able to recover sequences corresponding to 91% of the distinguishable individuals in a bulk environmental sample, as well as many species present as undistinguishable tissue. 454-pyrosequencing was able to recover 10 more families of arthropods and 30 more species than did conventional Sanger sequencing of each individual specimen. The use of other loci (16S and 18S ribosomal DNA gene regions) also added the detection of species of microbes associated with these terrestrial arthropods. This method greatly decreases the time and money necessary to perform DNA-based comparisons of biodiversity among ecosystem samples. This methodology opens the door to much cheaper and increased capacity for ecological and evolutionary studies applicable to a wide range of socio-economic issues, as well as a basic understanding of how the world works.	[Gibson, Joel; Shokralla, Shadi; King, Ian; van Konynenburg, Steven; Hajibabaei, Mehrdad] Univ Guelph, Dept Integrat Biol, Guelph, ON N1G 2W1, Canada; [Gibson, Joel; Shokralla, Shadi; King, Ian; van Konynenburg, Steven; Hajibabaei, Mehrdad] Univ Guelph, Biodivers Inst Ontario, Guelph, ON N1G 2W1, Canada; [Shokralla, Shadi] Mansoura Univ, Dept Microbiol, Mansoura 35516, Egypt; [Porter, Teresita M.] McMaster Univ, Dept Biol, Hamilton, ON L8S 4K1, Canada; [Janzen, Daniel H.; Hallwachs, Winnie] Univ Penn, Dept Biol, Philadelphia, PA 19104 USA	Janzen, DH (reprint author), Univ Penn, Dept Biol, Philadelphia, PA 19104 USA.	djanzen@sas.upenn.edu; mhajibab@uoguelph.ca	Porter, Teresita/H-4072-2011	King, Ian/0000-0002-8820-6956; Gibson, Joel/0000-0001-7786-0066	Government of Canada through Genome Canada; Ontario Genomics Institute through the Biomonitoring 2.0 project [OGI-050]; National Science Foundation Grant Division of Environmental Biology [0515699]; JRS Biodiversity Foundation; Wege Foundation of Grand Rapids, MI; Natural Sciences and Engineering Research Council of Canada	We thank Claudia Bertrand for help in sample collection; Stephanie Boilard for assistance with processing Sanger sequencing; M. Alex Smith for the use of photographic equipment; Hamid Nikbakht for assistance with bioinformatic analysis; and Angela Holliss and Jeff Gross for Sanger-based DNA sequencing. We are grateful to Area de Conservacion Guanacaste for protecting the forest habitat that we sampled. This project was funded by the Government of Canada through Genome Canada and the Ontario Genomics Institute through the Biomonitoring 2.0 project (OGI-050) (to M. H.), National Science Foundation Grant Division of Environmental Biology 0515699 (to D.H.J.), and the JRS Biodiversity Foundation and the Wege Foundation of Grand Rapids, MI, to the Guanacaste Dry Forest Conservation Fund. J.G. is also funded by a Natural Sciences and Engineering Research Council of Canada postdoctoral fellowship.		54	87	89	8	175	NATL ACAD SCIENCES	WASHINGTON	2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA	0027-8424			P NATL ACAD SCI USA	Proc. Natl. Acad. Sci. U. S. A.	Jun-03	2014	111	22					8007	8012		10.1073/pnas.1406468111				6	Multidisciplinary Sciences	Science & Technology - Other Topics	AI2KY	WOS:000336687900043	24808136	Bronze, Green Published			22-11-18
J	Lee, CC; Wang, J; Matsuura, K; Yang, CCS				Lee, Chih-Chi; Wang, John; Matsuura, Kenji; Yang, Chin-Cheng Scotty			The complete mitochondrial genome of yellow crazy ant, Anoplolepis gracilipes (Hymenoptera: Formicidae)	MITOCHONDRIAL DNA PART B-RESOURCES			English	Article						Yellow crazy ant; mitochondrial genome; invasive ant	ISLAND	The yellow crazy ant Anoplolepis gracilipes is an invasive species that threatens biodiversity in introduced ecosystems. We sequenced the A. gracilipes mitogenome using next-generation sequencing methods. The circular mitogenome of A. gracilipes was 16,943 bp included 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 893 bp. The base composition was AT-biased (72%). Three genomic rearrangements compared to ancestral insects were found. Phylogenetic analysis based on the concatenated nucleotide sequences of the 13 protein-coding genes supports A. gracilipes belonging to the Formicinae subfamily. We announce the A. gracilipes mitogenome as a DNA reference for further population genetic, phylogenetic, and evolutionary analyses.	[Lee, Chih-Chi; Matsuura, Kenji] Kyoto Univ, Grad Sch Agr, Lab Insect Ecol, Kyoto, Japan; [Lee, Chih-Chi; Yang, Chin-Cheng Scotty] Kyoto Univ, Res Inst Sustainable Humanosphere, Kyoto, Japan; [Wang, John] Acad Sinica, Biodivers Res Ctr, Taipei, Taiwan	Yang, CCS (reprint author), Kyoto Univ, Res Inst Sustainable Humanosphere, Kyoto, Japan.	ccyang@rish.kyoto-u.ac.jp						17	0	0	1	1	TAYLOR & FRANCIS LTD	ABINGDON	2-4 PARK SQUARE, MILTON PARK, ABINGDON OR14 4RN, OXON, ENGLAND	2380-2359			MITOCHONDRIAL DNA B	Mitochondrial DNA Part B-Resour.		2018	3	2					622	623		10.1080/23802359.2018.1467739				2	Genetics & Heredity	Genetics & Heredity	GU5BB	WOS:000445298500067					22-11-18
J	Tomberlin, JK; Crippen, TL; Tarone, AM; Chaudhury, MFB; Singh, B; Cammack, JA; Meisel, RP				Tomberlin, Jeffery K.; Crippen, Tawni L.; Tarone, Aaron M.; Chaudhury, Muhammad F. B.; Singh, Baneshwar; Cammack, Jonathan A.; Meisel, Richard P.			A Review of Bacterial Interactions With Blow Flies (Diptera: Calliphoridae) of Medical, Veterinary, and Forensic Importance	ANNALS OF THE ENTOMOLOGICAL SOCIETY OF AMERICA			English	Review						interkingdom communication; veterinary entomology; medical entomology; trophic interaction; succession	LUCILIA-SERICATA DIPTERA; COCHLIOMYIA-MACELLARIA DIPTERA; HORIZONTALLY TRANSMITTED PARASITES; LEVEL PHYSIOLOGICAL PROFILES; CUPRINA WIEDEMANN DIPTERA; MUSCA-DOMESTICA DIPTERA; INCUBATED BOVINE BLOOD; GRAVID SCREWWORM FLIES; GREEN BOTTLE FLY; MICROBIAL COMMUNITIES	Blow flies are commonly associated with decomposing material. In most cases, the larvae are found feeding on decomposing vertebrate remains; however, some species have specialized to feed on living tissue or can survive on other alternate resources like feces. Because of their affiliation with such septic environments, these insects have close associations with microbes. Historically, a tremendous amount of research focused on these insects due to their veterinary importance. Within the past 40 yr, efforts have expanded this research to include areas such as systems ecology, forensics, and even wound debridement (maggot) therapy. Initial research efforts examining the relationship between microbes and these insects were hampered by the technology available. However, with the advent of high-throughput sequencing and modern molecular techniques, new avenues of research examining these interactions have opened up. The purpose of this article is to highlight the research exploring the interactions between microbes and blow flies with regards to blow fly biology, the application of such information to benefit humanity, and potential future pathways of research.	[Tomberlin, Jeffery K.; Tarone, Aaron M.; Cammack, Jonathan A.] Texas A&M Univ, Dept Entomol, TAMU 2475, College Stn, TX 77843 USA; [Crippen, Tawni L.] Agr Res Serv, USDA, Southern Plains Agr Res Ctr, 2881 F&B Rd, College Stn, TX 77845 USA; [Chaudhury, Muhammad F. B.] Univ Nebraska, USDA ARS, SRU, Lincoln, NE USA; [Singh, Baneshwar] Virginia Commonwealth Univ, Dept Forens Sci, Richmond, VA 23284 USA; [Meisel, Richard P.] Univ Houston, Dept Biol & Biochem, 3455 Cullen Blvd, Houston, TX 77204 USA	Tomberlin, JK (reprint author), Texas A&M Univ, Dept Entomol, TAMU 2475, College Stn, TX 77843 USA.	jktomberlin@TAMU.edu; tawni.crippen@ars.usda.gov; tamlucilia@tamu.edu; Muhammad.Chaudhury@ars.usda.gov; bsingh@vcu.edu; jcammack_07@tamu.edu; rpmeisel@Central.UH.EDU		Crippen, Tawni/0000-0001-5129-2371; Meisel, Richard/0000-0002-7362-9307	Texas AM University; Texas A&M AgriLife Research; National Institute of Justice [2015-DN-BX-K020, 2010-DN-BX-K243]	A.M.T. and J.K.T. would like to thank Texas A&M University and Texas A&M AgriLife Research for providing support to develop this manuscript. We thank Robert Alaniz at Texas A&M for helpful discussions regarding gnotobiotic research and Natalie Gasz at Deakin University for reviewing this manuscript. AMT is funded by the National Institute of Justice grant 2015-DN-BX-K020. JKT, TLC, AMT, and BS were also funded by the National Institute of Justice grant 2010-DN-BX-K243. Points of view in this document are those of the authors do not necessarily represent the official position or policies of the U.S. Department of Justice.		222	5	5	9	27	OXFORD UNIV PRESS INC	CARY	JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA	0013-8746	1938-2901		ANN ENTOMOL SOC AM	Ann. Entomol. Soc. Am.	JAN	2017	110	1					19	36		10.1093/aesa/saw086				18	Entomology	Entomology	EP0QL	WOS:000397091700004					22-11-18
J	Weatherbee, CR; Pechal, JL; Benbow, ME				Weatherbee, Courtney R.; Pechal, Jennifer L.; Benbow, M. Eric			The Dynamic Maggot Mass Microbiome	ANNALS OF THE ENTOMOLOGICAL SOCIETY OF AMERICA			English	Article						Calliphoridae; decomposition; necrobiome; epinecrotic; community	BACTERIAL COMMUNITY SUCCESSION; CARRION DECOMPOSITION; POSTMORTEM INTERVAL; POTENTIAL USE; BLOW FLIES; XANTHOMONADACEAE; ECOLOGY; FLY	Necrophagous insect studies have shown that decomposing vertebrate remains are an important ephemeral resource within an ecosystem. However, the microbes (e.g., bacteria and archaea) that were a part of the once living organism and the exogenous taxa that colonize this postmortem resource remain largely underexplored. Also, it is not well understood how these two kingdoms interact to recycle decaying biomass, an important mechanistic question for ecosystem function ecology. To better understand microbial community dynamics throughout decomposition, we used swine carcasses (N = 6) as models for mammalian postmortem decomposition to characterize epinecrotic microbial communities from: the abdominal skin of replicate carcasses; the internal microbiome of individual necrophagous dipteran larvae (maggots); and the microbiome of dipteran larval masses that had colonized the carcasses. Sampling occurred every 12 h for the duration of the decomposition process. We characterized these microbial communities over time using high-throughput 16S amplicon sequencing. The relative abundance of microbial taxa changed over decomposition as well as across sampling locations, suggesting significant interactions between the environment, microbes, and insect larvae. Maggot masses were represented by multiple blow fly species in each mass: Phormia regina (Meigen), Lucilia coeruleiviridis (Macquart), and Cochliomyia macellaria (F.). Relative abundance of these species within the mass also changed as decomposition progressed, suggesting the presence of certain Calliphoridae species within a mass may be associated with temporal shifts of the microbial communities. These results provide new insight into the community ecology of carrion decomposition by providing new data on interactions of microbes and dipteran larvae over time.	[Weatherbee, Courtney R.; Pechal, Jennifer L.; Benbow, M. Eric] Michigan State Univ, Dept Entomol, 243 Nat Sci Bldg, E Lansing, MI 48824 USA; [Benbow, M. Eric] Michigan State Univ, Dept Osteopath Med Specialties, 243 Nat Sci Bldg, E Lansing, MI 48824 USA	Benbow, ME (reprint author), Michigan State Univ, Dept Entomol, 243 Nat Sci Bldg, E Lansing, MI 48824 USA.; Benbow, ME (reprint author), Michigan State Univ, Dept Osteopath Med Specialties, 243 Nat Sci Bldg, E Lansing, MI 48824 USA.	weath108@msu.edu; pechalje@msu.edu; benbow@msu.edu		Pechal, Jennifer/0000-0002-2588-2519	Michigan State University College of Agriculture and Natural Resources (Department of Entomology); College of Osteopathic Medicine (Department of Osteopathic Medical Specialties)	We would like to thank Trevor Stamper and Christine Picard for their collaboration in study design and resources. Trevor Stamper provided the swine carcasses, including their transport, and is greatly appreciated for support and hospitality during the course of this study. This study was conducted at the Forensic Entomology Research Compound facility on the campus of Purdue University, directed by Trevor Stamper. We also thank Charity Owings, Elizabeth Went, and Jarrett Hiatt for assistance with sample collections. We thank the Michigan State University College of Agriculture and Natural Resources (Department of Entomology) and the College of Osteopathic Medicine (Department of Osteopathic Medical Specialties) for funding this work.		42	3	3	3	18	OXFORD UNIV PRESS INC	CARY	JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA	0013-8746	1938-2901		ANN ENTOMOL SOC AM	Ann. Entomol. Soc. Am.	JAN	2017	110	1					45	53		10.1093/aesa/saw088				9	Entomology	Entomology	EP0QL	WOS:000397091700006					22-11-18
J	Zeng, V; Extavour, CG				Zeng, Victor; Extavour, Cassandra G.			ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species	DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION			English	Article							CRUSTACEAN PARHYALE-HAWAIENSIS; HEMIMETABOLOUS INSECT; ONCOPELTUS-FASCIATUS; PROTEIN FAMILIES; GENOME SEQUENCE; DROSOPHILA-MELANOGASTER; COPTOTERMES-FORMOSANUS; DEVELOPMENTAL GENETICS; TRIBOLIUM-CASTANEUM; RECENT IMPROVEMENTS	The increased throughput and decreased cost of next-generation sequencing (NGS) have shifted the bottleneck genomic research from sequencing to annotation, analysis and accessibility. This is particularly challenging for research communities working on organisms that lack the basic infrastructure of a sequenced genome, or an efficient way to utilize whatever sequence data may be available. Here we present a new database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository and search engine for transcriptomic data from arthropods that are of high interest to multiple research communities but currently lack sequenced genomes. We demonstrate the functionality and utility of ASGARD using de novo assembled transcriptomes from the milkweed bug Oncopeltus fasciatus, the cricket Gryllus bimaculatus and the amphipod crustacean Parhyale hawaiensis. We have annotated these transcriptomes to assign putative orthology, coding region determination, protein domain identification and Gene Ontology (GO) term annotation to all possible assembly products. ASGARD allows users to search all assemblies by orthology annotation, GO term annotation or Basic Local Alignment Search Tool. User-friendly features of ASGARD include search term auto-completion suggestions based on database content, the ability to download assembly product sequences in FASTA format, direct links to NCBI data for predicted orthologs and graphical representation of the location of protein domains and matches to similar sequences from the NCBI non-redundant database. ASGARD will be a useful repository for transcriptome data from future NGS studies on these and other emerging model arthropods, regardless of sequencing platform, assembly or annotation status. This database thus provides easy, one-stop access to multi-species annotated transcriptome information. We anticipate that this database will be useful for members of multiple research communities, including developmental biology, physiology, evolutionary biology, ecology, comparative genomics and phylogenomics.	[Zeng, Victor; Extavour, Cassandra G.] Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA	Extavour, CG (reprint author), Harvard Univ, Dept Organism & Evolutionary Biol, 16 Divin Ave, Cambridge, MA 02138 USA.	extavour@oeb.harvard.edu	Extavour, Cassandra/I-4567-2012	Extavour, Cassandra/0000-0003-2922-5855	Harvard Stem Cell Institute [SG-0057-10-00]; Ellison Medical Foundation [AG-NS-07010-10]; National Science Foundation [IOS-0817678]	The Harvard Stem Cell Institute (Seed Grant number SG-0057-10-00 to C. G. E.); the Ellison Medical Foundation (New Scholar Award number AG-NS-07010-10 to C. G. E.); the National Science Foundation (grant number IOS-0817678 to C.G.E.).		103	7	7	0	30	OXFORD UNIV PRESS	OXFORD	GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND	1758-0463			DATABASE-OXFORD	Database	Nov-23	2012									bas048	10.1093/database/bas048				17	Mathematical & Computational Biology	Mathematical & Computational Biology	105ZM	WOS:000316111200001	23180770	DOAJ Gold, Green Published			22-11-18
J	Pedro, PM; Piper, R; Neto, PB; Cullen, L; Dropa, M; Lorencao, R; Matte, MH; Rech, TC; Rufato, MO; Silva, M; Turati, DT				Pedro, Pedro M.; Piper, Ross; Neto, Pedro Bazilli; Cullen, Laury, Jr.; Dropa, Milena; Lorencao, Rogerio; Matte, Maria Helena; Rech, Tatiane Cristina; Rufato, Mauro Osmar, Jr.; Silva, Miriam; Turati, Daniele Turganti			Metabarcoding Analyses Enable Differentiation of Both Interspecific Assemblages and Intraspecific Divergence in Habitats With Differing Management Practices	ENVIRONMENTAL ENTOMOLOGY			English	Article						next-generation sequencing; metabarcoding; Beta diversity; insect dispersal	BIODIVERSITY ASSESSMENT; COFFEE PLANTATIONS; DNA BARCODES; ARTHROPODS; DIVERSITY; METAGENOMICS; PARADIGM; SEARCH; PEST	Spatial and temporal collections provide important data on the distribution and dispersal of species. Regional-scale monitoring invariably involves hundreds of thousands of samples, the identification of which is costly in both time and money. In this respect, metabarcoding is increasingly seen as a viable alternative to traditional morphological identification, as it eliminates the taxonomic bottleneck previously impeding such work. Here, we assess whether terrestrial arthropods collected from 12 pitfall traps in two farms of a coffee (Coffea arabica L.) growing region of Sao Paulo State, Brazil could differentiate the two locations. We sequenced a portion of the cytochrome oxidase 1 region from minimally processed pools of samples and assessed inter- and intraspecific parameters across the two locations. Our sequencing was sufficient to circumscribe the overall diversity, which was characterized by few dominant taxa, principally small Coleoptera species and Collembola. Thirty-four operational taxonomic units were detected and of these, eight were present in significantly different quantities between the two farms. Analysis of community-wide Beta diversity grouped collections based on farm provenance. Moreover, haplotype-based analyses for a species of Xyleborus beetle showed that there is significant population genetic structuring between the two farms, suggesting limited dispersal. We conclude that metabarcoding can provide important management input and, considering the rapidly declining cost of sequencing, suggest that large-scale monitoring is now feasible and can identify both the taxa present as well as contribute information about genetic diversity of focal species.	[Pedro, Pedro M.; Cullen, Laury, Jr.; Lorencao, Rogerio; Rufato, Mauro Osmar, Jr.] IPE Inst Ecol Res, BR-12960000 Nazare Paulista, SP, Brazil; [Piper, Ross] Univ Leeds, Fac Biol Sci, Leeds LS2 9JT, W Yorkshire, England; [Neto, Pedro Bazilli] Fazenda Sao Pedro, BR-13770000 Caconde, SP, Brazil; [Dropa, Milena; Matte, Maria Helena; Silva, Miriam] Univ Sao Paulo, Fac Saude Publ, BR-01246904 Sao Paulo, SP, Brazil; [Rech, Tatiane Cristina] AES Tiete, BR-16370000 Promissao, SP, Brazil; [Turati, Daniele Turganti] Sitio Sao Luis, BR-13770000 Caconde, SP, Brazil	Pedro, PM (reprint author), IPE Inst Ecol Res, BR-12960000 Nazare Paulista, SP, Brazil.	pedro@ipe.org.br	Dropa, Milena/A-3946-2013	Dropa, Milena/0000-0003-1459-915X	ANEEL (Agencia Nacional de Energia Eletrica) [0064-1035/2014]	This research received R&D funding from ANEEL (Agencia Nacional de Energia Eletrica; grant number 0064-1035/2014). Sample collections were undertaken with permit number 54835 administered by the Brazilian Federal agency SISBIO. We thank the contributions from two anonymous reviewers, who provided important considerations to this work.		45	1	1	2	7	OXFORD UNIV PRESS INC	CARY	JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA	0046-225X	1938-2936		ENVIRON ENTOMOL	Environ. Entomol.	DEC	2017	46	6					1381	1389		10.1093/ee/nvx166				9	Entomology	Entomology	FP6KH	WOS:000417734400025	29069398				22-11-18
J	Manirajan, BA; Maisinger, C; Ratering, S; Rusch, V; Schwiert, A; Cardinale, M; Schnell, S				Manirajan, Binoy Ambika; Maisinger, Corinna; Ratering, Stefan; Rusch, Volker; Schwiert, Andreas; Cardinale, Massimiliano; Schnell, Sylvia			Diversity, specificity, co-occurance and hub taxa of the bacterial-fungal pollen microbiome	FEMS MICROBIOLOGY ECOLOGY			English	Article						flower pollen; microbiome; inter-kingdom diversity; intra-kingdom diversity; core microbiome; hub species	SP-NOV.; POLLINATION; MICROORGANISMS; COMMUNITIES; SURFACES; ECOLOGY; NECTAR	Flower pollen represents a unique microbial habitat, however the factors driving microbial assemblages and microbe-microbe interactions remain largely unexplored. Here we compared the structure and diversity of the bacterial-fungal microbiome between eight different pollen species (four wind-pollinated and four insect-pollinated) from close geographical locations, using high-throughput sequencing of the 16S the rRNA gene fragment (bacteria) and the internal transcribed spacer 2 (ITS2, fungi). Proteobacteria and Ascomycota were the most abundant bacterial and fungal phyla, respectively. Pseudomonas (bacterial) and Cladosporium (fungal) were the most abundant genera. Both bacterial and fungal microbiota were significantly influenced by plant species and pollination type, but showed a core microbiome consisting of 12 bacterial and 33 fungal genera. Co-occurrence analysis highlighted significant inter- and intra-kingdom interactions, and the interaction network was shaped by four bacterial hub taxa: Methylobacterium (two OTUs), Friedmanniella and Rosenbergiella. Rosenbergiella prevailed in insect-pollinated pollen and was negatively correlated with the other hubs, indicating habitat complementarity Inter-kingdom co-occurrence showed a predominant effect of fungal on bacterial taxa. This study enhances our basic knowledge of pollen microbiota, and poses the basis for further inter- and intra-kingdom interaction studies in the plant reproductive organs.	[Manirajan, Binoy Ambika; Maisinger, Corinna; Ratering, Stefan; Cardinale, Massimiliano; Schnell, Sylvia] Justus Liebig Univ Giessen, Res Ctr BioSyst Land Use & Nutr IFZ, Inst Appl Microbiol, Heinrich Buff Ring 26-32, D-35392 Giessen, Germany; [Rusch, Volker] Stiftung Old Herborn Univ, Inst Integrat Biol, Herborn, Germany; [Schwiert, Andreas] MVZ Inst Mikrookol GmbH, D-35745 Herborn, Germany	Cardinale, M; Schnell, S (reprint author), Justus Liebig Univ Giessen, Res Ctr BioSyst Land Use & Nutr IFZ, Inst Appl Microbiol, Heinrich Buff Ring 26-32, D-35392 Giessen, Germany.	Sylvia.Schnell@umwelt.uni-giessen.de	Ratering, Stefan/N-9437-2013; Schnell, Sylvia/H-1639-2012	Ratering, Stefan/0000-0001-7572-6306; Schnell, Sylvia/0000-0003-3903-6089; Cardinale, Massimiliano/0000-0003-1421-722X				96	1	1	11	11	OXFORD UNIV PRESS	OXFORD	GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND	0168-6496	1574-6941		FEMS MICROBIOL ECOL	FEMS Microbiol. Ecol.	AUG	2018	94	8							fiy112	10.1093/femsec/fiy112				11	Microbiology	Microbiology	GP8XI	WOS:000441198800008	29878113				22-11-18
J	Fu, XH; Li, JJ; Tian, Y; Quan, WP; Zhang, S; Liu, Q; Liang, F; Zhu, XL; Zhang, LS; Wang, DP; Hu, J				Fu, Xinhua; Li, Jingjing; Tian, Yu; Quan, Weipeng; Zhang, Shu; Liu, Qian; Liang, Fan; Zhu, Xinlei; Zhang, Liangsheng; Wang, Depeng; Hu, Jiang			Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome	GIGASCIENCE			English	Article						firefly; Pyrocoelia pectoralis; genome; long reads; assembly	GENE; ANNOTATION; PREDICTION; COLEOPTERA; LAMPYRIDAE; ALIGNMENT; INSIGHTS; REVEALS; BEETLE; TOOL	Background: Fireflies are a family of insects within the beetle order Coleoptera, or winged beetles, and they are one of the most well-known and loved insect species because of their bioluminescence. However, the firefly is in danger of extinction because of the massive destruction of its living environment. In order to improve the understanding of fireflies and protect them effectively, we sequenced the whole genome of the terrestrial firefly Pyrocoelia pectoralis. Findings: Here, we developed a highly reliable genome resource for the terrestrial firefly Pyrocoelia pectoralis (E. Oliv., 1883; Coleoptera: Lampyridae) using single molecule real time (SMRT) sequencing on the PacBio Sequel platform. In total, 57.8 Gb of long reads were generated and assembled into a 760.4-Mb genome, which is close to the estimated genome size and covered 98.7% complete and 0.7% partial insect Benchmarking Universal Single-Copy Orthologs. The k-mer analysis showed that this genome is highly heterozygous. However, our long-read assembly demonstrates continuousness with a contig N50 length of 3.04 Mb and the longest contig length of 13.69 Mb. Furthermore, 135 589 SSRs and 341 Mb of repeat sequences were detected. A total of 23 092 genes were predicted; 88.44% of genes were annotated with one or more related functions. Conclusions: We assembled a high-quality firefly genome, which will not only provide insights into the conservation and biodiversity of fireflies, but also provide a wealth of information to study the mechanisms of their sexual communication, bio-luminescence, and evolution.	[Fu, Xinhua] Huazhong Agr Univ, Hubei Insect Resources Utilizat & Sustainable Pes, Coll Plant Sci & Technol, Shizishan St, Wuhan 430000, Hubei, Peoples R China; [Li, Jingjing; Tian, Yu; Quan, Weipeng; Zhang, Shu; Liang, Fan; Wang, Depeng; Hu, Jiang] Next Biosci Inst, 666 Gaoxin Rd, Wuhan 430000, Hubei, Peoples R China; [Zhu, Xinlei] Firefly Conservat Res Ctr, Shizishan St, Wuhan 430000, Hubei, Peoples R China; [Liu, Qian] Columbia Univ, Inst Genom Med, 116th St & Broadway, New York, NY 10032 USA; [Zhang, Liangsheng] Fujian Agr & Forestry Univ, Ctr Genom & Biotechnol, State Key Lab Ecol Pest Control Fujian & Taiwan C, Shangxiadian Rd, Fuzhou 350002, Fujian, Peoples R China	Wang, DP; Hu, J (reprint author), Next Biosci Inst, 666 Gaoxin Rd, Wuhan 430000, Hubei, Peoples R China.	wangdp@grandomics.com; huj@grandomics.com			National Science Foundation of China [31672349, 31372252]	We thank members of Huazhong Agricultural University for preparing samples. We also thank the staff at Nextomics Biosciences, who contributed to the sequencing of the firefly genome. We thank Huiwen Che and Kai Wang for revising and discussion. Financial assistance was provided by the National Science Foundation of China (#31672349 and #31372252).		50	1	1	7	8	OXFORD UNIV PRESS	OXFORD	GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND	2047-217X			GIGASCIENCE	GigaScience	Nov-24	2017	6	12								10.1093/gigascience/gix112				7	Multidisciplinary Sciences	Science & Technology - Other Topics	FS2XO	WOS:000419642900002		DOAJ Gold, Green Published			22-11-18
J	Monaghan, MT; Wild, R; Elliot, M; Fujisawa, T; Balke, M; Inward, DJ; Lees, DC; Ranaivosolo, R; Eggleton, P; Barraclough, TG; Vogler, AP				Monaghan, Michael T.; Wild, Ruth; Elliot, Miranda; Fujisawa, Tomochika; Balke, Michael; Inward, Daegan J. G.; Lees, David C.; Ranaivosolo, Ravo; Eggleton, Paul; Barraclough, Timothy G.; Vogler, Alfried P.			Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation	SYSTEMATIC BIOLOGY			English	Article						Biodiversity; coalescent; DNA barcoding; DNA taxonomy; endemism; GMYC; Madagascar; turnover	DNA TAXONOMY; MOLECULAR EVOLUTION; DUNG BEETLES; POPULATIONS; DIVERSITY; BARCODES; MITOCHONDRIAL; DELIMITATION; POLYMORPHISM; PROMISE	High-throughput DNA sequencing has the potential to accelerate species discovery if it is able to recognize evolutionary entities from sequence data that are comparable to species. The general mixed Yule-coalescent (GMYC) model estimates the species boundary from DNA surveys by identifying independently evolving lineages as a transition from coalescent to speciation branching patterns on a phylogenetic tree. Applied here to 12 families from 4 orders of insects in Madagascar, we used the model to delineate 370 putative species from mitochondrial DNA sequence variation among 1614 individuals. These were compared with data from the nuclear genome and morphological identification and found to be highly congruent (98% and 94%). We developed a modified GMYC that allows for a variable transition from coalescent to speciation among lineages. This revised model increased the congruence with morphology (97%), suggesting that a variable threshold better reflects the clustering of sequence data into biological species. Local endemism was pronounced in all 5 insect groups. Most species (60-91%) and haplotypes (88-99%) were found at only 1 of the 5 study sites (40-1000 km apart). This pronounced endemism resulted in a 37% increase in species numbers using diagnostic nucleotides in a population aggregation analysis. Sample sizes between 7 and 10 individuals represented a threshold above which there was minimal increase in genetic diversity, broadly agreeing with coalescent theory and other empirical studies. Our results from > 1.4 Mb of empirical data suggest that the GMYC model captures species boundaries comparable to those from traditional methods without the need for prior hypotheses of population coherence. This provides a method of species discovery and biodiversity assessment using single-locus data from mixed or environmental samples while building a globally available taxonomic database for future identifications.	[Monaghan, Michael T.] IGB, Leibniz Inst Freshwater Ecol & Inland Fisheries, D-12587 Berlin, Germany; [Monaghan, Michael T.; Wild, Ruth; Elliot, Miranda; Balke, Michael; Inward, Daegan J. G.; Lees, David C.; Eggleton, Paul; Vogler, Alfried P.] Nat Hist Museum, Dept Entomol, London SW7 5BD, England; [Monaghan, Michael T.; Wild, Ruth; Elliot, Miranda; Fujisawa, Tomochika; Barraclough, Timothy G.; Vogler, Alfried P.] Univ London Imperial Coll Sci Technol & Med, Div Biol, Ascot SL5 7PY, Berks, England; [Balke, Michael] Zool Staatssammlung, D-81247 Munich, Germany; [Ranaivosolo, Ravo] Univ Antananarivo, Dept Anim Biol, Antananarivo 101, Madagascar	Monaghan, MT (reprint author), IGB, Leibniz Inst Freshwater Ecol & Inland Fisheries, D-12587 Berlin, Germany.	monaghan@igb-berlin.de	Monaghan, Michael/A-2589-2009	Monaghan, Michael/0000-0001-6200-2376; Barraclough, Timothy/0000-0002-8084-2640	Madagascar Ministry of the Environment, Water and Forests; National Association for the Management of Protected Areas; Biotechnology and Biological Sciences Research Council [BBS/B/04358]	Field work would not have been possible without the generous support of staff at the Madagascar Institute for the Conservation of Tropical Ecosystems, especially Benjamin Andriamihaja, Liva Ravelonarivo, Benjy Randrianambina, and Jean-Marcel Rakotoarison. Sampling was conducted with the help of Doug Ottke, Roger Andriamparany, Kelly Inward, and Pierre Raza. ndraire. In Ranomafana, we thank Anigo Summer-Nielson, JeanPhilippe Puyravaud, and Patricia Wright. In London, Julia Llewellyn-Hughes, Claire Grif. n, Andie Hall, Lisa Smith, Jo Ingle, Anna Papadapoulou, Sandra Sterman, Alex Martin, and Sylvia Fabrizi supported each stage of the laboratory analysis. Johannes Bergsten, Jean-Luc Gattolliat, and Olivier Montreuil provided expertise with specimen identifications. Data analysis was assisted by Ben Isambert, Mafalda Lopez da Silva, Eleri Randall, Aline Moore, Gail Bartlett, Tom Conner, Toby Hunt, and Paul van Dyk. Comments from Anna Papadapoulou helped to improve an earlier draft. We thank Marshal Hedin and 3 anonymous reviewers for comments on the manuscript. Access to protected areas and permission to sample (Permit No. 175 MINENVEF/SG/DGEF/DPB/SCBLF) and export (Permit No. 354N-EV11/MG04) specimens for research was granted by the Madagascar Ministry of the Environment, Water and Forests and the National Association for the Management of Protected Areas.		87	379	385	8	96	OXFORD UNIV PRESS	OXFORD	GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND	1063-5157	1076-836X		SYST BIOL	Syst. Biol.	JUN	2009	58	3					298	311		10.1093/sysbio/syp027				14	Evolutionary Biology	Evolutionary Biology	496UL	WOS:000270004400002	20525585		Y	N	22-11-18
J	Lemmon, AR; Emme, SA; Lemmon, EM				Lemmon, Alan R.; Emme, Sandra A.; Lemmon, Emily Moriarty			Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics	SYSTEMATIC BIOLOGY			English	Article						Anchor regions; anchored enrichment; anchored phylogenomics; highly conserved regions; hybrid enrichment; phylogenetics; phylogeography; sequence capture; ultraconserved elements	SPECIES-TREE ESTIMATION; ULTRACONSERVED ELEMENTS; PHYLOGENETIC INFORMATIVENESS; BAYESIAN-ESTIMATION; VERTEBRATE TREE; EUKARYOTIC TREE; INSECT GENOMES; LIFE PROGRESS; GENE TREES; SELECTION	The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required labor-intensive marker development coupled with single-locus polymerase chain reaction and DNA sequencing on clade-by-clade and locus-by-locus basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of loci for potentially hundreds of individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target enrichment of >500 loci in highly conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency ill nonmodel species up to 508 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential not only to expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (similar to 1% of the cost of traditional Sanger sequencing and similar to 3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci x 100 individuals) and rapid data collection (similar to 2 weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or nonexistent genomic resources.	[Lemmon, Alan R.] Florida State Univ, Dept Sci Comp, Dirac Sci Lib, Tallahassee, FL 32306 USA; [Emme, Sandra A.; Lemmon, Emily Moriarty] Florida State Univ, Dept Biol Sci, Tallahassee, FL 32306 USA	Lemmon, AR (reprint author), Florida State Univ, Dept Sci Comp, Dirac Sci Lib, Tallahassee, FL 32306 USA.	alemmon@fsu.edu			Florida State University	This work was funded by Florida State University new faculty setup funds to Alan Lemmon and Emily Moriarty Lemmon.		54	256	257	7	142	OXFORD UNIV PRESS	OXFORD	GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND	1063-5157	1076-836X		SYST BIOL	Syst. Biol.	OCT	2012	61	5					727	744		10.1093/sysbio/sys049				18	Evolutionary Biology	Evolutionary Biology	988XG	WOS:000307524200003	22605266	Bronze	Y	N	22-11-18
J	Roossinck, MJ; Martin, DP; Roumagnac, P				Roossinck, Marilyn J.; Martin, Darren P.; Roumagnac, Philippe			Plant Virus Metagenomics: Advances in Virus Discovery	PHYTOPATHOLOGY			English	Review							TALLGRASS PRAIRIE PRESERVE; COMPLETE GENOME SEQUENCES; MILD MOTTLE VIRUS; MOLECULAR CHARACTERIZATION; DNA VIRUSES; SMALL RNAS; TERRESTRIAL ORCHIDS; WESTERN-AUSTRALIA; OSAGE COUNTY; WILD PLANT	In recent years plant viruses have been detected from many environments, including domestic and wild plants and interfaces between these systems-aquatic sources, feces of various animals, and insects. A variety of methods have been employed to study plant virus biodiversity, including enrichment for virus-like particles or virus-specific RNA or DNA, or the extraction of total nucleic acids, followed by next-generation deep sequencing and bioinformatic analyses. All of the methods have some shortcomings, but taken together these studies reveal our surprising lack of knowledge about plant viruses and point to the need for more comprehensive studies. In addition, many new viruses have been discovered, with most virus infections in wild plants appearing asymptomatic, suggesting that virus disease may be a byproduct of domestication. For plant pathologists these studies are providing useful tools to detect viruses, and perhaps to predict future problems that could threaten cultivated plants.	[Roossinck, Marilyn J.] Penn State Univ, Dept Plant Pathol & Environm Microbiol, Ctr Infect Dis Dynam, University Pk, PA 16802 USA; [Martin, Darren P.] Univ Cape Town, Computat Biol Grp, Inst Infect Dis & Mol Med, ZA-7925 Cape Town, South Africa; [Roumagnac, Philippe] CIRAD, UMR BGPI, F-34398 Montpellier 5, France	Roossinck, MJ (reprint author), Penn State Univ, Dept Plant Pathol & Environm Microbiol, Ctr Infect Dis Dynam, University Pk, PA 16802 USA.	mjr25@psu.edu			National Science Foundation [EF-0627108, EPS-0447262, IOS-0950579, IOS-1157148]; United States Department of Agriculture [OKLR-2007-01012]; Pennsylvania State University	We thank P. Bernardo, E. Fernandez, and D. Filloux for their invaluable help in achieving the large-scale VANA-based ecogenomic studies conducted in Camargue and Western Cape regions. M. J. Roossinck acknowledges the National Science Foundation grant numbers EF-0627108, EPS-0447262, IOS-0950579, and IOS-1157148 and the United States Department of Agriculture grant number OKLR-2007-01012 for previous and continuing research support, and the Pennsylvania State University.		97	63	70	5	69	AMER PHYTOPATHOLOGICAL SOC	ST PAUL	3340 PILOT KNOB ROAD, ST PAUL, MN 55121 USA	0031-949X	1943-7684		PHYTOPATHOLOGY	Phytopathology	JUN	2015	105	6					716	727		10.1094/PHYTO-12-14-0356-RVW				12	Plant Sciences	Plant Sciences	CL4VY	WOS:000356955500001	26056847		Y	N	22-11-18
J	Mata, VA; Amorim, F; Corley, MFV; McCracken, GF; Rebelo, H; Beja, P				Mata, Vanessa A.; Amorim, Francisco; Corley, Martin F. V.; McCracken, Gary F.; Rebelo, Hugo; Beja, Pedro			Female dietary bias towards large migratory moths in the European free-tailed bat (Tadarida teniotis)	BIOLOGY LETTERS			English	Article						resource partitioning; bat diet; gender segregation; Tadarida teniotis; metabarcoding; COI	EPTESICUS-FUSCUS; FORAGING BEHAVIOR; INSECTS; SEGREGATION; SEX	In bats, sexual segregation has been described in relation to differential use of roosting and foraging habitats. It is possible that variation may also exist between genders in the use of different prey types. However, until recently this idea was difficult to test owing to poorly resolved taxonomy of dietary studies. Here, we use high-throughput sequencing to describe gender-related variation in diet composition of the European free-tailed bat (Tadarida teniotis), while controlling for effects of age and season. We analysed guano pellets collected from 143 individuals mist-netted from April to October 2012 and 2013, in northeast Portugal. Moths (Lepidoptera; mainly Noctuidae and Geometridae) were by far the most frequently recorded prey, occurring in nearly all samples and accounting for 96 out of 115 prey taxa. There were significant dietary differences between males and females, irrespective of age and season. Compared to males, females tended to consume larger moths and more moths of migratory behaviour (e.g. Autographa gamma). Our study provides the first example of gender-related dietary variation in bats, illustrating the value of novel molecular tools for revealing intraspecific variation in food resource use in bats and other insectivores.	[Mata, Vanessa A.; Amorim, Francisco; Corley, Martin F. V.; Rebelo, Hugo; Beja, Pedro] Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO InBIO, P-4485661 Vairao, Portugal; [McCracken, Gary F.] Univ Tennessee, Dept Ecol & Evolutionary Biol, Knoxville, TN 37996 USA; [Rebelo, Hugo] Univ Bristol, Sch Biol Sci, Bristol BS8 1UG, Avon, England; [Rebelo, Hugo; Beja, Pedro] Univ Lisbon, Inst Super Agron, Ctr Ecol Aplicada Prof Baeta Neves, CEABN InBIO, P-1349017 Lisbon, Portugal	Mata, VA (reprint author), Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO InBIO, P-4485661 Vairao, Portugal.	vanessamata@cibio.up.pt	Mata, Vanessa/L-7375-2013; Rebelo, Hugo/C-9005-2009; Beja, Pedro/A-7851-2008	Mata, Vanessa/0000-0003-3005-9030; Rebelo, Hugo/0000-0002-7118-4068; Beja, Pedro/0000-0001-8164-0760; Amorim, Francisco/0000-0002-7731-9242	Fundacao para Ciencia e Tecnologia (FCT) [LTER/BIA-BEC/0004/2009]; EDP Biodiversity Chair; FCT [PD/BD/113462/2015, PD/BD/52606/2014, IF/00497/2013]	The study was funded by Fundacao para Ciencia e Tecnologia (FCT) (Project LTER/BIA-BEC/0004/2009) and EDP Biodiversity Chair. FCT funded Vanessa Mata (PD/BD/113462/2015), Francisco Amorim (PD/BD/52606/2014) and Hugo Rebelo (IF/00497/2013).		24	12	12	3	36	ROYAL SOC	LONDON	6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND	1744-9561	1744-957X		BIOL LETTERS	Biol. Lett.	Mar-01	2016	12	3							20150988	10.1098/rsbl.2015.0988				5	Biology; Ecology; Evolutionary Biology	Life Sciences & Biomedicine - Other Topics; Environmental Sciences & Ecology; Evolutionary Biology	DJ1AE	WOS:000373934700005	27009885	Green Published, Bronze			22-11-18
J	Poelchau, MF; Reynolds, JA; Elsik, CG; Denlinger, DL; Armbruster, PA				Poelchau, Monica F.; Reynolds, Julie A.; Elsik, Christine G.; Denlinger, David L.; Armbruster, Peter A.			Deep sequencing reveals complex mechanisms of diapause preparation in the invasive mosquito, Aedes albopictus	PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES			English	Article						Aedes albopictus; RNA-Seq; diapause preparation; embryonic development; molecular physiology; invasive species	CELL NUCLEAR ANTIGEN; LARGE GENE LISTS; INSECT DIAPAUSE; SARCOPHAGA-CRASSIPALPIS; DROSOPHILA-MELANOGASTER; EMBRYONIC-DEVELOPMENT; FLESH FLY; EXPRESSION; CULICIDAE; DIPTERA	Seasonal environments present fundamental physiological challenges to a wide range of insects. Many temperate insects surmount the exigencies of winter by undergoing photoperiodic diapause, in which photoperiod provides a token cue that initiates an alternative developmental programme leading to dormancy. Pre-diapause is a crucial preparatory phase of this process, preceding developmental arrest. However, the regulatory and physiological mechanisms of diapause preparation are largely unknown. Using high-throughput gene expression profiling in the Asian tiger mosquito, Aedes albopictus, we reveal major shifts in endocrine signalling, cell proliferation, metabolism, energy production and cellular structure across pre-diapause development. While some hallmarks of diapause, such as insulin signalling and stress response, were not important at the transcriptional level, two genes, Pepck and PCNA, appear to show diapause-induced transcriptional changes across insect taxa. These processes demonstrate physiological commonalities between Ae. albopictus pre-diapause and diapause strategies across insects, and support the idea of a genetic 'toolkit' for diapause. Observations of gene expression trends from a comparative developmental perspective suggest that individual physiological processes are delayed against a background of a fixed morphological ontogeny. Our results demonstrate how deep sequencing can provide new insights into elusive molecular bases of complex ecological adaptations.	[Poelchau, Monica F.; Armbruster, Peter A.] Georgetown Univ, Dept Biol, Washington, DC 20057 USA; [Reynolds, Julie A.; Denlinger, David L.] Ohio State Univ, Dept Entomol, Columbus, OH 43210 USA; [Elsik, Christine G.] Univ Missouri, Div Anim Sci, S134 D Anim Sci Res Ctr, Columbia, MO USA	Poelchau, MF (reprint author), Georgetown Univ, Dept Biol, 37th & O Str NW, Washington, DC 20057 USA.	mpoelchau@gmail.com	Elsik, Christine/C-4120-2017	Elsik, Christine/0000-0002-4248-7713; Poelchau, Monica/0000-0002-4584-6056	National Institutes of Health [5R21AI081041-02]; Georgetown University	We would like to thank the Armbruster, Elsik and Denlinger laboratories, and R. Scott Cornman for helpful comments and suggestions on this work. Comments from the Associate Editor and two anonymous referees greatly improved the quality of this manuscript. Christopher Childers was instrumental in setting up the website http://AlbopictusExpression.org. This work was supported by the National Institutes of Health (grant no. 5R21AI081041-02 to P. A. A., C. G. E. and D. L. D.) and Georgetown University.		61	47	50	2	51	ROYAL SOC	LONDON	6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND	0962-8452	1471-2954		P ROY SOC B-BIOL SCI	Proc. R. Soc. B-Biol. Sci.	May-22	2013	280	1759							20130143	10.1098/rspb.2013.0143				9	Biology; Ecology; Evolutionary Biology	Life Sciences & Biomedicine - Other Topics; Environmental Sciences & Ecology; Evolutionary Biology	124RA	WOS:000317482100011	23516243	Green Published, Bronze			22-11-18
J	Bekal, S; Domier, LL; Niblack, TL; Lambert, KN				Bekal, Sadia; Domier, Leslie L.; Niblack, Terry L.; Lambert, Kris N.			Discovery and initial analysis of novel viral genomes in the soybean cyst nematode	JOURNAL OF GENERAL VIROLOGY			English	Article							VIRUS-LIKE PARTICLES; ROOT-KNOT NEMATODE; CAENORHABDITIS-ELEGANS; HETERODERA-GLYCINES; NUCLEOTIDE-SEQUENCE; RNA VIRUS; REPLICATION; DISEASE; PLANT; TRANSMISSION	Nematodes are the most abundant multicellular animals on earth, yet little is known about their natural viral pathogens. To date, only two nematode virus genomes have been reported. Consequently, nematode viruses have been overlooked as important biotic factors in the study of nematode ecology. Here, we show that one plant parasitic nematode species, Heterodera glycines, the soybean cyst nematode (SCN), harbours four different RNA viruses. The nematode virus genomes were discovered in the SCN transcriptome after high-throughput sequencing and assembly. All four viruses have negative-sense RNA genomes, and are distantly related to nyaviruses and bornaviruses, rhabdoviruses, bunyaviruses and tenuiviruses. Some members of these families replicate in and are vectored by insects, and can cause significant diseases in animals and plants. The novel viral sequences were detected in both eggs and the second juvenile stage of SCN, suggesting that these viruses are transmitted vertically. While there was no evidence of integration of viral sequences into the nematode genome, we indeed detected transcripts from these viruses by using quantitative PCR. These data are the first finding of virus genomes in parasitic nematodes. This discovery highlights the need for further exploration for nematode viruses in all tropic groups of these diverse and abundant animals, to determine how the presence of these viruses affects the fitness of the nematode, strategies of viral transmission and mechanisms of viral pathogenesis.	[Domier, Leslie L.; Lambert, Kris N.] Univ Illinois, USDA, ARS, Dept Crop Sci, Urbana, IL 61810 USA	Lambert, KN (reprint author), Univ Illinois, USDA, ARS, Dept Crop Sci, Urbana, IL 61810 USA.	knlamber@illinois.edu			United Soybean Board; North Central Soybean Research Panel	We would like to thank the United Soybean Board and the North Central Soybean Research Panel for the financial support. We also thank Drs George Bruening and Joanna Shisler for their helpful comments on this manuscript.		41	35	35	2	19	SOC GENERAL MICROBIOLOGY	READING	MARLBOROUGH HOUSE, BASINGSTOKE RD, SPENCERS WOODS, READING RG7 1AG, BERKS, ENGLAND	0022-1317			J GEN VIROL	J. Gen. Virol.	AUG	2011	92		8				1870	1879		10.1099/vir.0.030585-0				10	Biotechnology & Applied Microbiology; Virology	Biotechnology & Applied Microbiology; Virology	802DF	WOS:000293488800016	21490246	Bronze			22-11-18
J	Evans, DM; Kitson, JJN; Lunt, DH; Straw, NA; Pocock, MJO				Evans, Darren M.; Kitson, James J. N.; Lunt, David H.; Straw, Nigel A.; Pocock, Michael J. O.			Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems	FUNCTIONAL ECOLOGY			English	Article						food webs; forestry; host-parasitoid interactions; invasive species; next-generation sequencing	FOOD-WEB STRUCTURE; MUTUALISTIC NETWORKS; POLLINATION NETWORKS; EVOLUTIONARY HISTORY; MOLECULAR-DETECTION; MAXIMUM-LIKELIHOOD; SEQUENCING DATA; CLIMATE-CHANGE; BIODIVERSITY; ROBUSTNESS	1. Significant advances in both mathematical and molecular approaches in ecology offer unprecedented opportunities to describe and understand ecosystem functioning. Ecological networks describe interactions between species, the underlying structure of communities and the function and stability of ecosystems. They provide the ability to assess the robustness of complex ecological communities to species loss, as well as a novel way of guiding restoration. However, empirically quantifying the interactions between entire communities remains a significant challenge. 2. Concomitantly, advances in DNA sequencing technologies are resolving previously intractable questions in functional and taxonomic biodiversity and provide enormous potential to determine hitherto difficult to observe species interactions. Combining DNA metabarcoding approaches with ecological network analysis presents important new opportunities for understanding large-scale ecological and evolutionary processes, as well as providing powerful tools for building ecosystems that are resilient to environmental change. 3. We propose a novel 'nested tagging' metabarcoding approach for the rapid construction of large, phylogenetically structured species-interaction networks. Taking tree-insect-parasitoid ecological networks as an illustration, we show how measures of network robustness, constructed using DNA metabarcoding, can be used to determine the consequences of tree species loss within forests, and forest habitat loss within wider landscapes. By determining which species and habitats are important to network integrity, we propose new directions for forest management. 4. Merging metabarcoding with ecological network analysis provides a revolutionary opportunity to construct some of the largest, phylogenetically structured species-interaction networks to date, providing new ways to: (i) monitor biodiversity and ecosystem functioning; (ii) assess the robustness of interacting communities to species loss; and (iii) build ecosystems that are more resilient to environmental change.	[Evans, Darren M.] Newcastle Univ, Sch Biol, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England; [Evans, Darren M.; Kitson, James J. N.; Lunt, David H.] Univ Hull, Sch Biol Biomed & Environm Sci, Kingston Upon Hull HU6 7RX, N Humberside, England; [Straw, Nigel A.] Alice Holt Lodge, Forest Res, Farnham GU10 4LH, Surrey, England; [Pocock, Michael J. O.] Ctr Ecol & Hydrol, Wallingford OX10 8BB, Oxon, England	Kitson, JJN (reprint author), Univ Hull, Sch Biol Biomed & Environm Sci, Kingston Upon Hull HU6 7RX, N Humberside, England.	KitsonJJN@gmail.com	Pocock, Michael/A-5632-2012	Pocock, Michael/0000-0003-4375-0445; Kitson, James/0000-0003-2405-1198	Natural Environment Research Council [ceh020002]			81	17	17	14	71	WILEY-BLACKWELL	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0269-8463	1365-2435		FUNCT ECOL	Funct. Ecol.	DEC	2016	30	12					1904	1916		10.1111/1365-2435.12659				13	Ecology	Environmental Sciences & Ecology	EF2ZU	WOS:000390195000004		Bronze, Green Published			22-11-18
J	Bellemain, E; Davey, ML; Kauserud, H; Epp, LS; Boessenkool, S; Coissac, E; Geml, J; Edwards, M; Willerslev, E; Gussarova, G; Taberlet, P; Brochmann, C				Bellemain, Eva; Davey, Marie L.; Kauserud, Havard; Epp, Laura S.; Boessenkool, Sanne; Coissac, Eric; Geml, Jozsef; Edwards, Mary; Willerslev, Eske; Gussarova, Galina; Taberlet, Pierre; Brochmann, Christian			Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost	ENVIRONMENTAL MICROBIOLOGY			English	Article							BASIDIOMYCETOUS YEAST; MICROBIAL DIVERSITY; ENVIRONMENTAL DNA; SPOROCARP DNA; SP NOV.; SOIL; ALPINE; ICE; COMMUNITIES; SEDIMENTS	The taxonomic and ecological diversity of ancient fungal communities was assessed by combining next generation sequencing and metabarcoding of DNA preserved in permafrost. Twenty-six sediment samples dated 1600032000 radiocarbon years old from two localities in Siberia were analysed for fungal ITS. We detected 75 fungal OTUs from 21 orders representing three phyla, although rarefaction analyses suggested that the full diversity was not recovered despite generating an average of 6677 +/- 3811 (mean +/- SD) sequences per sample and that preservation bias likely has considerable effect on the recovered DNA. Most OTUs (75.4%) represented ascomycetes. Due to insufficient sequencing depth, DNA degradation and putative preservation biases in our samples, the recovered taxa probably do not represent the complete historic fungal community, and it is difficult to determine whether the fungal communities varied geographically or experienced a composition shift within the period of 1600032000 bp. However, annotation of OTUs to functional ecological groups provided a wealth of information on the historic communities. About one-third of the OTUs are presumed plant-associates (pathogens, saprotrophs and endophytes) typical of graminoid- and forb-rich habitats. We also detected putative insect pathogens, coprophiles and keratinophiles likely associated with ancient insect and herbivore faunas. The detection of putative insect pathogens, mycoparasites, aquatic fungi and endophytes broadens our previous knowledge of the diversity of fungi present in Beringian palaeoecosystems. A large group of putatively psychrophilic/psychrotolerant fungi was also detected, most likely representing a modern, metabolically active fungal community.	[Bellemain, Eva; Epp, Laura S.; Boessenkool, Sanne; Gussarova, Galina; Brochmann, Christian] Univ Oslo, Nat Hist Museum, Natl Ctr Biosystemat, NO-0318 Oslo, Norway; [Davey, Marie L.; Kauserud, Havard] Univ Oslo, Dept Biol, MERG, N-0316 Oslo, Norway; [Davey, Marie L.] Norwegian Univ Life Sci, Dept Ecol & Nat Resource Management, N-1430 As, Norway; [Coissac, Eric; Taberlet, Pierre] Univ Grenoble 1, Lab Ecol Alpine, CNRS UMR 5553, F-38041 Grenoble 9, France; [Geml, Jozsef] Leiden Univ, Nationaal Herbarium Nederland, Kits van Waveren Fdn, NL-2300 RA Leiden, Netherlands; [Edwards, Mary] Univ Southampton, Southampton, Hants, England; [Willerslev, Eske] Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen K, Denmark	Bellemain, E (reprint author), SpyGen Savoie Technolac, 17 Allee Lac St Andre,BP 274 1, F-73375 Le Bourget Du Lac, France.	evabellemain@gmail.com	Geml, Jozsef/C-2223-2018; Gussarova, Galina/E-4758-2015; Taberlet, Pierre/D-1178-2010; Epp, Laura Saskia/J-5301-2016; Boessenkool, Sanne/K-4274-2017; Brochmann, Christian/A-4105-2009; Coissac, Eric/B-1077-2011	Geml, Jozsef/0000-0001-8745-0423; Gussarova, Galina/0000-0001-5388-7491; Taberlet, Pierre/0000-0002-3554-5954; Epp, Laura Saskia/0000-0002-2230-9477; Boessenkool, Sanne/0000-0001-8033-1165; Coissac, Eric/0000-0001-7507-6729; Davey, Marie/0000-0003-3911-8770	Research Council of Norway [191627/V40]; ECOCHANGE Project under the sixth Framework Programme of the European Commission [FP6-0368669]; National Science and Engineering Research Council of Canada (NSERC)	This work is part of the BarFrost project ('Reconstruction of past ecosystems by barcoding DNA preserved in permafrost') funded by the Research Council of Norway (Grant No. 191627/V40 to CB). It is conducted in collaboration with the ECOCHANGE Project (Contract No FP6-0368669) under the sixth Framework Programme of the European Commission. MLD's participation was financed by a postdoctoral fellowship from the National Science and Engineering Research Council of Canada (NSERC). We are grateful to Ludovic Orlando for running the analyses on Cytosine deamination for psychrophilic fungi.		83	34	36	4	134	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1462-2912	1462-2920		ENVIRON MICROBIOL	Environ. Microbiol.	APR	2013	15	4					1176	1189		10.1111/1462-2920.12020				14	Microbiology	Microbiology	122AM	WOS:000317287200015	23171292				22-11-18
J	Pechal, JL; Benbow, ME				Pechal, Jennifer L.; Benbow, M. Eric			Microbial ecology of the salmon necrobiome: evidence salmon carrion decomposition influences aquatic and terrestrial insect microbiomes	ENVIRONMENTAL MICROBIOLOGY			English	Article							TROUT ONCORHYNCHUS-MYKISS; FLIES DIPTERA; MAGGOT EXCRETIONS/SECRETIONS; STAPHYLOCOCCUS-AUREUS; INTERACTIVE TREE; RAIN-FOREST; BLOW FLIES; FOOD WEBS; DIVERSITY; BACTERIAL	Carrion decomposition is driven by complex relationships that affect necrobiome community (i.e. all organisms and their genes associated with a dead animal) interactions, such as insect species arrival time to carrion and microbial succession. Little is understood about how microbial communities interact with invertebrates at the aquatic-terrestrial habitat interface. The first objective of the study was to characterize internal microbial communities using high-throughput sequencing of 16S rRNA gene amplicons for aquatic insects (three mayfly species) in streams with salmon carcasses compared with those in streams without salmon carcasses. The second objective was to assess the epinecrotic microbial communities of decomposing salmon carcasses (Oncorhynchus keta) compared with those of terrestrial necrophagous insects (Calliphora terraenovae larvae and adults) associated with the carcasses. There was a significant difference in the internal microbiomes of mayflies collected in salmon carcass-bearing streams and in non-carcass streams, while the developmental stage of blow flies was the governing factor in structuring necrophagous insect internal microbiota. Furthermore, the necrophagous internal microbiome was influenced by the resource on which the larvae developed, and changes in the adult microbiome varied temporally. Overall, these carrion subsidy-driven networks respond to resource pulses with bottom-up effects on consumer microbial structure, as revealed by shifting communities over space and time.	[Pechal, Jennifer L.; Benbow, M. Eric] Michigan State Univ, Dept Entomol, 243 Nat Sci Bldg, E Lansing, MI 48824 USA; [Benbow, M. Eric] Michigan State Univ, Dept Osteopath Med Specialties, 243 Nat Sci Bldg, E Lansing, MI 48824 USA	Pechal, JL (reprint author), Michigan State Univ, Dept Entomol, 243 Nat Sci Bldg, E Lansing, MI 48824 USA.	pechalje@msu.edu		Pechal, Jennifer/0000-0002-2588-2519	Michigan State University College of Natural Resources and Agriculture (Department of Entomology); College of Osteopathic Medicine (Department of Osteopathic Medical Specialties)	The authors would like to thank CJ Picard for assistance in Calliphoridae adult collections along with DA Tallmon and J Hudson for their support and hospitality. The authors would like to thank four anonymous reviewers who made comments to improve a previous version of the manuscript. We thank the Michigan State University College of Natural Resources and Agriculture (Department of Entomology) and the College of Osteopathic Medicine (Department of Osteopathic Medical Specialties) for funding this work. The authors declare no conflict of interest.		77	10	10	0	21	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1462-2912	1462-2920		ENVIRON MICROBIOL	Environ. Microbiol.	MAY	2016	18	5					1511	1522		10.1111/1462-2920.13187				12	Microbiology	Microbiology	DL2QX	WOS:000375481200019	26690563				22-11-18
J	Manirajan, BA; Ratering, S; Rusch, V; Schwiertz, A; Geissler-Plaum, R; Cardinale, M; Schnell, S				Manirajan, Binoy Ambika; Ratering, Stefan; Rusch, Volker; Schwiertz, Andreas; Geissler-Plaum, Rita; Cardinale, Massimiliano; Schnell, Sylvia			Bacterial microbiota associated with flower pollen is influenced by pollination type, and shows a high degree of diversity and species-specificity	ENVIRONMENTAL MICROBIOLOGY			English	Article							IN-SITU HYBRIDIZATION; TARGETED OLIGONUCLEOTIDE PROBES; FLORAL NECTAR; CHEMICAL-COMPOSITION; SP NOV.; COMMUNITIES; PHYLLOSPHERE; MICROORGANISMS; IDENTIFICATION; ENVIRONMENT	Diverse microorganisms colonise the different plant-microhabitats, such as rhizosphere and phyllosphere, and play key roles for the host. However, bacteria associated with pollen are poorly investigated, despite its ecological, commercial and medical relevance. Due to structure and nutritive composition, pollen provides a unique microhabitat. Here the bacterial abundance, community structure, diversity and colonization pattern of birch, rye, rapes and autumn crocus pollens were examined, by using cultivation, high-throughput sequencing and microscopy. Cultivated bacteria belonged to Proteobacteria, Actinobacteria and Firmicutes, with remarkable differences at species level between pollen species. High-throughput sequencing of 16S rRNA gene amplicon libraries showed Proteobacteria as the dominant phylum in all pollen species, followed by Actinobacteria, Acidobacteria and Firmicutes. Both plant species and pollination type significant influenced structure and diversity of the pollen microbiota. The insect-pollinated species possessed a more similar microbiota in comparison to the wind-pollinated ones, suggesting a levelling effect by insect vectors. Scanning electron microscopy as well as fluorescent in situ hybridisation coupled with confocal laser scanning microscopy (FISH-CLSM) indicated the tectum surface as the preferred niche of bacterial colonisation. This work is the most comprehensive study of pollen microbiology, and strongly increases our knowledge on one of the less investigated plant-microhabitats.	[Manirajan, Binoy Ambika; Ratering, Stefan; Geissler-Plaum, Rita; Cardinale, Massimiliano; Schnell, Sylvia] Justus Liebig Univ, Res Ctr BioSyst Land Use & Nutr IFZ, Inst Appl Microbiol, Giessen, Germany; [Rusch, Volker] Stiftung Old Herborn Univ, Inst Integrat Biol, Herborn, Germany; [Schwiertz, Andreas] MVZ Inst Mikrookol GmbH, Herborn, Germany	Schnell, S (reprint author), Justus Liebig Univ, Res Ctr BioSyst Land Use & Nutr IFZ, Inst Appl Microbiol, Giessen, Germany.	Sylvia.Schnell@umwelt.uni-giessen.de	Ratering, Stefan/N-9437-2013; Cardinale, Massimiliano/B-8269-2014; Schnell, Sylvia/H-1639-2012	Ratering, Stefan/0000-0001-7572-6306; Cardinale, Massimiliano/0000-0003-1421-722X; Schnell, Sylvia/0000-0003-3903-6089				70	16	16	6	39	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1462-2912	1462-2920		ENVIRON MICROBIOL	Environ. Microbiol.	DEC	2016	18	12					5161	5174		10.1111/1462-2920.13524				14	Microbiology	Microbiology	EJ1CD	WOS:000392946900064	27612299				22-11-18
J	Pascual, J; von Hoermann, C; Rottler-Hoermann, AM; Nevo, O; Geppert, A; Sikorski, J; Huber, KJ; Steiger, S; Ayasse, M; Overmann, J				Pascual, Javier; von Hoermann, Christian; Rottler-Hoermann, Ann-Marie; Nevo, Omer; Geppert, Alicia; Sikorski, Johannes; Huber, Katharina J.; Steiger, Sandra; Ayasse, Manfred; Overmann, Joerg			Function of bacterial community dynamics in the formation of cadaveric semiochemicals during in situ carcass decomposition	ENVIRONMENTAL MICROBIOLOGY			English	Article							MICROBIAL COMMUNITIES; POTENTIAL USE; SUCCESSION; GUT; GENE; DIVERSITY; VOLATILES; DIPTERA; BEETLE; TOOL	The decomposition of dead mammalian tissue involves a complex temporal succession of epinecrotic bacteria. Microbial activity may release different cadaveric volatile organic compounds which in turn attract other key players of carcass decomposition such as scavenger insects. To elucidate the dynamics and potential functions of epinecrotic bacteria on carcasses, we monitored bacterial communities developing on still-born piglets incubated in different forest ecosystems by combining high-throughput Illumina 16S rRNA sequencing with gas chromatography-mass spectrometry of volatiles. Our results show that the community structure of epinecrotic bacteria and the types of cadaveric volatile compounds released over the time course of decomposition are driven by deterministic rather than stochastic processes. Individual cadaveric volatile organic compounds were correlated with specific taxa during the first stages of decomposition which are dominated by bacteria. Through best-fitting multiple linear regression models, the synthesis of acetic acid, indole and phenol could be linked to the activity of Enterobacteriaceae, Tissierellaceae and Xanthomonadaceae, respectively. These conclusions are also commensurate with the metabolism described for the dominant taxa identified for these families. The predictable nature of in situ synthesis of cadaveric volatile organic compounds by epinecrotic bacteria provides a new basis for future chemical ecology and forensic studies.	[Pascual, Javier; Geppert, Alicia; Sikorski, Johannes; Huber, Katharina J.; Overmann, Joerg] Leibniz Inst DSMZ Deutsch Sammlung Mikroorganisme, Dept Microbial Ecol & Divers Res, Braunschweig, Germany; [von Hoermann, Christian; Rottler-Hoermann, Ann-Marie; Nevo, Omer; Steiger, Sandra; Ayasse, Manfred] Ulm Univ, Inst Evolutionary Ecol & Conservat Genom, Dept Biol, Ulm, Germany; [Overmann, Joerg] Tech Univ Carolo Wilhelmina Braunschweig, Braunschweig, Germany	Pascual, J (reprint author), Leibniz Inst DSMZ Deutsch Sammlung Mikroorganisme, Dept Microbial Ecol & Divers Res, Braunschweig, Germany.	javier.pascual@dsmz.de		pascual, javier/0000-0002-1900-7099	DFG Priority Program 1374 "Infrastructure-Biodiversity-Exploratories' [AY 12/9-1, STE 1874/4-1, OV 20/21-1]	We thank the managers of the three Exploratories, Kirsten Reichel-Jung, Swen Renner, Katrin Lorenzen, Sonja Gockel, Kerstin Wiesner and Martin Gorke for their work in maintaining the plot and project infrastructure; Ralf Schlehahn and Ulf Pommer of the Local Management Team Schorfheide-Chorin for fieldwork assistance; Christiane Fischer and Simone Pfeiffer for giving support through the central office, Michael Owonibi for managing the central data base and Markus Fischer, Eduard Linsenmair, Dominik Hessenmoller, Jens Nieschulze, Daniel Prati, Ingo Schoning, Francois Buscot, Ernst-Detlef Schulze, Wolfgang W. Weisser and the late Elisabeth Kalko for their role in setting up the Biodiversity Exploratories project. The work has been (partly) funded by the DFG Priority Program 1374 "Infrastructure-Biodiversity-Exploratories' (AY 12/9-1, STE 1874/4-1, OV 20/21-1). Field work permits were issued by the responsible state environmental offices of Baden-Wurttemberg, Thuringen and Brandenburg (according to 72 BbgNatSchG). The authors declare no conflicts of interest.		62	1	1	3	19	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1462-2912	1462-2920		ENVIRON MICROBIOL	Environ. Microbiol.	AUG	2017	19	8			SI		3310	3322		10.1111/1462-2920.13828				13	Microbiology	Microbiology	FD8RB	WOS:000407790700029	28631411				22-11-18
J	Brodin, Y; Ejdung, G; Strandberg, J; Lyrholm, T				Brodin, Y.; Ejdung, G.; Strandberg, J.; Lyrholm, T.			Improving environmental and biodiversity monitoring in the Baltic Sea using DNA barcoding of Chironomidae (Diptera)	MOLECULAR ECOLOGY RESOURCES			English	Article						DNA barcoding; environmental DNA; insects; invertebrates	COMMUNITY STRUCTURE; IDENTIFICATION; PHYLOGENY; MACROINVERTEBRATES; INDICATORS; INFERENCE; TAXONOMY; COMPLEX; QUALITY; GENUS	As for many other regions, environmental and biodiversity monitoring of the brackish Baltic Sea suffers from low species resolution for several taxa. One such case is the benthic larvae of midges Chironomidae (Diptera), which are estimated to constitute about 30% of the macrozoobenthos species of the Baltic Sea and are important indicators of environmental quality. We assessed the usefulness of COI (cytochrome oxidase I) gene barcoding to improve species resolution and its potential for implementation in monitoring programmes. Neighbour-Joining, Maximum parsimony and Bayesian-inference analyses all provided high congruency with morphological analyses of adult males for almost all 42 species studied. Barcoding was helpful to elucidate some cases of taxonomical difficulties, such as synonyms. In contrast to the high identification accuracy when using our local database, there were a number of cases where matching with GenBank and BOLD provided puzzling results. For reliable species identification at least 15-30 specimens from 5-10 well-distributed sites within the geographical range of the species might be needed in a database to adequately cover the intraspecific variability of chironomids. Implementation of DNA barcoding, as applied here, in monitoring would result in an increase from at present less than 10% to more than 90% successful chironomid species identification of Baltic Sea benthic samples, as it also would for many nearby lakes. Routine monitoring of benthic environmental samples based on Next-Generation sequencing techniques would provide a cost effective way to obtain a taxonomically much more complete assessment of environmental quality and biodiversity, as required by EU directives and national legislation.	[Brodin, Y.; Strandberg, J.; Lyrholm, T.] Swedish Museum Nat Hist, S-10405 Stockholm, Sweden; [Ejdung, G.] Swedish Agcy Marine & Water Management, S-40439 Gothenburg, Sweden	Lyrholm, T (reprint author), Swedish Museum Nat Hist, Box 50007, S-10405 Stockholm, Sweden.	thomas.lyrholm@nrm.se			Swedish Environmental Protection Agency	We wish to express our gratitude to Dawn Williams for slide preparations and to Sara Berggren, Lars Bern, Bo Bjornsater, Caroline Essenberg, Jorgen Hellberg, Gunnar Hjertstrand, Axel Hullberg, Martin Irestedt, Hans Kautsky, Kristina Murray-Brodin, Jonas Rodhe and Miriam Talah for field sampling of chironomids. We are grateful for helpful comments by the reviewers. Funding was provided by the Swedish Environmental Protection Agency.		40	20	20	2	71	WILEY-BLACKWELL	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1755-098X	1755-0998		MOL ECOL RESOUR	Mol. Ecol. Resour.	NOV	2013	13	6			SI		996	1004		10.1111/1755-0998.12053				9	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	234FN	WOS:000325627700004	23280321				22-11-18
J	Clarke, LJ; Soubrier, J; Weyrich, LS; Cooper, A				Clarke, Laurence J.; Soubrier, Julien; Weyrich, Laura S.; Cooper, Alan			Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias	MOLECULAR ECOLOGY RESOURCES			English	Article						environmental DNA; insect; metabarcoding; PCR bias	SUBUNIT RIBOSOMAL-RNA; SECONDARY STRUCTURE; DNA BARCODES; 16S RDNA; GENE; IDENTIFICATION; COMMUNITIES; DIVERSITY; EVOLUTION; PRIMERS	Studies of insect assemblages are suited to the simultaneous DNA-based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR-amplification bias, as well as sufficient sequence divergence to resolve species. We used in silicoPCR to compare the taxonomic coverage and resolution of newly designed insect metabarcodes (targeting 16S) with that of existing markers [16S and cytochrome oxidase c subunit I (COI)] and then compared their efficiency in vitro. Existing metabarcoding primers amplified in silico <75% of insect species with complete mitochondrial genomes available, whereas new primers targeting 16S provided >90% coverage. Furthermore, metabarcodes targeting COI appeared to introduce taxonomic PCR-amplification bias, typically amplifying a greater percentage of Lepidoptera and Diptera species, while failing to amplify certain orders in silico. To test whether bias predicted in silico was observed in vitro, we created an artificial DNA blend containing equal amounts of DNA from 14 species, representing 11 insect orders and one arachnid. We PCR-amplified the blend using five primer sets, targeting either COI or 16S, with high-throughput amplicon sequencing yielding more than 6million reads. In vitro results typically corresponded to in silicoPCR predictions, with newly designed 16S primers detecting 11 insect taxa present, thus providing equivalent or better taxonomic coverage than COI metabarcodes. Our results demonstrate that in silicoPCR is a useful tool for predicting taxonomic bias in mixed template PCR and that researchers should be wary of potential bias when selecting metabarcoding markers.	[Clarke, Laurence J.; Soubrier, Julien; Weyrich, Laura S.; Cooper, Alan] Univ Adelaide, Australian Ctr Ancient DNA, Adelaide, SA 5005, Australia	Clarke, LJ (reprint author), Univ Adelaide, Australian Ctr Ancient DNA, Adelaide, SA 5005, Australia.	laurence.clarke@adelaide.edu.au	Clarke, Laurence/N-3579-2017	Clarke, Laurence/0000-0002-0844-4453; Weyrich, Laura/0000-0001-5243-4634	ARC	Thanks to Renate Faast and Oliver Wooley for supplying insect specimens; Douglas Green for supplying DNA extracts; and John Jennings, Gary Taylor and Remko Leijs for morphological identification. Bastien Llamas helped design the bioinformatic pipeline. Oliver Wooley helped produce Fig. S2 (Supporting information). We thank the ARC for funding and ACAD members for helpful comments and assistance.		49	70	71	9	99	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1755-098X	1755-0998		MOL ECOL RESOUR	Mol. Ecol. Resour.	NOV	2014	14	6					1160	1170		10.1111/1755-0998.12265				11	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	AR8DJ	WOS:000343805400006	24751203				22-11-18
J	Pinol, J; Mir, G; Gomez-Polo, P; Agusti, N				Pinol, J.; Mir, G.; Gomez-Polo, P.; Agusti, N.			Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods	MOLECULAR ECOLOGY RESOURCES			English	Article						annealing temperature; insects; Ion Torrent; PCR bias; PCR cycles	PREY DNA; BIODIVERSITY ASSESSMENT; PCR AMPLIFICATION; ION TORRENT; DIET; FECES; DIVERSITY; SAMPLES; COUNT	The quantification of the biological diversity in environmental samples using high-throughput DNA sequencing is hindered by the PCR bias caused by variable primer-template mismatches of the individual species. In some dietary studies, there is the added problem that samples are enriched with predator DNA, so often a predator-specific blocking oligonucleotide is used to alleviate the problem. However, specific blocking oligonucleotides could coblock nontarget species to some degree. Here, we accurately estimate the extent of the PCR biases induced by universal and blocking primers on a mock community prepared with DNA of twelve species of terrestrial arthropods. We also compare universal and blocking primer biases with those induced by variable annealing temperature and number of PCR cycles. The results show that reads of all species were recovered after PCR enrichment at our control conditions (no blocking oligonucleotide, 45 degrees C annealing temperature and 40 cycles) and high-throughput sequencing. They also show that the four factors considered biased the final proportions of the species to some degree. Among these factors, the number of primer-template mismatches of each species had a disproportionate effect (up to five orders of magnitude) on the amplification efficiency. In particular, the number of primer-template mismatches explained most of the variation (similar to 3/4) in the amplification efficiency of the species. The effect of blocking oligonucleotide concentration on nontarget species relative abundance was also significant, but less important (below one order of magnitude). Considering the results reported here, the quantitative potential of the technique is limited, and only qualitative results (the species list) are reliable, at least when targeting the barcoding COI region.	[Pinol, J.] Univ Autonoma Barcelona, Cerdanyola Del Valles 08193, Spain; [Pinol, J.] CREAF, Cerdanyola Del Valles 08193, Spain; [Mir, G.] UB, UAB, IRTA, CRAG,CSIC, Cerdanyola Del Valles 08193, Spain; [Mir, G.] Peter MacCallum Canc Ctr, East Melbourne, Vic, Australia; [Gomez-Polo, P.; Agusti, N.] IRTA, E-08348 Barcelona, Spain	Pinol, J (reprint author), Univ Autonoma Barcelona, Cerdanyola Del Valles 08193, Spain.	Jo-sep.Pinol@uab.es	Agusti, Nuria/C-8318-2011; Pinol, Josep/K-3577-2014	Agusti, Nuria/0000-0002-5908-4873; Pinol, Josep/0000-0002-4067-3301	MINECO [CGL2010-18182, AGL2011-24349]	We thank several anonymous reviewers and Bruce Deagle for useful suggestions on preliminary versions of the manuscript. Financial help was provided by the MINECO grants CGL2010-18182 and AGL2011-24349. Carla Romeu-Dalmau and Laia Mestre provided some of the DNA extracts used here. We thank Vanesa Vega, Merce Miquel, Oriol Casagran and Jordi Martinez-Vilalta for technical support.		46	55	60	10	126	WILEY-BLACKWELL	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1755-098X	1755-0998		MOL ECOL RESOUR	Mol. Ecol. Resour.	JUL	2015	15	4					819	830		10.1111/1755-0998.12355				12	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	CL1CJ	WOS:000356679800012	25454249				22-11-18
J	Mitchell, A				Mitchell, Andrew			Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens	MOLECULAR ECOLOGY RESOURCES			English	Article						COI; DNA barcodes; DNA sequencing; insect	LEPIDOPTERA; EVOLUTION; REVISION	Natural history museums are vastly underutilized as a source of material for DNA analysis because of perceptions about the limitations of DNA degradation in older specimens. Despite very few exceptions, most DNA barcoding projects, which aim to obtain sequence data from all species, generally use specimens collected specifically for that purpose, instead of the wealth of identified material in museums, constrained by the lack of suitable PCR methods. Any techniques that extend the utility of museum specimens for DNA analysis therefore are highly valuable. This study first tested the effects of specimen age and PCR amplicon size on PCR success rates in pinned insect specimens, then developed a PCR primer set and amplification strategy allowing greatly increased utilization of older museum specimens for DNA barcoding. PCR success rates compare favourably with the few published studies utilizing similar aged specimens, and this new strategy has the advantage of being easily automated for high-throughput laboratory workflows. The strategy uses hemi-nested, degenerate, M13-tailed PCR primers to amplify two overlapping amplicons, using two PCRs per amplicon (i.e. four PCRs per DNA sample). Initial PCR products are reamplified using an internal primer and a M13 primer. Together the two PCR amplicons yield 559bp of the COI gene from Coleoptera, Lepidoptera, Diptera, Hemiptera, Odonata and presumably also other insects. BARCODE standard-compliant data were recovered from 67% (56 of 84) of specimens up to 25years old, and 51% (102 of 197) of specimens up to 55years old. Given the time, cost and specialist expertise required for fieldwork and identification, collecting in collections' is a viable alternative allowing researchers to capitalize on the knowledge captured by curation work in decades past.	Australian Museum, Res Inst, Sydney, NSW 2010, Australia	Mitchell, A (reprint author), Australian Museum, Res Inst, 6 Coll St, Sydney, NSW 2010, Australia.	Andrew.Mitchell@austmus.gov.au	Mitchell, Andrew/B-7018-2008	Mitchell, Andrew/0000-0001-5022-5898	Australian Biological Resources Study	The author thanks Tom Weir, Marianne Horak and You Ning Su of the Australian National Insect Collection (ANIC), CSIRO, for the loan of beetle and moth specimens, and the Australian Centre for Wildlife Genomics for technical support. Funding was provided by the Australian Biological Resources Study.		19	9	9	1	55	WILEY-BLACKWELL	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1755-098X	1755-0998		MOL ECOL RESOUR	Mol. Ecol. Resour.	SEP	2015	15	5					1102	1111		10.1111/1755-0998.12380				10	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	CP1JH	WOS:000359631600009	25644663				22-11-18
J	Liu, SL; Wang, X; Xie, L; Tan, MH; Li, ZY; Su, X; Zhang, H; Misof, B; Kjer, KM; Tang, M; Niehuis, O; Jiang, H; Zhou, X				Liu, Shanlin; Wang, Xin; Xie, Lin; Tan, Meihua; Li, Zhenyu; Su, Xu; Zhang, Hao; Misof, Bernhard; Kjer, Karl M.; Tang, Min; Niehuis, Oliver; Jiang, Hui; Zhou, Xin			Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis	MOLECULAR ECOLOGY RESOURCES			English	Article						biodiversity; gene capture; microarray; mitochondrial genome	DE-NOVO ASSEMBLER; GENOMES; PHYLOGENY; BARCODE; EVOLUTION; SAMPLES; ARRAY	Biodiversity analyses based on next-generation sequencing (NGS) platforms have developed by leaps and bounds in recent years. A PCR-free strategy, which can alleviate taxonomic bias, was considered as a promising approach to delivering reliable species compositions of targeted environments. The major impediment of such a method is the lack of appropriate mitochondrial DNA enrichment ways. Because mitochondrial genomes (mitogenomes) make up only a small proportion of total DNA, PCR-free methods will inevitably result in a huge excess of data (>99%). Furthermore, the massive volume of sequence data is highly demanding on computing resources. Here, we present a mitogenome enrichment pipeline via a gene capture chip that was designed by virtue of the mitogenome sequences of the 1000 Insect Transcriptome Evolution project (1KITE, ). A mock sample containing 49 species was used to evaluate the efficiency of the mitogenome capture method. We demonstrate that the proportion of mitochondrial DNA can be increased by approximately 100-fold (from the original 0.47% to 42.52%). Variation in phylogenetic distances of target taxa to the probe set could in principle result in bias in abundance. However, the frequencies of input taxa were largely maintained after capture (R-2=0.81). We suggest that our mitogenome capture approach coupled with PCR-free shotgun sequencing could provide ecological researchers an efficient NGS method to deliver reliable biodiversity assessment.	[Liu, Shanlin; Wang, Xin; Tan, Meihua; Su, Xu; Tang, Min; Zhou, Xin] BGI Shenzhen, China Natl GeneBank Shenzhen, Shenzhen 518083, Guangdong, Peoples R China; [Liu, Shanlin; Wang, Xin; Xie, Lin; Tan, Meihua; Li, Zhenyu; Zhang, Hao; Tang, Min; Jiang, Hui; Zhou, Xin] BGI Shenzhen, Shenzhen 518083, Guangdong, Peoples R China; [Liu, Shanlin] Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, Oster Voldgade 5-7, DK-1350 Copenhagen, Denmark; [Su, Xu] Guizhou Prov Ctr Dis Control & Prevent, Guiyang 550004, Guizhou Provinc, Peoples R China; [Misof, Bernhard; Niehuis, Oliver] Zentrum Mol Biodiversitats Forsch, Zool Forsch Museum Alexander Koenig ZFMK, Bonn, Germany; [Kjer, Karl M.] Univ Calif Davis, Dept Entomol & Nematol, Davis, CA 95616 USA	Zhou, X (reprint author), BGI Shenzhen, China Natl GeneBank Shenzhen, Shenzhen 518083, Guangdong, Peoples R China.; Zhou, X (reprint author), BGI Shenzhen, Shenzhen 518083, Guangdong, Peoples R China.	xinzhou@genomics.cn	Zhou, Xin/D-4025-2009	Zhou, Xin/0000-0002-1407-7952; Tang, Min/0000-0002-6021-7282	National High Technology Research and Development Program of China - 863 Program [2012021601]; National Key Technology RD Program [2012BAK11B06]; Science and Technology Innovation of CAS, iFlora Cross and Cooperation Team [31129001]	We are thankful to Douglas Yu for his valuable advices. This work is supported by the National High Technology Research and Development Program of China - 863 Program (2012021601), the National Key Technology R&D Program (2012BAK11B06) and the Science and Technology Innovation of CAS, iFlora Cross and Cooperation Team (31129001). We would like to thank members of the 1KITE consortium (www.1kite.org) for allowing us to filter mitogenomes in transcriptome data.		45	24	26	1	42	WILEY-BLACKWELL	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1755-098X	1755-0998		MOL ECOL RESOUR	Mol. Ecol. Resour.	MAR	2016	16	2					470	479		10.1111/1755-0998.12472				10	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	DC3RS	WOS:000369137000010	26425990	Green Published			22-11-18
J	Reiskind, MOB; Coyle, K; Daniels, HV; Labadie, P; Reiskind, MH; Roberts, NB; Roberts, RB; Schaff, J; Vargo, EL				Reiskind, M. O. Burford; Coyle, K.; Daniels, H. V.; Labadie, P.; Reiskind, M. H.; Roberts, N. B.; Roberts, R. B.; Schaff, J.; Vargo, E. L.			Development of a universal double-digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa	MOLECULAR ECOLOGY RESOURCES			English	Article						double-digest RAD sequencing; high-throughput sequencing; reduced representation sequencing; restriction enzyme digests	POPULATION GENOMICS; ADAPTIVE RADIATION; HIGH-THROUGHPUT; READ ALIGNMENT; CICHLID FISHES; MARKERS; DIVERGENCE; PHYLOGENY; EVOLUTION; DISCOVERY	The generation of genome-scale data is critical for a wide range of questions in basic biology using model organisms, but also in questions of applied biology in nonmodel organisms (agriculture, natural resources, conservation and public health biology). Using a genome-scale approach on a diverse group of nonmodel organisms and with the goal of lowering costs of the method, we modified a multiplexed, high-throughput genomic scan technique utilizing two restriction enzymes. We analysed several pairs of restriction enzymes and completed double-digestion RAD sequencing libraries for nine different species and five genera of insects and fish. We found one particular enzyme pair produced consistently higher number of sequence-able fragments across all nine species. Building libraries off this enzyme pair, we found a range of usable SNPs between 4000 and 37000 SNPS per species and we found a greater number of usable SNPs using reference genomes than de novo pipelines in STACKS. We also found fewer reads in the Read 2 fragments from the paired-end Illumina Hiseq run. Overall, the results of this study provide empirical evidence of the utility of this method for producing consistent data for diverse nonmodel species and suggest specific considerations for sequencing analysis strategies.	[Reiskind, M. O. Burford; Daniels, H. V.] N Carolina State Univ, Dept Appl Ecol, Campus Box 7617, Raleigh, NC 27695 USA; [Coyle, K.; Roberts, N. B.; Roberts, R. B.] N Carolina State Univ, Dept Biol Sci, Raleigh, NC 27695 USA; [Labadie, P.; Reiskind, M. H.] N Carolina State Univ, Dept Entomol, Raleigh, NC 27695 USA; [Vargo, E. L.] Texas A&M Univ, Dept Entomol, College Stn, TX 77843 USA; [Schaff, J.] N Carolina State Univ, Genom Sci Lab, Raleigh, NC 27695 USA	Reiskind, MOB (reprint author), N Carolina State Univ, Dept Appl Ecol, Campus Box 7617, Raleigh, NC 27695 USA.	mbreiski@ncsu.edu		Burford Reiskind, Martha/0000-0001-6826-9215	Wynne Innovation Grant from the CAL Dean's Enrichment Grant Programme at NCSU; NSF [IOS-1456765]; Applied Ecology and Entomology Departments at NCSU	We thank the following for their assistance with collections of specimens: O. Blavin, C. Schal, W. Booth, A. A. Aguilar, A. Gill, B. Reading, P. Lounidos and I. Bargielowski. We thank C. Dashiell for assistance with the Bioanalyzer and sequencing logistics and E. Scholl for consultation on sequence alignment programs. R.W. Whetton for consultation on bioinformatic questions and T. Schultz for initial consultation on library building. Finally, we thank several anonymous reviewers for comments that improved this manuscript. This research was funded by the Wynne Innovation Grant from the CAL Dean's Enrichment Grant Programme at NCSU awarded to MO Burford Reiskind. Part of this research was also funded by the NSF, Grant IOS-1456765 awarded to RB Roberts. We also thank both the Applied Ecology and Entomology Departments at NCSU for providing matching funds to further fund this collaborative research.		40	5	5	6	36	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1755-098X	1755-0998		MOL ECOL RESOUR	Mol. Ecol. Resour.	NOV	2016	16	6					1303	1314		10.1111/1755-0998.12527				12	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	DZ5ZP	WOS:000385941500003	27739656				22-11-18
J	Carew, ME; Metzeling, L; St Clair, R; Hoffmann, AA				Carew, Melissa E.; Metzeling, Leon; St Clair, Rosalind; Hoffmann, Ary A.			Detecting invertebrate species in archived collections using next-generation sequencing	MOLECULAR ECOLOGY RESOURCES			English	Article						aquatic; DNA barcoding; insect; invertebrates; metagenomic	DNA BARCODES; WATER-QUALITY; RAPID ASSESSMENT; FAMILY-LEVEL; MACROINVERTEBRATES; AUSTRALIA; IDENTIFICATION; BIOASSESSMENT; AMPLIFICATION; SPECIMENS	Invertebrate biodiversity measured at mostly family level is widely used in biological monitoring programmes to assess anthropogenic impacts on ecosystems. However, next-generation sequencing (NGS) could allow development of new more sensitive biomonitoring tools by allowing rapid species identification. This could be accelerated if archived invertebrate collections and environmental information from past programmes are used to understand species distributions and their environmental responses. In this study, we take archived macroinvertebrate samples from two sites collected on multiple occasions and test whether NGS can successfully detect species. Samples had been stored in 70% ethanol at room temperature for up to 12 years. Three amplicons ranging from 197 to 274 bps within the DNA barcode region were amplified from samples and compared to DNA barcoding libraries to identify species. We were able to amplify partial DNA barcodes from most samples, and species were often detected with multiple amplicons. However, some singletons and taxa poorly covered by DNA barcoding were missed. This suggests additional DNA barcodes will be required to fill 'gaps' in current DNA barcode libraries for aquatic macroinvertebrates and/or that it may not be possible to detect all taxa in a sample. Furthermore, older samples often detected fewer taxa and were less reliable for amplification, suggesting NGS is best used on samples within 8 years of collection. Nevertheless, many common taxa with existing DNA barcodes were reliably identified with NGS and were often present at sites across multiple years, showing the potential of NGS for detecting common and abundant species in archived material.	[Carew, Melissa E.; Hoffmann, Ary A.] Univ Melbourne, Victorian Ctr Aquat Pollut Identificat & Manageme, Inst Bio21, Sch BioSci, 30 Flemington Rd, Melbourne, Vic 3010, Australia; [Metzeling, Leon; St Clair, Rosalind] Environm Protect Author Victoria, Ernest Jones Dr, Macleod, Vic 3085, Australia	Carew, ME (reprint author), Univ Melbourne, Victorian Ctr Aquat Pollut Identificat & Manageme, Inst Bio21, Sch BioSci, 30 Flemington Rd, Melbourne, Vic 3010, Australia.	mecarew@unimelb.edu.au			Australian Research Council; Melbourne Water Corporation; Victorian Government; EPA Victoria	The authors thank Michael Shackleton, David Cartwright and John Dean for the use of their DNA barcode information. We also thank Rahul Rane for his advice in the laboratory and on data analysis and Isabel Valenzuela for assistance with primer selection. This study was funded primarily by the Australian Research Council through their Linkage and Fellowship schemes, with additional support from Melbourne Water Corporation, the Victorian Government and EPA Victoria.		64	3	3	4	10	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1755-098X	1755-0998		MOL ECOL RESOUR	Mol. Ecol. Resour.	SEP	2017	17	5					915	930		10.1111/1755-0998.12644				16	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	FN3TF	WOS:000415921600008	27987268				22-11-18
J	Sproul, JS; Maddison, DR				Sproul, John S.; Maddison, David R.			Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA	MOLECULAR ECOLOGY RESOURCES			English	Article						high-throughput DNA sequencing; insects; museum specimens; natural history collections; sample preparation; type specimens	MUSEUM SPECIMENS; ANCIENT DNA; GENOMICS; RHODOPHYTA; PHYLOGENY; BEMBIDION; CAPTURE; MODELS; FUTURE; SHIFTS	Despite advances that allow DNA sequencing of old museum specimens, sequencing small-bodied, historical specimens can be challenging and unreliable as many contain only small amounts of fragmented DNA. Dependable methods to sequence such specimens are especially critical if the specimens are unique. We attempt to sequence small-bodied (3-6mm) historical specimens (including nomenclatural types) of beetles that have been housed, dried, in museums for 58-159years, and for which few or no suitable replacement specimens exist. To better understand ideal approaches of sample preparation and produce preparation guidelines, we compared different library preparation protocols using low amounts of input DNA (1-10ng). We also explored low-cost optimizations designed to improve library preparation efficiency and sequencing success of historical specimens with minimal DNA, such as enzymatic repair of DNA. We report successful sample preparation and sequencing for all historical specimens despite our low-input DNA approach. We provide a list of guidelines related to DNA repair, bead handling, reducing adapter dimers and library amplification. We present these guidelines to facilitate more economical use of valuable DNA and enable more consistent results in projects that aim to sequence challenging, irreplaceable historical specimens.	[Sproul, John S.; Maddison, David R.] Oregon State Univ, Dept Integrat Biol, 3029 Cordley Hall, Corvallis, OR 97331 USA	Sproul, JS (reprint author), Oregon State Univ, Dept Integrat Biol, 3029 Cordley Hall, Corvallis, OR 97331 USA.	johnssproul@gmail.com			Harold E. and Leona M. Rice Endowment Fund at Oregon State University; National Science Foundation [DEB-1258220]	We thank James Pflug, Kojun Kanda and Jeff Oliver for help with data analysis. We thank Kojun Kanda for reviewing the manuscript. We thank David Kavanaugh, Wendy Moore, Esteve Boutaud, Antonio Gomez, Olivia Boyd, Pietro Brandmayr and Jose Serrano for helpful discussions related to our findings. We are indebted to the technical support staff from New England Biolabs and Swift Biosciences for several hours of discussion as we implemented optimizations that deviated from their published protocols. We thank Terry Erwin (USNM), Philip Perkins (MCZ) Beulah Garner and Max Barclay (BMNH), Robert Davidson (CMNH), David Kavanaugh (CAS), Christopher Dietrich (INHS) and Wendy Moore (UAIC) for providing historical specimens. Thanks to Robert Davidson for providing information about the collection date for the paratype of Bembidion ulkei. For help in collecting context specimens, we thank K.W. Will, J.N. Caira, A. Gill, J.R. LaBonte, J.H.A. Maddison, A.E. Arnold, K. Kanda, K.T. Eldredge, W.Moore, S.D. Schoville, G.J. Binford, M. Lahti and D.H. Kavanaugh. This work was funded in part by the Harold E. and Leona M. Rice Endowment Fund at Oregon State University, as well as National Science Foundation grant DEB-1258220 to DRM.		37	4	4	6	14	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1755-098X	1755-0998		MOL ECOL RESOUR	Mol. Ecol. Resour.	NOV	2017	17	6					1183	1201		10.1111/1755-0998.12660				19	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	FN3TH	WOS:000415921900032	28199781	Bronze			22-11-18
J	Batovska, J; Lynch, SE; Cogan, NOI; Brown, K; Darbro, JM; Kho, EA; Blacket, MJ				Batovska, J.; Lynch, S. E.; Cogan, N. O. I.; Brown, K.; Darbro, J. M.; Kho, E. A.; Blacket, M. J.			Effective mosquito and arbovirus surveillance using metabarcoding	MOLECULAR ECOLOGY RESOURCES			English	Article						bulk sample; Culicidae; cytochrome c oxidase subunit I; DNA barcoding; pooled samples; virus	ROSS-RIVER-VIRUS; DNA; IDENTIFICATION; BIODIVERSITY; ARTHROPODS; ABUNDANCE; BARCODES; VECTORS; CAPTURE; SAMPLES	Effective vector and arbovirus surveillance requires timely and accurate screening techniques that can be easily upscaled. Next-generation sequencing (NGS) is a high-throughput technology that has the potential to modernize vector surveillance. When combined with DNA barcoding, it is termed 'metabarcoding.' The aim of our study was to establish a metabarcoding protocol to characterize pools of mosquitoes and screen them for virus. Pools contained 100 morphologically identified individuals, including one Ross River virus (RRV) infected mosquito, with three species present at different proportions: 1, 5, 94%. Nucleic acid extracted from both crude homogenate and supernatant was used to amplify a 269-bp section of the mitochondrial cytochrome c oxidase subunit I (COI) locus. Additionally, a 67-bp region of the RRV E2 gene was amplified from synthesized cDNA to screen for RRV. Amplicon sequencing was performed using an Illumina MiSeq, and bioinformatic analysis was performed using a DNA barcode database of Victorian mosquitoes. Metabarcoding successfully detected all mosquito species and RRV in every positive sample tested. The limits of species detection were also examined by screening a pool of 1000 individuals, successfully identifying the species and RRV from a single mosquito. The primers used for amplification, number of PCR cycles and total number of individuals present all have effects on the quantification of species in mixed bulk samples. Based on the results, a number of recommendations for future metabarcoding studies are presented. Overall, metabarcoding shows great promise for providing a new alternative approach to screening large insect surveillance trap catches.	[Batovska, J.; Lynch, S. E.; Cogan, N. O. I.; Brown, K.; Blacket, M. J.] Ctr AgriBiosci, Agr Victoria, AgriBio, Bundoora, Vic, Australia; [Cogan, N. O. I.] La Trobe Univ, Sch Appl Syst Biol, Bundoora, Vic, Australia; [Darbro, J. M.; Kho, E. A.] QIMR Berghofer Med Res Inst, Mosquito Control Lab, Brisbane, Qld, Australia	Batovska, J (reprint author), Ctr AgriBiosci, Agr Victoria, AgriBio, Bundoora, Vic, Australia.	jana.batovska@ecodev.vic.gov.au			Victorian Department of Health and Human Services; Department of Economic Development, Jobs, Transport and Resources	Victorian Department of Health and Human Services; Biosciences Research Innovation Fund Program through the Department of Economic Development, Jobs, Transport and Resources		52	0	0	8	10	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1755-098X	1755-0998		MOL ECOL RESOUR	Mol. Ecol. Resour.	JAN	2018	18	1					32	40		10.1111/1755-0998.12682				9	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	FU8OI	WOS:000424112000004	28417591	Other Gold			22-11-18
J	Birer, C; Tysklind, N; Zinger, L; Duplais, C				Birer, Caroline; Tysklind, Niklas; Zinger, Lucie; Duplais, Christophe			Comparative analysis of DNA extraction methods to study the body surface microbiota of insects: A case study with ant cuticular bacteria	MOLECULAR ECOLOGY RESOURCES			English	Article						16S rRNA; bacterial communities; cuticular microbiome; insect cuticle; metabarcoding	SKIN MICROBIOTA; COMMUNITIES; HYMENOPTERA; FORMICIDAE; STRATEGIES; DIVERSITY; EVOLUTION; SYMBIOSIS	High-throughput sequencing of the 16S rRNA gene has considerably helped revealing the essential role of bacteria living on insect cuticles in the ecophysiology and behaviour of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties of working with low bacterial DNA quantities as with individual insect cuticle samples, which are more prone to molecular biases and contaminations. Herein, we conducted a methodological benchmark on the cuticular bacterial loads retrieved from two Neotropical ant species of different body size and ecology: Atta cephalotes (similar to 15mm) and Pseudomyrmex penetrator (similar to 5mm). We evaluated the richness and composition of the cuticular microbiota, as well as the amount of biases and contamination produced by four DNA extraction protocols. We also addressed how bacterial community characteristics would be affected by the number of individuals or individual body size used for DNA extraction. Most extraction methods yielded similar results in terms of bacterial diversity and composition for A.cephalotes (similar to 15mm). In contrast, greater amounts of artefactual sequences and contaminations, as well as noticeable differences in bacterial community characteristics were observed between extraction methods for P.penetrator (similar to 5mm). We also found that large (similar to 15mm) and small (similar to 5mm) A.cephalotes individuals harbour different bacterial communities. Our benchmark suggests that cuticular microbiota of single individual insects can be reliably retrieved provided that blank controls, appropriate data cleaning, and individual body size and functional role within insect society are considered in the experiment.	[Birer, Caroline; Duplais, Christophe] Univ Guyane, Univ Antilles, CNRS, EcoFoG UMR8172,AgroParisTech,Cirad,INRA, Cayenne, France; [Tysklind, Niklas] Univ Guyane, Univ Antilles, CNRS, AgroParisTech,Cirad,INRA,UMR8172 EcoFoG, Kourou, French Guiana; [Zinger, Lucie] Univ Toulouse 3 Paul Sabatier, CNRS, ENFA, UMR 5174 EDB, Toulouse, France; [Zinger, Lucie] Paris Sci & Lettres Res Univ, Inst Biol Ecole Normale Super, INSERM, CNRS UMR 8197,U1024, F-75005 Paris, France	Birer, C (reprint author), CNRS, EcoFoG, UMR8172, Campus Agron, Kourou, France.	caroline@birer.fr	Zinger, Lucie/D-2527-2010	Zinger, Lucie/0000-0002-3400-5825; Duplais, Christophe/0000-0003-0926-9885	Agence Nationale de la Recherche [ANR-10-LABX-25-01]; CNRS; Investissement d'Avenir Grant	Agence Nationale de la Recherche, Grant/Award Number: ANR-10-LABX-25-01; CNRS; Investissement d'Avenir Grant		48	1	1	11	30	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1755-098X	1755-0998		MOL ECOL RESOUR	Mol. Ecol. Resour.	NOV	2017	17	6					e34	e45		10.1111/1755-0998.12688				12	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	FN3TH	WOS:000415921900004	28477337				22-11-18
J	Galan, M; Pons, JB; Tournayre, O; Pierre, E; Leuchtmann, M; Pontier, D; Charbonnel, N				Galan, Maxime; Pons, Jean-Baptiste; Tournayre, Orianne; Pierre, Eric; Leuchtmann, Maxime; Pontier, Dominique; Charbonnel, Nathalie			Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis	MOLECULAR ECOLOGY RESOURCES			English	Article						Arthropoda; Chiroptera; environmental DNA (eDNA); false positives; high-throughput sequencing; predator-prey interactions	DESMAN GALEMYS-PYRENAICUS; ENVIRONMENTAL DNA; PYRENEAN DESMAN; BIODIVERSITY; EXTRACTION; IDENTIFY; PLATFORM; BARCODE; FOOD	Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the "all at once" taxonomic identification of bats and their arthropod prey for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods, and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity and amplification biases. Our parallel identification strategy of predators and prey reduces the risk of mis-assigning prey to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing "chirosurveillance" and conservation strategies.	[Galan, Maxime; Tournayre, Orianne; Pierre, Eric; Charbonnel, Nathalie] Univ Montpellier, Montpellier SupAgro, INRA, CBGP,CIRAD,IRD, Montferrier Sur Lez, France; [Pons, Jean-Baptiste; Pontier, Dominique] Univ Lyon, LabEx ECOFECT Ecoevolutionary Dynam Infect Dis, Lyon, France; [Leuchtmann, Maxime] Nat Environm, Surgeres, France; [Pontier, Dominique] Univ Lyon 1, Univ Lyon, CNRS, Lab Biomet & Biol Evolut,UMR5558, Villeurbanne, France	Galan, M (reprint author), Univ Montpellier, Montpellier SupAgro, INRA, CBGP,CIRAD,IRD, Montferrier Sur Lez, France.	maxime.galan@inra.fr	charbonnel, Nathalie/B-2601-2013	charbonnel, Nathalie/0000-0002-7907-6539	Agence Nationale de la Recherche [ANR-11-LABX-0048]; LabEx ECOFECT [ANR-11LABX-0048]; CBGP laboratory	Agence Nationale de la Recherche, Grant/Award Number: ANR-11-LABX-0048; LabEx ECOFECT, Grant/Award Number: ANR-11LABX-0048; CBGP laboratory		55	1	1	38	38	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1755-098X	1755-0998		MOL ECOL RESOUR	Mol. Ecol. Resour.	MAY	2018	18	3					474	489		10.1111/1755-0998.12749				16	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	GG4JH	WOS:000432662400008	29288544				22-11-18
J	Wang, WY; Srivathsan, A; Foo, M; Yamane, SK; Meier, R				Wang, Wendy Y.; Srivathsan, Amrita; Foo, Maosheng; Yamane, Seiki K.; Meier, Rudolf			Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: Validating a reverse workflow for specimen processing	MOLECULAR ECOLOGY RESOURCES			English	Article						community ecology; DNA barcoding; insects; invertebrates; systematics	DNA BARCODES; BIOLOGICAL IDENTIFICATIONS; BIODIVERSITY ASSESSMENT; DIRECT PCR; TAXONOMY; ANTS; DELIMITATION; ORGANIZATION; PSEUDOGENES; EXTRACTION	Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an next-generation sequencing (NGS) barcoding pipeline that allows for cost-effective high-throughput generation of short specimen-specific barcodes (313bp of COI; laboratory cost <$0.50 per specimen) through next-generation sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3,290 of 4,032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases and yields precise abundance information.	[Wang, Wendy Y.; Foo, Maosheng; Meier, Rudolf] Natl Univ Singapore, Fac Sci, Lee Kong Chian Nat Hist Museum, Singapore, Singapore; [Srivathsan, Amrita; Meier, Rudolf] Natl Univ Singapore, Dept Biol Sci, Evolutionary Biol Lab, Singapore, Singapore; [Yamane, Seiki K.] Kagoshima Univ Museum, Kagoshima, Japan	Meier, R (reprint author), Natl Univ Singapore, Fac Sci, Lee Kong Chian Nat Hist Museum, Singapore, Singapore.	meier@nus.edu.sg	Meier, Rudolf/G-4213-2010	Meier, Rudolf/0000-0002-4452-2885	MOE [R-154-000A22-112]; NUS [R-154-000-648-646, R-154-000-648-733]	MOE, Grant/Award Number: R-154-000A22-112; NUS, Grant/Award Number: R-154-000-648-646, R-154-000-648-733		64	6	7	18	18	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1755-098X	1755-0998		MOL ECOL RESOUR	Mol. Ecol. Resour.	MAY	2018	18	3					490	501		10.1111/1755-0998.12751				12	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	GG4JH	WOS:000432662400009	29314756				22-11-18
J	Dupuis, JR; Bremer, FT; Kauwe, A; San Jose, M; Leblanc, L; Rubinoff, D; Geib, SM				Dupuis, Julian R.; Bremer, Forest T.; Kauwe, Angela; San Jose, Michael; Leblanc, Luc; Rubinoff, Daniel; Geib, Scott M.			HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing	MOLECULAR ECOLOGY RESOURCES			English	Article						Bactrocera; high-throughput sequencing; phylogenetics; systematics; Tephritidae	SPECIES TREE ESTIMATION; MAXIMUM-LIKELIHOOD PHYLOGENIES; ANCHORED HYBRID ENRICHMENT; FLIES DIPTERA TEPHRITIDAE; ULTRACONSERVED ELEMENTS; FRUIT-FLIES; TARGET ENRICHMENT; GENETIC-MARKERS; ORTHOLOG GROUPS; TRANSCRIPTOME	High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, 20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.	[Dupuis, Julian R.; Bremer, Forest T.; Kauwe, Angela; Geib, Scott M.] USDA ARS, Daniel K Inouye US Pacific Basin Agr Res Ctr, Hilo, HI 96720 USA; [Dupuis, Julian R.; Bremer, Forest T.; San Jose, Michael; Rubinoff, Daniel] Univ Hawaii Manoa, Dept Plant & Environm Protect Serv, Honolulu, HI 96822 USA; [Leblanc, Luc] Univ Idaho, Dept Entomol Plant Pathol & Nematol, Moscow, ID 83843 USA	Geib, SM (reprint author), USDA ARS, Daniel K Inouye US Pacific Basin Agr Res Ctr, Hilo, HI 96720 USA.	scott.geib@ars.usda.gov		Geib, Scott/0000-0002-9511-5139	USDA-ARS [3.0251.02, 3.0251.03, 3.0256.01, 3.0256.02, 3.0392.02, 3.0392.03]; USDA-APHIS [3.0251.02, 3.0251.03, 3.0256.01, 3.0256.02, 3.0392.02, 3.0392.03]	USDA-ARS and USDA-APHIS, Grant/Award Number: 3.0251.02, 3.0251.03, 3.0256.01, 3.0256.02, 3.0392.02, 3.0392.03		127	1	1	10	13	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1755-098X	1755-0998		MOL ECOL RESOUR	Mol. Ecol. Resour.	SEP	2018	18	5					1000	1019		10.1111/1755-0998.12783				20	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	GQ5SZ	WOS:000441753000008	29633537				22-11-18
J	Liu, SL; Li, YY; Lu, JL; Su, X; Tang, M; Zhang, R; Zhou, LL; Zhou, CR; Yang, Q; Ji, YQ; Yu, DW; Zhou, X				Liu, Shanlin; Li, Yiyuan; Lu, Jianliang; Su, Xu; Tang, Min; Zhang, Rui; Zhou, Lili; Zhou, Chengran; Yang, Qing; Ji, Yinqiu; Yu, Douglas W.; Zhou, Xin			SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons	METHODS IN ECOLOGY AND EVOLUTION			English	Article						high-throughput sequencing; metabarcoding; next-generation-sequencing; operational taxonomic units; phylogenetic diversity; species richness; standard barcode	ENVIRONMENTAL DNA; GENERATION; ALIGNMENT; BARCODE	Metabarcoding of mixed arthropod samples for biodiversity assessment has mostly been carried out on the 454 GS FLX sequencer (Roche, Branford, Connecticut, USA), due to its ability to produce long reads (400bp) that are believed to allow higher taxonomic resolution. The Illumina sequencing platforms, with their much higher throughputs, could potentially reduce sequencing costs and improve sequence quality, but the associated shorter read length (typically <150bp) has deterred their usage in next-generation-sequencing (NGS)-based analyses of eukaryotic biodiversity, which often utilize standard barcode markers (e.g. COI, rbcL, matK, ITS) that are hundreds of nucleotides long. We present a new Illumina-based pipeline to recover full-length COI barcodes from mixed arthropod samples. Our new assembly program, SOAPBarcode, a variant of the genome assembly program SOAPdenovo, uses paired-end reads of the standard COI barcode region as anchors to extract the correct pathways (sequences) out of otherwise chaotic de Bruijn graphs', which are caused by the presence of large numbers of COI homologs of high sequence similarity. Two bulk insect samples of known species composition have been analysed in a recently published 454 metabarcoding study (Yu etal. 2012) and are re-analysed by our analysis pipeline. Compared to the results of Roche 454 (c.400-bp reads), our pipeline recovered full-length COI barcodes (658bp) and 17-31% more species-level operational taxonomic units (OTUs) from bulk insect samples, with fewer untraceable (novel) OTUs. On the other hand, our PCR-based pipeline also revealed higher rates of contamination across samples, due to the Illumina's increased sequencing depth. On balance, the assembled full-length barcodes and increased OTU recovery rates resulted in more resolved taxonomic assignments and more accurate beta diversity estimation. The HiSeq 2000 and the SOAPBarcode pipeline together can achieve more accurate biodiversity assessment at a much reduced sequencing cost in metabarcoding analyses. However, greater precaution is needed to prevent cross-sample contamination during field preparation and laboratory operation because of greater ability to detect non-target DNA amplicons present in low-copy numbers.	[Liu, Shanlin; Li, Yiyuan; Lu, Jianliang; Su, Xu; Tang, Min; Zhang, Rui; Zhou, Lili; Zhou, Chengran; Yang, Qing; Zhou, Xin] BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Guangdong, Peoples R China; [Zhou, Chengran] Sichuan Univ, Coll Life Sci, Chengdu 610000, Sichuan Provinc, Peoples R China; [Ji, Yinqiu; Yu, Douglas W.] Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming 650223, Yunnan, Peoples R China; [Yu, Douglas W.] Univ E Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England	Zhou, X (reprint author), BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Guangdong, Peoples R China.	xinzhou@genomics.cn	Zhou, Xin/D-4025-2009	Zhou, Xin/0000-0002-1407-7952; Li, Yiyuan/0000-0003-1426-0033; Tang, Min/0000-0002-6021-7282	National High-tech Research and Development Project (863) of China [2012AA021601]; BGI; Yunnan Province [20080A001]; Chinese Academy of Sciences [0902281081, KSCX2-YW-Z-1027]; National Natural Science Foundation of China [31170498]; Ministry of Science and Technology of China [2012FY110800]; University of East Anglia; State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology	This study is supported by the National High-tech Research and Development Project (863) of China (2012AA021601) and by BGI. YQJ and DWY were supported by Yunnan Province (20080A001), the Chinese Academy of Sciences (0902281081, KSCX2-YW-Z-1027), the National Natural Science Foundation of China (31170498), the Ministry of Science and Technology of China (2012FY110800), the University of East Anglia, and the State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology.		28	23	25	2	77	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	2041-210X	2041-2096		METHODS ECOL EVOL	Methods Ecol. Evol.	DEC	2013	4	12					1142	1150		10.1111/2041-210X.12120				9	Ecology	Environmental Sciences & Ecology	266BS	WOS:000327997900005		Other Gold			22-11-18
J	Bittleston, LS; Baker, CCM; Strominger, LB; Pringle, A; Pierce, NE				Bittleston, Leonora S.; Baker, Christopher C. M.; Strominger, Lila B.; Pringle, Anne; Pierce, Naomi E.			Metabarcoding as a tool for investigating arthropod diversity in Nepenthes pitcher plants	AUSTRAL ECOLOGY			English	Article						18S amplicon sequencing; carnivorous plant; insect; microcosm; network	BIODIVERSITY ASSESSMENT; SARRACENIA-PURPUREA; HIGH-THROUGHPUT; COPY NUMBER; COMMUNITY; DNA; AMPLIFICATION; EVOLUTION; ALIGNMENT; RESOURCE	The biodiversity of tropical forests consists primarily of small organisms that are difficult to detect and characterize. Next-generation sequencing (NGS) methods can facilitate analyses of these arthropod and microbial communities, leading to a better understanding of existing diversity and factors influencing community assembly. The pitchers of carnivorous pitcher plants often house surprisingly discrete communities and provide ideal systems for analysis using an NGS approach. The plants digest insects in order to access essential nutrients while growing in poor soils; however, the pitchers are also home to communities of living organisms, called inquilines. Certain arthropods appear to have coevolved with their pitcher plant hosts and are not found in other environments. We used Illumina amplicon sequencing of 18S rDNA to characterize the eukaryotes in three species of Nepenthes (Nepenthaceae) pitcher plants - N.gracilis, N.rafflesiana and N.ampullaria - in each of three different parks in Singapore. The data reveal an unexpected diversity of eukaryotes, significant differences in community diversity among host species, variation in host specificity of inquilines and the presence of gregarine parasites. Counts of whole inquiline arthropods from the first collection year were roughly correlated with scaled 18S sequence abundances, indicating that amplicon sequencing is an effective means of gauging community structure. We barcoded a subset of the dipteran larvae using COI primers, and the resulting phylogenetic tree is mostly congruent with that found using the 18S locus, with the exception of one of five morphospecies. For many 18S and COI sequences, the best BLASTn matches showed low sequence identity, illustrating the need for better databases of Southeast Asian dipterans. Finally, networks of core arthropods and their host species were used to investigate degree of host specificity across multiple hosts, and this revealed significant specialization of certain arthropod fauna.	[Bittleston, Leonora S.; Baker, Christopher C. M.; Strominger, Lila B.; Pierce, Naomi E.] Harvard Univ, Dept Organism & Evolutionary Biol, 26 Oxford St, Cambridge, MA 02138 USA; [Bittleston, Leonora S.; Baker, Christopher C. M.; Strominger, Lila B.; Pierce, Naomi E.] Harvard Univ, Museum Comparat Zool, 26 Oxford St, Cambridge, MA 02138 USA; [Pringle, Anne] Harvard Univ, Harvard Forest, Petersham, MA USA	Bittleston, LS (reprint author), Harvard Univ, Dept Organism & Evolutionary Biol, 26 Oxford St, Cambridge, MA 02138 USA.; Bittleston, LS (reprint author), Harvard Univ, Museum Comparat Zool, 26 Oxford St, Cambridge, MA 02138 USA.	lbittles@fas.harvard.edu		Baker, Christopher/0000-0002-2675-1078; Bittleston, Leonora/0000-0003-4007-5405	NSF Graduate Research Predoctoral Fellowship; NSF Doctoral Dissertation Improvement Grant [DEB-1400982]; Templeton FQEB Grant	Our research was supported by an NSF Graduate Research Predoctoral Fellowship and NSF Doctoral Dissertation Improvement Grant DEB-1400982 to L.S.B., and a Templeton FQEB Grant to N.E.P. and A.P. We thank Singapore National Parks for issuing collecting permits (Research Permit: NP/RP11-096-1 to L.S.B.), and the many people who provided suggestions and assistance with fieldwork, including Matthew Lim, Shawn Lum, Stuart Davies, Kang Min Ngo, Su Shiyu and Kadeem Gilbert. Li Daiquin and Gregory Jedd graciously provided laboratory space in Singapore. We appreciate Charles Wolock's help with DNA extractions and inquiline taxonomic assignments, and Jon Sanders' support with sequencing preparation. We thank two anonymous reviewers for their suggestions that greatly improved the manuscript. This work was inspired in part by Roger Kitching's seminal contributions to the study of phytotelmata, and we are deeply grateful to him for his unflagging enthusiasm, generosity and intellectual leadership.		50	4	4	5	56	WILEY-BLACKWELL	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1442-9985	1442-9993		AUSTRAL ECOL	Austral Ecol.	APR	2016	41	2					120	132		10.1111/aec.12271				13	Ecology	Environmental Sciences & Ecology	DJ6EA	WOS:000374301600002					22-11-18
J	Tierney, SM; Friedrich, M; Humphreys, WF; Jones, TM; Warrant, EJ; Wcislo, WT				Tierney, Simon M.; Friedrich, Markus; Humphreys, William F.; Jones, Theresa M.; Warrant, Eric J.; Wcislo, William T.			Consequences of evolutionary transitions in changing photic environments	AUSTRAL ENTOMOLOGY			English	Review						adaptation; cave; dim-light; genomics; photoreceptors; vision	N-ACETYLTRANSFERASE ACTIVITY; BEE MEGALOPTA-GENALIS; DIM-LIGHT VISION; SUBTERRANEAN DIVING BEETLES; GENERA LIMBODESSUS GUIGNOT; NOCTURNAL BEE; DROSOPHILA-MELANOGASTER; UNDERGROUND WATERS; CIRCADIAN-RHYTHMS; VISUAL-SYSTEM	Light represents one of the most reliable environmental cues in the biological world. In this review we focus on the evolutionary consequences to changes in organismal photic environments, with a specific focus on the class Insecta. Particular emphasis is placed on transitional forms that can be used to track the evolution from (1) diurnal to nocturnal (dim-light) or (2) surface to subterranean (aphotic) environments, as well as (3) the ecological encroachment of anthropomorphic light on nocturnal habitats (artificial light at night). We explore the influence of the light environment in an integrated manner, highlighting the connections between phenotypic adaptations (behaviour, morphology, neurology and endocrinology), molecular genetics and their combined influence on organismal fitness. We begin by outlining the current knowledge of insect photic niches and the organismal adaptations and molecular modifications that have evolved for life in those environments. We then outline concepts and guidelines for future research in the fields of natural history, ethology, neurology, morphology and particularly the advantages that high throughput sequencing provides to these aspects of investigation. Finally, we highlight that the power of such integrative science lies in its ability to make phylogenetically robust comparative assessments of evolution, ones that are grounded by empirical evidence derived from a concrete understanding of organismal natural history.	[Tierney, Simon M.; Humphreys, William F.] Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia; [Friedrich, Markus] Wayne State Univ, Dept Biol Sci, 5047 Gullen Mall, Detroit, MI USA; [Friedrich, Markus] Wayne State Univ, Sch Med, Dept Anat & Cell Biol, 540 East Canfield Ave, Detroit, MI 48201 USA; [Humphreys, William F.] Western Australian Museum, Terrestrial Zool, Locked Bag 49, Welshpool, WA 6986, Australia; [Humphreys, William F.] Univ Western Australia, Sch Anim Biol, Nedlands, WA 6907, Australia; [Jones, Theresa M.] Univ Melbourne, Dept Zool, Melbourne, Vic 3010, Australia; [Warrant, Eric J.] Lund Univ, Dept Biol, Solvegatan 35, S-22362 Lund, Sweden; [Wcislo, William T.] Smithsonian Trop Res Inst, POB 0843 03092, Balboa, Panama	Tierney, SM (reprint author), Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia.	simon.tierney@adelaide.edu.au	Tierney, Simon/H-2410-2015	Tierney, Simon/0000-0002-8812-6753; Humphreys, William/0000-0002-8998-9323	Australian Entomological Society	This collaboration was facilitated by a symposium and workshop funded by a Research Seeding Grant from the Australian Entomological Society, awarded to S. M. T. We thank Steve Cooper for helpful comments on a draft manuscript and Dan-Eric Nilsson for the use of his artwork. This paper is dedicated to the memory of Charles Duncan Michener, 1918-2015.		276	9	10	3	25	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	2052-1758	2052-174X		AUSTRAL ENTOMOL	Austral Entomol.	FEB	2017	56	1					23	46		10.1111/aen.12264				24	Entomology	Entomology	EP3EK	WOS:000397265400003					22-11-18
J	Morales-Hojas, R				Morales-Hojas, Ramiro			Molecular ecology of insect pests of agricultural importance: the case of aphids	ECOLOGICAL ENTOMOLOGY			English	Article; Proceedings Paper	29th International Symposium and National Science Meeting of the Royal-Entomological-Society	SEP, 2017	Newcastle Univ, Newcastle upon Tyne, ENGLAND	Royal Entomol Soc	Newcastle Univ	Agricultural landscapes; aphids; landscape genetics; migration; natural history collections; next generation sequencing; phylogeography; species distribution models	CLIMATE-CHANGE PREDICTIONS; MYZUS-PERSICAE HEMIPTERA; AVENAE F HEMIPTERA; PEA APHID; GENETIC-VARIATION; SITOBION-AVENAE; NICHE MODELS; HOST-PLANT; POPULATION DIFFERENTIATION; MICROSATELLITE MARKERS	1. Ongoing environmental change is predicted to have a strong impact on biodiversity. Studies have already noted a range shift in many species as they track their favoured environments. A key challenge entomologists are facing is to understand how insect pest species are responding to this rapid environmental change, and molecular ecology has a central role to play in this task. In the present paper, I argue that molecular ecology has much relevance in relation to the monitoring of insect pests of agricultural importance, with a focus on aphids. 2. First, I examine how the combination of phylogeography and species distribution modelling can be a powerful approach to understanding species responses to climate change and to forecasting future distributions. Despite such a joint approach being increasingly used to understand these questions (e.g. in conservation biology), there are still very few studies that concern pest species of agricultural importance. 3. I then discuss how the use of samples from natural history collections represent an opportunity to directly observe the evolution of species, enhancing our knowledge of the evolutionary processes occurring at ecological time scales. I introduce the Rothamsted Insect Survey (RIS) sample archive and the central role it plays in the studies of pest species of agricultural importance. 4. Lastly, I assess how the advances in DNA sequencing technologies have allowed us to investigate genetic variation at the genome-wide level. Thus, they provide us with the opportunity of studying a variety of questions about the dynamics of pest insects that were previously impossible as well as unmanageable.	[Morales-Hojas, Ramiro] Rothamsted Res, Rothamsted Insect Survey, Harpenden, Herts, England	Morales-Hojas, R (reprint author), Rothamsted Res, Rothamsted Insect Survey, Harpenden, Herts, England.	ramiro.morales-hojas@rothamsted.ac.uk		Morales Hojas, Ramiro/0000-0002-4120-5964	BBSRC	The Rothamsted Insect Survey is a National Capability funded by BBSRC. I would like to thank the people at the Rothamsted Insect Survey for providing valuable information about aphids for this manuscript. The author reports no conflicts of interest. The head of the Rothamsted Insect Survey, James Bell, and the Agroecology Department, Angela Karp, provided helpful comments on the manuscript. I would also like to thank the reviewers, Hugh D. Loxdale and an anonymous reviewer, for providing useful comments on the manuscript which have helped improve the final version.		118	1	1	7	30	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0307-6946	1365-2311		ECOL ENTOMOL	Ecol. Entomol.	AUG	2017	42			1	SI		18	27		10.1111/een.12445				10	Entomology	Entomology	FF4MD	WOS:000408922400003		Bronze			22-11-18
J	Wachi, N; Matsubayashi, KW; Maeto, K				Wachi, Nakatada; Matsubayashi, Kei W.; Maeto, Kaoru			Application of next-generation sequencing to the study of non-model insects	ENTOMOLOGICAL SCIENCE			English	Review						amplicon sequencing; high-throughput sequencing; MIG-seq; non-model organism; RAD-seq; RNA-seq; target capture	ULTRACONSERVED ELEMENTS; PHYLOGENOMICS RESOLVES; TARGET-ENRICHMENT; GENETIC-VARIATION; GENOME; PHYLOGENETICS; EVOLUTIONARY; SPECIATION; PLATFORM; DIVERSIFICATION	Recent developments in, and widespread availability of, platforms, technologies, and computer software and hardware have enhanced the use of genetic markers to address major scientific questions in non-model organisms, even by researchers with limited expertise in genomics. However, there are few studies investigating the genomes of non-model insects using these approaches. This review discusses the application of next-generation sequencing (NGS) technologies to the study of genomes of wild organisms. We first introduce currently available NGS-based methods-including restriction site-associated DNA sequencing; multiplexed inter-simple sequence repeat genotyping by sequencing; target capture; and amplicon, transcriptome, and whole genome sequencing-as useful tools for studies of non-model insects. We also provide guidelines for first-time users of NGS systems. In addition to the massive amount of information that it provides, a major advantage of NGS data is the scalability to future research projects. Studies using NGS technology can answer questions related to basic entomology by focusing on the unique nature of non-model insects in wild environments in a way that is not possible for model organisms.	[Wachi, Nakatada] Biohist Res Hall, Takatsuki, Osaka, Japan; [Matsubayashi, Kei W.] Kyushu Univ, Fac Arts & Sci, Fukuoka, Fukuoka, Japan; [Maeto, Kaoru] Kobe Univ, Grad Sch Agr Sci, Kobe, Hyogo, Japan; [Wachi, Nakatada] Res Inst Environm Agr & Fisheries, Dept Environm Res, Shakudo 442, Habikino, Osaka 5830862, Japan	Wachi, N (reprint author), Res Inst Environm Agr & Fisheries, Dept Environm Res, Shakudo 442, Habikino, Osaka 5830862, Japan.	nwachi@kyudai.jp			JSPS KAKENHI from the Japan Society for the Promotion of Science [JP15K21705, JP25292034]	This research was supported by JSPS KAKENHI (grant nos. JP15K21705 to N.W. and JP25292034 to K.M.) from the Japan Society for the Promotion of Science.		64	2	2	10	16	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1343-8786	1479-8298		ENTOMOL SCI	Entomol. Sci.	MAR	2018	21	1					3	11		10.1111/ens.12281				9	Entomology	Entomology	GL0JO	WOS:000436767700001		Bronze			22-11-18
J	Swift, JF; Lance, RF; Guan, X; Britzke, ER; Lindsay, DL; Edwards, CE				Swift, Joel F.; Lance, Richard F.; Guan, Xin; Britzke, Eric R.; Lindsay, Denise L.; Edwards, Christine E.			Multifaceted DNA metabarcoding: Validation of a noninvasive, next-generation approach to studying bat populations	EVOLUTIONARY APPLICATIONS			English	Article						bats; DNA metabarcoding; next-generation DNA sequencing; noninvasive sampling; population assessment	WHITE-NOSE SYNDROME; ELUSIVE ANIMALS; DIET; IDENTIFICATION; PRIMERS; PHYLOGEOGRAPHY; MICROBIOTA; TAXONOMY; ACCURACY; WILDLIFE	As multiple species of bats are currently experiencing dramatic declines in populations due to white-nose syndrome (WNS) and other factors, conservation managers have an urgent need for data on the ecology and overall status of populations of once-common bat species. Standard approaches to obtain data on bat populations often involve capture and handling, requiring extensive expertise and unavoidably resulting in stress to the bats. New methods to rapidly obtain critical data are needed that minimize both the stress on bats and the spread of WNS. Guano provides a noninvasive source of DNA that includes information from the bat, but also dietary items, parasites, and pathogens. DNA metabarcoding is a high-throughput, DNA-based identification technique to assess the biodiversity of environmental or fecal samples. We investigated the use of multifaceted DNA metabarcoding (MDM), a technique combining next-generation DNA sequencing (NGS), DNA barcodes, and bioinformatic analysis, to simultaneously collect data on multiple parameters of interest (bat species composition, individual genotype, sex ratios, diet, parasites, and presence of WNS) from fecal samples using a single NGS run. We tested the accuracy of each MDM assay using samples in which these parameters were previously determined using conventional approaches. We found that assays for bat species identification, insect diet, parasite diversity, and genotype were both sensitive and accurate, the assay to detect WNS was highly sensitive but requires careful sample processing steps to ensure the reliability of results, while assays for nectivorous diet and sex showed lower sensitivity. MDM was able to quantify multiple data classes from fecal samples simultaneously, and results were consistent whether we included assays for a single data class or multiple data classes. Overall, MDM is a useful approach that employs noninvasive sampling and a customizable suite of assays to gain important and largely accurate information on bat ecology and population dynamics.	[Swift, Joel F.; Edwards, Christine E.] Missouri Bot Garden, Ctr Conservat & Sustainable Dev, POB 299, St Louis, MO 63166 USA; [Lance, Richard F.; Britzke, Eric R.; Lindsay, Denise L.] US Army, Environm Lab, Engineer Res & Dev Ctr, Vicksburg, MS USA; [Guan, Xin] Bennett Aerosp, Cary, NC USA	Edwards, CE (reprint author), Missouri Bot Garden, Ctr Conservat & Sustainable Dev, POB 299, St Louis, MO 63166 USA.	christine.edwards@mobot.org		Edwards, Christine/0000-0001-8837-4872	U.S. Department of Defense's Environmental Security Technology Certification Program (ESTCP) [14 E-RC3-018]	This work was supported by the U.S. Department of Defense's Environmental Security Technology Certification Program (ESTCP Grant number 14 E-RC3-018).		72	1	1	29	29	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	1752-4571			EVOL APPL	Evol. Appl.	AUG	2018	11	7			SI		1120	1138		10.1111/eva.12644				19	Evolutionary Biology	Evolutionary Biology	GN9HT	WOS:000439505200007	30026801	DOAJ Gold			22-11-18
J	Behura, SK				Behura, Susanta K.			Molecular marker systems in insects: current trends and future avenues	MOLECULAR ECOLOGY			English	Review						insect; microarray; molecular marker; SNP; SFP; transposon display	FRAGMENT-LENGTH-POLYMORPHISM; QUANTITATIVE TRAIT LOCI; SINGLE NUCLEOTIDE POLYMORPHISMS; GENETIC-LINKAGE MAP; RICE GALL MIDGE; ORYZAE WOOD-MASON; MITOCHONDRIAL-DNA SEQUENCES; BEMISIA-TABACI HEMIPTERA; MOSQUITO AEDES-AEGYPTI; INDIVIDUAL HONEY-BEES	Insects comprise the largest species composition in the entire animal kingdom and possess a vast undiscovered genetic diversity and gene pool that can be better explored using molecular marker techniques. Current trends of application of DNA marker techniques in diverse domains of insect ecological studies show that mitochondrial DNA (mtDNA), microsatellites, random amplified polymorphic DNA (RAPD), expressed sequence tags (EST) and amplified fragment length polymorphism (AFLP) markers have contributed significantly for progresses towards understanding genetic basis of insect diversity and for mapping medically and agriculturally important genes and quantitative trait loci in insect pests. Apart from these popular marker systems, other novel approaches including transposon display, sequence-specific amplification polymorphism (S-SAP), repeat-associated polymerase chain reaction (PCR) markers have been identified as alternate marker systems in insect studies. Besides, whole genome microarray and single nucleotide polymorphism (SNP) assays are becoming more popular to screen genome-wide polymorphisms in fast and cost effective manner. However, use of such methodologies has not gained widespread popularity in entomological studies. The current study highlights the recent trends of applications of molecular markers in insect studies and explores the technological advancements in molecular marker tools and modern high throughput genotyping methodologies that may be applied in entomological researches for better understanding of insect ecology at molecular level.	Univ Illinois, Dept Entomol, Urbana, IL 61801 USA	Behura, SK (reprint author), Univ Illinois, Dept Entomol, 349 Morrill Hall,505 S Goodwin Ave, Urbana, IL 61801 USA.	susanta@life.uiuc.edu		BEHURA, SUSANTA/0000-0002-0654-6288				259	141	159	1	70	WILEY-BLACKWELL	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0962-1083	1365-294X		MOL ECOL	Mol. Ecol.	OCT	2006	15	11					3087	3113		10.1111/j.1365-294X.2006.03014.x				27	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	083FC	WOS:000240440800001	16968257				22-11-18
J	Thomsen, PF; Kielgast, J; Iversen, LL; Wiuf, C; Rasmussen, M; Gilbert, MTP; Orlando, L; Willerslev, E				Thomsen, Philip Francis; Kielgast, Jos; Iversen, Lars L.; Wiuf, Carsten; Rasmussen, Morten; Gilbert, M. Thomas P.; Orlando, Ludovic; Willerslev, Eske			Monitoring endangered freshwater biodiversity using environmental DNA	MOLECULAR ECOLOGY			English	Article						biological diversity; molecular detection; pyrosequencing; threatened species; wildlife conservation	CONSERVATION; PERSISTENCE; PERMAFROST; STABILITY; SEDIMENTS; SAMPLES; ICE	Freshwater ecosystems are among the most endangered habitats on Earth, with thousands of animal species known to be threatened or already extinct. Reliable monitoring of threatened organisms is crucial for data-driven conservation actions but remains a challenge owing to nonstandardized methods that depend on practical and taxonomic expertise, which is rapidly declining. Here, we show that a diversity of rare and threatened freshwater animalsrepresenting amphibians, fish, mammals, insects and crustaceanscan be detected and quantified based on DNA obtained directly from small water samples of lakes, ponds and streams. We successfully validate our findings in a controlled mesocosm experiment and show that DNA becomes undetectable within 2 weeks after removal of animals, indicating that DNA traces are near contemporary with presence of the species. We further demonstrate that entire faunas of amphibians and fish can be detected by high-throughput sequencing of DNA extracted from pond water. Our findings underpin the ubiquitous nature of DNA traces in the environment and establish environmental DNA as a tool for monitoring rare and threatened species across a wide range of taxonomic groups.	[Thomsen, Philip Francis; Kielgast, Jos; Rasmussen, Morten; Gilbert, M. Thomas P.; Orlando, Ludovic; Willerslev, Eske] Univ Copenhagen, Ctr GeoGenet, Nat Hist Museum Denmark, DK-1350 Copenhagen, Denmark; [Iversen, Lars L.] Univ Copenhagen, Freshwater Biol Sect, Dept Biol, DK-3400 Hillerod, Denmark; [Wiuf, Carsten] Aarhus Univ, Bioinformat Res Ctr BiRC, DK-8000 Aarhus, Denmark	Willerslev, E (reprint author), Univ Copenhagen, Ctr GeoGenet, Nat Hist Museum Denmark, Oster Voldgade 5-7, DK-1350 Copenhagen, Denmark.	ewillerslev@snm.ku.dk	Wiuf, Carsten/H-6320-2011; Gilbert, Marcus/A-8936-2013; Orlando, Ludovic/A-8932-2013	Wiuf, Carsten/0000-0002-1302-4445; Gilbert, Marcus/0000-0002-5805-7195; Orlando, Ludovic/0000-0003-3936-1850; Thomsen, Philip Francis/0000-0002-9867-4366	University of Copenhagen; Natural History Museum of Denmark; Danish National Research Foundation	We thank Dr. P. R. Moller (Natural History Museum of Denmark), A. Drews (LLUR, Schleswig-Holstein), A. Linnet (Danish Nature Agency, Thy) and Martin Hesselsoe (Amphi-Consult Aps) for generously supplying monitoring data. All work involving live animals was conducted under permit number SNS-441-00116 of the Danish Nature Agency. This study was supported by the University of Copenhagen, The Natural History Museum of Denmark and the Danish National Research Foundation.		39	318	333	22	492	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0962-1083	1365-294X		MOL ECOL	Mol. Ecol.	JUN	2012	21	11					2565	2573		10.1111/j.1365-294X.2011.05418.x				9	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	946WZ	WOS:000304389500004	22151771		Y	N	22-11-18
J	Yu, DW; Ji, YQ; Emerson, BC; Wang, XY; Ye, CX; Yang, CY; Ding, ZL				Yu, Douglas W.; Ji, Yinqiu; Emerson, Brent C.; Wang, Xiaoyang; Ye, Chengxi; Yang, Chunyan; Ding, Zhaoli			Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring	METHODS IN ECOLOGY AND EVOLUTION			English	Article						454 Genome Sequencer FLX System; DNA barcoding; high-throughput sequencing; metagenetics; metagenomics; OTU picking; phylogenetic diversity	16S RIBOSOMAL-RNA; ENVIRONMENTAL DNA; DIVERSITY; SEQUENCES; COMMUNITIES; PITFALLS; ACCURATE; PRIMERS; PROGRAM; BARCODE	1. Traditional biodiversity assessment is costly in time, money and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for auditing by neutral parties, which is necessary for dispute resolution. 2. We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass-PCR amplification of the COI barcode gene, pyrosequencing and bioinformatic analysis, which together we call metabarcoding. 3. We construct seven communities of arthropods (mostly insects) and show that it is possible to recover a substantial proportion of the original taxonomic information. We further demonstrate, for the first time, that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within-community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information inherent to metabarcoding. 4. Alpha and beta diversity metrics are the raw materials of ecology and the environmental sciences, facilitating assessment of the state of the environment with a broad and efficient measure of biodiversity.	[Yu, Douglas W.; Ji, Yinqiu; Wang, Xiaoyang; Ye, Chengxi; Yang, Chunyan] Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, ECEC, Kunming 650223, Yunnan, Peoples R China; [Yu, Douglas W.; Emerson, Brent C.] Univ E Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England; [Ding, Zhaoli] Chinese Acad Sci, Kunming Inst Zool, Kunming Biodivers Large Apparat Reg Ctr, Kunming 650223, Yunnan, Peoples R China	Yu, DW (reprint author), Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, ECEC, Kunming 650223, Yunnan, Peoples R China.	dougwyu@gmail.com		Emerson, Brent/0000-0003-4067-9858	Yunnan Province [20080A001]; Chinese Academy of Sciences [0902281081, KSCX2-YW-Z-1027]; National Natural Science Foundation of China [31170498]; University of East Anglia	For support, we thank Yunnan Province (20080A001), the Chinese Academy of Sciences (0902281081, KSCX2-YW-Z-1027), the National Natural Science Foundation of China (31170498), and the University of East Anglia. We thank Ricardo Ramirez-Gonzalez for early access to PyroClean, Sam Ma for advice, Kasper Munch, Mohammadreza Ghodsi, David Nipperess, and Xiaolin Hao for help with their respective software packages, and two anonymous reviewers for comments.		57	202	217	19	285	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	2041-210X	2041-2096		METHODS ECOL EVOL	Methods Ecol. Evol.	AUG	2012	3	4					613	623		10.1111/j.2041-210X.2012.00198.x				11	Ecology	Environmental Sciences & Ecology	981JA	WOS:000306961700001			Y	N	22-11-18
J	Fukatsu, T				Fukatsu, Takema			Next-generation sequencing sheds light on intricate regulation of insect gut microbiota	MOLECULAR ECOLOGY			English	News Item						co-evolution; gut bacteria; host-symbiont interactions; Pyrrhocoris apterus; symbiosis	PYRRHOCORIS-APTERUS HETEROPTERA; DIVERSITY; SYMBIONT	Next-generation sequencing (NGS) technologies are getting cheaper and easier and hence becoming readily accessible for many researchers in biological disciplines including ecology. In this issue of Molecular Ecology, Sudakaran etal. (2012) show how the NGS revolution contributes to our better and more comprehensive understanding of ecological interactions between gut symbiotic microbiota and the host organism. Using the European red firebug Pyrrhocoris apterus as a model system, they demonstrated that the gut microbiota consists of a small number of major bacterial phylotypes plus other minor bacterial associates. The major bacteria are localized in a specific anoxic section of the midgut and quantitatively account for most of the gut microbiota irrespective of host's geographic populations. The specific gut microbiota is established through early nymphal development of the host insect. Interestingly, the host feeding on different food, namely linden seeds, sunflower seeds or wasp larvae, scarcely affected the symbiont composition, suggesting homoeostatic control over the major symbiotic microbiota in the anoxic section of the midgut. Some of the minor components of the gut microbiota, which conventional PCR/cloning/sequencing approaches would have failed to detect, were convincingly shown to be food-derived. These findings rest on the robust basis of high-throughput sequencing data, and some of them could not be practically obtained by conventional molecular techniques, highlighting the significant impact of NGS approaches on ecological aspects of hostsymbiont interactions in a nonmodel organism.	Natl Inst Adv Ind Sci & Technol, Tsukuba, Ibaraki 3058566, Japan	Fukatsu, T (reprint author), Natl Inst Adv Ind Sci & Technol, Tsukuba, Ibaraki 3058566, Japan.	t-fukatsu@aist.go.jp						15	5	5	0	71	WILEY-BLACKWELL	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0962-1083			MOL ECOL	Mol. Ecol.	DEC	2012	21	24					5908	5910		10.1111/mec.12090				3	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	051SI	WOS:000312147300002	23355979	Bronze			22-11-18
J	Russell, JA; Weldon, S; Smith, AH; Kim, KL; Hu, Y; Lukasik, P; Doll, S; Anastopoulos, I; Novin, M; Oliver, KM				Russell, Jacob A.; Weldon, Stephanie; Smith, Andrew H.; Kim, Kyungsun L.; Hu, Yi; Lukasik, Piotr; Doll, Steven; Anastopoulos, Ioannis; Novin, Matthew; Oliver, Kerry M.			Uncovering symbiont-driven genetic diversity across North American pea aphids	MOLECULAR ECOLOGY			English	Article						biodiversity; co-infection; endosymbiont; strain diversity; Wolbachia	FACULTATIVE BACTERIAL ENDOSYMBIONTS; HOST-PLANT SPECIALIZATION; ACYRTHOSIPHON-PISUM; SECONDARY SYMBIONTS; NATURAL-POPULATIONS; HORIZONTAL TRANSFER; HIGH-THROUGHPUT; DEFENSIVE SYMBIONTS; SEQUENCE ALIGNMENT; BEMISIA-TABACI	Heritable genetic variation is required for evolution, and while typically encoded within nuclear and organellar genomes, several groups of invertebrates harbour heritable microbes serving as additional sources of genetic variation. Hailing from the symbiont-rich insect order Hemiptera, pea aphids (Acyrthosiphon pisum) possess several heritable symbionts with roles in host plant utilization, thermotolerance and protection against natural enemies. As pea aphids vary in the numbers and types of harboured symbionts, these bacteria provide heritable and functionally important variation within field populations. In this study, we quantified the cytoplasmically inherited genetic variation contributed by symbionts within North American pea aphids. Through the use of Denaturing Gradient Gel Electrophoresis (DGGE) and 454 amplicon pyrosequencing of 16S rRNA genes, we explored the diversity of bacteria harboured by pea aphids from five populations, spanning three locations and three host plants. We also characterized strain variation by analysing 16S rRNA, housekeeping and symbiont-associated bacteriophage genes. Our results identified eight species of facultative symbionts, which often varied in frequency between locations and host plants. We detected 28 cytoplasmic genotypes across 318 surveyed aphids, considering only the various combinations of secondary symbiont species infecting single hosts. Yet the detection of multiple Regiella insecticola, Hamiltonella defensa and Rickettsia strains, and diverse bacteriophage genotypes from H.defensa, suggest even greater diversity. Combined, these findings reveal that heritable bacteria contribute substantially to genetic variation in A.pisum. Given the costs and benefits of these symbionts, it is likely that fluctuating selective forces play a role in the maintenance of this diversity.	[Russell, Jacob A.; Smith, Andrew H.; Hu, Yi; Lukasik, Piotr; Doll, Steven; Anastopoulos, Ioannis; Novin, Matthew] Drexel Univ, Dept Biol, Philadelphia, PA 19104 USA; [Weldon, Stephanie; Kim, Kyungsun L.; Oliver, Kerry M.] Univ Georgia, Dept Entomol, Athens, GA 30602 USA	Russell, JA (reprint author), Drexel Univ, Dept Biol, 3245 Chestnut St, Philadelphia, PA 19104 USA.	jar337@drexel.edu	Lukasik, Piotr/E-8869-2011; Russell, Jacob/H-7996-2015; oliver, kerry/H-4498-2017; Yi, Hu/F-5157-2017	Lukasik, Piotr/0000-0002-4164-6487; oliver, kerry/0000-0002-2835-4017; Weldon, Stephanie/0000-0001-5384-9946	NSF [1050128, 1050098]	The authors thank Anthony Ives, Ted Evans, Nick Tuttle and Rachae DiSciullo for assistance with aphid collections, and three anonymous reviewers for helpful suggestions on the manuscript. This work was funded by NSF grant #1050128 to KMO and #1050098 to JAR.		76	93	97	2	187	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0962-1083	1365-294X		MOL ECOL	Mol. Ecol.	APR	2013	22	7					2045	2059		10.1111/mec.12211				15	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	112ET	WOS:000316575800020	23379399				22-11-18
J	Boucias, DG; Cai, YP; Sun, YJ; Lietze, VU; Sen, R; Raychoudhury, R; Scharf, ME				Boucias, Drion G.; Cai, Yunpeng; Sun, Yijun; Lietze, Verena-Ulrike; Sen, Ruchira; Raychoudhury, Rhitoban; Scharf, Michael E.			The hindgut lumen prokaryotic microbiota of the termite Reticulitermes flavipes and its responses to dietary lignocellulose composition	MOLECULAR ECOLOGY			English	Article						16S rRNA gene; 454 pyrosequencing; bTEFAP; cellulose; Microbial symbionts	BACTERIAL COMMUNITY STRUCTURE; FEEDING HIGHER TERMITE; RNA SEQUENCE DATA; PHYLOGENETIC DIVERSITY; SYMBIOTIC METHANOGENS; COPTOTERMES-FORMOSANUS; PHYSIOLOGICAL ECOLOGY; FLAGELLATED PROTISTS; SUBTERRANEAN TERMITE; SPECIES RICHNESS	Reticulitermes flavipes (Isoptera: Rhinotermitidae) is a highly eusocial insect that thrives on recalcitrant lignocellulosic diets through nutritional symbioses with gut-dwelling prokaryotes and eukaryotes. In the R.flavipes hindgut, there are up to 12 eukaryotic protozoan symbionts; the number of prokaryotic symbionts has been estimated in the hundreds. Despite its biological relevance, this diverse community, to date, has been investigated only by culture- and cloning-dependent methods. Moreover, it is unclear how termite gut microbiomes respond to diet changes and what roles they play in lignocellulose digestion. This study utilized high-throughput 454 pyrosequencing of 16S V5-V6 amplicons to sample the hindgut lumen prokaryotic microbiota of R.flavipes and to examine compositional changes in response to lignin-rich and lignin-poor cellulose diets after a 7-day feeding period. Of the 475000 high-quality reads that were obtained, 99.9% were annotated as bacteria and 0.11% as archaea. Major bacterial phyla included Spirochaetes (24.9%), Elusimicrobia (19.8%), Firmicutes (17.8%), Bacteroidetes (14.1%), Proteobacteria (11.4%), Fibrobacteres (5.8%), Verrucomicrobia (2.0%), Actinobacteria (1.4%) and Tenericutes (1.3%). The R.flavipes hindgut lumen prokaryotic microbiota was found to contain over 4761 species-level phylotypes. However, diet-dependent shifts were not statistically significant or uniform across colonies, suggesting significant environmental and/or host genetic impacts on colony-level microbiome composition. These results provide insights into termite gut microbiome diversity and suggest that (i) the prokaryotic gut microbiota is much more complex than previously estimated, and (ii) environment, founding reproductive pair effects and/or host genetics influence microbiome composition.	[Boucias, Drion G.; Lietze, Verena-Ulrike] Univ Florida, Dept Entomol & Nematol, Gainesville, FL 32610 USA; [Cai, Yunpeng] Chinese Acad Sci, Shenzhen Inst Adv Technol, Shenzhen, Peoples R China; [Sun, Yijun] Univ Florida, Interdisciplinary Ctr Biotechnol Res, Gainesville, FL 32610 USA; [Sen, Ruchira; Raychoudhury, Rhitoban; Scharf, Michael E.] Purdue Univ, Dept Entomol, W Lafayette, IN 47907 USA	Boucias, DG (reprint author), Univ Florida, Dept Entomol & Nematol, Gainesville, FL 32610 USA.	pathos@ufl.edu	Cai, Yunpeng/O-8823-2018		Consortium for Plant Biotechnology Research Inc; DOE [DE-FG3602GO12026]; National Science Foundation [DBI-1062362]	We thank Amit Sethi for many helpful suggestions on this work and manuscript drafts. This work was supported by funds provided by The Consortium for Plant Biotechnology Research Inc. and DOE prime Agreement No. DE-FG3602GO12026 (Scharf and Boucias), by the O.W. Rollins/Orkin Endowment (Scharf) and by the National Science Foundation under grant DBI-1062362 awarded to Y. Sun.		93	62	65	3	113	WILEY-BLACKWELL	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0962-1083			MOL ECOL	Mol. Ecol.	APR	2013	22	7					1836	1853		10.1111/mec.12230				18	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	112ET	WOS:000316575800007	23379767				22-11-18
J	Martinson, EO; Wheeler, D; Wright, J; Mrinalini; Siebert, AL; Werren, JH				Martinson, Ellen O.; Wheeler, David; Wright, Jeremy; Mrinalini; Siebert, Aisha L.; Werren, John H.			Nasonia vitripennis venom causes targeted gene expression changes in its fly host	MOLECULAR ECOLOGY			English	Article						enhancer of split; extended phenotype; parasitoid wasps; venom	WASP PIMPLA-HYPOCHONDRIACA; CULTURED INSECT CELLS; ECTOPARASITIC WASP; FLESH FLY; WALKER HYMENOPTERA; SARCOPHAGA-BULLATA; DROSOPHILA; PTEROMALIDAE; METABOLISM; EVOLUTION	Parasitoid wasps are diverse and ecologically important insects that use venom to modify their host's metabolism for the benefit of the parasitoid's offspring. Thus, the effects of venom can be considered an extended phenotype' of the wasp. The model parasitoid wasp Nasonia vitripennis has approximately 100 venom proteins, 23 of which do not have sequence similarity to known proteins. Envenomation by N.vitripennis has previously been shown to induce developmental arrest, selective apoptosis and alterations in lipid metabolism in flesh fly hosts. However, the full effects of Nasonia venom are still largely unknown. In this study, we used high throughput RNA sequencing (RNA-Seq) to characterize global changes in Sarcophaga bullata (Diptera) gene expression in response to envenomation by N.vitripennis. Surprisingly, we show that Nasonia venom targets a small subset of S.bullata loci, with similar to 2% genes being differentially expressed in response to envenomation. Strong upregulation of enhancer of split complex genes provides a potential molecular mechanism that could explain the observed neural cell death and developmental arrest in envenomated hosts. Significant increases in antimicrobial peptides and their corresponding regulatory genes provide evidence that venom could be selectively activating certain immune responses of the hosts. Further, we found differential expression of genes in several metabolic pathways, including glycolysis and gluconeogenesis that may be responsible for the decrease in pyruvate levels found in envenomated hosts. The targeting of Nasonia venom effects to a specific and limited set of genes provides insight into the interaction between the ectoparasitoid wasp and its host.	[Martinson, Ellen O.; Wheeler, David; Wright, Jeremy; Mrinalini; Werren, John H.] Univ Rochester, Dept Biol, Rochester, NY 14627 USA; [Siebert, Aisha L.] Univ Rochester, Sch Med & Dent, Translat Biomed Sci Dept, Rochester, NY 14627 USA	Martinson, EO (reprint author), Univ Rochester, Dept Biol, Rochester, NY 14627 USA.	e.martinson@rochester.edu		, Mrinalini/0000-0002-9878-4661; Werren, John/0000-0001-9353-2070; Wheeler, David/0000-0001-5538-8119; Siebert, Aisha/0000-0001-6954-9163	National Institutes of Health [RO1GM098667]; Provost Multidisciplinary Award (University of Rochester)	We thank the National Institutes of Health (RO1GM098667) and the Provost Multidisciplinary Award (University of Rochester) for financial support, and M Williams, R Edwards and A Dolan for technical assistance and VG Martinson for helpful discussion.		48	25	26	1	31	WILEY-BLACKWELL	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0962-1083	1365-294X		MOL ECOL	Mol. Ecol.	DEC	2014	23	23					5918	5930		10.1111/mec.12967				13	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	AU5ET	WOS:000345630700020	25319487	Green Accepted			22-11-18
J	Mcfrederick, QS; Rehan, SM				Mcfrederick, Quinn S.; Rehan, Sandra M.			Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee	MOLECULAR ECOLOGY			English	Article						Ceratina calcarata; Lactobacillus; microbiome; palynology; pollination ecology; Polylectic pollen forager	NAIVE BAYESIAN CLASSIFIER; GUT MICROBIOTA; GEN. NOV.; CERATINA-CALCARATA; HIGH-THROUGHPUT; BUMBLE BEES; HONEY-BEES; SEQUENCES; ALIGNMENT; DIVERSITY	Many insects obtain gut microbes from their diet, but how a mother's foraging patterns influence the microbes found in her offspring's food remains an open question. To address this gap, we studied a bee that forages for pollen from multiple species of plants and may therefore acquire diverse bacteria from different plants. We tested the hypothesis that pollen diversity correlates with bacterial diversity by simultaneously characterizing these two communities in bee brood provisions for the first time. We used deep sequencing of the plant RBCL gene and the bacterial 16S rRNA gene to characterize pollen and bacterial diversity. We then tested for associations between pollen and bacterial species richness and community composition, as well as co-occurrence of specific bacteria and pollen types. We found that both pollen and bacterial communities were extremely diverse, indicating that mother bees visit a wide variety of flowers for pollen and nectar and subsequently bring a diversity of microbes back into their nests. Pollen and bacterial species richness and community composition, however, were not correlated. Certain pollen types significantly co-occurred with the most proportionally abundant bacteria, indicating that the plants these pollen types came from may serve as reservoirs for these bacteria. Even so, the overall diversity of these communities appears to mask these associations at a broader scale. Further study of these pollen and bacteria associations will be important for understanding the complicated relationship between bacteria and wild bees.	[Mcfrederick, Quinn S.] Univ Calif Riverside, Dept Entomol, 900 Univ Ave, Riverside, CA 92521 USA; [Rehan, Sandra M.] Univ New Hampshire, Dept Biol Sci, 46 Coll Rd, Durham, NH 03824 USA	Mcfrederick, QS (reprint author), Univ Calif Riverside, Dept Entomol, 900 Univ Ave, Riverside, CA 92521 USA.	quinn.mcfrederick@ucr.edu			University of California, Riverside; New Hampshire Agricultural Experiment Station; Tuttle Research Foundation; University of New Hampshire	We thank Sean Lombard and Nicholas Pizzi for assistance with nest collections, Krista Ciaccio and Wyatt Shell for brood cell processing, Kaleigh Russell for help with DNA extractions and library preparation, Glenn Hicks of UCR's IIGB for advice on primer design, and Jason Rothman, Peter Graystock, Hoang Vuong, Kaleigh Russell, Alexander Keller and an anonymous reviewer for comments on an earlier draft. Funding from the University of California, Riverside to QSM, the New Hampshire Agricultural Experiment Station, Tuttle Research Foundation, and the University of New Hampshire to SMR supported this work.		59	16	16	3	65	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0962-1083	1365-294X		MOL ECOL	Mol. Ecol.	MAY	2016	25	10					2302	2311		10.1111/mec.13608				10	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	DN4HF	WOS:000377024200015	26945527				22-11-18
J	Koneru, SL; Salinas, H; Flores, GE; Hong, RL				Koneru, Sneha L.; Salinas, Heilly; Flores, Gilberto E.; Hong, Ray L.			The bacterial community of entomophilic nematodes and host beetles	MOLECULAR ECOLOGY			English	Article						bacteria; beetles; entomophilic nematodes; microbiome; next-generation sequencing	N.-SP NEMATODA; ENTOMOPATHOGENIC NEMATODES; PRISTIONCHUS-PACIFICUS; PHYLOGENETIC-RELATIONSHIPS; OSCHEIUS-CAROLINENSIS; ORIENTALIS COLEOPTERA; GENUS PRISTIONCHUS; NATURAL VARIATION; RHABDITIDAE; SCARABAEIDAE	Insects form the most species-rich lineage of Eukaryotes and each is a potential host for organisms from multiple phyla, including fungi, protozoa, mites, bacteria and nematodes. In particular, beetles are known to be associated with distinct bacterial communities and entomophilic nematodes. While entomopathogenic nematodes require symbiotic bacteria to kill and reproduce inside their insect hosts, the microbial ecology that facilitates other types of nematode-insect associations is largely unknown. To illuminate detailed patterns of the tritrophic beetle-nematode-bacteria relationship, we surveyed the nematode infestation profiles of scarab beetles in the greater Los Angeles area over a five-year period and found distinct nematode infestation patterns for certain beetle hosts. Over a single season, we characterized the bacterial communities of beetles and their associated nematodes using high-throughput sequencing of the 16S rRNA gene. We found significant differences in bacterial community composition among the five prevalent beetle host species, independent of geographical origin. Anaerobes Synergistaceae and sulphate-reducing Desulfovibrionaceae were most abundant in Amblonoxia beetles, while Enterobacteriaceae and Lachnospiraceae were common in Cyclocephala beetles. Unlike entomopathogenic nematodes that carry bacterial symbionts, insect-associated nematodes do not alter the beetles' native bacterial communities, nor do their microbiomes differ according to nematode or beetle host species. The conservation of Diplogastrid nematodes associations with Melolonthinae beetles and sulphate-reducing bacteria suggests a possible link between beetle-bacterial communities and their associated nematodes. Our results establish a starting point towards understanding the dynamic interactions between soil macroinvertebrates and their microbiota in a highly accessible urban environment.	[Koneru, Sneha L.; Salinas, Heilly; Flores, Gilberto E.; Hong, Ray L.] Calif State Univ Northridge, Dept Biol, 18111 Nordhoff St, Northridge, CA 91330 USA; [Koneru, Sneha L.] Univ London Imperial Coll Sci Technol & Med, Dept Life Sci, London, England	Hong, RL (reprint author), Calif State Univ Northridge, Dept Biol, 18111 Nordhoff St, Northridge, CA 91330 USA.	ray.hong@csun.edu		Koneru, Sneha Latha/0000-0003-0305-8059	CSUN Biology Department; NIH [1SC3GM105579]	We thank the dedicated beetle collectors, especially the Nelson-Riecks family. We are grateful for R. Mackelprang for computational assistance; E. Bernal, J. Go, V. Guizar, V. Lewis, M. Gonzalez, and J. Shibata for technical assistance; T. Renahan for comments on the manuscript; as well as J. Hogue for beetle identification. This study was funded by CSUN Biology Department and NIH award 1SC3GM105579 to R.L.H.		60	9	9	4	33	WILEY-BLACKWELL	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0962-1083	1365-294X		MOL ECOL	Mol. Ecol.	MAY	2016	25	10					2312	2324		10.1111/mec.13614				13	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	DN4HF	WOS:000377024200016	26992100	Green Accepted			22-11-18
J	Zhang, K; Lin, SL; Ji, YQ; Yang, CX; Wang, XY; Yang, CY; Wang, HS; Jiang, HS; Harrison, RD; Yu, DW				Zhang, Kai; Lin, Siliang; Ji, Yinqiu; Yang, Chenxue; Wang, Xiaoyang; Yang, Chunyan; Wang, Hesheng; Jiang, Haisheng; Harrison, Rhett D.; Yu, Douglas W.			Plant diversity accurately predicts insect diversity in two tropical landscapes	MOLECULAR ECOLOGY			English	Article						Arthropoda; biodiversity; biomonitoring; host specificity; insect-plant interactions; surrogate species	SPECIES RICHNESS ESTIMATORS; BIODIVERSITY ASSESSMENT; HERBIVOROUS INSECTS; HOST-SPECIFICITY; MAXIMUM-LIKELIHOOD; BETA DIVERSITY; FOREST; PERFORMANCE; SEQUENCES; DNA	Plant diversity surely determines arthropod diversity, but only moderate correlations between arthropod and plant species richness had been observed until Basset et al. (Science, 338, 2012 and 1481) finally undertook an unprecedentedly comprehensive sampling of a tropical forest and demonstrated that plant species richness could indeed accurately predict arthropod species richness. We now require a high-throughput pipeline to operationalize this result so that we can (i) test competing explanations for tropical arthropod megadiversity, (ii) improve estimates of global eukaryotic species diversity, and (iii) use plant and arthropod communities as efficient proxies for each other, thus improving the efficiency of conservation planning and of detecting forest degradation and recovery. We therefore applied metabarcoding to Malaise-trap samples across two tropical landscapes in China. We demonstrate that plant species richness can accurately predict arthropod (mostly insect) species richness and that plant and insect community compositions are highly correlated, even in landscapes that are large, heterogeneous and anthropogenically modified. Finally, we review how metabarcoding makes feasible highly replicated tests of the major competing explanations for tropical megadiversity.	[Zhang, Kai; Ji, Yinqiu; Yang, Chenxue; Wang, Xiaoyang; Yang, Chunyan; Yu, Douglas W.] Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming 650223, Peoples R China; [Zhang, Kai; Wang, Xiaoyang] Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650204, Peoples R China; [Lin, Siliang; Wang, Hesheng] South China Normal Univ, Sch Life Sci, Guangzhou 510631, Guangdong, Peoples R China; [Wang, Hesheng] Hainan Yinggeling Natl Nat Reserve, Baisha 572800, Peoples R China; [Harrison, Rhett D.] East & Cent Asia Reg Off, World Agroforestry Ctr, Kunming 650201, Peoples R China; [Harrison, Rhett D.] Chinese Acad Sci, Kunming Inst Bot, Ctr Mt Ecosyst Studies CMES, Kunming 650201, Peoples R China; [Yu, Douglas W.] Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England; [Harrison, Rhett D.] East & Southern Africa Reg, World Agroforestry Ctr, 13 Elm Rd, Lusaka, Zambia	Yu, DW (reprint author), Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming 650223, Peoples R China.; Harrison, RD (reprint author), East & Cent Asia Reg Off, World Agroforestry Ctr, Kunming 650201, Peoples R China.; Yu, DW (reprint author), Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England.; Harrison, RD (reprint author), East & Southern Africa Reg, World Agroforestry Ctr, 13 Elm Rd, Lusaka, Zambia.	r.harrison@cgiar.org; dougwyu@gmail.com		Lin, Siliang/0000-0003-1660-2543	GIZ/BMZ on behalf of the Government of the Federal Republic of Germany [08.7860.3-001.00, 13.1432.7-001.00]; National Natural Science Foundation of China [31400470, 41661144002]; Ministry of Science and Technology of China [2012FY110800]; University of East Anglia and its GRACE computing cluster; State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology [GREKF13-13, GREKF14-13, GREKF16-09]	We are very grateful to the three reviewers and to the editor for comments and suggestions. We thank Mei Long for field assistance, Zhaoli Ding for sequencing, Philip Beckschafer for providing the Mengsong GIS layer, and Mengsong village, Bulong Nature Reserve and Hainan Yinggeling National Nature Reserve for field support. Funding for fieldwork in Mengsong was provided by GIZ/BMZ (Project Nos. 08.7860.3-001.00, 13.1432.7-001.00) on behalf of the Government of the Federal Republic of Germany. CYY and DWY were supported by the National Natural Science Foundation of China (31400470, 41661144002), the Ministry of Science and Technology of China (2012FY110800), the University of East Anglia and its GRACE computing cluster, and the State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology (GREKF13-13, GREKF14-13 and GREKF16-09).		64	6	7	5	70	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0962-1083	1365-294X		MOL ECOL	Mol. Ecol.	SEP	2016	25	17					4407	4419		10.1111/mec.13770				13	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	DW0PS	WOS:000383343800021	27474399				22-11-18
J	Nakadai, R; Kawakita, A				Nakadai, Ryosuke; Kawakita, Atsushi			Patterns of temporal and enemy niche use by a community of leaf cone moths (Caloptilia) coexisting on maples (Acer) as revealed by metabarcoding	MOLECULAR ECOLOGY			English	Article						closely related species; herbivorous insect; metabarcoding; parasitoid; phenology; species coexistence	PLANT-FEEDING INSECTS; SYMPATRIC HOST RACES; REPRODUCTIVE ISOLATION; HERBIVORE ASSEMBLAGES; AREA RELATIONSHIPS; SPECIES-AREA; GUT CONTENTS; DIVERSITY; DNA; DIVERSIFICATION	The diversity of herbivorous insects is often considered a function of host plant diversity. However, recent research has uncovered many examples of closely related herbivores using the same host plant(s), suggesting that partitioning of host plants is not the only mechanism generating diversity. Herbivores sharing hosts may utilize different parts of the same plant, but such resource partitioning is often not apparent; hence, the factors that allow closely related herbivores to coexist are still largely undetermined. We examined whether partitioning of phenology or natural enemies may explain the coexistence of leaf cone moths (Caloptilia; Gracillariidae) associated with maples (Acer; Sapindaceae). Larval activity of 10 sympatric Caloptilia species found on nine maple species was monitored every 2-3 weeks for a total of 13 sampling events, and an exhaustive search for internal parasitoid wasps was conducted using high-throughput sequencing. Blocking primers were used to facilitate the detection of wasp larvae inside moth tissue. We found considerable phenological overlap among Caloptilia species, with two clear peaks in July and September-October. Coexisting Caloptilia species also had largely overlapping parasitoid communities; a total of 13 chalcid and ichneumon wasp species attacked Caloptilia in a nonspecific fashion at an overall parasitism rate of 46.4%. Although coexistence may be facilitated by factors not accounted for in this study, it appears that niche partitioning is not necessary for closely related herbivores to stably coexist on shared hosts. Co-occurrence without resource partitioning may provide an additional axis along which herbivorous insects attain increased species richness.	[Nakadai, Ryosuke; Kawakita, Atsushi] Kyoto Univ, Ctr Ecol Res, Hirano 2-509-3, Otsu, Shiga 5202113, Japan	Nakadai, R (reprint author), Kyoto Univ, Ctr Ecol Res, Hirano 2-509-3, Otsu, Shiga 5202113, Japan.	r.nakadai@ecology.kyoto-u.ac.jp	Nakadai, Ryosuke/R-6927-2016	Nakadai, Ryosuke/0000-0002-9512-8511	JSPS KAKENHI [26650165, 15H04421, 15H05241];  [15J00601]	We thank staff members of Ashiu Forest Research Station for field assistance and S. Fujinaga, Y. Okazaki, S. Matsuoka and M. Ushio for advice on DNA experiments. We also thank the subject editor W. Symondson and two anonymous reviewers for comments that improved the manuscript. This work was supported by a grant from Grant-in-Aid for JSPS Fellows Grant Number 15J00601 and the JSPS KAKENHI Grant Number 26650165, 15H04421, 15H05241.		61	2	2	4	18	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0962-1083	1365-294X		MOL ECOL	Mol. Ecol.	JUN	2017	26	12					3309	3319		10.1111/mec.14105				11	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	EW9JX	WOS:000402836700018	28316099				22-11-18
J	Kocher, A; de Thoisy, B; Catzeflis, F; Valiere, S; Banuls, AL; Murienne, J				Kocher, Arthur; de Thoisy, Benoit; Catzeflis, Francois; Valiere, Sophie; Banuls, Anne-Laure; Murienne, Jerome			iDNA screening: Disease vectors as vertebrate samplers	MOLECULAR ECOLOGY			English	Article						bloodmeal; dipteran; feeding preference; insect; mosquito; sand fly	PANAMANIAN PHLEBOTOMINE SANDFLIES; NATURAL HOST PREFERENCES; HIGH-THROUGHPUT; BLOOD MEALS; SOUTH-AMERICA; FRENCH-GUIANA; RAIN-FOREST; SAND FLIES; IDENTIFICATION; BIODIVERSITY	In the current context of global change and human-induced biodiversity decline, there is an urgent need for developing sampling approaches able to accurately describe the state of biodiversity. Traditional surveys of vertebrate fauna involve time-consuming and skill-demanding field methods. Recently, the use of DNA derived from invertebrate parasites (leeches and blowflies) was suggested as a new tool for vertebrate diversity assessment. Bloodmeal analyses of arthropod disease vectors have long been performed to describe their feeding behaviour, for epidemiological purposes. On the other hand, this existing expertise has not yet been applied to investigate vertebrate fauna per se. Here, we evaluate the usefulness of hematophagous dipterans as vertebrate samplers. Blood-fed sand flies and mosquitoes were collected in Amazonian forest sites and analysed using high-throughput sequencing of short mitochondrial markers. Bloodmeal identifications highlighted contrasting ecological features and feeding behaviour among dipteran species, which allowed unveiling arboreal and terrestrial mammals of various body size, as well as birds, lizards and amphibians. Additionally, lower vertebrate diversity was found in sites undergoing higher levels of human-induced perturbation. These results suggest that, in addition to providing precious information on disease vector host use, dipteran bloodmeal analyses may represent a useful tool in the study of vertebrate communities. Although further effort is required to validate the approach and consider its application to large-scale studies, this first work opens up promising perspectives for biodiversity monitoring and eco-epidemiology.	[Kocher, Arthur; Murienne, Jerome] Univ Toulouse III Paul Sabatier, CNRS, ENFA, UMR5174 EDB,Lab Evolut & Divers Biol, Toulouse, France; [Kocher, Arthur; Banuls, Anne-Laure] Univ Montpellier, CNRS, UMR MIVEGEC, IRD 224 5290, Montpellier, France; [de Thoisy, Benoit] Inst Pasteur, Cayenne, French Guiana; [de Thoisy, Benoit] Assoc Kwata, Cayenne, French Guiana; [Catzeflis, Francois] Univ Montpellier 2, CNRS, Inst Sci Evolut, UMR 5554, Case Courrier 064, Montpellier, France; [Valiere, Sophie] INRA Auzeville, Genotoul, GeT PlaGe, Castanet Tolosan, France	Kocher, A (reprint author), Univ Toulouse III Paul Sabatier, CNRS, ENFA, UMR5174 EDB,Lab Evolut & Divers Biol, Toulouse, France.	arthur.kocher@gmail.com		Banuls, Anne-Laure/0000-0002-2106-8667; Kocher, Arthur/0000-0002-9499-6472; Murienne, Jerome/0000-0003-1474-7829	Agence Nationale de la Recherche [ANR-10-LABX-25-01, ANR-10-LABX-41, ANR-11-IDEX-0002-02]; LABEX DRIIHM	Agence Nationale de la Recherche, Grant/Award Number: ANR-10-LABX-25-01, ANR-10-LABX-41, ANR-11-IDEX-0002-02, LABEX DRIIHM		66	3	3	6	23	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0962-1083	1365-294X		MOL ECOL	Mol. Ecol.	NOV	2017	26	22					6478	6486		10.1111/mec.14362				9	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	FO9UH	WOS:000417241800020	28926155				22-11-18
J	Parfrey, LW; Moreau, CS; Russell, JA				Parfrey, Laura Wegener; Moreau, Corrie S.; Russell, Jacob A.			Introduction: The host-associated microbiome: Pattern, process and function	MOLECULAR ECOLOGY			English	Article						community assembly; experiments; high-throughput sequencing; microbiota; symbiosis	GUT MICROBIOTA; BACTERIAL COMMUNITIES; ROOT MICROBIOME; EVOLUTIONARY ECOLOGY; HORIZONTAL TRANSFER; CORAL-REEFS; DIVERSITY; SYMBIOSIS; APHIDS; INSECTS		[Parfrey, Laura Wegener] Univ British Columbia, Biodivers Res Ctr, Dept Bot, Vancouver, BC, Canada; [Parfrey, Laura Wegener] Univ British Columbia, Dept Zool, Vancouver, BC, Canada; [Moreau, Corrie S.] Field Museum Nat Hist, Dept Sci & Educ, Chicago, IL 60605 USA; [Russell, Jacob A.] Drexel Univ, Dept Biol, Philadelphia, PA 19104 USA	Parfrey, LW (reprint author), Univ British Columbia, Biodivers Res Ctr, Dept Bot, Vancouver, BC, Canada.	Lwparfrey@botany.ubc.ca						129	1	1	26	26	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0962-1083	1365-294X		MOL ECOL	Mol. Ecol.	APR	2018	27	8			SI		1749	1765		10.1111/mec.14706				17	Biochemistry & Molecular Biology; Ecology; Evolutionary Biology	Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology	GF1BV	WOS:000431667800001	29727917				22-11-18
J	Yeo, D; Puniamoorthy, J; Ngiam, RWJ; Meier, R				Yeo, Darren; Puniamoorthy, Jayanthi; Ngiam, Robin Wen Jiang; Meier, Rudolf			Towards holomorphology in entomology: rapid and cost-effective adult-larva matching using NGS barcodes	SYSTEMATIC ENTOMOLOGY			English	Article							SPECIES DELIMITATION; MOLECULAR-IDENTIFICATION; ANISOPTERA AESHNIDAE; ODONATA AESHNIDAE; NATURAL-HISTORY; DNA-SEQUENCES; INSTAR LARVA; TAXONOMY; DIPTERA; ASSOCIATION	In many taxa the morphology of females and immatures is poorly known because species descriptions and identification tools have a male bias. The root causes are problems with matching life-history stages and genders belonging to the same species. Such matching is time-consuming when conventional methods are used (e.g. rearing) and expensive when the stages are matched with DNA barcodes. Unfortunately, the lack of associations is not a trivial problem because it renders a large part of the phenome of insects unexplored, although larvae and females are useful sources of characters for descriptive and phylogenetic purposes. In addition, many collectors intentionally avoid females and immature stages, which skews survey results, interferes with collecting life-history information, and makes it less likely that rare species are discovered. These problems even exist for well-studied taxa like Odonata, where obtaining adult-larva matches relies largely on rearing. Here we demonstrate how the matching problem can be addressed with cost-effective tagged amplicon sequencing of a 313-bp segment of cox1 with next-generation sequencing (NGS) ('NGS barcoding'). We illustrate the value of this approach based on Singapore's odonate fauna which is of a similar size as the European fauna (Singapore, 122 extant species; Europe, 138 recorded species). We match the larvae and adults of 59 species by first creating a barcode database for 338 identified adult specimens representing 83 species. We then sequence 1178 larvae from a wide range of sources. We successfully barcode 1123 specimens, which leads to adult-larva matches for 59 species based on our own barcodes (55) and online barcode databases (4). With these additions, 84 of the 131 species recorded in Singapore have now been associated with a species name. Most common species are now matched (83%), and good progress has been made for vulnerable/near-threatened (55%), endangered (53%), and critically endangered species (38%). We used nondestructive DNA extraction methods in order to be able to use high-resolution imaging of matched larvae to establish a publicly available digital reference collection for odonates which is incorporated into 'Biodiversity of Singapore' (https://singapore.biodiversity.online/). We suggest that the methods described here are suitable for many insect taxa because NGS barcoding allows for fast and low-cost matching of well-studied life-history stages with neglected semaphoronts (eggs, larvae, females). We estimate that the specimen-specific amplicons in this study (c. 1500 specimens) can now be obtained within eight working days and that the laboratory and sequencing cost is c. US$600 (<US$0.40 per specimen).	[Yeo, Darren; Meier, Rudolf] Natl Univ Singapore, Dept Biol Sci, 14 Sci Dr 4,05-20, Singapore 117543, Singapore; [Puniamoorthy, Jayanthi] Lee Kong Chian Nat Hist Museum, Singapore, Singapore; [Ngiam, Robin Wen Jiang] Natl Pk Board, Singapore, Singapore	Meier, R (reprint author), Natl Univ Singapore, Dept Biol Sci, 14 Sci Dr 4,05-20, Singapore 117543, Singapore.	meier@nus.edu.sg	Meier, Rudolf/G-4213-2010		NUS SEABIG [R-154-000-648-646, R-154-000-648-733]	We would like to thank Dr Esther Clews and her team from the TMSI for providing larval specimens and expertise, Foo Maosheng and Siti Maimon Bte Hussin for providing assistance with the larval imaging, Tang Hung Bun for providing photographs for the graphical abstract, as well as Dr Yuchen Ang and Jonathan Ho Kit Ian for their work on the Biodiversity of Singapore digital reference collection. We would like to acknowledge grant support from NUS SEABIG (R-154-000-648-646 and R-154-000-648-733).		94	2	2	12	12	WILEY	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0307-6970	1365-3113		SYST ENTOMOL	Syst. Entomol.	OCT	2018	43	4					678	691		10.1111/syen.12296				14	Evolutionary Biology; Entomology	Evolutionary Biology; Entomology	GS2TS	WOS:000443411300004					22-11-18
J	Maddison, DR; Cooper, KW				Maddison, David R.; Cooper, Kenneth W.			Species delimitation in the ground beetle subgenus Liocosmius (Coleoptera: Carabidae: Bembidion), including standard and next-generation sequencing of museum specimens	ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY			English	Article						Bembidiini; Bembidion; DNA; Illumina; morphology; museum specimens; species delimitation; systematics	DOMAIN PROTEINS MSP-300; DNA EXTRACTION; NORTH; PRESERVATION; INFERENCE; KLARSICHT; ALIGNMENT; GENOMICS; INSECTS; AMERICA	The species of subgenus LiocosmiusCasey of genus BembidionLatreille are delimited and documented using DNA sequences from eight genes, morphological data, and geography. The subgenus consists of six known species, three of which are described as new: Bembidion orionCooper and Maddison (California), B.darlingtonielumCooper and Maddison (California), and B.cooperiMaddison (New Mexico and Arizona). The group ranges from British Columbia south to Baja California, and east to Colorado and New Mexico, with the centre of diversity in California. DNA from a pinned specimen collected in 1968 was sequenced using an Illumina platform, resulting in accurate data of all eight genes studied. Identification tools and descriptions of each species are provided.(c) 2014 The Linnean Society of London	[Maddison, David R.] Oregon State Univ, Dept Integrat Biol, Corvallis, OR 97331 USA; [Cooper, Kenneth W.] Univ Calif Riverside, Dept Biol, Riverside, CA 92521 USA	Maddison, DR (reprint author), Oregon State Univ, Dept Integrat Biol, 3029 Cordley Hall, Corvallis, OR 97331 USA.	david.maddison@science.oregonstate.edu			Harold E and Leona M. Rice Endowment Fund at Oregon State University; National Science Foundation [DEB-1258220]	This work was funded in part by the Harold E and Leona M. Rice Endowment Fund at Oregon State University, as well as National Science Foundation grant DEB-1258220 to DRM.		51	7	8	0	36	WILEY-BLACKWELL	HOBOKEN	111 RIVER ST, HOBOKEN 07030-5774, NJ USA	0024-4082	1096-3642		ZOOL J LINN SOC-LOND	Zool. J. Linn. Soc.	DEC	2014	172	4					741	770		10.1111/zoj.12188				30	Zoology	Zoology	AU4OC	WOS:000345589900001		Other Gold			22-11-18
J	James, TY; Marino, JA; Perfecto, I; Vandermeer, J				James, Timothy Y.; Marino, John A.; Perfecto, Ivette; Vandermeer, John			Identification of Putative Coffee Rust Mycoparasites via Single-Molecule DNA Sequencing of Infected Pustules	APPLIED AND ENVIRONMENTAL MICROBIOLOGY			English	Article							FUNGAL ENDOPHYTES; THEOBROMA-CACAO; LECANICILLIUM-LECANII; VERTICILLIUM-LECANII; ENTOMOGENOUS FUNGUS; HEMILEIA-VASTATRIX; DIVERSITY; BIODIVERSITY; BIOCONTROL; AGROECOSYSTEM	The interaction of crop pests with their natural enemies is a fundament to their control. Natural enemies of fungal pathogens of crops are poorly known relative to those of insect pests, despite the diversity of fungal pathogens and their economic importance. Currently, many regions across Latin America are experiencing unprecedented epidemics of coffee rust (Hemileia vastatrix). Identification of natural enemies of coffee rust could aid in developing management strategies or in pinpointing species that could be used for biocontrol. In the present study, we characterized fungal communities associated with coffee rust lesions by single-molecule DNA sequencing of fungal rRNA gene bar codes from leaf discs (approximate to 28 mm(2)) containing rust lesions and control discs with no rust lesions. The leaf disc communities were hyperdiverse in terms of fungi, with up to 69 operational taxonomic units (putative species) per control disc, and the diversity was only slightly reduced in rust-infected discs, with up to 63 putative species. However, geography had a greater influence on the fungal community than whether the disc was infected by coffee rust. Through comparisons between control and rust-infected leaf discs, as well as taxonomic criteria, we identified 15 putative mycoparasitic fungi. These fungi are concentrated in the fungal family Cordycipitaceae and the order Tremellales. These data emphasize the complexity of diverse fungi of unknown ecological function within a leaf that might influence plant disease epidemics or lead to the development of species for biocontrol of fungal disease.	[James, Timothy Y.; Marino, John A.; Vandermeer, John] Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA; [Perfecto, Ivette] Univ Michigan, Sch Nat Resources & Environm, Ann Arbor, MI 48109 USA	James, TY (reprint author), Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA.	tyjames@umich.edu						43	6	7	1	35	AMER SOC MICROBIOLOGY	WASHINGTON	1752 N ST NW, WASHINGTON, DC 20036-2904 USA	0099-2240	1098-5336		APPL ENVIRON MICROB	Appl. Environ. Microbiol.	JAN	2016	82	2					631	639		10.1128/AEM.02639-15				9	Biotechnology & Applied Microbiology; Microbiology	Biotechnology & Applied Microbiology; Microbiology	DC7BL	WOS:000369373200022	26567299	Green Published, Bronze			22-11-18
J	Duguma, D; Hall, MW; Smartt, CT; Neufeld, JD				Duguma, Dagne; Hall, Michael W.; Smartt, Chelsea T.; Neufeld, Josh D.			Effects of Organic Amendments on Microbiota Associated with the Culex nigripalpus Mosquito Vector of the Saint Louis Encephalitis and West Nile Viruses	MSPHERE			English	Article						aquatic chemistry; bacteria; disease vectors; food web; life stages; microbiome; mosquito; pollution	HIGH WOLBACHIA DENSITY; DIPTERA-CULICIDAE; BACILLUS-THURINGIENSIS; BACTERIAL COMMUNITIES; NUTRIENT ENRICHMENT; ANOPHELES-GAMBIAE; AEDES-AEGYPTI; QUINQUEFASCIATUS DIPTERA; THORSELLIA-ANOPHELIS; FEEDING-BEHAVIOR	Pollution from nutrients in aquatic habitats has been linked to increases in disease vectors, including mosquitoes and other pestiferous insects. One possibility is that changes in mosquito microbiomes are impacted by nutrient enrichments and that these changes affect various traits, including larval development, susceptibility to larval control agents, and susceptibility of the adult mosquitoes to pathogens. We tested this hypothesis using field mesocosms supplemented with low-and high-organic-nutrient regimens and then sampled microbial communities associated with the naturally colonizing Culex nigripalpus mosquito vector. By high-throughput sequencing of 16S rRNA gene sequences, we found no significant differences in overall microbial communities associated with sampled mosquitoes, despite detecting discernible differences in environmental variables, including pH, dissolved oxygen, and nutrient amendments. Nevertheless, indicator species analysis revealed that members of the Clostridiales were significantly associated with mosquitoes that originated from high-nutrient enrichments. In contrast, members of the Burkholderiales were associated with mosquitoes from the low-nutrient enrichment. High bacterial variability associated with the life stages of the C. nigripalpus was largely unaffected by levels of nutrient enrichments that impacted larval microbial resources, including bacteria, ciliates, and flagellates in the larval environments. IMPORTANCE Mosquito microbiota provide important physiological and ecological attributes to mosquitoes, including an impact on their susceptibility to pathogens, fitness, and sensitivity to mosquito control agents. Culex nigripalpus mosquito populations transmit various pathogens, including the Saint Louis and West Nile viruses, and proliferate in nutrient-rich environments, such as in wastewater treatment wet-lands. Our study examined whether increases in nutrients within larval mosquito developmental habitats impact microbial communities associated with C. nigripalpus mosquitoes. We characterized the effects of organic enrichments on microbiomes associated with C. nigripalpus mosquitoes and identified potential bacterial microbiota that will be further investigated for whether they alter mosquito life history traits and for their potential role in the development of microbial-based control strategies.	[Duguma, Dagne; Smartt, Chelsea T.] Univ Florida, IFAS, Florida Med Entomol Lab, Vero Beach, FL USA; [Hall, Michael W.] Dalhousie Univ, Fac Comp Sci, Halifax, NS, Canada; [Neufeld, Josh D.] Univ Waterloo, Dept Biol, Waterloo, ON, Canada	Duguma, D (reprint author), Univ Florida, IFAS, Florida Med Entomol Lab, Vero Beach, FL USA.	duguma@ufl.edu			Florida Department of Agriculture and Consumer Services [00123786]; Natural Sciences and Engineering Research Council of Canada (NSERC); University of Florida	D.D. was supported by funding from Florida Department of Agriculture and Consumer Services (project no. 00123786). J.D.N. was supported by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (NSERC). Publication of this article was funded in part by the University of Florida Open Access Publishing Fund. The funders had no role in study design, data collection and interpretation, nor the decision to submit the work for publication.		77	5	5	4	11	AMER SOC MICROBIOLOGY	WASHINGTON	1752 N ST NW, WASHINGTON, DC 20036-2904 USA	2379-5042			MSPHERE	mSphere	JAN	2017	2	1							e00387-16	10.1128/mSphere.00387-16				12	Microbiology	Microbiology	EL3WL	WOS:000394549900025	28168223	DOAJ Gold, Green Published			22-11-18
J	Zhou, X; Li, YY; Liu, SL; Yang, Q; Su, X; Zhou, LL; Tang, M; Fu, RB; Li, JG; Huang, QF				Zhou, Xin; Li, Yiyuan; Liu, Shanlin; Yang, Qing; Su, Xu; Zhou, Lili; Tang, Min; Fu, Ribei; Li, Jiguang; Huang, Quanfei			Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification	GIGASCIENCE			English	Article								Background: Next-generation-sequencing (NGS) technologies combined with a classic DNA barcoding approach have enabled fast and credible measurement for biodiversity of mixed environmental samples. However, the PCR amplification involved in nearly all existing NGS protocols inevitably introduces taxonomic biases. In the present study, we developed new Illumina pipelines without PCR amplifications to analyze terrestrial arthropod communities. Results: Mitochondrial enrichment directly followed by Illumina shotgun sequencing, at an ultra-high sequence volume, enabled the recovery of Cytochrome c Oxidase subunit 1 (COI) barcode sequences, which allowed for the estimation of species composition at high fidelity for a terrestrial insect community. With 15.5 Gbp Illumina data, approximately 97% and 92% were detected out of the 37 input Operational Taxonomic Units (OTUs), whether the reference barcode library was used or not, respectively, while only 1 novel OTU was found for the latter. Additionally, relatively strong correlation between the sequencing volume and the total biomass was observed for species from the bulk sample, suggesting a potential solution to reveal relative abundance. Conclusions: The ability of the new Illumina PCR-free pipeline for DNA metabarcoding to detect small arthropod specimens and its tendency to avoid most, if not all, false positives suggests its great potential in biodiversity-related surveillance, such as in biomonitoring programs. However, further improvement for mitochondrial enrichment is likely needed for the application of the new pipeline in analyzing arthropod communities at higher diversity.	[Zhou, Xin; Li, Yiyuan; Liu, Shanlin; Yang, Qing; Su, Xu; Zhou, Lili; Tang, Min; Fu, Ribei; Li, Jiguang; Huang, Quanfei] BGI Shenzhen, Beishan Ind Zone, Shenzhen 518083, Guangdong, Peoples R China	Zhou, X (reprint author), BGI Shenzhen, Beishan Ind Zone, Shenzhen 518083, Guangdong, Peoples R China.	xinzhou@genomics.cn	Zhou, Xin/D-4025-2009	Zhou, Xin/0000-0002-1407-7952; Li, Yiyuan/0000-0003-1426-0033				0	128	134	7	67	OXFORD UNIV PRESS	OXFORD	GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND	2047-217X			GIGASCIENCE	GigaScience	Mar-27	2013	2								4	10.1186/2047-217X-2-4				12	Multidisciplinary Sciences	Science & Technology - Other Topics	172XZ	WOS:000321041600001	23587339	DOAJ Gold, Green Published			22-11-18
J	Fuller, ZL; Nino, EL; Patch, HM; Bedoya-Reina, OC; Baumgarten, T; Muli, E; Mumoki, F; Ratan, A; McGraw, J; Frazier, M; Masiga, D; Schuster, S; Grozinger, CM; Miller, W				Fuller, Zachary L.; Nino, Elina L.; Patch, Harland M.; Bedoya-Reina, Oscar C.; Baumgarten, Tracey; Muli, Elliud; Mumoki, Fiona; Ratan, Aakrosh; McGraw, John; Frazier, Maryann; Masiga, Daniel; Schuster, Stephen; Grozinger, Christina M.; Miller, Webb			Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools	BMC GENOMICS			English	Article						Apis mellifera; Galaxy; Genome sequencing; Adaptive evolution	DIVISION-OF-LABOR; POSITIVE DARWINIAN SELECTION; DROSOPHILA-MELANOGASTER; MITOCHONDRIAL-DNA; JUVENILE-HORMONE; SOCIAL INSECTS; VARROA-DESTRUCTOR; NATURAL-SELECTION; VENOM ALLERGEN; GENETIC THEORY	Background: With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including FST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions. Results: We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea. Conclusions: These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows (http://usegalaxy.org/r/kenyanbee) that can be applied to any model system with genomic information.	[Fuller, Zachary L.] Penn State Univ, Dept Biol, University Pk, PA 16802 USA; [Nino, Elina L.; Patch, Harland M.; Baumgarten, Tracey; Frazier, Maryann; Grozinger, Christina M.] Penn State Univ, Dept Entomol, Ctr Pollinator Res, University Pk, PA 16802 USA; [Bedoya-Reina, Oscar C.; Ratan, Aakrosh; Schuster, Stephen; Miller, Webb] Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA; [Muli, Elliud] SEKU, Dept Biol Sci, Kitui, Kenya; [Mumoki, Fiona; Masiga, Daniel] Icipe, Nairobi, Kenya; [McGraw, John] Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA	Fuller, ZL (reprint author), Penn State Univ, Dept Biol, University Pk, PA 16802 USA.	zlf105@psu.edu	Fuller, Zachary/N-3926-2017	Fuller, Zachary/0000-0003-4765-9227; Masiga, Daniel/0000-0001-7513-0887	National Science Foundation-BREAD grant [0965441]; USDA-AFRI Post-doctoral Fellowship	We would like to thank Joseph Kilonzo and James Kilmani for assistance with the field collections, and Stephen Schaeffer and Soojin Yi for insightful comments. We would also like to thank the comments of two anonymous reviewers. This work was supported by funding from a National Science Foundation-BREAD grant #0965441 to J. Tumlinson, M. Frazier, J. Frazier, C. Grozinger, D. Masiga, E. Muli, H. Patch and a USDA-AFRI Post-doctoral Fellowship to E. L. Nino.		107	10	10	1	66	BIOMED CENTRAL LTD	LONDON	236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND	1471-2164			BMC GENOMICS	BMC Genomics	Jul-10	2015	16								518	10.1186/s12864-015-1712-0				18	Biotechnology & Applied Microbiology; Genetics & Heredity	Biotechnology & Applied Microbiology; Genetics & Heredity	CM4EJ	WOS:000357636800003	26159619	DOAJ Gold, Green Published			22-11-18
J	Ulrich, J; Dao, VA; Majumdar, U; Schmitt-Engel, C; Schwirz, J; Schultheis, D; Strohlein, N; Troelenberg, N; Grossmann, D; Richter, T; Donitz, J; Gerischer, L; Leboulle, G; Vilcinskas, A; Stanke, M; Bucher, G				Ulrich, Julia; Dao, Van Anh; Majumdar, Upalparna; Schmitt-Engel, Christian; Schwirz, Jonas; Schultheis, Dorothea; Stroehlein, Nadi; Troelenberg, Nicole; Grossmann, Daniela; Richter, Tobias; Doenitz, Juergen; Gerischer, Lizzy; Leboulle, Gerard; Vilcinskas, Andreas; Stanke, Mario; Bucher, Gregor			Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target	BMC GENOMICS			English	Article						Pest control; RNAi; RNAi target gene; iBeetle; Tribolium; Proteasome	DOUBLE-STRANDED-RNA; INSECTICIDE RESISTANCE; LARVAL RNAI; INTERFERENCE; CASTANEUM; BEETLE; DROSOPHILA; COLEOPTERA; DATABASE; GENOME	Background: Insect pest control is challenged by insecticide resistance and negative impact on ecology and health. One promising pest specific alternative is the generation of transgenic plants, which express double stranded RNAs targeting essential genes of a pest species. Upon feeding, the dsRNA induces gene silencing in the pest resulting in its death. However, the identification of efficient RNAi target genes remains a major challenge as genomic tools and breeding capacity is limited in most pest insects impeding whole-animal-high-throughput-screening. Results: We use the red flour beetle Tribolium castaneum as a screening platform in order to identify the most efficient RNAi target genes. From about 5,000 randomly screened genes of the iBeetle RNAi screen we identify 11 novel and highly efficient RNAi targets. Our data allowed us to determine GO term combinations that are predictive for efficient RNAi target genes with proteasomal genes being most predictive. Finally, we show that RNAi target genes do not appear to act synergistically and that protein sequence conservation does not correlate with the number of potential off target sites. Conclusions: Our results will aid the identification of RNAi target genes in many pest species by providing a manageable number of excellent candidate genes to be tested and the proteasome as prime target. Further, the identified GO term combinations will help to identify efficient target genes from organ specific transcriptomes. Our off target analysis is relevant for the sequence selection used in transgenic plants.	[Ulrich, Julia; Schmitt-Engel, Christian; Schwirz, Jonas; Grossmann, Daniela; Doenitz, Juergen; Bucher, Gregor] Univ Gottingen, GZMB, Johann Friedrich Blumenbach Inst, D-37077 Gottingen, Germany; [Majumdar, Upalparna; Schultheis, Dorothea; Stroehlein, Nadi; Troelenberg, Nicole; Richter, Tobias] Univ Erlangen Nurnberg, Entwicklungsbiol, Dept Biol, D-91058 Erlangen, Germany; [Dao, Van Anh] Univ Cologne, Inst Entwicklungsbiol, D-50674 Cologne, Germany; [Gerischer, Lizzy; Stanke, Mario] Ernst Moritz Arndt Univ Greifswald, Inst Math & Informat, D-17487 Greifswald, Germany; [Leboulle, Gerard] Free Univ Berlin, Neurobiol, Inst Biol, D-14195 Berlin, Germany; [Vilcinskas, Andreas] Univ Giessen, Inst Phytopathol & Angew Zool, D-35392 Giessen, Germany	Bucher, G (reprint author), Univ Gottingen, GZMB, Johann Friedrich Blumenbach Inst, Justus von Liebig Weg 11, D-37077 Gottingen, Germany.	gbucher1@uni-goettingen.de		Donitz, Jurgen/0000-0002-8401-8851; Bucher, Gregor/0000-0002-4615-6401	German Research Foundation (DFG) [FOR1234]; Gottingen University	We acknowledge support by the German Research Foundation (DFG), which funded the iBeetle project (FOR1234) but was not involved in design or analysis of the data or its publication. Further, we acknowledge the Open Access Publication Funds of the Gottingen University. We thank Claudia Hinners for technical assistance, Maike Tech for extracting the gene lists from the database.		30	26	26	0	50	BIOMED CENTRAL LTD	LONDON	236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND	1471-2164			BMC GENOMICS	BMC Genomics	Sep-03	2015	16								674	10.1186/s12864-015-1880-y				9	Biotechnology & Applied Microbiology; Genetics & Heredity	Biotechnology & Applied Microbiology; Genetics & Heredity	CQ4XE	WOS:000360607100014	26334912	DOAJ Gold, Green Published			22-11-18
J	Shearer, PW; West, JD; Walton, VM; Brown, PH; Svetec, N; Chiu, JC				Shearer, Peter W.; West, Jessica D.; Walton, Vaughn M.; Brown, Preston H.; Svetec, Nicolas; Chiu, Joanna C.			Seasonal cues induce phenotypic plasticity of Drosophila suzukii to enhance winter survival	BMC ECOLOGY			English	Article						Drosophila suzukii; Phenotypic plasticity; Cold tolerance; Diapause; High-throughput sequencing; Transcriptome	SPOTTED WING DROSOPHILA; GENE-EXPRESSION; DIPTERA DROSOPHILIDAE; COLD TOLERANCE; REPRODUCTIVE DIAPAUSE; RANGE EXPANSION; BODY-SIZE; MELANOGASTER; TEMPERATURE; EVOLUTION	Background: As global climate change and exponential human population growth intensifies pressure on agricultural systems, the need to effectively manage invasive insect pests is becoming increasingly important to global food security. Drosophila suzukii is an invasive pest that drastically expanded its global range in a very short time since 2008, spreading to most areas in North America and many countries in Europe and South America. Preliminary ecological modeling predicted a more restricted distribution and, for this reason, the invasion of D. suzukii to northern temperate regions is especially unexpected. Investigating D. suzukii phenology and seasonal adaptations can lead to a better understanding of the mechanisms through which insects express phenotypic plasticity, which likely enables invasive species to successfully colonize a wide range of environments. Results: We describe seasonal phenotypic plasticity in field populations of D. suzukii. Specifically, we observed a trend of higher proportions of flies with the winter morph phenotype, characterized by darker pigmentation and longer wing length, as summer progresses to winter. A laboratory-simulated winter photoperiod and temperature (12: 12 L:D and 10 degrees C) were sufficient to induce the winter morph phenotype in D. suzukii. This winter morph is associated with increased survival at 1 degrees C when compared to the summer morph, thus explaining the ability of D. suzukii to survive cold winters. We then used RNA sequencing to identify gene expression differences underlying seasonal differences in D. suzukii physiology. Winter morph gene expression is consistent with known mechanisms of cold-hardening such as adjustments to ion transport and up-regulation of carbohydrate metabolism. In addition, transcripts involved in oogenesis and DNA replication were down-regulated in the winter morph, providing the first molecular evidence of a reproductive diapause in D. suzukii. Conclusions: To date, D. suzukii cold resistance studies suggest that this species cannot overwinter in northern locations, e.g. Canada, even though they are established pests in these regions. Combining physiological investigations with RNA sequencing, we present potential mechanisms by which D. suzukii can overwinter in these regions. This work may contribute to more accurate population models that incorporate seasonal variation in physiological parameters, leading to development of better management strategies.	[Shearer, Peter W.; Brown, Preston H.] Oregon State Univ, Mid Columbia Agr Res & Extens Ctr, 3005 Expt Stn Dr, Hood River, OR 97331 USA; [West, Jessica D.; Chiu, Joanna C.] Univ Calif Davis, Dept Entomol & Nematol, Davis, CA 95616 USA; [Walton, Vaughn M.] Oregon State Univ, Dept Hort, Corvallis, OR 97331 USA; [Svetec, Nicolas] Univ Calif Davis, Dept Ecol & Evolut, Davis, CA 95616 USA	Chiu, JC (reprint author), Univ Calif Davis, Dept Entomol & Nematol, Davis, CA 95616 USA.	jcchiu@ucdavis.edu			USDA Specialty Crops Research Initiative Grant [2010-51181-21167]; Clarence and Estelle Albaugh Endowment; NSF [IOS-1456297]; NIH-IMSD [GM56765]; HHMI [52005892]; NIGMS-MARC-U-STAR [GM083894]	We thank Tuck Contreas for noticing the seasonal morph phenotypes while monitoring D. suzukii traps, Kala M. Gonsler, Sarah Hieber, Joana R. Kemper, Matthew T. Riek and Kelley E. Schwaner for measuring fly phenotype parameters, and Kelly A. Hamby, Frank G. Zalom, Ernest K. Lee for fruitful discussions. We thank Christine A. Tabuloc for her assistance in fly dissections. This work was supported by funds received from the USDA Specialty Crops Research Initiative Grant (award number 2010-51181-21167) awarded to PWS and VMW, and the Clarence and Estelle Albaugh Endowment and NSF IOS-1456297 to JCC. JDW is a participant of the BUSP Program at UC Davis, which is supported by NIH-IMSD GM56765 and HHMI Grant 52005892, and a participant of BSHARP program, supported by NIGMS-MARC-U-STAR GM083894.		81	36	36	13	115	BIOMED CENTRAL LTD	LONDON	236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND	1472-6785			BMC ECOL	BMC Ecol.	Mar-22	2016	16								11	10.1186/s12898-016-0070-3				18	Ecology	Environmental Sciences & Ecology	DH0SP	WOS:000372494700001	27001084	DOAJ Gold, Green Published			22-11-18
J	Sadd, BM; Barribeau, SM; Bloch, G; de Graaf, DC; Dearden, P; Elsik, CG; Gadau, J; Grimmelikhuijzen, CJP; Hasselmann, M; Lozier, JD; Robertson, HM; Smagghe, G; Stolle, E; Van Vaerenbergh, M; Waterhouse, RM; Bornberg-Bauer, E; Klasberg, S; Bennett, AK; Caamara, F; Guigo, R; Hoff, K; Mariotti, M; Munoz-Torres, M; Murphy, T; Santesmasses, D; Amdam, GV; Beckers, M; Beye, M; Biewer, M; Bitondi, MMG; Blaxter, ML; Bourke, AFG; Brown, MJF; Buechel, SD; Cameron, R; Cappelle, K; Carolan, JC; Christiaens, O; Ciborowski, KL; Clarke, DF; Colgan, TJ; Collins, DH; Cridge, AG; Dalmay, T; Dreier, S; du Plessis, L; Duncan, E; Erler, S; Evans, J; Falcon, T; Flores, K; Freitas, FCP; Fuchikawa, T; Gempe, T; Hartfelder, K; Hauser, F; Helbing, S; Humann, FC; Irvine, F; Jermiin, LS; Johnson, CE; Johnson, RM; Jones, AK; Kadowaki, T; Kidner, JH; Koch, V; Kohler, A; Kraus, FB; Lattorff, HMG; Leask, M; Lockett, GA; Mallon, EB; Antonio, DSM; Marxer, M; Meeus, I; Moritz, RFA; Nair, A; Napflin, K; Nissen, I; Niu, J; Nunes, FMF; Oakeshott, JG; Osborne, A; Otte, M; Pinheiro, DG; Rossie, N; Rueppell, O; Santos, CG; Schmid-Hempel, R; Schmitt, BD; Schulte, C; Simoes, ZLP; Soares, MPM; Swevers, L; Winnebeck, EC; Wolschin, F; Yu, N; Zdobnov, EM; Aqrawi, PK; Blankenburg, KP; Coyle, M; Francisco, L; Hernandez, AG; Holder, M; Hudson, ME; Jackson, L; Jayaseelan, J; Joshi, V; Kovar, C; Lee, SL; Mata, R; Mathew, T; Newsham, IF; Ngo, R; Okwuonu, G; Pham, C; Pu, LL; Saada, N; Santibanez, J; Simmons, D; Thornton, R; Venkat, A; Walden, KKO; Wu, YQ; Debyser, G; Devreese, B; Asher, C; Blommaert, J; Chipman, AD; Chittka, L; Fouks, B; Liu, J; O'Neill, MP; Sumner, S; Puiu, D; Qu, J; Salzberg, SL; Scherer, SE; Muzny, DM; Richards, S; Robinson, GE; Gibbs, RA; Schmid-Hempel, P; Worley, KC				Sadd, Ben M.; Barribeau, Seth M.; Bloch, Guy; de Graaf, Dirk C.; Dearden, Peter; Elsik, Christine G.; Gadau, Juergen; Grimmelikhuijzen, Cornelis J. P.; Hasselmann, Martin; Lozier, Jeffrey D.; Robertson, Hugh M.; Smagghe, Guy; Stolle, Eckart; Van Vaerenbergh, Matthias; Waterhouse, Robert M.; Bornberg-Bauer, Erich; Klasberg, Steffen; Bennett, Anna K.; Camara, Francisco; Guigo, Roderic; Hoff, Katharina; Mariotti, Marco; Munoz-Torres, Monica; Murphy, Terence; Santesmasses, Didac; Amdam, Gro V.; Beckers, Matthew; Beye, Martin; Biewer, Matthias; Bitondi, Marcia M. G.; Blaxter, Mark L.; Bourke, Andrew F. G.; Brown, Mark J. F.; Buechel, Severine D.; Cameron, Rossanah; Cappelle, Kaat; Carolan, James C.; Christiaens, Olivier; Ciborowski, Kate L.; Clarke, David F.; Colgan, Thomas J.; Collins, David H.; Cridge, Andrew G.; Dalmay, Tamas; Dreier, Stephanie; du Plessis, Louis; Duncan, Elizabeth; Erler, Silvio; Evans, Jay; Falcon, Tiago; Flores, Kevin; Freitas, Flavia C. P.; Fuchikawa, Taro; Gempe, Tanja; Hartfelder, Klaus; Hauser, Frank; Helbing, Sophie; Humann, Fernanda C.; Irvine, Frano; Jermiin, Lars S.; Johnson, Claire E.; Johnson, Reed M.; Jones, Andrew K.; Kadowaki, Tatsuhiko; Kidner, Jonathan H.; Koch, Vasco; Koehler, Arian; Kraus, F. Bernhard; Lattorff, H. Michael G.; Leask, Megan; Lockett, Gabrielle A.; Mallon, Eamonn B.; Antonio, David S. Marco; Marxer, Monika; Meeus, Ivan; Moritz, Robin F. A.; Nair, Ajay; Napflin, Kathrin; Nissen, Inga; Niu, Jinzhi; Nunes, Francis M. F.; Oakeshott, John G.; Osborne, Amy; Otte, Marianne; Pinheiro, Daniel G.; Rossie, Nina; Rueppell, Olav; Santos, Carolina G.; Schmid-Hempel, Regula; Schmitt, Bjoern D.; Schulte, Christina; Simoes, Zila L. P.; Soares, Michelle P. M.; Swevers, Luc; Winnebeck, Eva C.; Wolschin, Florian; Yu, Na; Zdobnov, Evgeny M.; Aqrawi, Peshtewani K.; Blankenburg, Kerstin P.; Coyle, Marcus; Francisco, Liezl; Hernandez, Alvaro G.; Holder, Michael; Hudson, Matthew E.; Jackson, LaRonda; Jayaseelan, Joy; Joshi, Vandita; Kovar, Christie; Lee, Sandra L.; Mata, Robert; Mathew, Tittu; Newsham, Irene F.; Ngo, Robin; Okwuonu, Geoffrey; Pham, Christopher; Pu, Ling-Ling; Saada, Nehad; Santibanez, Jireh; Simmons, DeNard; Thornton, Rebecca; Venkat, Aarti; Walden, Kimberly K. O.; Wu, Yuan-Qing; Debyser, Griet; Devreese, Bart; Asher, Claire; Blommaert, Julie; Chipman, Ariel D.; Chittka, Lars; Fouks, Bertrand; Liu, Jisheng; O'Neill, Meaghan P.; Sumner, Seirian; Puiu, Daniela; Qu, Jiaxin; Salzberg, Steven L.; Scherer, Steven E.; Muzny, Donna M.; Richards, Stephen; Robinson, Gene E.; Gibbs, Richard A.; Schmid-Hempel, Paul; Worley, Kim C.			The genomes of two key bumblebee species with primitive eusocial organization	GENOME BIOLOGY			English	Article							BEE APIS-MELLIFERA; SEX-DETERMINATION PATHWAY; MULTIPLE SEQUENCE ALIGNMENT; BOMBUS-TERRESTRIS LINNAEUS; MALE COURTSHIP BEHAVIOR; HONEY-BEE; DROSOPHILA-MELANOGASTER; PHYLOGENETIC ANALYSES; DNA METHYLATION; HIGH-THROUGHPUT	Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.	[Sadd, Ben M.] Illinois State Univ, Sch Biol Sci, Normal, IL 61790 USA; [Sadd, Ben M.; Barribeau, Seth M.; Buechel, Severine D.; Marxer, Monika; Napflin, Kathrin; Schmid-Hempel, Regula; Schmid-Hempel, Paul] ETH, Inst Integrat Biol, Expt Ecol, CH-8092 Zurich, Switzerland; [Barribeau, Seth M.] E Carolina Univ, Dept Biol, Greenville, NC 27858 USA; [Bloch, Guy; Fuchikawa, Taro; Chipman, Ariel D.] Hebrew Univ Jerusalem, Alexander Silberman Inst Life Sci, Dept Ecol Evolut & Behav, Jerusalem, Israel; [de Graaf, Dirk C.; Van Vaerenbergh, Matthias] Univ Ghent, Fac Sci, Lab Zoophysiol, B-9000 Ghent, Belgium; [Dearden, Peter; Cameron, Rossanah; Cridge, Andrew G.; Duncan, Elizabeth; Irvine, Frano; Leask, Megan; Nair, Ajay; Osborne, Amy; Blommaert, Julie] Univ Otago, Dept Biochem, Labo Evolut & Dev Genet, Dunedin 9054, New Zealand; [Dearden, Peter; Cameron, Rossanah; Cridge, Andrew G.; Duncan, Elizabeth; Irvine, Frano; Leask, Megan; Nair, Ajay; Osborne, Amy; Blommaert, Julie; O'Neill, Meaghan P.] Univ Otago, Dept Biochem, Natl Res Ctr Growth & Dev, Dunedin 9054, New Zealand; [Elsik, Christine G.] Univ Missouri, Div Plant Sci, Div Anim Sci, Columbia, MO 65211 USA; [Elsik, Christine G.] Univ Missouri, MU Informat Inst, Columbia, MO 65211 USA; [Elsik, Christine G.; Bennett, Anna K.; Munoz-Torres, Monica; Venkat, Aarti] Georgetown Univ, Dept Biol, Washington, DC 20057 USA; [Gadau, Juergen; Amdam, Gro V.; Wolschin, Florian] Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA; [Grimmelikhuijzen, Cornelis J. P.; Hauser, Frank] Univ Copenhagen, Dept Biol, Ctr Funct & Comparat Insect Gen, Copenhagen, Denmark; [Hasselmann, Martin; Biewer, Matthias] Univ Hohenheim, Inst Anim Sci, D-70599 Stuttgart, Germany; [Lozier, Jeffrey D.] Univ Alabama, Dept Biol Sci, Tuscaloosa, AL 35487 USA; [Robertson, Hugh M.; Cappelle, Kaat; Johnson, Claire E.; Walden, Kimberly K. O.] Univ Illinois, Dept Entomol, Urbana, IL 61801 USA; [Smagghe, Guy; Christiaens, Olivier; Meeus, Ivan; Niu, Jinzhi; Yu, Na; Liu, Jisheng] Univ Ghent, Fac Biosci Engn, Dept Crop Protect, Lab Agrozool, B-9000 Ghent, Belgium; [Stolle, Eckart; Erler, Silvio; Helbing, Sophie; Kidner, Jonathan H.; Kraus, F. Bernhard; Lattorff, H. Michael G.; Moritz, Robin F. A.; Otte, Marianne; Fouks, Bertrand] Univ Halle Wittenberg, Inst Biol, Wittenberg, Germany; [Waterhouse, Robert M.; Zdobnov, Evgeny M.] Univ Geneva, Sch Med, Dept Genet Med & Dev, CH-1211 Geneva, Switzerland; [Waterhouse, Robert M.; Zdobnov, Evgeny M.] Swiss Inst Bioinformat, CH-1211 Geneva, Switzerland; [Waterhouse, Robert M.] MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA; [Waterhouse, Robert M.] MIT & Harvard, Broad Inst, Cambridge Ctr 7, Cambridge, MA 02142 USA; [Bornberg-Bauer, Erich; Klasberg, Steffen] Univ Munster, Inst Evolut & Biodivers, D-48149 Munster, Germany; [Camara, Francisco; Guigo, Roderic; Mariotti, Marco; Santesmasses, Didac] Ctr Genom Regulat CRG, Barcelona 08003, Spain; [Camara, Francisco; Guigo, Roderic; Mariotti, Marco; Santesmasses, Didac] UPF, Barcelona, Spain; [Hoff, Katharina] Ernst Moritz Arndt Univ Greifswald, Inst Math & Comp Sci, D-17487 Greifswald, Germany; [Munoz-Torres, Monica] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA; [Murphy, Terence] Natl Lib Med, Natl Ctr Biotechnol Informat, Bethesda, MD 20894 USA; [Amdam, Gro V.; Wolschin, Florian] Norwegian Univ Food Sci, Dept Chem Biotechnol & Food Sci, N-1432 As, Norway; [Beckers, Matthew] Univ E Anglia, Sch Comp Sci, Norwich NR4 7TJ, Norfolk, England; [Beye, Martin; Gempe, Tanja; Koch, Vasco; Koehler, Arian; Nissen, Inga; Rossie, Nina; Schmitt, Bjoern D.; Schulte, Christina] Univ Dusseldorf, Inst Evolut Genet, D-40225 Dusseldorf, Germany; [Biewer, Matthias] Univ Cologne, Inst Genet, Cologne, Germany; [Bitondi, Marcia M. G.; Simoes, Zila L. P.] Univ Sao Paulo, Dept Biol, Fac Filosofia Ciencias & Letras Ribeirao Preto, BR-14040901 Ribeirao Preto, Brazil; [Blaxter, Mark L.] Univ Edinburgh, Ashworth Labs, Inst Evolutionary Biol & Edinburgh Gen, Edinburgh EH9 3FL, Midlothian, Scotland; [Bourke, Andrew F. G.; Collins, David H.; Dalmay, Tamas] Univ E Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England; [Brown, Mark J. F.] Royal Holloway Univ London, Sch Biol Sci, London, England; [Carolan, James C.] Maynooth Univ, Dept Biol, Co, Kildare, Ireland; [Ciborowski, Kate L.; Sumner, Seirian] Univ Bristol, Sch Biol Sci, Bristol BS8 1TQ, Avon, England; [Clarke, David F.; Jermiin, Lars S.; Oakeshott, John G.] CSIRO, Land & Water Flagship, Canberra, ACT, Australia; [Colgan, Thomas J.] Trin Coll Dublin, Sch Nat Sci, Dept Zool, Dublin, Ireland; [Dreier, Stephanie; Asher, Claire] Zool Soc London, Inst Zool, London NW1 4RY, England; [du Plessis, Louis] ETH, Inst Integrat Biol, Theoret Biol, CH-8092 Zurich, Switzerland; [du Plessis, Louis] Swiss Inst Bioinformat, Lausanne, Switzerland; [du Plessis, Louis] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Computat Evolut, Basel, Switzerland; [Evans, Jay] USDA ARS, Bee Res Lab, Washington, DC 20250 USA; [Falcon, Tiago; Freitas, Flavia C. P.; Hartfelder, Klaus; Antonio, David S. Marco; Soares, Michelle P. M.] Univ Sao Paulo, Dept Genet, Fac Med Ribeirao Preto, BR-14040900 Ribeirao Preto, Brazil; [Flores, Kevin] N Carolina State Univ, Ctr Res Sci Computat, Raleigh, NC 27695 USA; [Fuchikawa, Taro] Kyoto Univ, Grad Sch Agr, Lab Insect Ecol, Kyoto, Japan; [Santos, Carolina G.] Univ Sao Paulo, Dept Biol Celular & Mol & Bioagentes Patogen, Fac Med Ribeirao Preto, BR-14040900 Ribeirao Preto, Brazil; [Humann, Fernanda C.] Inst Fed Educ Ciencia & Tecnol Sao Paulo, BR-15991502 Matao, Brazil; [Johnson, Reed M.] Ohio State Univ, Dept Entomol, Wooster, OH 44791 USA; [Jones, Andrew K.] Oxford Brookes Univ, Fac Hlth & Life Sci, Dept Biol & Med Sci, Oxford OX3 0BP, England; [Kadowaki, Tatsuhiko] Xian Jiaotong Liverpool Univ, Dept Biol Sci, Suzhou, Peoples R China; [Kraus, F. Bernhard] Univ Hosp Halle Saale, Dept Lab Med, Halle, Germany; [Lattorff, H. Michael G.] German Ctr Integrat Biodivers Res iDiv, Leipzig, Germany; [Lockett, Gabrielle A.] Univ Southampton, Southampton, Hants, England; [Mallon, Eamonn B.] Univ Leicester, Dept Biol, Leicester, Leics, England; [Nunes, Francis M. F.] Univ Fed Sao Carlos, Ctr Ciencias Biol & Saude, Dept Genet & Evolucao, BR-13565905 Sao Carlos, SP, Brazil; [Pinheiro, Daniel G.] Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Tecnol, BR-14884900 Jaboticabal, Brazil; [Rueppell, Olav; Fouks, Bertrand] Univ N Carolina, Dept Biol, Greensboro, NC 27403 USA; [Swevers, Luc] Natl Ctr Sci Res Demokritos, Inst Biosci & Applicat, Athens, Greece; [Winnebeck, Eva C.] Univ Munich, Munich, Germany; [Aqrawi, Peshtewani K.; Blankenburg, Kerstin P.; Coyle, Marcus; Francisco, Liezl; Holder, Michael; Jackson, LaRonda; Jayaseelan, Joy; Joshi, Vandita; Kovar, Christie; Lee, Sandra L.; Mata, Robert; Mathew, Tittu; Ngo, Robin; Okwuonu, Geoffrey; Pham, Christopher; Pu, Ling-Ling; Saada, Nehad; Santibanez, Jireh; Simmons, DeNard; Thornton, Rebecca; Wu, Yuan-Qing; Qu, Jiaxin; Muzny, Donna M.; Richards, Stephen; Gibbs, Richard A.; Worley, Kim C.] Baylor Coll Med, Dept Mol & Human Genet, Human Genome Sequencing Ctr, Houston, TX 77030 USA; [Hernandez, Alvaro G.] Univ Illinois, Roy J Carver Biotechnol, Urbana, IL 61801 USA; [Hudson, Matthew E.] Univ Illinois, Dept Crop Sci, Urbana, IL 61801 USA; [Hudson, Matthew E.] Univ Illinois, Inst Genom Biol, Urbana, IL 61801 USA; [Newsham, Irene F.] MD Anderson Canc Ctr, Sch Hlth Profess, Mol Genet Technol Program, Unit 2, Houston, TX 77025 USA; [Venkat, Aarti] Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA; [Debyser, Griet; Devreese, Bart] Univ Ghent, Dept Biochem & Microbiol, Lab Prot Biochem & Biomol Engn, B-9000 Ghent, Belgium; [Chittka, Lars] Queen Mary Univ London, Sch Biol & Chem Sci, Dept Biol & Expt Psychol, London E1 4NS, England; [Liu, Jisheng; Scherer, Steven E.] Guangzhou Univ, Sch Life Sci, Guangzhou, Guangdong, Peoples R China; [Puiu, Daniela; Salzberg, Steven L.] Johns Hopkins Univ, McKusick Nathans Inst Genet Med, Ctr Computat Biol, Baltimore, MD 21205 USA; [Robinson, Gene E.] Univ Illinois, Neurosci Program, Dept Entomol, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA	Sadd, BM (reprint author), Illinois State Univ, Sch Biol Sci, Normal, IL 61790 USA.	bmsadd@ilstu.edu	Dearden, Peter/B-7607-2008; JAYASEELAN, JOY CHRISTINA/F-9824-2015; Hartfelder, Klaus/A-4293-2009; Erler, Silvio/B-4162-2012; Kraus, Frank Bernhard/B-8172-2011; Guigo, Roderic/D-1303-2010; Hauser, Frank/M-2952-2014; Freitas, Flavia/M-4720-2014; Jermiin, Lars/C-2458-2009; Camara Ferreira, Francisco/G-9841-2015; Elsik, Christine/C-4120-2017; Bourke, Andrew/E-5271-2011; Bornberg-Bauer, Erich/A-1563-2013; Lattorff, H. Michael/F-6287-2010; Waterhouse, Robert/A-1858-2010; Lopes, Tiago/G-3409-2016; Blaxter, Mark/B-4113-2010; Oakeshott, John/B-5365-2009; Hudson, Matthew/A-4438-2008; Zdobnov, Evgeny/K-1133-2012; Marco Antonio, David/G-2642-2012; Evans, Jay/C-8408-2012; Nunes, Francis/F-5871-2010; Moritz, Robin/K-6053-2012; Johnson, Reed/H-3742-2011; Bitondi, Marcia/E-8014-2012; Chittka, Lars/C-3110-2012	Dearden, Peter/0000-0001-7790-9675; JAYASEELAN, JOY CHRISTINA/0000-0002-7759-0139; Hartfelder, Klaus/0000-0001-7981-8427; Erler, Silvio/0000-0002-9425-8103; Kraus, Frank Bernhard/0000-0003-4354-9952; Guigo, Roderic/0000-0002-5738-4477; Hauser, Frank/0000-0001-5563-2345; Freitas, Flavia/0000-0002-3162-4890; Jermiin, Lars/0000-0002-9619-3809; Camara Ferreira, Francisco/0000-0002-1971-5466; Elsik, Christine/0000-0002-4248-7713; Bornberg-Bauer, Erich/0000-0002-1826-3576; Lattorff, H. Michael/0000-0002-8603-6332; Waterhouse, Robert/0000-0003-4199-9052; Lopes, Tiago/0000-0002-8936-0381; Blaxter, Mark/0000-0003-2861-949X; Oakeshott, John/0000-0001-8324-7874; Hudson, Matthew/0000-0002-4737-0936; Evans, Jay/0000-0002-0036-4651; Nunes, Francis/0000-0002-7769-3058; Moritz, Robin/0000-0003-0791-887X; Johnson, Reed/0000-0002-2431-0180; Bitondi, Marcia/0000-0002-5619-6378; Chittka, Lars/0000-0001-8153-1732; Blommaert, Julie/0000-0003-1411-2313; Lockett, Gabrielle A./0000-0003-3759-2145; Chipman, Ariel/0000-0001-6696-840X; Hasselmann, Martin/0000-0003-3305-4024; Jones, Andrew/0000-0002-7835-0890; Stolle, Eckart/0000-0001-7638-4061; Childers, Anna/0000-0002-0747-8539; Rueppell, Olav/0000-0001-5370-4229; Grimmelikhuijzen, Cornelis/0000-0001-6486-2046; Napflin, Kathrin/0000-0002-1088-5282; Barribeau, Seth/0000-0001-6643-0562; Winnebeck, Eva/0000-0002-0717-9432; Sadd, Ben/0000-0003-3136-5144; Fouks, Bertrand/0000-0002-3675-3499; Cridge, Andrew/0000-0002-1399-5188; Otte, Marianne/0000-0001-7433-2444; Dalmay, Tamas/0000-0003-1492-5429; Guariz Pinheiro, Daniel/0000-0001-7062-5936; Bloch, Guy/0000-0003-1624-4926; Leask, Megan/0000-0003-3199-5277; Duncan, Elizabeth/0000-0002-1841-504X	National Institutes of Health (NIH) [DP1 OD006416, U54 HG003273]; Agriculture and Food Research Initiative Competitive grant from the USDA National Institute of Food and Agriculture [2010-65106-21301]; Research Council of Norway (NFR); PEW Charitable Trust; University of East Anglia, UK; Israel Science Foundation (ISF); Biotechnology and Biological Sciences Research Council, UK; University of East Anglia; University of Alabama College of Arts and Sciences; Sao Paulo Research Foundation grant (FAPESP) [11/03171-5]; Marie Curie International Outgoing Fellowship [PIOF-GA-2011-303312]; Swiss National Science Foundation [31003A-125350, 31003A-143936]; New Faculty Initiative Grant (NFIG) from Illinois State University College of Arts and Sciences; DFG; Instituto Nacional de Bioinformatica (INB) from ISCIII in Spain; Natural Environment Research Council [NE/K011316/1, NBAF010003]; Biotechnology and Biological Sciences Research Council [BB/I023585/1, BB/K020161/1, BB/G00661X/1]; Medical Research Council [MR/K001744/1, G0900740]	The sequencing, annotation, and assembly of the B. impatiens genome was supported by National Institutes of Health (NIH) Pioneer Award DP1 OD006416 (GER). The B. terrestris genome sequencing, assembly and project coordination was supported by NIH grant U54 HG003273 (RAG). Contributions from members of the CGE lab were supported by Agriculture and Food Research Initiative Competitive grant no. 2010-65106-21301 from the USDA National Institute of Food and Agriculture. GVA was supported by the Research Council of Norway (NFR) and the PEW Charitable Trust. MB was supported by a student fellowship from the University of East Anglia, UK. GB was supported by the Israel Science Foundation (ISF). DHC was supported by a studentship funded by the Biotechnology and Biological Sciences Research Council, UK, and the University of East Anglia. JDL was supported by the University of Alabama College of Arts and Sciences. ZPLS was supported by a Sao Paulo Research Foundation grant (FAPESP number 11/03171-5). RMW was supported by Marie Curie International Outgoing Fellowship PIOF-GA-2011-303312 and by Swiss National Science Foundation awards 31003A-125350 and 31003A-143936 to EMZ. BMS was supported by a New Faculty Initiative Grant (NFIG) from Illinois State University College of Arts and Sciences. MHasselmann received financial support from the DFG. The work of FC, RG, and MM was supported by the Instituto Nacional de Bioinformatica (INB) from ISCIII in Spain. We thank Justin Reese and Christopher Childers for setting up genome annotation tools at Hymenoptera Genome Database.		213	103	106	15	200	BMC	LONDON	CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND	1474-760X			GENOME BIOL	Genome Biol.	Apr-24	2015	16								76	10.1186/s13059-015-0623-3				31	Biotechnology & Applied Microbiology; Genetics & Heredity	Biotechnology & Applied Microbiology; Genetics & Heredity	CG9YT	WOS:000353676700001	25908251	DOAJ Gold, Green Published			22-11-18
J	Diaz, S; Villavicencio, B; Correia, N; Costa, J; Haag, KL				Diaz, Sebastian; Villavicencio, Bianca; Correia, Nathalia; Costa, Jane; Haag, Karen L.			Triatomine bugs, their microbiota and Trypanosoma cruzi: asymmetric responses of bacteria to an infected blood meal	PARASITES & VECTORS			English	Article						Triatomine bugs; Chagas disease; Trypanosoma cruzi; Arsenophonus; Microbiota; Metabarcoding; 16 rRNA	RHODNIUS-PROLIXUS; CHAGAS-DISEASE; GUT MICROBIOTA; ARSENOPHONUS-TRIATOMINARUM; INDEPENDENT METHODS; SYMBIOTIC BACTERIA; VECTOR COMPETENCE; ANTERIOR MIDGUT; UNITED-STATES; BRASILIENSIS	Background: Triatomine bugs (Hemiptera: Reduviidae) are vectors of the flagellate Trypanosoma cruzi, the causative agent of Chagas disease. The study of triatomine gut microbiota has gained relevance in the last years due to its possible role in vector competence and prospective use in control strategies. The objective of this study is to examine changes in the gut microbiota composition of triatomines in response to a T. cruzi-infected blood meal and identifying key factors determining those changes. Results: We sampled colony-reared individuals from six triatomine vectors (Panstrongylus megistus, Rhodnius prolixus, Triatoma brasiliensis, T. infestans, T. juazeirensis and T. sherlocki) comparing experimentally T. cruzi strain 0354-challenged and non-challenged insects. The microbiota of gut and gonad tissues was characterized using high throughput sequencing of region V3-V4 of bacterial 16S rRNA gene. The triatomine microbiota had a low intra-individual diversity, and a high inter-individual variation within the same host species. Arsenophonous appeared as the dominant triatomine bacterial symbiont in our study (59% of the total 16S coverage), but there were significant differences in the distribution of bacterial genera among vectors. In Rhodnius prolixus the dominant symbiont was Pectobacterium. Conclusions: Trypanosoma cruzi-challenge significantly affects microbiota composition, with challenged vectors harbouring a significantly more diverse bacterial community, both in the gut and the gonads. Our results show that blood-feeding with T. cruzi epimastigotes strongly affects microbiota composition in a species-specific manner. We suggest that triatomine-adapted enterobacteria such as Arsenophonus could be used as stable vectors for genetic transformation of triatomine bugs and control of Chagas disease.	[Diaz, Sebastian; Haag, Karen L.] Univ Fed Rio Grande do Sul, Programa Posgrad Genet & Biol Mol, Porto Alegre, RS, Brazil; [Villavicencio, Bianca; Haag, Karen L.] Univ Fed Rio Grande do Sul, Programa Posgrad Biol Celular & Mol, Porto Alegre, RS, Brazil; [Correia, Nathalia; Costa, Jane] Inst Oswaldo Cruz Fiocruz, Lab oio Biodiversidade Entomol, Rio De Janeiro, Brazil; [Haag, Karen L.] Univ Fed Rio Grande do Sul, Inst Biociencias, Dept Genet, Porto Alegre, RS, Brazil	Haag, KL (reprint author), Univ Fed Rio Grande do Sul, Programa Posgrad Genet & Biol Mol, Porto Alegre, RS, Brazil.; Haag, KL (reprint author), Univ Fed Rio Grande do Sul, Programa Posgrad Biol Celular & Mol, Porto Alegre, RS, Brazil.	karen.haag@ufrgs.br			Fundacao de Amparo a Pesquisa do Estado do Rio Grande do Sul (FAPERGS) [1993-2551/13-1]; Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) [470228/2013-0]	Funding was provided by Fundacao de Amparo a Pesquisa do Estado do Rio Grande do Sul (FAPERGS) grant number 1993-2551/13-1 and Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) grant number 470228/2013-0.		60	11	11	3	17	BIOMED CENTRAL LTD	LONDON	236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND	1756-3305			PARASITE VECTOR	Parasites Vectors	Dec-09	2016	9								636	10.1186/s13071-016-1926-2				11	Parasitology; Tropical Medicine	Parasitology; Tropical Medicine	EI3DV	WOS:000392370800003	27938415	DOAJ Gold, Green Published			22-11-18
J	Toju, H; Baba, YG				Toju, Hirokazu; Baba, Yuki G.			DNA metabarcoding of spiders, insects, and springtails for exploring potential linkage between above- and below-ground food webs	ZOOLOGICAL LETTERS			English	Article						Above-and below-ground linkage; Collembola (springtails); DNA barcoding; Ecological communities; Food webs; Illumina sequencing; Insects; Networks; Molecular gut content analyses; Predator-prey interactions		Background: Understanding feedback between above-and below-ground processes of biological communities is a key to the effective management of natural and agricultural ecosystems. However, as above-and below-ground food webs are often studied separately, our knowledge of material flow and community dynamics in terrestrial ecosystems remains limited. Results: We developed a high-throughput sequencing method for examining how spiders link above-and below-ground food webs as generalist predators. To overcome problems related to DNA-barcoding-based analyses of arthropod-arthropod interactions, we designed spider-specific blocking primers and Hexapoda-specific primers for the selective PCR amplification of Hexapoda prey sequences from spider samples. By applying the new DNA metabarcoding framework to spider samples collected in a temperate secondary forest in Japan, we explored the structure of a food web involving 15 spider species and various taxonomic groups of Hexapoda prey. These results support the hypothesis that multiple spider species in a community can prey on both above-and below-ground prey species, potentially coupling above-and below-ground food-web dynamics. Conclusions: The PCR primers and metabarcoding pipeline described in this study are expected to accelerate nuclear marker-based analyses of food webs, illuminating poorly understood trophic interactions in ecosystems.	[Toju, Hirokazu] Kyoto Univ, Ctr Ecol Res, Hirano 2-509-3, Otsu, Shiga 5202113, Japan; [Toju, Hirokazu] Japan Sci & Technol Agcy, Precursory Res Embryon Sci & Technol PRESTO, Honcho 4-1-8, Kawaguchi, Saitama 3320012, Japan; [Baba, Yuki G.] NARO, Inst Agroenvironm Sci, Kannondai 3-1-3, Tsukuba, Ibaraki 3058604, Japan	Toju, H (reprint author), Kyoto Univ, Ctr Ecol Res, Hirano 2-509-3, Otsu, Shiga 5202113, Japan.; Toju, H (reprint author), Japan Sci & Technol Agcy, Precursory Res Embryon Sci & Technol PRESTO, Honcho 4-1-8, Kawaguchi, Saitama 3320012, Japan.	toju.hirokazu.4c@kyoto-u.ac.jp	Toju, Hirokazu/S-7307-2017	Toju, Hirokazu/0000-0002-3362-3285	JSPS KAKENHI Grant [26650144]; JST PRESTO [JPMJPR16Q6]	This work was financially supported by JSPS KAKENHI Grant (Nos. 26650144) and JST PRESTO (JPMJPR16Q6) to H.T.		76	0	0	15	20	BIOMED CENTRAL LTD	LONDON	236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND	2056-306X			ZOOL LETT	Zool. Lett.	Feb-15	2018	4								4	10.1186/s40851-018-0088-9				12	Zoology	Zoology	FW2MI	WOS:000425137000001	29468086	DOAJ Gold, Green Published			22-11-18
J	Belda, E; Pedrola, L; Pereto, J; Martinez-Blanch, JF; Montagud, A; Navarro, E; Urchueguia, J; Ramon, D; Moya, A; Porcar, M				Belda, Eugeni; Pedrola, Laia; Pereto, Juli; Martinez-Blanch, Juan F.; Montagud, Arnau; Navarro, Emilio; Urchueguia, Javier; Ramon, Daniel; Moya, Andres; Porcar, Manuel			Microbial Diversity in the Midguts of Field and Lab-Reared Populations of the European Corn Borer Ostrinia nubilalis	PLOS ONE			English	Article							CELLULOLYTIC BACTERIUM; GLYCOSIDE HYDROLASES; FUNCTIONAL-ANALYSIS; MULTIPLE ALIGNMENT; COMMUNITY; GUT; METAGENOMICS; RECONSTRUCTION; LEPIDOPTERA; ENVIRONMENT	Background: Insects are associated with microorganisms that contribute to the digestion and processing of nutrients. The European Corn Borer (ECB) is a moth present world-wide, causing severe economical damage as a pest on corn and other crops. In the present work, we give a detailed view of the complexity of the microorganisms forming the ECB midgut microbiota with the objective of comparing the biodiversity of the midgut-associated microbiota and explore their potential as a source of genes and enzymes with biotechnological applications. Methodological/Principal Findings: A high-throughput sequencing approach has been used to identify bacterial species, genes and metabolic pathways, particularly those involved in plant-matter degradation, in two different ECB populations (field-collected vs. lab-reared population with artificial diet). Analysis of the resulting sequences revealed the massive presence of Staphylococcus warneri and Weissella paramesenteroides in the lab-reared sample. This enabled us to reconstruct both genomes almost completely. Despite the apparently low diversity, 208 different genera were detected in the sample, although most of them at very low frequency. By contrast, the natural population exhibited an even higher taxonomic diversity along with a wider array of cellulolytic enzyme families. However, in spite of the differences in relative abundance of major taxonomic groups, not only did both metagenomes share a similar functional profile but also a similar distribution of non-redundant genes in different functional categories. Conclusions/Significance: Our results reveal a highly diverse pool of bacterial species in both O. nubilalis populations, with major differences: The lab-reared sample is rich in gram-positive species (two of which have almost fully sequenced genomes) while the field sample harbors mainly gram-negative species and has a larger set of cellulolytic enzymes. We have found a clear relationship between the diet and the midgut microbiota, which reveals the selection pressure of food on the community of intestinal bacteria.	[Belda, Eugeni; Pereto, Juli; Moya, Andres; Porcar, Manuel] Univ Valencia, Inst Cavanilles Biodiversitat & Biol Evolutiva, Valencia, Spain; [Belda, Eugeni; Montagud, Arnau; Urchueguia, Javier] Univ Politecn Valencia, Inst Univ Matemat Pura & Aplicada, E-46071 Valencia, Spain; [Pedrola, Laia; Martinez-Blanch, Juan F.; Ramon, Daniel] Lifesequencing, Valencia, Spain; [Navarro, Emilio] Univ Malaga, Dept Lenguajes & Ciencias Computac, E-29071 Malaga, Spain	Belda, E (reprint author), CEA GENOSCOPE, Lab Anal Bioinformat Genom & Metab, Evry, France.	manuel.porcar@uv.es	Navarro, Emilio/A-1420-2013; Porcar, Manuel/D-2503-2010; Montagud, Arnau/B-8001-2008; Moya, Andres/A-8190-2008; Pereto, Juli/G-5969-2015	Navarro, Emilio/0000-0002-0608-2129; Porcar, Manuel/0000-0002-7916-9479; Montagud, Arnau/0000-0002-7696-1241; Moya, Andres/0000-0002-2867-1119; Pereto, Juli/0000-0002-5756-1517; Pedrola, Laia/0000-0002-3031-6124; Urchueguia, Javier F./0000-0002-3054-3431; Belda, Eugeni/0000-0003-4307-5072	Spanish Ministerio de Ciencia e Innovacion [CIT-010000-2008-5]; MICINN (Ministerio de Ciencia e Innovacion) [TIN2009-12359]; Generalitat Valenciana grant [BFPI/2007/283]	The research was funded by the Spanish Ministerio de Ciencia e Innovacion, under grant agreement CIT-010000-2008-5 and by a MICINN (Ministerio de Ciencia e Innovacion) TIN2009-12359 ArtBioCom project. Arnau Montagud acknowledges Generalitat Valenciana grant BFPI/2007/283. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.		44	26	27	1	25	PUBLIC LIBRARY SCIENCE	SAN FRANCISCO	1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA	1932-6203			PLOS ONE	PLoS One	Jun-30	2011	6	6							e21751	10.1371/journal.pone.0021751				14	Multidisciplinary Sciences	Science & Technology - Other Topics	786GP	WOS:000292291800039	21738787	DOAJ Gold, Green Published			22-11-18
J	Ventura, T; Manor, R; Aflalo, ED; Chalifa-Caspi, V; Weil, S; Sharabi, O; Sagi, A				Ventura, Tomer; Manor, Rivka; Aflalo, Eliahu D.; Chalifa-Caspi, Vered; Weil, Simy; Sharabi, Omri; Sagi, Amir			Post-Embryonic Transcriptomes of the Prawn Macrobrachium rosenbergii: Multigenic Succession through Metamorphosis	PLOS ONE			English	Article							METHYL FARNESOATE; LIFE-CYCLE; MICROARRAY ANALYSIS; GENE-EXPRESSION; HEDGEHOG; LARVAL; GENOMICS; ANNOTATION; DROSOPHILA; CRUSTACEAN	Like many metazoans, the freshwater prawn Macrobrachium rosenbergii begins its post-embryonic life with a set of morphologically distinct planktonic larval stages, followed by a benthic post-larval stage during which the maturing organism differs from the larvae both ecologically and physiologically. Understanding of the molecular basis underlying morphogenesis in crustaceans is limited to the observation that methyl farnesoate, the non-epoxidated form of the insect juvenile hormone, acts as the active crustacean juvenoid. Molt steroids were also linked to morphogenesis and several other molecular pathways, such as Hedgehog and Wnt, are known to underlie morphogenesis in all metazoans examined and, as such, are thought to do the same in crustaceans. Using next generation sequencing, we deep-sequenced the transcriptomes of several larval and post-larval stages. De novo assembly, followed by bioinformatics analysis, revealed that many novel transcripts are over-expressed in either larvae-or post-larvae-stage prawn, shedding light on the molecular basis underlying M. rosenbergii metamorphosis. Fast larval molting rates and periodic morphological changes were reflected in over-expression of transcripts annotated to the cell cycle, DNA replication and morphogenic pathways (i.e., Hedgehog and Wnt). Further characterization of transcripts assigned to morphogenic pathways by real-time RT-PCR reconfirmed their over-expression in larvae, albeit with a more complex expression pattern when examined in the individual developmental stages. The expression level of an orthologue of cytochrome P450, 15A1, known to epoxidize methyl farnesoate in insects, was increased in the late larval and early post-larval stages, in accordance with the role of methyl farnesoate in crustacean metamorphosis. This study exemplifies the applicability of a high-throughput sequencing approach for studying complex traits, including metamorphosis, providing new insight into this unexplored area of crustacean research.	[Ventura, Tomer; Manor, Rivka; Aflalo, Eliahu D.; Weil, Simy; Sharabi, Omri; Sagi, Amir] Ben Gurion Univ Negev, Dept Life Sci, IL-84105 Beer Sheva, Israel; [Ventura, Tomer; Manor, Rivka; Aflalo, Eliahu D.; Chalifa-Caspi, Vered; Weil, Simy; Sharabi, Omri; Sagi, Amir] Ben Gurion Univ Negev, Natl Inst Biotechnol Negev, IL-84105 Beer Sheva, Israel	Sagi, A (reprint author), Ben Gurion Univ Negev, Dept Life Sci, IL-84105 Beer Sheva, Israel.	sagia@bgu.ac.il		Ventura, Tomer/0000-0002-0777-2367; Sagi, Amir/0000-0002-4229-1059	Tiran, Ltd. through BGNegev; National Institute for Biotechnology in the Negev (NIBN); Wolfson Family Charitable Trust	This study was funded by grants from Tiran, Ltd. through BGNegev and the National Institute for Biotechnology in the Negev (NIBN) and the Wolfson Family Charitable Trust. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.		42	24	24	0	25	PUBLIC LIBRARY SCIENCE	SAN FRANCISCO	1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA	1932-6203			PLOS ONE	PLoS One	Jan-25	2013	8	1							e55322	10.1371/journal.pone.0055322				9	Multidisciplinary Sciences	Science & Technology - Other Topics	093RV	WOS:000315210400088	23372848	DOAJ Gold, Green Published			22-11-18
J	McCarthy, CB; Santini, MS; Pimenta, PFP; Diambra, LA				McCarthy, Christina B.; Soledad Santini, Maria; Pimenta, Paulo F. P.; Diambra, Luis A.			First Comparative Transcriptomic Analysis of Wild Adult Male and Female Lutzomyia longipalpis, Vector of Visceral Leishmaniasis	PLOS ONE			English	Article							CYTOCHROME-C-OXIDASE; PROTEIN-COUPLED RECEPTORS; PERMETHRIN INDUCES OVEREXPRESSION; MOSQUITO ANOPHELES-GAMBIAE; DROSOPHILA ACTIN GENES; AEDES-AEGYPTI; PERITROPHIC MATRIX; SAND FLIES; CUTANEOUS LEISHMANIASIS; INSECTICIDE RESISTANCE	Leishmaniasis is a vector-borne disease with a complex epidemiology and ecology. Visceral leishmaniasis (VL) is its most severe clinical form as it results in death if not treated. In Latin America VL is caused by the protist parasite Leishmania infantum (syn. chagasi) and transmitted by Lutzomyia longipalpis. This phlebotomine sand fly is only found in the New World, from Mexico to Argentina. However, due to deforestation, migration and urbanisation, among others, VL in Latin America is undergoing an evident geographic expansion as well as dramatic changes in its transmission patterns. In this context, the first VL outbreak was recently reported in Argentina, which has already caused 7 deaths and 83 reported cases. Insect vector transcriptomic analyses enable the identification of molecules involved in the insect's biology and vector-parasite interaction. Previous studies on laboratory reared Lu. longipalpis have provided a descriptive repertoire of gene expression in the whole insect, midgut, salivary gland and male reproductive organs. Nevertheless, the study of wild specimens would contribute a unique insight into the development of novel bioinsecticides. Given the recent VL outbreak in Argentina and the compelling need to develop appropriate control strategies, this study focused on wild male and female Lu. longipalpis from an Argentine endemic (Posadas, Misiones) and a Brazilian non-endemic (Lapinha Cave, Minas Gerais) VL location. In this study, total RNA was extracted from the sand flies, submitted to sequence independent amplification and high-throughput pyrosequencing. This is the first time an unbiased and comprehensive transcriptomic approach has been used to analyse an infectious disease vector in its natural environment. Transcripts identified in the sand flies showed characteristic profiles which correlated with the environment of origin and with taxa previously identified in these same specimens. Among these, various genes represented putative targets for vector control via RNA interference (RNAi).	[McCarthy, Christina B.; Diambra, Luis A.] Univ Nacl La Plata, Ctr Reg Estudios Genom, Fac Ciencias Exactas, Buenos Aires, DF, Argentina; [McCarthy, Christina B.] Univ Nacl Noroeste Prov Buenos Aires, Dept Informat & Tecnol, Buenos Aires, DF, Argentina; [Soledad Santini, Maria] Minist Salud, Ctr Nacl Diagnost & Invest Endemoepidemias, Adm Nacl Labs, Buenos Aires, DF, Argentina; [Soledad Santini, Maria] Minist Salud, Inst Salud, Buenos Aires, DF, Argentina; [Pimenta, Paulo F. P.] Fundacao Oswaldo Cruz FIOCRUZ, Lab Med Entomol, Ctr Pesquisas Rene Rachou, Belo Horizonte, MG, Brazil	McCarthy, CB (reprint author), Univ Nacl La Plata, Ctr Reg Estudios Genom, Fac Ciencias Exactas, Buenos Aires, DF, Argentina.	mccarthychristina@gmail.com	Diambra, Luis/F-6319-2015	Diambra, Luis/0000-0001-8052-4880	Fundacion Bunge y Born grant [FBBEI5/08]; Agencia Nacional de Promocion Cientifica y Tecnologica (ANPCyT) [PICT PRH 112]	This research was supported by a Fundacion Bunge y Born grant (FBBEI5/08) and an Agencia Nacional de Promocion Cientifica y Tecnologica (ANPCyT) grant (PICT PRH 112) to CBM. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.		147	6	7	0	18	PUBLIC LIBRARY SCIENCE	SAN FRANCISCO	1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA	1932-6203			PLOS ONE	PLoS One	Mar-12	2013	8	3							e58645	10.1371/journal.pone.0058645				20	Multidisciplinary Sciences	Science & Technology - Other Topics	107WV	WOS:000316252500036	23554910	DOAJ Gold, Green Published			22-11-18
J	Staats, M; Erkens, RHJ; van de Vossenberg, B; Wieringa, JJ; Kraaijeveld, K; Stielow, B; Geml, J; Richardson, JE; Bakker, FT				Staats, Martijn; Erkens, Roy H. J.; van de Vossenberg, Bart; Wieringa, Jan J.; Kraaijeveld, Ken; Stielow, Benjamin; Geml, Jozsef; Richardson, James E.; Bakker, Freek T.			Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens	PLOS ONE			English	Article							ANCIENT DNA-SEQUENCES; MISCODING LESIONS; EXTRACTION; AMPLIFICATION; PATTERNS; FUNGI; PLANT; ENRICHMENT; EVOLUTION; ALIGNMENT	Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22-82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4-97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2-71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well.	[Staats, Martijn; Wieringa, Jan J.; Bakker, Freek T.] Wageningen Univ, Biosystemat Grp, NL-6700 AP Wageningen, Netherlands; [Erkens, Roy H. J.] Maastricht Univ, Maastricht Sci Program, Maastricht, Netherlands; [Erkens, Roy H. J.] Univ Utrecht, Dept Biol, Ecol & Biodivers Grp, Utrecht, Netherlands; [van de Vossenberg, Bart] Dutch Natl Plant Protect Org, Natl Reference Ctr, Wageningen, Netherlands; [Wieringa, Jan J.] Wageningen Univ, Herbarium Vadense WAG, Netherlands Ctr Biodivers Nat, Sect NHN, NL-6700 AP Wageningen, Netherlands; [Kraaijeveld, Ken] Leiden Univ, Dept Human Genet, Med Ctr, Leiden Genome Technol Ctr, NL-2300 RA Leiden, Netherlands; [Stielow, Benjamin] Cent Bur Schimmelcultures Fungal Biodivers Ctr CB, Utrecht, Netherlands; [Geml, Jozsef] Nat Biodivers Ctr, Sect Natl Herbarium Netherlands, Leiden, Netherlands; [Richardson, James E.] Royal Bot Garden Edinburgh, Edinburgh, Midlothian, Scotland; [Richardson, James E.] Univ Los Andes, Lab Bot & Sistemat, Bogota, Colombia	Bakker, FT (reprint author), Wageningen Univ, Biosystemat Grp, NL-6700 AP Wageningen, Netherlands.	freek.bakker@wur.nl	Geml, Jozsef/C-2223-2018; Erkens, Roy/B-9961-2008; Wieringa, Jan/D-9517-2015; Richardson, James-Edward/L-2768-2016	Geml, Jozsef/0000-0001-8745-0423; Erkens, Roy/0000-0002-1093-0370; Wieringa, Jan/0000-0003-0566-372X; Richardson, James-Edward/0000-0001-9014-4865; van de Vossenberg, Bart T.L.H./0000-0003-1205-6119	European Community Research Infrastructures program [226506-CP-CSA-Infra]; Innovational Research Incentives Scheme (VENI) (NWO-ALW, The Netherlands) [863.09.017]	The work was funded by the European Community Research Infrastructures program under FP7 call 'Synthesis of Systematic Resources', grant number 226506-CP-CSA-Infra. RHJE was supported via the Innovational Research Incentives Scheme (VENI, nr. 863.09.017; NWO-ALW, The Netherlands). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.		49	60	65	0	86	PUBLIC LIBRARY SCIENCE	SAN FRANCISCO	1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA	1932-6203			PLOS ONE	PLoS One	Jul-29	2013	8	7							e69189	10.1371/journal.pone.0069189				11	Multidisciplinary Sciences	Science & Technology - Other Topics	204MP	WOS:000323369700021	23922691	DOAJ Gold, Green Published			22-11-18
J	Estes, AM; Hearn, DJ; Snell-Rood, EC; Feindler, M; Feeser, K; Abebe, T; Hotopp, JCD; Moczek, AP				Estes, Anne M.; Hearn, David J.; Snell-Rood, Emilie C.; Feindler, Michele; Feeser, Karla; Abebe, Tselotie; Hotopp, Julie C. Dunning; Moczek, Armin P.			Brood Ball-Mediated Transmission of Microbiome Members in the Dung Beetle, Onthophagus taurus (Coleoptera: Scarabaeidae)	PLOS ONE			English	Article							16S RIBOSOMAL-RNA; DEVELOPMENTAL-STAGES; LARVAE COLEOPTERA; HIGH-THROUGHPUT; PLANT LITTER; BACTERIA; GUT; ENDOSYMBIONTS; IDENTIFICATION; SYMBIONTS	Insects feeding on plant sap, blood, and other nutritionally incomplete diets are typically associated with mutualistic bacteria that supplement missing nutrients. Herbivorous mammal dung contains more than 86% cellulose and lacks amino acids essential for insect development and reproduction. Yet one of the most ecologically necessary and evolutionarily successful groups of beetles, the dung beetles (Scarabaeinae) feeds primarily, or exclusively, on dung. These associations suggest that dung beetles may benefit from mutualistic bacteria that provide nutrients missing from dung. The nesting behaviors of the female parent and the feeding behaviors of the larvae suggest that a microbiome could be vertically transmitted from the parental female to her offspring through the brood ball. Using sterile rearing and a combination of molecular and culture-based techniques, we examine transmission of the microbiome in the bull-headed dung beetle, Onthophagus taurus. Beetles were reared on autoclaved dung and the microbiome was characterized across development. A similar to 1425 bp region of the 16S rRNA identified Pseudomonadaceae, Enterobacteriaceae, and Comamonadaceae as the most common bacterial families across all life stages and populations, including cultured isolates from the 3rd instar digestive system. Finer level phylotyping analyses based on lepA and gyrB amplicons of cultured isolates placed the isolates closest to Enterobacter cloacae, Providencia stuartii, Pusillimonas sp., Pedobacter heparinus, and Lysinibacillus sphaericus. Scanning electron micrographs of brood balls constructed from sterile dung reveals secretions and microbes only in the chamber the female prepares for the egg. The use of autoclaved dung for rearing, the presence of microbes in the brood ball and offspring, and identical 16S rRNA sequences in both parent and offspring suggests that the O. taurus female parent transmits specific microbiome members to her offspring through the brood chamber. The transmission of the dung beetle microbiome highlights the maintenance and likely importance of this newly-characterized bacterial community.	[Estes, Anne M.; Hearn, David J.; Feindler, Michele; Feeser, Karla; Abebe, Tselotie] Towson Univ, Dept Biol Sci, Baltimore, MD USA; [Estes, Anne M.; Hotopp, Julie C. Dunning] Univ Maryland, Sch Med, Inst Genome Sci, Baltimore, MD 21201 USA; [Snell-Rood, Emilie C.; Moczek, Armin P.] Indiana Univ, Dept Biol, Bloomington, IN USA; [Hotopp, Julie C. Dunning] Univ Maryland, Sch Med, Dept Microbiol & Immunol, Baltimore, MD 21201 USA; [Hearn, David J.] J Craig Venter Inst Inc, Plant Genom, Rockville, MD USA	Estes, AM (reprint author), Towson Univ, Dept Biol Sci, Baltimore, MD USA.	anneestes@gmail.com		Estes, Anne/0000-0002-8775-2656; Feeser, Karla/0000-0003-0030-9449	Towson University Fisher College; Towson University; Orchid Society of Arizona; NSF REU [DBI0552654]; NSF IOS [0445661, 0718522]; State of Maryland	This research was supported in part through funds from: the Towson University Fisher College Undergraduate Research Awards (KF, TA), a Towson University Undergraduate Research Award (KF), Orchid Society of Arizona funding (AME), NSF REU DBI0552654 (MF), NSF IOS 0445661 (AM), NSF IOS 0718522 (AM), and State of Maryland internal funds (JDH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.		77	21	22	3	62	PUBLIC LIBRARY SCIENCE	SAN FRANCISCO	1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA	1932-6203			PLOS ONE	PLoS One	Nov-01	2013	8	11							UNSP e79061	10.1371/journal.pone.0079061				15	Multidisciplinary Sciences	Science & Technology - Other Topics	245XZ	WOS:000326499300050	24223880	DOAJ Gold, Green Published			22-11-18
J	Tin, MMY; Economo, EP; Mikheyev, AS				Tin, Mandy Man-Ying; Economo, Evan Philip; Mikheyev, Alexander Sergeyevich			Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics	PLOS ONE			English	Article							SINGLE-STRANDED-DNA; HAWAIIAN DROSOPHILA; DRAFT GENOME; EXTRACTION; DISCOVERY; ANCIENT; COLLECTIONS; MARKERS; DAMAGE; COST	Ancient and archival DNA samples are valuable resources for the study of diverse historical processes. In particular, museum specimens provide access to biotas distant in time and space, and can provide insights into ecological and evolutionary changes over time. However, archival specimens are difficult to handle; they are often fragile and irreplaceable, and typically contain only short segments of denatured DNA. Here we present a set of tools for processing such samples for state-of-the-art genetic analysis. First, we report a protocol for minimally destructive DNA extraction of insect museum specimens, which produced sequenceable DNA from all of the samples assayed. The 11 specimens analyzed had fragmented DNA, rarely exceeding 100 bp in length, and could not be amplified by conventional PCR targeting the mitochondrial cytochrome oxidase I gene. Our approach made these samples amenable to analysis with commonly used next-generation sequencing-based molecular analytic tools, including RAD-tagging and shotgun genome re-sequencing. First, we used museum ant specimens from three species, each with its own reference genome, for RAD-tag mapping. Were able to use the degraded DNA sequences, which were sequenced in full, to identify duplicate reads and filter them prior to base calling. Second, we re-sequenced six Hawaiian Drosophila species, with millions of years of divergence, but with only a single available reference genome. Despite a shallow coverage of 0.37 +/- 0.42 per base, we could recover a sufficient number of overlapping SNPs to fully resolve the species tree, which was consistent with earlier karyotypic studies, and previous molecular studies, at least in the regions of the tree that these studies could resolve. Although developed for use with degraded DNA, all of these techniques are readily applicable to more recent tissue, and are suitable for liquid handling automation.	[Tin, Mandy Man-Ying; Economo, Evan Philip; Mikheyev, Alexander Sergeyevich] Okinawa Inst Sci & Technol, Onna Son, Okinawa, Japan	Mikheyev, AS (reprint author), Okinawa Inst Sci & Technol, Onna Son, Okinawa, Japan.	sasha@homologo.us	Mikheyev, Alexander/O-7670-2014	Mikheyev, Alexander/0000-0003-4369-1019	Okinawa Institute of Science and Technology; Japan Society for the Promotion of Science [13058556]	This study was funded by the Okinawa Institute of Science and Technology, and a Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research # 13058556 to ASM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.		45	44	46	1	88	PUBLIC LIBRARY SCIENCE	SAN FRANCISCO	1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA	1932-6203			PLOS ONE	PLoS One	May-14	2014	9	5							e96793	10.1371/journal.pone.0096793				9	Multidisciplinary Sciences	Science & Technology - Other Topics	AI4TJ	WOS:000336857400037	24828244	DOAJ Gold, Green Published			22-11-18
J	You, L; Simmons, DR; Bateman, CC; Short, DPG; Kasson, MT; Rabaglia, RJ; Hulcr, J				You, Li; Simmons, David Rabern; Bateman, Craig C.; Short, Dylan P. G.; Kasson, Matthew T.; Rabaglia, Robert J.; Hulcr, Jiri			New Fungus-Insect Symbiosis: Culturing, Molecular, and Histological Methods Determine Saprophytic Polyporales Mutualists of Ambrosiodmus Ambrosia Beetles	PLOS ONE			English	Article							RIBOSOMAL DNA; COLEOPTERA; SCOLYTIDAE; EVOLUTION; IDENTIFICATION; AGRICULTURE; EUWALLACEA; DIVERSITY	Ambrosia symbiosis is an obligate, farming-like mutualism between wood-boring beetles and fungi. It evolved at least 11 times and includes many notorious invasive pests. All ambrosia beetles studied to date cultivate ascomycotan fungi: early colonizers of recently killed trees with poor wood digestion. Beetles in the widespread genus Ambrosiodmus, however, colonize decayed wood. We characterized the mycosymbionts of three Ambrosiodmus species using quantitative culturing, high-throughput metabarcoding, and histology. We determined the fungi to be within the Polyporales, closely related to Flavodon flavus. Culture-independent sequencing of Ambrosiodmus minor mycangia revealed a single operational taxonomic unit identical to the sequences from the cultured Flavodon. Histological sectioning confirmed that Ambrosiodmus possessed preoral mycangia containing dimitic hyphae similar to cultured F. cf. flavus. The Ambrosiodmus-Flavodon symbiosis is unique in several aspects: it is the first reported association between an ambrosia beetle and a basidiomycotan fungus; the mycosymbiont grows as hyphae in the mycangia, not as budding pseudo-mycelium; and the mycosymbiont is a white-rot saprophyte rather than an early colonizer: a previously undocumented wood borer niche. Few fungi are capable of turning rotten wood into complete animal nutrition. Several thousand beetle-fungus symbioses remain unstudied and promise unknown and unexpected mycological diversity and enzymatic innovations.	[You, Li; Simmons, David Rabern; Hulcr, Jiri] Univ Florida, Inst Food & Agr Sci, Sch Forest Resources & Conservat, Gainesville, FL 32611 USA; [Bateman, Craig C.; Hulcr, Jiri] Univ Florida, Inst Food & Agr Sci, Dept Entomol & Nematol, Gainesville, FL 32611 USA; [Short, Dylan P. G.; Kasson, Matthew T.] W Virginia Univ, Div Plant & Soil Sci, Morgantown, WV 26506 USA; [Rabaglia, Robert J.] ARS, Forest Hlth Protect State & Private Forestry, USDA, Washington, DC USA	Hulcr, J (reprint author), Univ Florida, Inst Food & Agr Sci, Sch Forest Resources & Conservat, Gainesville, FL 32611 USA.	hulcr@ufl.edu			USDA-FS-SRS [14-CA-11330130-032]; USDA-FS-FHP [12-CA-11420004-042]; USDA [14-8130-0377-CA]; NSF [DEB 1256968]; West Virginia Agricultural Experiment Station; University of Florida Opportunity Seed fund	This research was funded by USDA-FS-SRS Coop agreement 14-CA-11330130-032, USDA-FS-FHP Coop agreement 12-CA-11420004-042, USDA Farm Bill agreement 14-8130-0377-CA, NSF DEB 1256968, the West Virginia Agricultural Experiment Station, and a University of Florida Opportunity Seed fund.		49	3	4	0	73	PUBLIC LIBRARY SCIENCE	SAN FRANCISCO	1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA	1932-6203			PLOS ONE	PLoS One	Sep-14	2015	10	9							e0137689	10.1371/journal.pone.0137689				13	Multidisciplinary Sciences	Science & Technology - Other Topics	CR8KS	WOS:000361601100109	26367271	DOAJ Gold, Green Published			22-11-18
J	Kanda, K; Pflug, JM; Sproul, JS; Dasenko, MA; Maddison, DR				Kanda, Kojun; Pflug, James M.; Sproul, John S.; Dasenko, Mark A.; Maddison, David R.			Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing	PLOS ONE			English	Article							ANCIENT DNA; TARGETED ENRICHMENT; BEMBIDION LATREILLE; NEANDERTHAL GENOME; PLEISTOCENE HORSE; COLEOPTERA; SPECIMENS; CARABIDAE; PRESERVATION; EVOLUTION	In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced.	[Kanda, Kojun; Pflug, James M.; Sproul, John S.; Maddison, David R.] Oregon State Univ, Dept Integrat Biol, Corvallis, OR 97331 USA; [Dasenko, Mark A.] Oregon State Univ, Ctr Genome Res & Biocomp, Corvallis, OR 97331 USA	Kanda, K (reprint author), Oregon State Univ, Dept Integrat Biol, Corvallis, OR 97331 USA.	coniontis@gmail.com			Harold E. and Leona M. Rice Endowment Fund at Oregon State University; National Science Foundation [DEB-1258220]	This work was funded in part by the Harold E. and Leona M. Rice Endowment Fund at Oregon State University, as well as National Science Foundation grant DEB-1258220 to DRM.		95	15	16	4	25	PUBLIC LIBRARY SCIENCE	SAN FRANCISCO	1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA	1932-6203			PLOS ONE	PLoS One	Dec-30	2015	10	12							e0143929	10.1371/journal.pone.0143929				53	Multidisciplinary Sciences	Science & Technology - Other Topics	DA0TN	WOS:000367510500008	26716693	DOAJ Gold, Green Published			22-11-18
J	Berlanga, M; Llorens, C; Comas, J; Guerrero, R				Berlanga, Mercedes; Llorens, Carlos; Comas, Jaume; Guerrero, Ricardo			Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana	PLOS ONE			English	Article							WOOD-FEEDING COCKROACHES; H-2 PLUS CO2; TERMITE-GUT; PERIPLANETA-AMERICANA; MICROBIAL COMMUNITY; ATLANTIC FOREST; DIVERSITY; DICTYOPTERA; PHYLOGENY; PROTISTS	Cryptocercus punctulatus and Parasphaeria boleiriana are two distantly related xylophagous and subsocial cockroaches. Cryptocercus is related to termites. Xylophagous cockroaches and termites are excellent model organisms for studying the symbiotic relationship between the insect and their microbiota. In this study, high-throughput 454 pyrosequencing of 16S rRNA was used to investigate the diversity of metagenomic gut communities of C. punctulatus and P. boleiriana, and thereby to identify possible shifts in symbiont allegiances during cockroaches evolution. Our results revealed that the hindgut prokaryotic communities of both xylophagous cockroaches are dominated by members of four Bacteria phyla: Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Other identified phyla were Spirochaetes, Planctomycetes, candidatus Saccharibacteria (formerly TM7), and Acidobacteria, each of which represented 1-2% of the total population detected. Community similarity based on phylogenetic relatedness by unweighted UniFrac analyses indicated that the composition of the bacterial community in the two species was significantly different (P < 0.05). Phylogenetic analysis based on the characterized clusters of Bacteroidetes, Spirochaetes, and Deltaproteobacteria showed that many OTUs present in both cockroach species clustered with sequences previously described in termites and other cockroaches, but not with those from other animals or environments. These results suggest that, during their evolution, those cockroaches conserved several bacterial communities from the microbiota of a common ancestor. The ecological stability of those microbial communities may imply the important functional role for the survival of the host of providing nutrients in appropriate quantities and balance.	[Berlanga, Mercedes] Univ Barcelona, Fac Pharm, Dept Microbiol & Parasitol, Barcelona, Spain; [Llorens, Carlos; Comas, Jaume] Univ Barcelona CCiTUB, Unity Genom, Sci Ctr, Barcelona, Spain; [Llorens, Carlos; Comas, Jaume] Univ Barcelona CCiTUB, Unity Genom, Technol Ctr, Barcelona, Spain; [Llorens, Carlos] Biotechvana, Valencia, Spain; [Guerrero, Ricardo] Univ Barcelona, Fac Med, Lab Mol Microbiol & Antimicrobials, Dept Pathol & Expt Therapeut,IDIBELL, Barcelona 7, Spain; [Guerrero, Ricardo] Acad Europaea, Barcelona Knowledge Hub, Barcelona, Spain	Berlanga, M (reprint author), Univ Barcelona, Fac Pharm, Dept Microbiol & Parasitol, Barcelona, Spain.	mberlanga@ub.edu		Berlanga, Mercedes/0000-0002-7305-7046; Guerrero, Ricardo/0000-0001-5019-9933	Spanish Ministry of Science and Technology [CGL2009-08922]; Biotechvana	This study was funded by CGL2009-08922 (Spanish Ministry of Science and Technology) to Ricardo Guerrero. Author Carlos Llorens is employed by Biotechvana during the study. Biotechvana provided support in the form of salary for author CL, but did not provide specific funding for this study and did not have any additional role in the study design, data collection, decision to publish, or preparation of the manuscript. This specific role of this author is articulated in the 'author contributions' section.		66	3	3	4	31	PUBLIC LIBRARY SCIENCE	SAN FRANCISCO	1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA	1932-6203			PLOS ONE	PLoS One	Apr-07	2016	11	4							e0152400	10.1371/journal.pone.0152400				16	Multidisciplinary Sciences	Science & Technology - Other Topics	DI6KO	WOS:000373608000019	27054320	DOAJ Gold, Green Published			22-11-18
J	Blaimer, BB; Lloyd, MW; Guillory, WX; Brady, SG				Blaimer, Bonnie B.; Lloyd, Michael W.; Guillory, Wilson X.; Brady, Sean G.			Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens	PLOS ONE			English	Article							LARGE CARPENTER BEES; GENUS XYLOCOPA HYMENOPTERA; MUSEUM SPECIMENS; MOLECULAR PHYLOGENY; DNA BARCODES; ANCIENT DNA; COLLECTIONS; APIDAE; PRESERVATION; BIOGEOGRAPHY	Obtaining sequence data from historical museum specimens has been a growing research interest, invigorated by next-generation sequencing methods that allow inputs of highly degraded DNA. We applied a target enrichment and next-generation sequencing protocol to generate ultraconserved elements (UCEs) from 51 large carpenter bee specimens (genus Xylocopa), representing 25 species with specimen ages ranging from 2-121 years. We measured the correlation between specimen age and DNA yield (pre- and post-library preparation DNA concentration) and several UCE sequence capture statistics (raw read count, UCE reads on target, UCE mean contig length and UCE locus count) with linear regression models. We performed piecewise regression to test for specific breakpoints in the relationship of specimen age and DNA yield and sequence capture variables. Additionally, we compared UCE data from newer and older specimens of the same species and reconstructed their phylogeny in order to confirm the validity of our data. We recovered 6-972 UCE loci from samples with pre-library DNA concentrations ranging from 0.06-9.8 ng/mu L. All investigated DNA yield and sequence capture variables were significantly but only moderately negatively correlated with specimen age. Specimens of age 20 years or less had significantly higher pre- and post-library concentrations, UCE contig lengths, and locus counts compared to specimens older than 20 years. We found breakpoints in our data indicating a decrease of the initial detrimental effect of specimen age on pre- and post-library DNA concentration and UCE contig length starting around 21-39 years after preservation. Our phylogenetic results confirmed the integrity of our data, giving preliminary insights into relationships within Xylocopa. We consider the effect of additional factors not measured in this study on our age-related sequence capture results, such as DNA fragmentation and preservation method, and discuss the promise of the UCE approach for large-scale projects in insect phylogenomics using museum specimens.	[Blaimer, Bonnie B.; Lloyd, Michael W.; Brady, Sean G.] Smithsonian Inst, Natl Museum Nat Hist, Dept Entomol, Washington, DC 20560 USA; [Guillory, Wilson X.] Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA	Blaimer, BB (reprint author), Smithsonian Inst, Natl Museum Nat Hist, Dept Entomol, Washington, DC 20560 USA.	bonnieblaimer@gmail.com	Lloyd, Michael/C-8430-2017	Lloyd, Michael/0000-0003-1021-8129	Smithsonian Institution Competitive Grants Program for Science; Smithsonian Global Genome Initiative; NHRE - NSF-REU program [EAR-1062692]	Funding for this study was provided by the Smithsonian Institution Competitive Grants Program for Science and a Smithsonian Global Genome Initiative (www.ggi.si.edu) grant (to SGB). WXG was supported by an NHRE summer research internship for undergraduates funded by the NSF-REU program (grant number EAR-1062692, awarded to Elizabeth Cottrell and Gene Hunt). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.		54	22	22	1	20	PUBLIC LIBRARY SCIENCE	SAN FRANCISCO	1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA	1932-6203			PLOS ONE	PLoS One	Aug-24	2016	11	8							e0161531	10.1371/journal.pone.0161531				20	Multidisciplinary Sciences	Science & Technology - Other Topics	DU5NI	WOS:000382258100049	27556533	DOAJ Gold, Green Published			22-11-18
J	Sigut, M; Kostovcik, M; Sigutova, H; Hulcr, J; Drozd, P; Hrcek, J				Sigut, Martin; Kostovcik, Martin; Sigutova, Hana; Hulcr, Jiri; Drozd, Pavel; Hrcek, Jan			Performance of DNA metabarcoding, standard barcoding, and morphological approach in the identification of host-parasitoid interactions	PLOS ONE			English	Article							TAXONOMIC CLASSIFICATION; BIODIVERSITY ASSESSMENT; NATURAL-HISTORY; FOOD WEBS; DIVERSITY; COMMUNITY; SYMBIONTS; PITFALLS; PRIMERS; PLANTS	Understanding interactions between herbivores and parasitoids is essential for successful biodiversity protection and monitoring and for biological pest control. Morphological identifications employ insect rearing and are complicated by insects' high diversity and crypsis. DNA barcoding has been successfully used in studies of host-parasitoid interactions as it can substantially increase the recovered real host-parasitoid diversity distorted by overlooked species complexes, or by species with slight morphological differences. However, this approach does not allow the simultaneous detection and identification of host(s) and parasitoid(s). Recently, high-throughput sequencing has shown high potential for surveying ecological communities and trophic interactions. Using mock samples comprising insect larvae and their parasitoids, we tested the potential of DNA metabarcoding for identifying individuals involved in host-parasitoid interactions to different taxonomic levels, and compared it to standard DNA barcoding and morphological approaches. For DNA metabarcoding, we targeted the standard barcoding marker cytochrome oxidase subunit I using highly degenerate primers, 2*300 bp sequencing on a MiSeq platform, and RTAX classification using paired-end reads. Additionally, using a large host-parasitoid dataset from a Central European floodplain forest, we assess the completeness and usability of a local reference library by confronting the number of Barcoding Index Numbers obtained by standard barcoding with the number of morphotypes. Overall, metabarcoding recovery was high, identifying 92.8% of the taxa present in mock samples, and identification success within individual taxonomic levels did not significantly differ among metabarcoding, standard barcoding, and morphology. Based on the current local reference library, 39.4% parasitoid and 90.7% host taxa were identified to the species level. DNA barcoding estimated higher parasitoid diversity than morphotyping, especially in groups with high level of crypsis. This study suggests the potential of metabarcoding for effectively recovering host-parasitoid diversity, together with more accurate identifications obtained from building reliable and comprehensive reference libraries, especially for parasitoids.	[Sigut, Martin; Sigutova, Hana; Drozd, Pavel] Univ Ostrava, Inst Environm Technol, Dept Biol & Ecol, Ostrava, Czech Republic; [Kostovcik, Martin] Charles Univ Prague, Dept Genet & Microbiol, Prague, Czech Republic; [Kostovcik, Martin] Acad Sci Czech Republ, Inst Microbiol, BIOCEV, Vestec, Czech Republic; [Hulcr, Jiri] Univ Florida IFAS, Sch Forest Resources & Conservat, Gainesville, FL USA; [Hulcr, Jiri] Univ Florida IFAS, Dept Entomol & Nematol, Gainesville, FL USA; [Hrcek, Jan] Czech Acad Sci, Biol Ctr, Inst Entomol, Ceske Budejovice, Czech Republic	Sigutova, H; Drozd, P (reprint author), Univ Ostrava, Inst Environm Technol, Dept Biol & Ecol, Ostrava, Czech Republic.	sigutova.hanka@gmail.com; pavel.drozd@osu.cz	Drozd, Pavel/J-3943-2013; Hrcek, Jan/D-7335-2015	Drozd, Pavel/0000-0002-4602-8856; Hrcek, Jan/0000-0003-0711-6447	European Regional Development Fund BIOCEV [CZ.1.05/1.1.00/02.0109]; Ministry of Education, Youth and Sports of the Czech Republic [L01208]; Institute of Environmental Technologies [CZ.1.05/ 2.1.00/03.0100]; Czech Science Foundation [GA14-04258S, P506/11/2302]; NextGenProject [CZ.1.07/2.3120.0303]; Grant Agency of University of Ostrava [SGS28/PrF/2014, SGS20/PrF/2015]	This work was supported by the European Regional Development Fund BIOCEV (CZ.1.05/1.1.00/02.0109) (MK), http://www.biocev.eu/en/; Ministry of Education, Youth and Sports of the Czech Republic (L01208) (MS, PD), http://www.msmt.cz/?lang=2; Institute of Environmental Technologies (CZ.1.05/ 2.1.00/03.0100) MS PD); Czech Science Foundation (GA14-04258S; P506/11/2302) PD), https.//gacr.cz/eni; NextGenProject (CZ.1.07/2.3120.0303) (MS), http://nextgen.ivb.cz/; Grant Agency of University of Ostrava (No. SGS28/PrF/2014 and SGS20/PrF/2015) (MS), http://www.osu.eu/, and Institute of Environmental Technologies (CZ.1.05/ 2.1.00/03.0100) (HS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.		70	0	0	4	10	PUBLIC LIBRARY SCIENCE	SAN FRANCISCO	1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA	1932-6203			PLOS ONE	PLoS One	Dec-13	2017	12	12							e0187803	10.1371/journal.pone.0187803				18	Multidisciplinary Sciences	Science & Technology - Other Topics	FP8HS	WOS:000417884100007	29236697	DOAJ Gold, Green Published			22-11-18
J	Bridgeman, B; Morgan-Richards, M; Wheeler, D; Trewick, SA				Bridgeman, Benjamin; Morgan-Richards, Mary; Wheeler, David; Trewick, Steven A.			First detection of Wolbachia in the New Zealand biota	PLOS ONE			English	Article							CYTOPLASMIC INCOMPATIBILITY; HORIZONTAL TRANSMISSION; GENE-SEQUENCES; DIVERSITY; INSECTS; INFECTION; PHYLOGENY; EVOLUTION; ENDOSYMBIONT; POPULATIONS	Wolbachia is one of the most widespread intracellular bacteria on earth, estimated to infect between 40 and 66% of arthropod species in most ecosystems that have been surveyed. Their significance rests not only in their vast distribution, but also in their ability to modify the reproductive biology of their hosts, which can ultimately affect genetic diversity and speciation of infected populations. Wolbachia has yet to be formally identified in the fauna of New Zealand which has high levels of endemic biodiversity and this represents a gap in our understanding of the global biology of Wolbachia. Using High Throughput Sequencing (HTS) of host DNA in conjunction with traditional molecular techniques we identified six endemic Orthoptera species that were positive for Wolbachia infection. In addition, short-sequence amplification with Wolbachia specific primers applied to New Zealand and introduced invertebrates detected a further 153 individuals positive for Wolbachia. From these short-range DNA amplification products sequence data was obtained for the ftsZ gene region from 86 individuals representing 10 host species. Phylogenetic analysis using the sequences obtained in this study reveals that there are two distinct Wolbachia bacteria lineages in New Zealand hosts belonging to recognised Wolbachia supergroups (A and B). These represent the first described instances of Wolbachia in the New Zealand native fauna, including detection in putative parasitoids of infected Orthoptera suggesting a possible transmission path. Our detection of Wolbachia infections of New Zealand species provides the opportunity to study local transmission of Wolbachia and explore their role in the evolution of New Zealand invertebrates.	[Bridgeman, Benjamin; Morgan-Richards, Mary; Trewick, Steven A.] Massey Univ, Coll Sci, Ecol Grp, Palmerston North, New Zealand; [Wheeler, David] Massey Univ, Inst Fundamental Sci, Palmerston North, New Zealand	Bridgeman, B (reprint author), Massey Univ, Coll Sci, Ecol Grp, Palmerston North, New Zealand.	b.bridgeman@outlook.com		Bridgeman, Benjamin/0000-0003-1620-5927	National Science Foundation [SBE-1338614, SBE-1338626]; NZ Department of Conservation; Royal Society of New Zealand Te Aparangi Marsden Fund grant [MAU1201]; Department of Conservation Taxonomic Units Fund [4076]; Massey University Research Fund	This research was supported by the National Science Foundation, Grant Nos. SBE-1338614 and SBE-1338626.; Briar Taylor-Smith provided DNA extractions of many Hemiandrus specimens. HTS datasets were generated as part of other studies supported by TIFBIS funding from the NZ Department of Conservation; Royal Society of New Zealand Te Aparangi Marsden Fund grant (MAU1201), Department of Conservation Taxonomic Units Fund (contract 4076), Massey University Research Fund ("What limits a weta?" to MMR). We thank John Early, Auckland War Memorial Museum for providing specimens of Archaeoteleia. This paper was improved by comments from two anonymous reviewers.		60	1	1	6	6	PUBLIC LIBRARY SCIENCE	SAN FRANCISCO	1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA	1932-6203			PLOS ONE	PLoS One	Apr-25	2018	13	4							e0195517	10.1371/journal.pone.0195517				16	Multidisciplinary Sciences	Science & Technology - Other Topics	GD8ZI	WOS:000430802400033	29694414	DOAJ Gold			22-11-18
J	Kikuchi, T; Cotton, JA; Dalzell, JJ; Hasegawa, K; Kanzaki, N; McVeigh, P; Takanashi, T; Tsai, IJ; Assefa, SA; Cock, PJA; Otto, TD; Hunt, M; Reid, AJ; Sanchez-Flores, A; Tsuchihara, K; Yokoi, T; Larsson, MC; Miwa, J; Maule, AG; Sahashi, N; Jones, JT; Berriman, M				Kikuchi, Taisei; Cotton, James A.; Dalzell, Jonathan J.; Hasegawa, Koichi; Kanzaki, Natsumi; McVeigh, Paul; Takanashi, Takuma; Tsai, Isheng J.; Assefa, Samuel A.; Cock, Peter J. A.; Otto, Thomas Dan; Hunt, Martin; Reid, Adam J.; Sanchez-Flores, Alejandro; Tsuchihara, Kazuko; Yokoi, Toshiro; Larsson, Mattias C.; Miwa, Johji; Maule, Aaron G.; Sahashi, Norio; Jones, John T.; Berriman, Matthew			Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus	PLOS PATHOGENS			English	Article							PINE WOOD NEMATODE; HORIZONTAL GENE-TRANSFER; CAENORHABDITIS-ELEGANS; PHYLUM NEMATODA; MELOIDOGYNE-INCOGNITA; HETERODERA-GLYCINES; PHYLOGENETIC TREE; ESOPHAGEAL GLAND; HIGH-THROUGHPUT; WILT DISEASE	Bursaphelenchus xylophilus is the nematode responsible for a devastating epidemic of pine wilt disease in Asia and Europe, and represents a recent, independent origin of plant parasitism in nematodes, ecologically and taxonomically distinct from other nematodes for which genomic data is available. As well as being an important pathogen, the B. xylophilus genome thus provides a unique opportunity to study the evolution and mechanism of plant parasitism. Here, we present a high-quality draft genome sequence from an inbred line of B. xylophilus, and use this to investigate the biological basis of its complex ecology which combines fungal feeding, plant parasitic and insect-associated stages. We focus particularly on putative parasitism genes as well as those linked to other key biological processes and demonstrate that B. xylophilus is well endowed with RNA interference effectors, peptidergic neurotransmitters (including the first description of ins genes in a parasite) stress response and developmental genes and has a contracted set of chemosensory receptors. B. xylophilus has the largest number of digestive proteases known for any nematode and displays expanded families of lysosome pathway genes, ABC transporters and cytochrome P450 pathway genes. This expansion in digestive and detoxification proteins may reflect the unusual diversity in foods it exploits and environments it encounters during its life cycle. In addition, B. xylophilus possesses a unique complement of plant cell wall modifying proteins acquired by horizontal gene transfer, underscoring the impact of this process on the evolution of plant parasitism by nematodes. Together with the lack of proteins homologous to effectors from other plant parasitic nematodes, this confirms the distinctive molecular basis of plant parasitism in the Bursaphelenchus lineage. The genome sequence of B. xylophilus adds to the diversity of genomic data for nematodes, and will be an important resource in understanding the biology of this unusual parasite.	[Kikuchi, Taisei; Kanzaki, Natsumi; Takanashi, Takuma; Yokoi, Toshiro; Sahashi, Norio] Forestry & Forest Prod Res Inst, Tsukuba, Ibaraki 305, Japan; [Kikuchi, Taisei; Cotton, James A.; Tsai, Isheng J.; Assefa, Samuel A.; Otto, Thomas Dan; Hunt, Martin; Reid, Adam J.; Sanchez-Flores, Alejandro; Berriman, Matthew] Wellcome Trust Sanger Inst, Hinxton, England; [Dalzell, Jonathan J.; McVeigh, Paul; Maule, Aaron G.] Queens Univ Belfast, Ctr Med Biol, Inst Agri Food & Land Use, Sch Biol Sci, Belfast BT9 7BL, Antrim, North Ireland; [Hasegawa, Koichi; Miwa, Johji] Chubu Univ, Coll Biosci & Biotechnol, Kasugai, Aichi 487, Japan; [Takanashi, Takuma; Tsuchihara, Kazuko; Larsson, Mattias C.; Jones, John T.] Doshisha Univ, Neurosensing & Bionav Res Ctr, Kyoto 602, Japan; [Cock, Peter J. A.] James Hutton Inst, Plant Pathol Programme, Invergowrie, Scotland; [Larsson, Mattias C.] Swedish Univ Agr Sci, Dept Plant Protect Biol, Div Chem Ecol, Alnarp, Sweden	Kikuchi, T (reprint author), Forestry & Forest Prod Res Inst, Tsukuba, Ibaraki 305, Japan.	kikuchit@affrc.go.jp	Cock, Peter/D-8730-2013; Tsai, Isheng/H-6606-2014; Larsson, Mattias/E-4791-2014; Berriman, Matthew/A-7618-2011; Cotton, James/B-8806-2008; Sanchez-Flores, Alejandro/L-9454-2016	Cock, Peter/0000-0001-9513-9993; Berriman, Matthew/0000-0002-9581-0377; Cotton, James/0000-0001-5475-3583; Sanchez-Flores, Alejandro/0000-0003-0476-3139; Otto, Thomas/0000-0002-1246-7404; Reid, Adam/0000-0002-5926-7768; Hunt, Martin/0000-0002-8060-4335; Dalzell, Johnathan/0000-0001-9597-3945; Tsai, Isheng Jason/0000-0002-2123-5058	KAKENHI [23248024, 23380092]; FFPRI [200704]; JSPS; Wellcome Trust [WT 085775/Z/08/Z]; European Union [FP7/2007-2013, nu242095: EVIMalaR]; Scottish Government; COST Action 872; ERASMUS MUNDUS [2008-102]; Swedish Science Council; Carl Trygger Foundation; Linnaeus initiative "Insect Chemical Ecology, Ethology and Evolution" (ICE3)	This work was partially supported by Grants-in-Aid for Scientific Research (KAKENHI 23248024 and 23380092) (http://www.jsps.go.jp/) and research grant #200704 of FFPRI (http://www.ffpri.affrc.go.jp/). TK was supported by JSPS Postdoctoral Fellowships for Research Abroad (http://www.jsps.go.jp/). JAC, IJT, SAS, AJR, AS-F, and MB are supported by the Wellcome Trust [grant WT 085775/Z/08/Z] (http://www.wellcome.ac.uk/). TDO is supported by European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement nu242095: EVIMalaR - Towards the establishment of a permanent European Virtual Institute dedicated to Malaria Research (EVIMalaR) (http://cordis.europa.eu/fp7/). JH Institute receives funding from the Scottish Government. This work benefited from links funded though COST Action 872 (http://www.cost.esf.org/) and through ERASMUS MUNDUS project 2008-102 (EUMAINE) (http://www.eumaine.ugent.be). Swedish University of Agricultural Sciences was supported by Swedish Science Council, Carl Trygger Foundation (http://www.carltryggersstiftelse.se/), the Linnaeus initiative "Insect Chemical Ecology, Ethology and Evolution" (ICE3). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.		91	160	171	15	80	PUBLIC LIBRARY SCIENCE	SAN FRANCISCO	1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA	1553-7366	1553-7374		PLOS PATHOG	PLoS Pathog.	SEP	2011	7	9							e1002219	10.1371/journal.ppat.1002219				17	Microbiology; Parasitology; Virology	Microbiology; Parasitology; Virology	827DY	WOS:000295409000023	21909270	DOAJ Gold, Green Published	Y	N	22-11-18
J	Huestis, DL; Marshall, JL				Huestis, Diana L.; Marshall, Jeremy L.			From Gene Expression to Phenotype in Insects: Non-microarray Approaches for Transcriptome Analysis	BIOSCIENCE			English	Article						expressed sequence tags; mRNA differential display PCR; RNAi; suppression subtractive hybridization; pyrosequencing	SUPPRESSION SUBTRACTIVE HYBRIDIZATION; RNA DIFFERENTIAL DISPLAY; QUANTITATIVE RT-PCR; DOUBLE-STRANDED-RNA; MESSENGER-RNA; SERIAL ANALYSIS; BOMBYX-MORI; ACYRTHOSIPHON-PISUM; SAGE ANALYSIS; HOST-PLANT	Transcripts and their expression levels link an organism's genotype and phenotype, so understanding this relationship can aid our understanding of phenotypic evolution at the gene-expression level. The emerging field of functional genomics is concerned primarily with understanding how allelic and gene-expression variation is linked to observable, biologically relevant phenotypes. Insects are particularly well studied in this area because they are good laboratory systems and have incredible biodiversity and agricultural and public-health importance. Technology developed over the last decade or so permits gene expression studies in any insect system, thus advancing the field of functional genomics beyond traditional genetic model systems such as Drosophila. In this article we provide an overview of commonly used non-microarray gene-expression techniques in insect systems and review several empirical studies that use each technique. We also discuss RNA interference as a means to test the link between gene expression and phenotype for candidate loci. We end with a discussion of how new high-throughput sequencing methods are advancing the field of functional genomics.	[Marshall, Jeremy L.] Kansas State Univ, Dept Entomol, Manhattan, KS 66506 USA		dituestis@ksit.edu; cricket@ksu.edu		Huestis, Diana/0000-0001-6649-4785	EPA STAR GRO [GAD MA916584]; Kansas Agricultural Experiment Station [08-368-J]; National Science Foundation [DEB-0746316]	The authors thank three anonymous reviewers for comments on an earlier version of this manuscript. During the preparation of the manuscript, the authors were supported by an EPA STAR GRO feflowship to D. L. H. (GAD MA916584) and funding to J.L.M. from the Kansas Agricultural Experiment Station (contribution 08-368-J) and the National Science Foundation (DEB-0746316).		77	4	4	0	5	AMER INST BIOLOGICAL SCI	WASHINGTON	1444 EYE ST, NW, STE 200, WASHINGTON, DC 20005 USA	0006-3568			BIOSCIENCE	Bioscience	MAY	2009	59	5					373	384		10.1525/bio.2009.59.5.5				12	Biology	Life Sciences & Biomedicine - Other Topics	439HP	WOS:000265618500005					22-11-18
J	Jedlicka, JA; Vo, ATE; Almeida, RPP				Jedlicka, Julie A.; Vo, Anh-Thu E.; Almeida, Rodrigo P. P.			Molecular scatology and high-throughput sequencing reveal predominately herbivorous insects in the diets of adult and nestling Western Bluebirds (Sialia mexicana) in California vineyards	AUK			English	Article						DNA barcoding; diet analysis; ecosystem function; fecal/faecal samples; insectivore; nest box; noninvasive; trophic ecology	INSECTIVOROUS BIRDS; ECOSYSTEM SERVICES; PREDATORS; HABITAT; COMMUNITIES; LIBRARIES; CAPTURE; QUALITY; SAMPLES; GROWTH	Determining the ecosystem function of high-order predators is critical for evaluation of food web interactions. Insectivorous birds are abundant predators in many ecosystems yet because they forage upon small taxa, it remains largely unknown whether birds are providing ecosystem services in the form of pest control or disservices by preying upon predaceous arthropod species. We extracted DNA from noninvasive fecal samples of adult and nestling Western Bluebirds (Sialia mexicana) in California vineyards. Using universal arthropod-specific primers, we sequenced prey items via massively parallel sequencing on the Illumina MiSeq platform. Bluebirds consumed a broad diet comprising 66 unique arthropod species from 6 orders and 28 families. Aedes sp. (mosquitoes: Culicidae), a previously unknown prey, was the most common item recovered, occurring in 49.5% of the fecal samples. Ectoparasitic bird blowfly (Protocalliphora) DNA was found in 7% of adult and 11% of nestling samples, presenting clear evidence of active feeding by the avian hosts on adult or larval ectoparasites. Herbivorous insects, primarily from the orders Hemiptera and Lepidoptera, represented over half (56%) of the prey items in bluebird diets. Intraguild predation (consumption of predator or parasitoid arthropods) represented only 3% of adult and nestling dietary items. Diets of adults were significantly different from nestlings as were diets from birds sampled in different vineyard blocks. Sex, date, number of young, and individual bird (based on resampled individuals) were all insignificant factors that did not explain diet variability. Nestling age was a significant factor in explaining a small amount of the variability in dietary components. In addition, our analysis of subsampling larger fecal samples and processing them independently revealed highly dissimilar results in all 10 trials and we recommend avoiding this common methodology. Molecular scatology offers powerfully informative techniques that can reveal the ecosystem function and services provided by abundant yet cryptic avian foragers.	[Jedlicka, Julie A.] Missouri Western State Univ, Dept Biol, St Joseph, MO USA; [Vo, Anh-Thu E.] Univ Calif Berkeley, Museum Vertebrate Zool, Berkeley, CA 94720 USA; [Vo, Anh-Thu E.] Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA; [Almeida, Rodrigo P. P.] Univ Calif Berkeley, Dept Environm Sci Policy & Management, Berkeley, CA 94720 USA	Jedlicka, JA (reprint author), Missouri Western State Univ, Dept Biol, St Joseph, MO USA.	jjedlicka@missouriwestern.edu		Almeida, Rodrigo/0000-0003-2888-9617	National Science Foundation [DBI-1103583]; American Vineyard Foundation [2012-1343]	National Science Foundation (DBI-1103583) and American Vineyard Foundation (2012-1343) provided funding for this project.		53	4	4	11	81	AMER ORNITHOLOGISTS UNION	LAWRENCE	ORNITHOLOGICAL SOC NORTH AMER PO BOX 1897, LAWRENCE, KS 66044-8897 USA	0004-8038	1938-4254		AUK	AUK	APR	2017	134	1					116	127		10.1642/AUK-16-103.1				12	Ornithology	Zoology	EI1AB	WOS:000392206100011					22-11-18
J	Mansor, MS; Nor, SM; Ramli, R				Mansor, Mohammad Saiful; Nor, Shukor Md.; Ramli, Rosli			Assessing Diet of the Rufous-Winged Philentoma (Philentoma pyrhoptera) in Lowland Tropical Forest using Next-Generation Sequencing	SAINS MALAYSIANA			English	Article						Dietary ecology; MiSeq; next-generation sequencing (NGS); Philentoma pyrhoptera; tropical birds	MOLECULAR ANALYSIS; MYOTIS-LUCIFUGUS; RAIN-FORESTS; PREY; RESOURCE; PREDATOR; CONSUMPTION; GENERALIST; MALAYSIA; HABITAT	Dietary study provides understanding in predator-prey relationships, yet diet of tropical forest birds is poorly understood. In this study, a non-invasive method, next-generation sequencing (Illumina MiSeq platform) was used to identify prey in the faecal samples of the Rufous-winged Philentoma (Philentoma pyrhoptera). Dietary samples were collected in lowland tropical forest of central Peninsular Malaysia. A general invertebrate primer pair was used for the first time to assess diet of tropical birds. The USEARCH was used to cluster the COI mtDNA sequences into Operational Taxonomic Unit (OTU). OTU sequences were aligned and queried through the GenBank or Biodiversity of Life Database (BOLD). We identified 26 distinct arthropod taxa from 31 OTUs. Of all OTUs, there was three that could be identified up to species level, 20 to genus level, three to family level and five could not assigned to any taxa (the BLAST hits were poor). All sequences were identified to class Insecta belonging to 18 families from four orders, where Lepidoptera representing major insect order consumed by study bird species. This non-invasive molecular approach provides a practical and rapid technique to understand of how energy flows across ecosystems. This technique could be very useful to screen for possible particular pest insects consumed by insectivores (e.g. birds and bats) in crop plantation. A comprehensive arthropod studies and local reference sequences need to be added to the database to improve the proportion of sequences that can be identified.	[Mansor, Mohammad Saiful; Nor, Shukor Md.] Univ Kebangsaan Malaysia, Sch Environm & Nat Resource Sci, Fac Sci & Technol, Ukm Bangi 43600, Selangor Darul, Malaysia; [Ramli, Rosli] Univ Malaya, Inst Biol Sci, Kuala Lumpur 50603, Federal Territo, Malaysia	Mansor, MS (reprint author), Univ Kebangsaan Malaysia, Sch Environm & Nat Resource Sci, Fac Sci & Technol, Ukm Bangi 43600, Selangor Darul, Malaysia.	msaifulmansor@ukm.edu.my	Ramli, Rosli/A-8498-2010	Ramli, Rosli/0000-0003-0410-9604	Universiti Kebangsaan Malaysia [GGPM-2017-055]; University of Malaya [PG019-2013B]	We are grateful to Universiti Kebangsaan Malaysia Research Fund (GGPM-2017-055) and University of Malaya Research Fund [PG019-2013B] that provide financial support for this wildlife research. We thank the Department of Wildlife and National Parks, Hassan Kassim, Mohamad Nazli Mahamad Zain, Aziz Che Man, and Khairul Nizam Kamaruddin for their help and permission to perform this research in the Krau Wildlife Reserve. We also thank Muhd Fadhil Abdul Rasid, Mohd Sanusi Mohamed, Muhammad Rasul Abdullah Halim, Muhammad Firdaus Abdullah Sani and lab members for field assistance.		33	0	0	9	9	UNIV KEBANGSAAN MALAYSIA	SELANGOR	FACULTY SCIENCE & TECHNOLOGY, BANGI, SELANGOR, 43600, MALAYSIA	0126-6039			SAINS MALAYS	Sains Malays.	MAY	2018	47	5					1045	1050		10.17576/jsm-2018-4705-22				6	Multidisciplinary Sciences	Science & Technology - Other Topics	GJ7IE	WOS:000435559100022		Bronze			22-11-18
J	Minard, G; Tran, FH; Dubost, A; Van, TV; Mavingui, P; Moro, CV				Minard, Guillaume; Tran, Florence-Helene; Dubost, Audrey; Van Tran-Van; Mavingui, Patrick; Moro, Claire Valiente			Pyrosequencing 16S rRNA genes of bacteria associated with wild tiger mosquito Aedes albopictus: a pilot study	FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY			English	Article						high-throughput sequencing; 16S rDNA; bacterial diversity; Wolbachia; field-caught mosquitoes	CHIKUNGUNYA VIRUS; GUT MICROBIOTA; CYTOPLASMIC INCOMPATIBILITY; WOLBACHIA; DIVERSITY; SYMBIONTS; VECTOR; POPULATIONS; MADAGASCAR; INFECTION	The Asian tiger mosquito Aedes (Stegomya) albopictus is an invasive species that has spread across the world in the last two decades, showing a great capacity to adapt to contrasting climates and environments. While demonstrated in many insects, the contribution of bacterial symbionts in Aedes ecology is a challenging aspect that needs to be investigated. Also some bacterial species have already been identified in Ae. albopictus using classical methods, but a more accurate survey of mosquito-associated bacterial diversity is needed to decipher the potential biological functions of bacterial symbionts in mediating or constraining insect adaptation. We surveyed the bacteria associated with field populations of Ae. albopictus from Madagascar by pyrosequencing 16S rRNA gene amplicons. Different aspects of amplicon preparation and sequencing depth were tested to optimize the breadth of bacterial diversity identified. The results revealed that all mosquitoes collected from different sites have a bacterial microbiota dominated by a single taxon, Wolbachia pipientis, which accounted for about 99% of all 92,615 sequences obtained. As Ae. albopictus is known to harbor two Wolbachia strains (wAlbA and wAlbB), a quantitative PCR was used to estimate the relative densities, (i.e., the bacteria-to-host gene ratios) of each strains in individual mosquitoes. Relative densities were between 6.25 x 10(0.01) and 5.47 x 10(0.1) for wAlbA and between 2.03 x 10(0.1) and 1.4 x 10(1) for wAlbB. Apart from Wolbachia, a total of 31 bacterial taxa were identified at the genus level using different method variations. Diversity index values were low and probably underestimated the true diversity due to the high abundance of Wolbachia sequences vastly outnumbering sequences from other taxa. Further studies should implement alternative strategies to specifically discard from analysis any sequences from Wolbachia, the dominant endosymbiotic bacterium in Ae. albopictus from this area.	[Minard, Guillaume; Tran, Florence-Helene; Dubost, Audrey; Van Tran-Van; Mavingui, Patrick; Moro, Claire Valiente] Univ Lyon 1, UMR CNRS 5557, USC INRA 1364, VetAgro Sup,FR41 BioEnvironm & Hlth, F-69100 Villeurbanne, France	Mavingui, P (reprint author), Univ Lyon 1, UMR CNRS 5557, Batiment Lwoff,10,Rue Raphael Dubois, F-69100 Villeurbanne, France.	patrick.mavingui@univ-lyon1.fr; claire.valiente-moro@univ-lyon1.fr		valiente moro, claire/0000-0002-7193-405X; DUBOST, Audrey/0000-0003-0572-7834	CNRS [EC2CO]; CMIRA Region Rhone-Alpes; ERA-NET BiodivERsA; FRB France; FWF Austria; DFG Germany	We thank Maxime Bruto for his help in phylogeny analysis. Funding for this project was provided by grants from EC2CO CNRS and CMIRA Region Rhone-Alpes. This research was also partially funded by the ERA-NET BiodivERsA, with the national funders FRB France, FWF Austria, and DFG Germany, part of the 2012-2013 BiodivERsA call for research proposals, and was carried out within the frameworks of GDRIs "Biodiversite et Developpement Durable a Madagascar" and "Biodiversity and Infectious Diseases in Southeast Asia."		51	26	27	0	16	FRONTIERS RESEARCH FOUNDATION	LAUSANNE	PO BOX 110, LAUSANNE, 1015, SWITZERLAND	2235-2988			FRONT CELL INFECT MI	Front. Cell. Infect. Microbiol.	MAY	2014	4								59	10.3389/fcimb.2014.00059				9	Immunology; Microbiology	Immunology; Microbiology	AL2WR	WOS:000338986800006	24860790	DOAJ Gold, Green Published			22-11-18
J	Mitter, EK; de Freitas, JR; Germida, JJ				Mitter, Eduardo K.; de Freitas, J. Renato; Germida, James J.			Bacterial Root Microbiome of Plants Growing in Oil Sands Reclamation Covers	FRONTIERS IN MICROBIOLOGY			English	Article						oil sands; land reclamation; rhizosphere bacteria; endophytic bacteria; 16S rRNA gene sequencing; NGS analysis	CANOLA BRASSICA-NAPUS; RHIZOSPHERE MICROBIOME; CONTAMINATED SOIL; HYDROCARBON DEGRADATION; TAXONOMIC DIVERSITY; NITROGEN-FIXATION; YERSINIA-PESTIS; SP-NOV; RHIZOBIUM; GROWTH	Oil sands mining in northern Alberta impacts a large footprint, but the industry is committed to reclaim all disturbed land to an ecologically healthy state in response to environmental regulations. However, these newly reconstructed landscapes may be limited by several factors that include low soil nutrient levels and reduced microbial activity. Rhizosphere microorganisms colonize plant roots providing hosts with nutrients, stimulating growth, suppressing disease and increasing tolerance to abiotic stress. High-throughput sequencing techniques can be used to provide a detailed characterization of microbial community structure. This study used 16S rRNA amplicon sequencing to characterize the bacterial root microbiome associated with annual barley (Hordeum vulgare) and sweet clover (Melilotus albus) growing in an oil sands reclamation area. Our results indicate that Proteobacteria dominated the endosphere, whereas other phyla such as Acidobacteria and Gemmatimonadetes were restricted to the rhizosphere, suggesting that plants have the ability to select for certain soil bacterial consortia. The bacterial community in the endosphere compartments were less rich and diverse compared to the rhizosphere. Furthermore, it was apparent that sweet clover plants were more selective, as the community exhibited a lower richness and diversity compared to barley. Members of the family Rhizobiaceae, such as Sinorhizobium and Rhizobium were mainly associated with clover, whereas Acholeplasma (wall-less bacteria transmitted by insects) was unique to barley. Genera from the Enterobacteriaceae family, such as Yersinia and Lentzea were also mostly detected in barley, while other genera such Pseudomonas and Pantoea were able to successfully colonize both plants. Endophytic bacterial profiles varied within the same plant species at different sampling locations; however, these differences were driven by factors other than slope positions or cover management. Our results suggest that bacterial endophytic communities of plants growing in land reclamation systems are a subset of the rhizosphere community and selection is driven by plant factors.	[Mitter, Eduardo K.] Univ Saskatchewan, Dept Food & Bioprod Sci, Saskatoon, SK, Canada; [de Freitas, J. Renato; Germida, James J.] Univ Saskatchewan, Dept Soil Sci, Saskatoon, SK, Canada	Germida, JJ (reprint author), Univ Saskatchewan, Dept Soil Sci, Saskatoon, SK, Canada.	jim.germida@usask.ca		Sheibani Tezerji, Raheleh/0000-0002-1025-646X; Antonielli, Livio/0000-0002-7140-8359	Natural Sciences and Engineering Research Council of Canada Collaborative Research and Development Program; Suncor Energy Inc.; Syncrude Canada Ltd.; Canadian Natural Resources Limited; Total; Tervita Corporation; Alberta Newsprint Company; Alberta-Pacific Forest Industries; Hinton Pulp; Millar Western Forest Products Ltd.; Slave Lake Pulp; Oil Sands Research and Information Network; Environment Canada	We would like to thank the Forest Watershed and Riparian Disturbance Project (FORWARD III) funded by the Natural Sciences and Engineering Research Council of Canada Collaborative Research and Development Program and Suncor Energy Inc., Syncrude Canada Ltd., Canadian Natural Resources Limited, Total, Tervita Corporation, Alberta Newsprint Company, Alberta-Pacific Forest Industries, Hinton Pulp, Millar Western Forest Products Ltd., Slave Lake Pulp, Oil Sands Research and Information Network and Environment Canada. Thanks to Jorge Cordero Elvia and Dr. Bobbi Helgason for their valuable comments and suggestions.		88	23	23	14	38	FRONTIERS MEDIA SA	LAUSANNE	PO BOX 110, EPFL INNOVATION PARK, BUILDING I, LAUSANNE, 1015, SWITZERLAND	1664-302X			FRONT MICROBIOL	Front. Microbiol.	May-16	2017	8								849	10.3389/fmicb.2017.00849				14	Microbiology	Microbiology	EV2GT	WOS:000401574200001	28559882	DOAJ Gold, Green Published	Y	N	22-11-18
J	Gao, GQ; Gao, J; Hao, CF; Dai, LL; Chen, H				Gao, Guanqun; Gao, Jing; Hao, Chunfeng; Dai, Lulu; Chen, Hui			Biodiversity and Activity of Gut Fungal Communities across the Life History of Trypophloeus klimeschi (Coleoptera: Curculionidae: Scolytinae)	INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES			English	Article						Trypophloeus klimeschi; life stages; intestinal fungal; fungal communities; integrated pest management	BARK BEETLES; CELLULOLYTIC ACTIVITIES; COLD TOLERANCE; INSECTS; BACTERIAL; BIOLOGY; MICROORGANISMS; DECOMPOSERS; DIVERSITY; DYNAMICS	We comprehensively investigated the biodiversity of fungal communities in different developmental stages of Trypophloeus klimeschi and the difference between sexes and two generations by high throughput sequencing. The predominant species found in the intestinal fungal communities mainly belong to the phyla Ascomycota and Basidiomycota. Fungal community structure varies with life stage. The genera Nakazawaea, Trichothecium, Aspergillus, Didymella, Villophora, and Auricularia are most prevalent in the larvae samples. Adults harbored high proportions of Graphium. The fungal community structures found in different sexes are similar. Fusarium is the most abundant genus and conserved in all development stages. Gut fungal communities showed notable variation in relative abundance during the overwintering stage. Fusarium and Nectriaceae were significantly increased in overwintering mature larvae. The data indicates that Fusarium might play important roles in the survival of T. klimeschi especially in the overwintering stage. The authors speculated that Graphium plays an important role in the invasion and colonization of T. klimeschi. The study will contribute to the understanding of the biological role of the intestinal fungi in T. klimeschi, which might provide an opportunity and theoretical basis to promote integrated pest management (IPM) of T. klimeschi.	[Gao, Guanqun; Gao, Jing; Dai, Lulu; Chen, Hui] Northwest A&F Univ, Coll Forestry, Yangling 712100, Shaanxi, Peoples R China; [Hao, Chunfeng] Tianjin Forestry Pest Control & Quarantine Stn, Tianjin 300000, Peoples R China; [Chen, Hui] South China Agr Univ, Coll Forestry & Landscape Architecture, State Key Lab Conservat & Utilizat Subtrop Agrobi, Guangzhou 510642, Guangdong, Peoples R China	Chen, H (reprint author), Northwest A&F Univ, Coll Forestry, Yangling 712100, Shaanxi, Peoples R China.; Chen, H (reprint author), South China Agr Univ, Coll Forestry & Landscape Architecture, State Key Lab Conservat & Utilizat Subtrop Agrobi, Guangzhou 510642, Guangdong, Peoples R China.	ggqun@nwafu.edu.cn; sxllgaojing@nwafu.edu.cn; wjx2017@nwafu.edu.cn; dailulu@nwafu.edu.cn; chenhui@nwsuaf.edu.cn			Natural Science Basic Research Plan in Shanxi Province of China [2017ZDJC-03]; National Key Research and Development Program of China [2017YFD0600104]; Fundamental Research Funds for the Central Universities [Z109021640]	We acknowledge the financial support of the Natural Science Basic Research Plan in Shanxi Province of China (2017ZDJC-03), the National Key Research and Development Program of China (2017YFD0600104), the Fundamental Research Funds for the Central Universities (Z109021640).		66	0	0	4	4	MDPI	BASEL	ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND	1422-0067			INT J MOL SCI	Int. J. Mol. Sci.	JUL	2018	19	7							2010	10.3390/ijms19072010				24	Biochemistry & Molecular Biology; Chemistry, Multidisciplinary	Biochemistry & Molecular Biology; Chemistry	GR6UX	WOS:000442807400189	29996485	DOAJ Gold			22-11-18
J	Kajtoch, L				Kajtoch, Lukasz			A DNA Metabarcoding Study of a Polyphagous Beetle Dietary Diversity: the Utility of Barcodes and Sequencing Techniques	FOLIA BIOLOGICA-KRAKOW			English	Article						Molecular ecology; chloroplast DNA; rbcL gene; trnL intron; phytophagy; Centricnemus leucogrammus	CENTRICNEMUS-LEUCOGRAMMUS COLEOPTERA; LAND PLANTS; POLYDRUSUS-INUSTUS; EASTERN-EUROPE; CURCULIONIDAE; CONSERVATION; GRASSLANDS; INSECT; CHRYSOMELIDAE; HERBIVORES	Recently developed techniques of DNA barcoding and next-generation sequencing (NGS) overcome previous limitations of evaluation of animal diet composition and together are promising method in molecular ecology. The objective was to compare standard ABI Sanger sequencing with new high throughput sequencing (Illumina MiSeq) technique and the two selected plant barcodes (rbeL gene and trnL intron) in terms of the identification of host plant composition for the selected beetle species the Centricnemus leucogrammus weevil. A comparison of two sequencing techniques showed that NUS (in this case Illumina) gave more exhaustive results than the Sanger method. Moreover, it was proven that a two-locus barcoding systems (rbct, and trnL) is sufficient for host plant identification from DNA isolated from insect bodies, at least at the genus level. A comparison of host plant composition among distant populations revealed that the studied species did not feed uniformly across its range. This probably reveals an ecological adaptation of geographically and genetically isolated populations. These findings, beside broadening basic knowledge on the use of barcoding and sequencing techniques for host plant identifications in insect populations, can have implications for conservation studies and strategies for rare and endangered species.	Polish Acad Sci, Inst Systemat & Evolut Anim, PL-31049 Krakow, Poland	Kajtoch, L (reprint author), Polish Acad Sci, Inst Systemat & Evolut Anim, Slawkowska 17, PL-31049 Krakow, Poland.	kajtoch@isez.pan.krakow.pl	Kajtoch, Lukasz/B-4236-2012	Kajtoch, Lukasz/0000-0001-7345-9400	Polish National Science Centre [UMO-2011/01/B/NZ8/01491]	Supported by grant UMO-2011/01/B/NZ8/01491 from the Polish National Science Centre.		56	7	9	4	74	POLISH ACAD SCIENCES, INST SYSTEMATICS EVOLUTION ANIMALS	KRAKOW	EDITORIAL OFFICE, SLAWKOWSKA 17, KRAKOW, 31-016, POLAND	0015-5497	1734-9168		FOLIA BIOL-KRAKOW	Folia Biol.-Krakow		2014	62	3					223	234		10.3409/fb62_3.223				12	Biology	Life Sciences & Biomedicine - Other Topics	AN0ZU	WOS:000340313300009	25412510				22-11-18
J	Gomez-Zurita, J; Cardoso, A; Coronado, I; De la Cadena, G; Jurado-Rivera, JA; Maes, JM; Montelongo, T; Nguyen, DT; Papadopoulou, A				Gomez-Zurita, Jesus; Cardoso, Anabela; Coronado, Indiana; De la Cadena, Gissela; Jurado-Rivera, Jose A.; Maes, Jean-Michel; Montelongo, Tinguaro; Dinh Thi Nguyen; Papadopoulou, Anna			High-throughput biodiversity analysis: Rapid assessment of species richness and ecological interactions of Chrysomelidae (Coleoptera) in the tropics	ZOOKEYS			English	Article						Angiosperms; Biodiversity; Chrysomelidae; insect-plant interaction; molecular ecology; molecular taxonomy; tropics	MULTILOCUS SEQUENCE DATA; INTEGRATIVE TAXONOMY; DNA BARCODES; MOLECULAR CHARACTERIZATION; DELIMITATION; IDENTIFICATION; SYSTEMATICS; HERBIVORES; DIVERSITY; DISCOVERY	Biodiversity assessment has been the focus of intense debate and conceptual and methodological advances in recent years. The cultural, academic and aesthetic impulses to recognise and catalogue the diversity in our surroundings, in this case of living objects, is furthermore propelled by the urgency of understanding that we may be responsible for a dramatic reduction of biodiversity, comparable in magnitude to geological mass extinctions. One of the most important advances in this attempt to characterise biodiversity has been incorporating DNA-based characters and molecular taxonomy tools to achieve faster and more efficient species delimitation and identification, even in hyperdiverse tropical biomes. In this assay we advocate for a broad understanding of Biodiversity as the inventory of species in a given environment, but also the diversity of their interactions, with both aspects being attainable using molecular markers and phylogenetic approaches. We exemplify the suitability and utility of this framework for large-scale biodiversity assessment with the results of our ongoing projects trying to characterise the communities of leaf beetles and their host plants in several tropical setups. Moreover, we propose that approaches similar to ours, establishing the inventories of two ecologically inter-related and species-rich groups of organisms, such as insect herbivores and their angiosperm host-plants, can serve as the foundational stone to anchor a comprehensive assessment of diversity, also in tropical environments, by subsequent addition of trophic levels.	[Gomez-Zurita, Jesus; Cardoso, Anabela; De la Cadena, Gissela; Montelongo, Tinguaro; Dinh Thi Nguyen; Papadopoulou, Anna] Univ Pompeu Fabra, CSIC, Inst Evolutionary Biol, Anim Biodivers & Evolut, Barcelona 08003, Spain; [Coronado, Indiana] Univ Nacl Autonoma Nicaragua, Herbario & Jardin Bot Ambiental, Leon, Spain; [Jurado-Rivera, Jose A.] Univ Illes Balears, Dept Biol, Palma De Mallorca 07122, Spain; [Maes, Jean-Michel] Museo Entomol Leon, Leon, Nicaragua; [Dinh Thi Nguyen] Vietnam Acad Sci & Technol, Inst Ecol & Biol Resources, 18 Hoang Quoc Viet, Hanoi, Vietnam; [Papadopoulou, Anna] CSIC, Estn Biol Donana, Conservat & Evolutionary Genet, Seville 41092, Spain	Gomez-Zurita, J (reprint author), Univ Pompeu Fabra, CSIC, Inst Evolutionary Biol, Anim Biodivers & Evolut, Barcelona 08003, Spain.	j.gomez-zurita@csic.es	CSIC, EBD Donana/C-4157-2011; Papadopoulou, Anna/K-5492-2014; Gomez-Zurita, Jesus/C-4248-2008; De la Cadena Mendoza, Gissela Nathali/H-4863-2018	CSIC, EBD Donana/0000-0003-4318-6602; Papadopoulou, Anna/0000-0002-4656-4894; Gomez-Zurita, Jesus/0000-0001-7337-6541; De la Cadena Mendoza, Gissela Nathali/0000-0003-4437-2992	'Fundacion BBVA' (Spain) [BIOCON08-045]; AECID predoctoral studentship (Spanish Ministry of Foreign Affairs and Cooperation); SENESCYT scholarship (Secretariat of High Education, Science, Technology and Innovation, Ecuador); National Geographic Society [8380-07]; Percy Sladen Memorial Fund of the Linnean Society of London; Harvard University; MICINN [CGL2008-00007/BOS]; Spanish High Research Council (CSIC); Vietnamese Academy of Sciences	The 'Fundacion BBVA' (Spain) has funded the bulk of this work thanks to their support for our large-scale biodiversity assessment initiative in Nicaraguan tropical dry forests (project BIOCON08-045, IP: JGZ). Our work in Nicaragua has benefited from a postdoctoral 'Juan de la Cierva' contract (Spanish Ministry of Science and Innovation, MICINN) to AP, and an AECID predoctoral studentship (Spanish Ministry of Foreign Affairs and Cooperation) and a SENESCYT scholarship (Secretariat of High Education, Science, Technology and Innovation, Ecuador) to GDC. The National Geographic Society supported most of our research in New Caledonia (project 8380-07, IP: JGZ) with help from a travel grant awarded by the Percy Sladen Memorial Fund of the Linnean Society of London to JGZ. The Spanish High Research Council (CSIC), in the framework of a cooperation agreement with the Vietnamese Academy of Sciences, supports our work in dry tropical forests of southern Vietnam (IP: JGZ) as well as a predoctoral studentship to DTN. Several EU Synthesys research stays (GB-TAF-1840, SE-TAF-1893, DE-TAF-4348) and a Mayr Travel Grant (Harvard University) as well as project CGL2008-00007/BOS (MICINN, IP: JGZ) have contributed to the discovery of a new tropical species of Calligrapha, and the latter also framed the predoctoral studentship to TM.		80	3	3	1	19	PENSOFT PUBL	SOFIA	12 PROF GEORGI ZLATARSKI ST, SOFIA, 1700, BULGARIA	1313-2989	1313-2970		ZOOKEYS	ZooKeys		2016		597			SI		3	26		10.3897/zookeys.597.7065				24	Zoology	Zoology	DO8TD	WOS:000378055800002	27408583	DOAJ Gold, Green Published			22-11-18
J	Elbrecht, V; Taberlet, P; Dejean, T; Valentini, A; Usseglio-Polatera, P; Beisel, JN; Coissac, E; Boyer, F; Leese, F				Elbrecht, Vasco; Taberlet, Pierre; Dejean, Tony; Valentini, Alice; Usseglio-Polatera, Philippe; Beisel, Jean-Nicolas; Coissac, Eric; Boyer, Frederic; Leese, Florian			Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects	PEERJ			English	Article						Biodiversity assessment; Stream monitoring; Small ribosomal subunit; High throughput sequencing; DNA metabarcoding; Method testing; Freshwater invertebrates; Stream ecosystems; Primer bias; Illumina sequencing	BIODIVERSITY; BARCODE; EPHEMEROPTERA; TRICHOPTERA; ARTHROPODS; PLECOPTERA; DIVERSITY; CHURCHILL; PATTERNS; MANITOBA	Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable prinier binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate.	[Elbrecht, Vasco] Ruhr Univ Bochum, Dept Anim Ecol Evolut & Biodivers, Univ Str 150, Bochum, Germany; [Elbrecht, Vasco; Leese, Florian] Univ Duisburg Essen, Aquat Ecosyst Res, Essen, Germany; [Taberlet, Pierre; Coissac, Eric; Boyer, Frederic] CNRS, Lab Ecol Alpine LECA, Grenoble, France; [Taberlet, Pierre; Coissac, Eric; Boyer, Frederic] Univ Grenoble Alpes, Lab Ecol Alpine LECA, Grenoble, France; [Dejean, Tony; Valentini, Alice] SPYGEN, Le Bourget Du Lac, France; [Usseglio-Polatera, Philippe] Univ Lorraine, Lab Interdisciplinaire Environm Continentaux LIEC, Metz, France; [Beisel, Jean-Nicolas] Ecole Natl Genie Eau & Environm Strasbourg, Strasbourg, France; [Beisel, Jean-Nicolas] Univ Strasbourg, CNRS, UMR 7362, LIVE, Strasbourg, France; [Leese, Florian] Univ Duisburg Essen, Ctr Water & Environm Res ZWU Essen, Essen, Germany	Leese, F (reprint author), Univ Duisburg Essen, Aquat Ecosyst Res, Essen, Germany.; Leese, F (reprint author), Univ Duisburg Essen, Ctr Water & Environm Res ZWU Essen, Essen, Germany.	florian.leese@uni-due.de	Leese, Florian/D-4277-2012	Leese, Florian/0000-0002-5465-913X; valentini, alice/0000-0001-5829-5479; Boyer, Frederic/0000-0003-0021-9590; Coissac, Eric/0000-0001-7507-6729	Kurt Eberhard Bode foundation; Agence Nationale de la Recherche (aquaDNA) [ANR-13-ECOT-0002-01]	Florian Leese and Vasco Elbrecht are supported by a grant from the Kurt Eberhard Bode foundation to Florian Leese. Pierre Taberlet, Eric Coissac, Tony Dejean, Alice Valentini, Philippe Usseglio-Polatera, Jean-Nicolas Beisel and Frederic Boyerwere were supported by a grant from Agence Nationale de la Recherche (aquaDNA; ANR-13-ECOT-0002-01). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.		35	13	14	6	63	PEERJ INC	LONDON	341-345 OLD ST, THIRD FLR, LONDON, EC1V 9LL, ENGLAND	2167-8359			PEERJ	PeerJ	Apr-19	2016	4								e1966	10.7717/peerj.1966				12	Multidisciplinary Sciences	Science & Technology - Other Topics	DK2MJ	WOS:000374748300007	27114891	DOAJ Gold, Green Published			22-11-18
J	Datlof, EM; Amend, AS; Earl, K; Hayward, J; Morden, CW; Wade, R; Zahn, G; Hynson, NA				Datlof, Erin M.; Amend, Anthony S.; Earl, Kamala; Hayward, Jeremy; Morden, Clifford W.; Wade, Rachael; Zahn, Geoffrey; Hynson, Nicole A.			Uncovering unseen fungal diversity from plant DNA banks	PEERJ			English	Article						Microbial diversity; DNA banks; Fungi; Biodiversity; Biobanks	BIODIVERSITY HOTSPOTS; ENDOPHYTE COMMUNITIES; DISTANCE DECAY; PHYLLOSPHERE; ECOSYSTEMS; LIFE; IDENTIFICATION; CONSERVATION; SIMILARITY; MAGNITUDE	Throughout the world DNA banks are used as storage repositories for genetic diversity of organisms ranging from plants to insects to mammals. Designed to preserve the genetic information for organisms of interest, these banks also indirectly preserve organisms associated mcrobiomes,including fungi associated with plant tissues. Studies of fungal biodiversity lag far behind those of macroorganisms, such as p and estimates of global fungal richness are still widely debated. Utilizing previously collected specimens to study patterns of fungal diversity could significantly increase our understanding of overall patterns of biodiversity from snapshots in time. Here, we investigated the fungi inhabiting the phylloplane among species of the endemic Hawaiian plant genus, Clermontin (Campanulaceae). Utilizing next generation DNA amplicon sequencing, we uncovered approximately 1,780 fungal operational taxonomic nits from just 20 DNA bank samples collected throughout the main Hawaiian Islands. Using these historical samples, we tested the macroecological pattern of decreasing community similarity with decreasing geographic proximity. We found a significant distance decay pattern among Clermontia associated fungal, communities. This study provides the first insights into elucidating patterns of microbial diversity through the use of DNA bank repository samples.	[Datlof, Erin M.; Amend, Anthony S.; Hayward, Jeremy; Morden, Clifford W.; Wade, Rachael; Zahn, Geoffrey; Hynson, Nicole A.] Univ Hawaii Manoa, Dept Bot, Honolulu, HI 96822 USA; [Earl, Kamala] Univ Florida, Sch Forest Resources & Conservat, Gainesville, FL 32611 USA	Hynson, NA (reprint author), Univ Hawaii Manoa, Dept Bot, Honolulu, HI 96822 USA.	nhynson@hawaii.edu		Zahn, Geoffrey/0000-0002-8691-692X	Illumina Corporation; National Science Foundation [1255972]	The following grant information was disclosed by the authors:; Illumina Corporation and National Science Foundation: 1255972.		66	4	4	3	6	PEERJ INC	LONDON	341-345 OLD ST, THIRD FLR, LONDON, EC1V 9LL, ENGLAND	2167-8359			PEERJ	PeerJ	Aug-28	2017	5								e3730	10.7717/peerj.3730				18	Multidisciplinary Sciences	Science & Technology - Other Topics	FI4PD	WOS:000411953700004	28875077	DOAJ Gold, Green Published			22-11-18
J	Carew, ME; Coleman, RA; Hoffman, AA				Carew, Melissa E.; Coleman, Rhys A.; Hoffman, Ary A.			Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding?	PEERJ			English	Article						DNA barcoding; Aquatic; Metagenomics; Insect; Macroinvertebrates; Bioassessment; Freshwater	ARTHROPODS; BARCODES; CHIRONOMIDAE; DIVERSITY; BIODIVERSITY; COLLECTION; PITFALLS; TAXONOMY; PROTOCOL; PRIMERS	Background. High throughput DNA sequencing of bulk invertebrate samples or metabarcoding is becoming increasingly used to provide profiles of biological communities for environmental monitoring. As metabarcoding becomes more widely applied, new reference DNA barcodes linked to individual specimens identified by taxonomists are needed. This can be achieved through using DNA extraction methods that are not only suitable for metabarcoding but also for building reference DNA barcode libraries. Methods. In this study, we test the suitability of a rapid non-destructive DNA extraction method for metabarcoding of freshwater invertebrate samples. Results. This method resulted in detection of taxa from many taxonomic groups, comparable to results obtained with two other tissue-based extraction methods. Most taxa could also be successfully used for subsequent individual-based DNA barcoding and taxonomic identification. The method was successfully applied to field-collected invertebrate samples stored for taxonomic studies in 70% ethanol at room temperature, a commonly used storage method for freshwater samples. Discussion. With further refinement and testing, non-destructive extraction has the potential to rapidly characterise species biodiversity in invertebrate samples, while preserving specimens for taxonomic investigation.	[Carew, Melissa E.; Hoffman, Ary A.] Univ Melbourne, Sch Biosci, Melbourne, Vic, Australia; [Coleman, Rhys A.] Melbourne Water Corp, Appl Res, Melbourne, Vic, Australia	Carew, ME (reprint author), Univ Melbourne, Sch Biosci, Melbourne, Vic, Australia.	mecarew@unimelb.edu.au			Australian Research Council [LP150100876, FL100100066]; Melbourne Water Corporation	All funding for this study was from the Australian Research Council through their grant (grant number LP150100876) and Fellowship (grant number FL100100066), with additional support from Melbourne Water Corporation. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.		55	0	0	14	14	PEERJ INC	LONDON	341-345 OLD ST, THIRD FLR, LONDON, EC1V 9LL, ENGLAND	2167-8359			PEERJ	PeerJ	Jun-13	2018	6								e4980	10.7717/peerj.4980				24	Multidisciplinary Sciences	Science & Technology - Other Topics	GJ2XX	WOS:000435138900008	29915700	DOAJ Gold			22-11-18
J	Davies, AP; Lange, CL; O'Neill, SL				Davies, A. P.; Lange, C. L.; O'Neill, S. L.			A rapid single-step multiplex method for discriminating between Trichogramma (Hymenoptera : Trichogrammatidae) species in Australia	JOURNAL OF ECONOMIC ENTOMOLOGY			English	Article						Trichogramma australicum; Trichogramma pretiosum; internal transcribed spacer-2 identification	ALLOZYMIC VARIATION; RIBOSOMAL GENE; IDENTIFICATION; PRETIOSUM; SEQUENCES; MINUTUM; COMPLEX; MARKERS; HYM	Inaccurate species identification confounds insect ecological studies. Examining aspects of Trichogramma ecology pertinent to the novel insect resistance management strategy for future transgenic cotton, Gossypium hirsutum L., production in the Ord River Irrigation Area (ORIA) of Western Australia required accurate differentiation between morphologically similar Trichogramma species. Established molecular diagnostic methods for Trichogramma identification use species-specific sequence difference in the internal transcribed spacer (ITS) -2 chromosomal region; yet, difficulties arise discerning polymerase chain reaction (PCR) fragments of similar base pair length by gel electrophoresis. This necessitates the restriction enzyme digestion of PCR-amplified ITS-2 fragments to readily differentiate Trichogramma australicum Girault and Trichogramma pretiosum Riley. To overcome the time and expense associated with a two-step diagnostic procedure, we developed a "one-step" multiplex PCR technique using species-specific primers designed to the ITS-2 region. This approach allowed for a high-throughput analysis of samples as part of ongoing ecological studies examining Trichogramma biological control potential in the ORIA where these two species occur in sympatry.	Univ Queensland, Sch Integrat Biol, St Lucia, Qld 4072, Australia	Davies, AP (reprint author), Cotton Catchment Comm Cooperat Res Ctr, Dept Primary Ind Fisheries & Mines, Katherine Res Stn, POB 1346, Katherine, NT 0851, Australia.		O'Neill, Scott/B-3568-2009	O'Neill, Scott/0000-0002-4131-3615				31	13	15	0	10	OXFORD UNIV PRESS INC	CARY	JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA	0022-0493	1938-291X		J ECON ENTOMOL	J. Econ. Entomol.	DEC	2006	99	6					2142	2145						4	Entomology	Entomology	112YV	WOS:000242565000030	17195685				22-11-18