#NEXUS [written 05/07/2021] BEGIN DATA; DIMENSIONS NTAX=23 NCHAR=228; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4"; MATRIX Tupaia 0-000010100110000200010011001010000110001010010(01)00001-1101100000000010100000001100100000011200010010000000?0--00?0000001000100000022?0000000001001020000-000011001010000000010110000000001101010000010011001111101000000100000000000 zzMimolagus 11?212??1?1-????????1?0??????????0?1????????????110201111-1010100-0111101001101011111000012?01?00??0??0??1?20?30?00110?0?0???100???0????????????????????????????????????????????????????????1???0?0?01(0 1)10011100010111101011?0100000? zzMimotona 111212?0111-110201001000110210100001?101???1??01111201111-101010020111101001101(01)11111000012?00?00??0?10001?201?0?00110?010???100???0????????????????????????????????????????????????????????1???????????????????????0??????????????? zzGomphos 101212?0111-110201001101110211100001110001110001110101111-101010000101102000101111111000012001?000001?000?110140?001100000?101010000??1?0111322111020100-0000100?????100100??01100001100?1??101010000011001111000100010101?0?1100001 zzPalaeolagus (01)11111?1111-1103030-2201110210400011210031110201111102111-103030020221001001221020011000012001?00??0110001?20141100110?011111101001001??11?13221?1?30?00-1000100?00101000001?1??0100110001??10101?2011010011110011101111110?01?000?? zzProlagus_sardus 1(01)1111?1111-1103030-22011102104001-1210031110211111102111-1030300-0221101001221020011000012001?00000110001?20111000110?0101111000000010012?1322211?30000-1010100?302?1??0000?11111110101110?10101020110100111100111011111100?1100000 Lepus_californicus 11111121111-1103030-2201110210400011210031110211111102111-1030300-0-21001001221020011000012001000000110001120141200110?011111101001?010111213222110300010100010003020100000111111111110111001010102011010011110011000111111001100001 Lepus_timidus 11111121111-1103030-2201110210400011210031110211111102111-1030300-0-21001001221020011000012001100000110001120141200110?0111111010011010111213222110300010100010003020100000111111111110111001010102011010011110011001111111001100001 Lepus_europaeus 11111121111-1103030-2201110210400011210031110211111102111-1030300-0-21001001221020011000012001100000110001120141200110?0111111010011010111213222110300010100010003020100000111111111110111001010102011010011110011001111111001100001 Lepus_americanus 11111121111-1103030-2201110210400011210031110211111102111-1030300-0-21001001221020011000012001100000110001120141200110?011111101001?010111213222110300010100010003020100000111111111110111001010102011010011110011001111111001100001 Brachylagus_idahoensis 11111121111-1103030-2201110210400011210031110211111102111-1030300-0-210020?12210200110000120011100001000011201412001?0?011111101001101?11121322210030101010001000302?1000001011?1111110?11001010102011?1001111?0?2?0?111111001100001 Bunolagus_monticularis 11111121111-1103030-2?01110210400011210031110211111102111-1030300-0-210020?12210200110000120011100001000011201411001?0?011111001001001?1112132221?030?01010001000302?1000001111?1111110?11001010102011?1001111?0???0?111111001100001 Caprolagus_hispidus 11111121111-1103030-2?01110210400011210031110211111102111-1030300-0-210020?12210200110000120010100001000011201411001?0?011111101001001?11121322210030?01010001000302?1000001?11?1111110?11001010102011?1001111?0???0?111111001100001 Nesolagus_timminsi 11111121111-1103030-2?01110210400011210031110211111102111-1030300-0-210010?12210200110000120010100001000011201411001?0?011111101001001??1121322210030001010001000302?1000001011?1111110?11001010102011?1001111?0???0?111111001100001 Pentalagus_furnessi 11111121111-1103030-2201110210400011210031110211111102111-1030300-0-210020?1221020011000112001?100001000011201411001?0?011111101001001?11121322210030001010001000302?1000001111?1111110?11001010102011?1001111?0?2?0?111111001100001 Poelagus_marjorita 11111121111-1103030-2?01110210400011210031110211111102111-1030300-0-210020?12210200110000120011100001000011201411001?0?011111101001001?11121322210030001010001000302?1000001111?1111110?11001010102011?1001111?0???01111111001100001 Romerolagus_diazi 11111121111-1103030-2201110210400011210031110210111102111-1030300-0-210020?12210200110000120010100001000011201411001?0?011111101001001?11121322211030?01010001000302?1000001011?1111110?11001010102011?1001111?0?2?0?111111001100001 Pronolagus_crassicaudatus 11111121111-1103030-2101110?10400011210031110211111102111-1030300-0-210020?12210200110000120011100001000011201411001?0?011111101001101?11121322210030?01010001000302??000001111?1111110?11?01010102011?1?01111?0?2?0?111111001100001 Oryctolagus_cuniculus 11111121111-1103030-2201110210400011210031110210111102111-1030300-0-210010012210200110000120011101001000(01)1120141100100?011111001001101311121322210030101010001000302?10000010111111111001100101010201101001111100200(01)111111001100001 Ochotona_pallasi 10111121111-110?030-2201110210400011210031110211111102111-1030300-0221101001?21020011000112001000100110001120111000110?010111100000001001221322211(01)300010102010002021100000110111111010(01)11001010102011010011110011101111110001100000 Ochotona_princeps 10111121111-1103030-2201110210400011210031110211111102111-1030300-0221101001221020011000112001000100110001120111000110?010111100000001001221322211(01)300010102010002021100000110111111010(01)11001010102011010011110011101111110001100000 Sylvilagus_audubonii 11111121111-1103030-2101110210400011210031110210111102111-1010300-0-210020112210200110000120010100001000(01)1120141200110?011111101001101311121322210030101010001000302?100000101101111110011001010102011110011110012000111111001100001 Sylvilagus_bachmanii 11111121111-1103030-2101110210400011210031110210111102111-1010300-0-21002011221020011000012001?100001000(01)1120141200110?011111101001101311121322210030101010001000302?10000010110111111001100101010201111001111001200011111100?100001 ; END; begin mrbayes; [start logfile] log start filename="leporid_morpho_bayescal_cal_constrained"; [close after running] set autoclose=yes nowarn=yes; [outgroup] outgroup Tupaia; [constrain ingroup] [constrain clades] constraint ingroup = 2-.; constraint Lepus = 7-10; constraint Ochotona = 20-21; constraint Sylvilagus = 22-23; constraint Leporids = Lepus_californicus Lepus_timidus Lepus_europaeus Lepus_americanus Brachylagus_idahoensis Bunolagus_monticularis Caprolagus_hispidus Nesolagus_timminsi Pentalagus_furnessi Poelagus_marjorita Romerolagus_diazi Pronolagus_crassicaudatus Oryctolagus_cuniculus Sylvilagus_audubonii Sylvilagus_bachmanii; constraint clade_one = zzProlagus_sardus Ochotona_pallasi Ochotona_princeps; constraint clade_two = Nesolagus_timminsi Poelagus_marjorita Pronolagus_crassicaudatus; constraint clade_three = Caprolagus_hispidus Bunolagus_monticularis Oryctolagus_cuniculus Pentalagus_furnessi; constraint clade_four = Romerolagus_diazi Brachylagus_idahoensis Sylvilagus_audubonii Sylvilagus_bachmanii; [helps to seep up analysis, reach convergence and correct rooting] prset topologypr=constraints(ingroup, Lepus, Ochotona, Sylvilagus, Leporids, clade_one, clade_two, clade_three, clade_four); [set character evol model] lset coding=variable rates=gamma; [Mkv+G] [set prior parameters for rate variation among characters] prset ratepr=variable; [set hyperprior parameters for rate variation among charatcers] prset shapepr=exponential (1.0); [Tree model] [tip calibrations] calibrate zzMimolagus=uniform(37,40) zzMimotona=uniform(56,62) zzGomphos=uniform(37,56) zzPalaeolagus=uniform(20,34) zzProlagus_sardus=uniform(0.012,0.7) [constraint node calibrations] [ingroup=offsetexp(23.32,39.26)] Lepus=offsetexp(4.03,5.90) Ochotona=offsetexp(23.31,39.26) Sylvilagus=offsetexp(2.43,6.65) [Leporids=offsetexp(12.20,20.23)] [clade_two=offsetexp(8.1,15.98)] [clade_three=offsetexp(6.11,12.14)] [clade_four=offsetexp(6.43,12.65)]; prset nodeagepr=calibrated; [activates the fossilized birth-death tree model] prset brlenspr = clock:fossilization; [FBD] [broad prior on the net diversification rate] prset speciationpr = exp(10); [flat prior on the relative extinction (turnover) rate] prset extinctionpr = beta(1,1); [flat prior on the relative fossilization rate (sampling proportion)] prset fossilizationpr = beta(1,1); [prior on the fraction of extant species that are sampled in the analysis = 18/23] prset sampleprob = 0.78; [strategy under which species were sampled = maximize diversity since species were sampled to represent all major lineages/families] prset samplestrat = diversity; [places a soft upper bound constrain on the age of the tree] [mimotona dos Reis et al.2013] prset treeagepr = offsetexp(69,80); [clock model] [base of clock rate: clockrate informative prior based on previous nonclock analysis = median value for tree height in substitutions from posterior trees/ age of the tree based on the median of the distribution for the root prior] prset clockratepr=lognorm(-3.204691,1.04); [clock model for rate variation among lineages: IGR - relaxed uncorrelated clock with values sampled from a gamma distribution] prset clockvarpr=IGR; [hyperprior on shape of gamma distribution from IGR clock] prset igrvarpr=exp(10); [analysis parameters] mcmcp ngen= 7000000 relburnin=yes burninfrac=0.5 printfreq=1000 samplefreq=1000 temp=0.4 nruns=2 nchains=6 nswaps=3 savebrlens=yes; [start running] mcmc; [summarize parameters] sump; [summarize trees] sumt contype=allcompat Outputname=Leporid_Morpho_Bayescal_cal_constrained_AllCompCon.t; [MC tree] sumt contype=halfcompat Outputname=Leporid_Morpho_Bayescal_cal_constrained_MRC.t; [MRC tree] [close logfile] log stop; end;