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\beginsupplement
\section*{Supplemental Materials}

\begin{center}
\captionof{table}{Specimen locality data for newly sequenced transcriptomes.  For additional locality data see \cite{bond_phylogenomics_2014}, \cite{fernandez_phylogenomic_2014} and \cite{sanggaard_spider_2014}.}
\centering
\renewcommand{\arraystretch}{1.2}
\begin{longtable}{|p{2.2cm}|p{2.4cm}|p{1cm}|p{1cm}|p{1.8cm}|p{1cm}|} 
\hline
\multicolumn{1}{|c|}{\textbf{Family}} & 
\multicolumn{1}{c|}{\textbf{Genus}} & 
\multicolumn{1}{c|}{\textbf{Specific Epithet}} &
\multicolumn{1}{c|}{\textbf{Specimen ID}} &
\multicolumn{1}{c|}{\textbf{Locality}} &
\multicolumn{1}{c|}{\textbf{Latitude/Longitude}}\\  \hline
\endfirsthead
\multicolumn{6}{c}{{\bfseries \textbf{Supplemental Table 1} -- continued from previous page}}\\
\hline
\multicolumn{1}{|c|}{\textbf{Family}} & 
\multicolumn{1}{c|}{\textbf{Genus}} & 
\multicolumn{1}{c|}{\textbf{Specific Epithet}} &
\multicolumn{1}{c|}{\textbf{Specimen ID}} &
\multicolumn{1}{c|}{\textbf{Locality}} &
\multicolumn{1}{c|}{\textbf{Latitude/Longitude}}\\ \hline  
\endhead 
\\
Agelenidae & \textit{Agelenopsis} & \textit{emertoni} & AUMS5739 & Auburn, Lee Co, AL, USA & 32.6028°N 85.4554°W\\ \hline
Amaurobiidae & \textit{Callobius} & \textit{sp.} & AUMS11930 & Muir Woods, Marin Co, CA, USA & 37.8922°N 122.5717°W\\ \hline
Amphinectidae & \textit{Metaltella} & \textit{simoni} & AUMS11905 & Auburn University, Lee Co, AL, USA & 32.5986°N 85.4833°W\\ \hline
Amphinectidae & \textit{Metaltella} & \textit{simoni} & AUMS11915 & SanDiego Co, CA, USA & NA\\ \hline
Antrodiaetidae & \textit{Aliatypus} & \textit{coylei} & AUMS56 & near Monterey, Monterey Co, CA, USA & 36.5714°N 121.9043°W\\ \hline
Antrodiaetidae & \textit{Antrodiaetus} & \textit{unicolor} & MY2335 & near Hendersonville, Transylvania Co, NC, USA & 35.2192°N 82.7794°W\\ \hline
Anyphaenidae & \textit{Hibana} & \textit{sp.} & AUMS11902 & Louise Kreher Forest Ecology Preserve, Auburn, Lee Co, AL, USA & 32.6603°W 85.4836°W\\ \hline
Araneidae & \textit{Micrathena} & \textit{gracilis} & AUMS5620 & Dadeville, Co, AL, USA & 32.8318°N 85.7636°W\\ \hline
Araneidae & \textit{Verrucosa} & \textit{arenata} & AUMS11901 & Louise Kreher Forest Ecology Preserve, Auburn, Lee Co, AL, USA & 32.6603°N 85.4836°W\\ \hline
Atypidae & \textit{Sphodros} & \textit{rufipes} & AUMS146 & EV Smith Research Station, Macon Co, AL, USA & 32.4257°N 85.9015°W\\ \hline
Barychelidae & \textit{Trichopelma} & \textit{laselva} & AUMS8485 & La Selva, CR & 10.4295°N 84.0095°W\\ \hline
Caponiidae & \textit{Calponia} & \textit{harrisonfordi} & 1347-JML-001 & Russian Ridge Open Space Park, San Mateo Co, CA, USA & 37.3149°N 122.1872°W\\ \hline
Ctenidae & \textit{Anahita} & \textit{punctulata} & AUMS11932 & Auburn, Lee Co, AL, USA & 32.6028°N 85.4554°W\\ \hline
Ctenizidae & \textit{Cyclocosmia} & \textit{truncata} & AUMS120 & Grove Hill, Auburn, Lee Co, AL, USA & 32.5841°N 85.4604°W\\ \hline
Ctenizidae & \textit{Hebestatis} & \textit{theveneti} & AUMS152 & Tuolumne Co, CA, USA & 38.0453°N 119.9747°W\\ \hline
Deinopidae & \textit{Deinopis} & \textit{longipes} & AUMS8783 & La Selva, CR & 10.4295°N 84.0095°W\\ \hline
Desidae & \textit{Badumna} & \textit{longinqua} & AUMS11914 & Petaluma, Sonoma Co, CA, USA & 38.2247°N 122.6264°W\\ \hline
Dictynidae & \textit{Cicurina} & \textit{vibora} & HED003 & Temples of Thor Cave, Williamson Co, TX, USA & NA\\ \hline
Diguetidae & \textit{Diguetia} & \textit{sp.} & AUMS11919 & Iperial Co, CA, USA & NA\\ \hline
Dipluridae & \textit{Microhexura} & \textit{montivaga} & HED001 & Mt Gibbes, Mt Mitchell SP, Yancey Co, NC, USA & 35.7394°N 82.2850°W\\ \hline
Dysderidae & \textit{Dysdera} & \textit{crocata} & AUMS11924 & Golden Gate Park, San Francisco Co, CA, USA & 37.7686°N 122.4659°W\\ \hline
Euctenizidae & \textit{Aptostichus} & \textit{atomarius} & MY4002 & Winchester, Riverside Co, CA, USA & 33.7069°N 117.0844°W\\ \hline
Euctenizidae & \textit{Aptostichus} & \textit{stephencolberti} & AUMS20 & Marina Dunes State Park, Monterey Co, CA, USA & 36.7035°N 121.8068°W\\ \hline
Euctenizidae & \textit{Promyrmekiaphila} & \textit{clathrata} & AUMS5761 & near Cazadero, Sonoma Co, CA, USA & 38.5231°N 123.0845°W\\ \hline
Filistatidae & \textit{Kukulcania} & \textit{hibernalis} & AUMS8597 & Auburn, Lee Co, AL, USA & 32.6094°N 85.4544°W\\ \hline
Gnaphosidae & \textit{Sergiolus} & \textit{capulatus} & AUMS5674 & Opelika, Lee Co, AL, USA & 32.6887°N 85.4012°W\\ \hline
Hahniidae & \textit{Calymmaria} & \textit{persica} & AUMS11926 & Petaluma, Sonoma Co, CA, USA & 38.2247°N 122.6264°W\\ \hline
Homalonychidae & \textit{Homalonychus} & \textit{theologus} & AUMS11917 & Imperial Co, CA, USA & NA\\ \hline
Hypochilidae & \textit{Hypochilus} & \textit{pococki} & AUMS155 & Laurel Falls Trail, Sevier Co, TN, USA & 35.6782°N 83.5929°W\\ \hline
Idiopidae & \textit{Idiops} & \textit{bersebaensis} & AUMS6746 & Namibia, Africa & 17.0021°S 13.2445°E\\ \hline
Leptonetidae & \textit{Calileptoneta} & \textit{californica} & 1348-JML-001 & Mount Diablo State Park, Contra Co, CA, USA & 37.8745°N 121.9616°W\\ \hline
Linyphiidae & \textit{Frontinella} & \textit{communis} & AUMS5733 & Auburn University, Lee Co, AL, USA & 32.5987°N  85.4835°W\\ \hline
Liphistiidae & \textit{Liphistius} & \textit{sp.} & AUMS5743 & Thailand & NA\\ \hline
Lycosidae & \textit{Schizocosa} & \textit{rovneri} & AUMS5122 & Oxford, Lafayette Co, MS, USA & 32.4116°N 89.4183°W\\ \hline
Mecicobothriidae & \textit{Megahexura} & \textit{fulva} & AUMS154 & East of Groveland, Tuolumne Co, CA, USA & 38.0453°N 119.9747°W\\ \hline
Mimetidae & \textit{Ero} & \textit{leonina} & AUMS8817 & Tuskegee National Forest, Macon Co, AL, USA & 32.4418°N 85.6328°W\\ \hline
Nemesiidae & \textit{Calisoga} & \textit{longitarsis} & AUMS47 & Jasper Ridge, San Mateo Co, CA, USA & 37.4132°N 122.2050°W\\ \hline
Nemesiidae & \textit{Damarchus} & \textit{sp.} & AUMS5127 & Ramnagar Nepal & NA\\ \hline
Nemesiidae & \textit{Pionothele} & \textit{n.sp.} & AUMS6718 & Namibia, Africa & 23.5698°S 15.0398°E\\ \hline
Nephilidae & \textit{Nephila} & \textit{clavipes} & AUMS5736 & Donald E. Davis Arboretum, Auburn University, Lee Co, AL, USA & 32.5950°N 85.4834°W\\ \hline
Nesticidae & \textit{Nesticus} & \textit{cooperi} & HED002 & Nantahala River Gorge, Swain Co, NC, USA & 35.4111°N 83.5220°W\\ \hline
Oecobiidae & \textit{Oecobius} & \textit{navus} & AUMS5741 & Auburn University, Lee Co, AL, USA & 32.6000°N 85.4823°W\\ \hline
Oxyopidae & \textit{Peucetia} & \textit{longipalpis} & AUMS5740 & Opelika, Lee Co, AL, USA & 32.6887°N 85.4012°W\\ \hline
Paratropididae & \textit{Paratropis} & \textit{sp.} & AUMS148 & Socotá, Departamento Boyaca, Columbia & 6.08976°N 72.6198°W\\ \hline
Pholcidae & \textit{Pholcus} & \textit{phalangioides} & AUMS5732 & Auburn University, Lee Co, AL, USA & 32.6000°N 85.4823°W\\ \hline
Pholcidae & \textit{Pholcus} & \textit{phalangioides} & 1304-JML-001 & Petaluma, Sonoma Co, CA, USA & 38.2247°N 122.6264°W\\ \hline
Pimoidae & \textit{Pimoa} & \textit{sp.} & AUMS14951 & Del Norte Co, CA & NA\\ \hline
Pisauridae & \textit{Dolomedes} & \textit{triton} & AUMS11906 & Opelika, Lee Co, AL, USA & 32.6544°N 85.3973°W\\ \hline
Salticidae & \textit{Habronattus} & \textit{signatus} & HED004 & Ocotillo, Imperial Co, CA, USA & 32.7386°N 115.9941°W\\ \hline
Scytodidae & \textit{Scytodes} & \textit{thoracica} & AUMS5673 & Grove Hill, Lee Co, AL, USA & 32.5841°N 85.4604°W\\ \hline
Segestriidae & \textit{Segestria} & \textit{sp.} & AUMS11925 & Golden Gate Park, San Francisco, CA, USA & 37.7686°N 122.4659°W\\ \hline
Sicariidae & \textit{Loxosceles} & \textit{deserta} & 1346-JML-001 & Yarnell, Yavapai Co, AZ & 32.0756°N 110.6258°W\\ \hline
Tetragnathidae & \textit{Leucauge} & \textit{venusta} & AUMS11903 & Chewacla State Park, Auburn, Lee Co, AL, USA & 32.5536°N 85.4845°W\\ \hline
Tetragnathidae & \textit{Tetragnatha} & \textit{versicolor} & AUMS5738 & Donald E. Davis Arboretum, Auburn University, Lee Co, AL, USA & 32.5950°N 85.4834°W\\ \hline
Theraphosidae & \textit{Aphonopelma} & \textit{iviei} & APH2038 & East of Plymouth, Amador Co, CA, USA & 38.4759°N 120.8230°W\\ \hline
Theridiidae & \textit{Theridion} & \textit{sp.} & AUMS5737 & Donald E. Davis Arboretum, Auburn University, AL, USA & 32.5950°N 85.4834°W\\ \hline
Thomisidae & \textit{Misumenoides} & \textit{formosipes} & AUMS6454 & Opelika, Lee Co, AL, USA & 32.6887°N 85.4012°W\\ \hline
Uloboridae & \textit{Philopenella} & \textit{herediae} & AUMS8784 & La Selva, CR & 10.4295°N 84.0095°W\\ \hline
Uloboridae & \textit{Uloborus} & \textit{glomosus} & AUMS11904 & Chewacla State Park, Auburn, Lee Co, AL, USA & 32.5536°N 85.4845°W\\ \hline
\end{longtable}
\addtocounter{table}{-1}
\pagebreak
\captionof{table}{Transcriptome sequence and assembly data.}
\centering
\renewcommand{\arraystretch}{1.2}
\begin{longtable}{|p{2.3cm}|p{2.2cm}|p{1.8cm}|p{1cm}|p{1cm}|p{1cm}|p{.8cm}|p{.8cm}|}
\hline
\multicolumn{1}{|c|}{\textbf{Family}} &
\multicolumn{1}{c|}{\textbf{Species}} &
\multicolumn{1}{c|}{\textbf{Reads}} &
\multicolumn{1}{c|}{\textbf{Contigs}} &
\multicolumn{1}{c|}{\textbf{Ave. Len.}} &
\multicolumn{1}{c|}{\textbf{TransDecoder}} &
\multicolumn{1}{c|}{\textbf{ARTH}} &
\multicolumn{1}{c|}{\textbf{SPID}}\\ \hline 
\endfirsthead
\multicolumn{8}{c}{{\bfseries \textbf{Supplemental Table 2} -- continued from previous page}} \\ \hline 
\multicolumn{1}{|c|}{\textbf{Family}} &
\multicolumn{1}{c|}{\textbf{Species}} &
\multicolumn{1}{c|}{\textbf{Reads}} &
\multicolumn{1}{c|}{\textbf{Contigs}} &
\multicolumn{1}{c|}{\textbf{Ave. Len.}} &
\multicolumn{1}{c|}{\textbf{TransDecoder}} &
\multicolumn{1}{c|}{\textbf{ARTH}} &
\multicolumn{1}{c|}{\textbf{SPID}}\\ \hline 
\endhead 
\hline
Agelenidae & \textit{Agelenopsis emertoni} & 27264400 & 20517 & 719.7 & 8192 & 751 & 2613\\ \hline
Amaurobiidae & \textit{Amaurobius ferox} & 12549070 & 202311 & 530.8 & 35361 & 976 & 3247\\ \hline
Amaurobiidae & \textit{Callobius sp.} & 26240373 & 62055 & 499 & 21591 & 919 & 3401\\ \hline
Amphinectidae & \textit{Metaltella simoni} & 14728368 & 42301 & 574.7 & 18716 & 889 & 3039\\ \hline
Amphinectidae & \textit{Metaltella simoni} & 12935049 & 62734 & 612.4 & 23086 & 950 & 3174\\ \hline
Antrodiaetidae & \textit{Aliatypus coylei} & 29958173 & 23447 & 744.6 & 6098 & 695 & 2222\\ \hline
Antrodiaetidae & \textit{Antrodiaetus unicolor} & 32624239 & 14062 & 550.2 & 9850 & 756 & 2745\\ \hline
Anyphaenidae & \textit{Hibana sp.} & 40346328 & 55291 & 615.1 & 15212 & 909 & 2789\\ \hline
Araneidae & \textit{Verrucosa arenata} & 14468378 & 94721 & 911.9 & 41450 & 976 & 3993\\ \hline
Araneidae & \textit{Gasteracantha hasselti} & 12564452 & 50554 & 858.2 & 19944 & 978 & 4020\\ \hline
Araneidae & \textit{Macracantha arcuata} & 17523883 & 34411 & 787.9 & 16560 & 949 & 3826\\ \hline
Araneidae & \textit{Neoscona arabesca} & 28551664 & 161311 & 745.6 & 47096 & 992 & 3834\\ \hline
Araneidae & \textit{Micrathena gracilis} & 56963267 & 38210 & 856.6 & 16269 & 935 & 3719\\ \hline
Atypidae & \textit{Sphodros rufipes} & 51968533 & 27266 & 715.5 & 11504 & 915 & 3704\\ \hline
Barychelidae & \textit{Trichopelma laselva} & 27264400 & 33544 & 665.4 & 9061 & 807 & 2861\\ \hline
Buthidae & \textit{Centruroides vittatus} & 45691843 & 17788 & 378.2 & 4854 & 660 & 1099\\ \hline
Caponiidae & \textit{Calponia harrisonfordi} & 59921781 & 14397 & 542.1 & 4297 & 551 & 1604\\ \hline
Ctenidae & \textit{Anahita punctulata} & 44538794 & 75653 & 483.4 & 23111 & 961 & 3407\\ \hline
Ctenizidae & \textit{Cyclocosmia truncata} & 33664901 & 26408 & 604.7 & 8446 & 736 & 2679\\ \hline
Ctenizidae & \textit{Hebestatis theveneti} & 40097804 & 16167 & 650 & 6711 & 713 & 2647\\ \hline
Deinopidae & \textit{Deinopis longipes} & 39222056 & 36976 & 705.7 & 12764 & 880 & 3375\\ \hline
Desidae & \textit{Badumna longinqua} & 16455974 & 85746 & 661.9 & 34737 & 968 & 3557\\ \hline
Dictynidae & \textit{Cicurina vibora} & 29071083 & 175943 & 412.7 & 20256 & 852 & 3293\\ \hline
Diguetidae & \textit{Diguetia sp.} & 19838746 & 6816 & 306.9 & 1368 & 309 & 457\\ \hline
Dipluridae & \textit{Microhexura montivaga} & 24680385 & 19680 & 635.8 & 8286 & 761 & 2695\\ \hline
Dysderidae & \textit{Dysdera crocata} & 1718572 & 18286 & 452.8 & 5058 & 566 & 932\\ \hline
Eresidae & \textit{Stegodyphus mimosarum} & NA & NA & NA & 26888 & 965 & 4055\\ \hline
Euctenizidae & \textit{Aptostichus atomarius} & 27431535 & 14152 & 709.2 & 5795 & 643 & 2149\\ \hline
Euctenizidae & \textit{Aptostichus stephencolberti} & 30904990 & 13267 & 779.5 & 5344 & 589 & 1944\\ \hline
Euctenizidae & \textit{Promyrmekia- phila clathrata} & 24733435 & 22423 & 669.4 & 8445 & 758 & 2646\\ \hline
Filistatidae & \textit{Kukulcania hibernalis} & 42693292 & 29491 & 702.4 & 11121 & 835 & 3141\\ \hline
Gnaphosidae & \textit{Sergiolus capulatus} & 32765239 & 28757 & 725.6 & 11340 & 820 & 2989\\ \hline
Hahniidae & \textit{Calymmaria persica} & 19286137 & 110707 & 644.9 & 20501 & 982 & 2165\\ \hline
Homalonychidae & \textit{Homalonychus theologus} & 31165362 & 40734 & 462.1 & 13258 & 933 & 3167\\ \hline
Hypochilidae & \textit{Hypochilus pococki} & 25747925 & 19793 & 540.2 & 7561 & 796 & 2860\\ \hline
Idiopidae & \textit{Idiops bersebaensis} & 23040778 & 6270 & 649.1 & 2897 & 421 & 1151\\ \hline
Ixodidae & \textit{Ixodes  scapularis} & NA & 18810 & 668.4 & 17799 & 815 & 2726\\ \hline
Leptonetidae & \textit{Calileptoneta californica} & 59806212 & 37641 & 582 & 11687 & 875 & 3240\\ \hline
Linyphiidae & \textit{Frontinella communis} & 28476743 & 27195 & 757.1 & 11753 & 862 & 3126\\ \hline
Liphistiidae & \textit{Liphistius sp.} & 54043289 & 7830 & 370.5 & 1938 & 333 & 667\\ \hline
Liphistiidae & \textit{Liphistius malayanus} & 62897982 & 83669 & 515.4 & 19784 & 941 & 3568\\ \hline
Lycosidae & \textit{Schizocosa rovneri} & 132349831 & 42744 & 871.6 & 14965 & 911 & 3584\\ \hline
Mecicobothriidae & \textit{Megahexura fulva} & 59599533 & 40526 & 671.9 & 15303 & 964 & 4147\\ \hline
Mimetidae & \textit{Ero leonina} & 32363996 & 78785 & 801.7 & 24565 & 980 & 3971\\ \hline
Mysmenidae & \textit{Microdipoena guttata} & 16972695 & 156439 & 617.5 & 70785 & 998 & 3940\\ \hline
Nemesiidae & \textit{Calisoga longitarsis} & 30773715 & 20721 & 574.8 & 7674 & 743 & 2635\\ \hline
Nemesiidae & \textit{Damarchus sp.} & 21876221 & 13519 & 707.8 & 5558 & 623 & 2089\\ \hline
Nemesiidae & \textit{Pionothele n.sp.} & 20155275 & 5158 & 631.7 & 2283 & 368 & 970\\ \hline
Nephilidae & \textit{Nephila clavipes} & 34853551 & 32305 & 753.9 & 15200 & 935 & 3653\\ \hline
Nesticidae & \textit{Nesticus cooperi} & 20188741 & 41169 & 714 & 15744 & 945 & 3715\\ \hline
Oecobiidae & \textit{Oecobius navus} & 25031200 & 24989 & 695.4 & 12582 & 881 & 3183\\ \hline
Oxyopidae & \textit{Peucetia longipalpis} & 23273514 & 18810 & 668.4 & 7994 & 737 & 2536\\ \hline
Paratropididae & \textit{Paratropis sp.} & 18409810 & 9021 & 605 & 3694 & 473 & 1463\\ \hline
Pholcidae & \textit{Pholcus phalangioides} & 24861584 & 17870 & 556.9 & 6698 & 703 & 3183\\ \hline
Pholcidae & \textit{Pholcus phalangioides} & 58019035 & 40396 & 760.8 & 11883 & 902 & 2129\\ \hline
Phrynichidae & \textit{Damon variegatus} & 64733221 & 83669 & 515.4 & 27304 & 944 & 3327\\ \hline
Pimoidae & \textit{Pimoa sp.} & 46352103 & 160889 & 978.3 & 47496 & 998 & 3915\\ \hline
Pisauridae & \textit{Dolomedes triton} & 13590617 & 81075 & 625.3 & 32520 & 951 & 3209\\ \hline
Pisauridae & \textit{Pisaurina mira} & 6887470 & 129530 & 563.8 & 27116 & 958 & 3219\\ \hline
Salticidae & \textit{Habronattus signatus} & 75391275 & 26276 & 574.9 & 10447 & 843 & 3259\\ \hline
Scytodidae & \textit{Scytodes thoracica} & 30924460 & 59599 & 855.7 & 18223 & 962 & 3657\\ \hline
Segestriidae & \textit{Segestria sp.} & 38407502 & 191839 & 708.3 & 54753 & 987 & 3804\\ \hline
Sicariidae & \textit{Loxosceles deserta} & 61963685 & 40702 & 582.5 & 11078 & 876 & 3256\\ \hline
Tetragnathidae & \textit{Leucauge venusta} & 15567091 & 127727 & 919 & 51004 & 988 & 3972\\ \hline
Tetragnathidae & \textit{Tetragnatha versicolor} & 33465090 & 34328 & 815.4 & 15917 & 938 & 3672\\ \hline
Tetranychidae & \textit{Tetranychus cinnabarinus} & 26040173 & 30288 & 963.8 & 17083 & 938 & 3063\\ \hline
Thelyphonidae & \textit{Mastigoproctus giganteus} & 25983006 & 157263 & 623.7 & 43626 & 994 & 3785\\ \hline
Theraphosidae & \textit{Acanthoscurria  geniculata} & NA & NA & NA & 76237 & 933 & 4249\\ \hline
Theraphosidae & \textit{Aphonopelma iviei} & 36326210 & 13442 & 605.1 & 4717 & 596 & 2035\\ \hline
Theridiidae & \textit{Latrodectus tredecimguttatus} & 27605467 & 10259 & 1110.6 & 9266 & 904 & 3399\\ \hline
Theridiidae & \textit{Theridion sp.} & 37459365 & 24669 & 733.7 & 10013 & 800 & 2810\\ \hline
Thomisidae & \textit{Misumenoides formosipes} & 25351927 & 58396 & 570.4 & 21546 & 810 & 2161\\ \hline
Trachelidae & \textit{Trachelas tranquillus} & 15506968 & 118533 & 467.9 & 30037 & 950 & 3546\\ \hline
Uloboridae & \textit{Philoponella herediae} & 47234871 & 40659 & 655.9 & 16468 & 947 & 3656\\ \hline
Uloboridae & \textit{Uloborus glomosus} & 12362545 & 114137 & 657 & 40782 & 970 & 3810\\ \hline
\end{longtable}
\end{center}

\pagebreak
\subsection*{Supplemental Table 3}
See /Supplemental\_Material/AnnotationTable\_S3.tex :too large to compile within main.tex

\begin{center}
\begin{figure}[ht]
\centering
\includegraphics[width=16cm]{Supplemental_Material/F1_MissingData_positive_850}
\caption{Clustering/heatmap analysis depicting degree of shared data between each species pair; missing data reduction (matrix 3, Table 2). Degree of positive data overlap indicated by a color-coded heatmap (yellow = low, red = high); species order from right to left in the same order as listed from top to bottom on right side of figure. Lack of phylogenetic clustering indicates bias from shared data does not explain relationships seen in phylogenomic analyses.}
\label{fig:S1}
\end{figure}

\begin{figure}[ht]\centering
\includegraphics[width=16cm]{Supplemental_Material/F2_MissingData_positive_1700}
\caption{Clustering/heatmap analysis depicting degree of shared data between each species pair; missing data reduction (matrix 2, Table 2). Degree of positive data overlap indicated by a color-coded heatmap (yellow = low, red = high); species order from right to left in the same order as listed from top to bottom on right side of figure. Lack of phylogenetic clustering indicates bias from shared data does not explain relationships seen in phylogenomic analyses.}
\label{fig:S2}
\end{figure}

\begin{figure}[ht]\centering
\includegraphics[width=16cm]{Supplemental_Material/F3_MissingData_positive_BCC}
\caption{Clustering/heatmap analysis depicting degree of shared data between each species pair; BaCoCa reduced matrix (matrix 4, Table 2). Degree of positive data overlap indicated by a color-coded heatmap (yellow = low, red = high); species order from right to left in the same order as listed from top to bottom on right side of figure. Lack of phylogenetic clustering indicates bias from shared data does not explain relationships seen in phylogenomic analyses.}
\label{fig:S3}
\end{figure}

\begin{figure}[ht]\centering
\includegraphics[width=16cm]{Supplemental_Material/F4_MissingData_positive_FullArthropod}
\caption{Clustering/heatmap analysis depicting degree of shared data between each species pair;  arthropod core ortholog matrix (matrix 5, Table 2). Degree of positive data overlap indicated by a color-coded heatmap (yellow = low, red = high); species order from right to left in the same order as listed from top to bottom on right side of figure. Lack of phylogenetic clustering indicates bias from shared data does not explain relationships seen in phylogenomic analyses.}
\label{fig:S4}
\end{figure}

\begin{figure}[ht]\centering
\includegraphics[width=16cm]{Supplemental_Material/F5_MissingData_positive_FullSpider}
\caption{Clustering/heatmap analysis depicting degree of shared data between each species pair; full spider ortholog matrix (matrix 1, Table 2). Degree of positive data overlap indicated by a color-coded heatmap (yellow = low, red = high); species order from right to left in the same order as listed from top to bottom on right side of figure. Lack of phylogenetic clustering indicates bias from shared data does not explain relationships seen in phylogenomic analyses.}
\label{fig:S5}
\end{figure}

\begin{figure}[ht]\centering
\includegraphics[width=16cm]{Supplemental_Material/F6_MissingData_positive_MARE}
\caption{Clustering/heatmap analysis depicting degree of shared data between each species pair; MARE matrix (matrix 7, Table 2). Degree of positive data overlap indicated by a color-coded heatmap (yellow = low, red = high); species order from right to left in the same order as listed from top to bottom on right side of figure. Lack of phylogenetic clustering indicates bias from shared data does not explain relationships seen in phylogenomic analyses.}
\label{fig:S6}
\end{figure}

\begin{figure}[ht]\centering
\includegraphics[width=16cm]{Supplemental_Material/F7_fullspider_matrix}
\caption{Gene occupancy of matrix 1 (see Table 2). Colored squares represent partitions present in matrix for each OTU (x-axis, in descending order of OTU representation from left to right) and each partition or gene (y-axis, in ascending order of partition representation).}
\label{fig:S7}
\end{figure}

\begin{figure}[ht]\centering
\includegraphics[width=16cm]{Supplemental_Material/F8_1700spider_matrix}
\caption{Gene occupancy of matrix 2 (see Table 2).  Colored squares represent partitions present in matrix for each OTU (x-axis, in descending order of OTU representation from left to right) and each partition or gene (y-axis, in ascending order of partition representation).}
\label{fig:S8}
\end{figure}

\begin{figure}[ht]\centering
\includegraphics[width=16cm]{Supplemental_Material/F9_850spider_matrix}
\caption{Gene occupancy of matrix 3 (see Table 2). Colored squares represent partitions present in matrix for each OTU (y-axis, in descending order of OTU representation from bottom to top) and each partition or gene (x-axis, in descending order of partition representation from left to right).}
\label{fig:S9}
\end{figure}

\begin{figure}[ht]\centering
\includegraphics[width=16cm]{Supplemental_Material/F10_BCCspider_matrix}
\caption{Gene occupancy of matrix 4 (see Table 2). Colored squares represent partitions present in matrix for each OTU (y-axis, in descending order of OTU representation from bottom to top) and each partition or gene (x-axis, in descending order of partition representation from left to right).}
\label{fig:S10}
\end{figure}

\begin{figure}[ht]\centering
\includegraphics[width=16cm]{Supplemental_Material/F11_MAREspider_matrix}
\caption{Gene occupancy of matrix 7 (see Table 2). Colored squares represent partitions present in matrix for each OTU (y-axis, in descending order of OTU representation from bottom to top) and each partition or gene (x-axis, in descending order of partition representation from left to right).}
\label{fig:S11}
\end{figure}

\begin{figure}[ht]\centering
\includegraphics[width=16cm]{Supplemental_Material/F12_arthropod_matrix}
\caption{Gene occupancy of matrix 5 (see Table 2). Colored squares represent partitions present in matrix for each OTU (y-axis, in descending order of OTU representation from bottom to top) and each partition or gene (x-axis, in descending order of partition representation from left to right).}
\label{fig:S12}
\end{figure}

\begin{figure}[ht]\centering
\includegraphics[width=16cm]{Supplemental_Material/Level2_CommonOrth}
\caption{Gene Ontology molecular functions, levels 2 for OGs shared by Arthropod and Spider Core sets.  Figures generated by Blast2GO analysis.}
\label{fig:S13}
\end{figure}

\begin{figure}[ht]\centering
\includegraphics[width=16cm]{Supplemental_Material/Level3_CommonOrth}
\caption{Gene Ontology molecular functions, level 3 for OGs shared by Arthropod and Spider Core sets.  Figures generated by Blast2GO analysis.}
\label{fig:S14}
\end{figure}
\end{center}
\end{document}