pythonVersion 2.7.16 pythonImplementation CPython false Birds true This can be deleted tree1 Supplementary data 7 To create, take original file, then in R: tree <- read.tree("1-s2.0-S1055790317300477-mmc7.new") tips <- strsplit(tree$tip.label, "_") g <- unlist(lapply(tips, "[", 1)) s <- unlist(lapply(tips, "[", 2)) spp <- paste(g, s, sep="_") tree2 <- tree tree2$tip.label <- as.character(spp) indices <- 1:length(tree$tip.label) dups <- spp[duplicated(spp)] toReplace <- indices[tree2$tip.label %in% dups] tree2$tip.label[tree2$tip.label %in% dups] <- tree$tip.label[toReplace] write.tree(tree2, "forImport.tree") tree1 otu145 otu146 otu15 otu16 otu168 otu169 otu176 otu177 otu185 otu186 otu211 otu212 otu226 otu227 otu228 otu231 otu23 otu24 otu25 otu31 otu29 otu30 otu44 otu45 otu47 otu48 otu5 otu6 otu61 otu62 otu67 otu68 otu84 otu85 ^ot:comment ^ot:nodeLabelMode ^ot:nodeLabelTimeUnit ^ot:reasonsToExcludeFromSynthesis ^ot:ottId merge check (EJM) eliotmiller Emily Jane McTavish 1020138 Picidae ot_2017 Shakya, S. B., Fuchs, J., Pons, J.-M., & Sheldon, F. H. (2017). Tapping the woodpecker tree for evolutionary insight. Molecular Phylogenetics and Evolution, 116, 182–191. doi:10.1016/j.ympev.2017.09.005 2017 Indicator indicator Indicator indicator JF4138 Picumnus varzeae Picumnus varzeae LSU25565 Celeus obrien Celeus obrieni AMNH242687 Celeus spectabilis LSU45460 Colaptes aurulentus FMNH395722 Piculus chrysochloros K53 149826 Piculus chrysochloros Piculus flavigula LSU12780 Piculus callopterus LSU51433 Piculus leucolaemus LSU6795 Piculus litae LSU11800 Colaptes auratus AMNHPAC820 Colaptes chrysoides LSU5756 Picumnus minutissimus YPM137243 Colaptes auricularis FMNH394211 Colaptes atricollis LSU100056 Colaptes rubiginosus LSU32995 Colaptes campestris LSU26064 Colaptes punctigula LSU7274 Colaptes melanochloros NRM947052 Colaptes rivolii LSU31804 Colaptes pitius KU11678 Colaptes rupicola LSU26059 Blythipicus pyrrhotis MNHN1562 Picumnus spilogaster KU5851 Blythipicus rubiginosus ZMUC115602 Chrysocolaptes validus LSU38653 Chrysocolaptes lucidus MNHN042D Chrysocolaptes erythrocephalus UAM25329 Chrysocolaptes haematribon UAM29073 Campephilus haematogaster ZMUC114730 Campephilus imperialis MCZ302882 Campephilus principalis USNM195199 Campephilus magellanicus KU11713 Campephilus leucopogon USNM609524 Picumnus temminckii ZMUC115793 Campephilus robustus UMMZ200730 Campephilus rubricollis LSU48392 Campephilus pollens LSU32066 Campephilus guatemalensis DA05 Campephilus gayaquilensis LSU66134 Campephilus melanoleucos NRM966949 Sphyrapicus thyroideus LSU51542 Sphyrapicus varius CAS89230 Sphyrapicus nuchalis LSU55515 Sphyrapicus ruber USNM621107 Picumnus steindachneri LSU44105 Melanerpes striatus KU8014 Melanerpes lewis LSU24677 Melanerpes erythrocephalus LSU55063 Melanerpes herminieri K14 925306 Melanerpes herminieri Melanerpes portoricensis LSU11314 Melanerpes formicivorus CAS92857 576224 Melanerpes formicivorus Melanerpes formicivorus UWBM81380 576224 Melanerpes formicivorus Melanerpes cactorum LSU38143 Melanerpes candidus LSU37801 Melanerpes chrysauchen LSU41588 Picumnus albosquamatus FMNH334415 3600241 Picumnus albosquamatus Melanerpes pucherani LSU46624 Melanerpes cruentatus LSU42572 Melanerpes flavifrons NRM967085 Melanerpes hypopolius LSU30254 Melanerpes pygmaeus KU2009 Melanerpes chrysogenys LSU30250 Melanerpes hoffmanni Z11 3600222 Melanerpes hoffmannii Melanerpes rubricapillus LSU16528 Melanerpes uropygialis LSU36940 Melanerpes radiolatus FMNH331073 Picumnus albosquamatus Z16 3600241 Picumnus albosquamatus Melanerpes superciliaris FMNH431721 Melanerpes santacruzi LSU60740 Melanerpes aurifrons LSU29763 Melanerpes carolinus USNM626309 Picoides arcticus MVZ177838 Picoides dorsalis LSU10193 Picoides tridactylus ZMUC115007 Yungipicus canicapillus M44 701707 Dendrocopos canicapillus Yungipicus moluccensis AMNH9620 377175 Dendrocopos moluccensis Yungipicus moluccensis USNM583026 377175 Dendrocopos moluccensis Picumnus cirratus LSU25725 Yungipicus maculatus FMNH344963 Yungipicus kizuki UWBM47379 Yungipicus temminckii MNHNCG18971343 Leiopicus mahrattensis USNM586658 Dendrocoptes auriceps AMNH5534 Dendrocoptes dorae BMNH1938101823 Dendrocoptes medius ZMUC130576 499959 Dendrocopos medius Dendrocoptes medius DD34 499959 Dendrocopos medius Dendropicos namaquus MNHNCG2013272 Dendropicos pyrrhogaster FMNH396512 Picumnus dorbignyanus LSU34601 Dendropicos xantholophos D01 Dendropicos obsoletus DA71 Dendropicos stierlingi DB90 Dendropicos goertae JF566 Dendropicos spodocephalus DC14 Dendropicos griseocephalus ZMUC120456 329876 Dendropicos griseocephalus Dendropicos griseocephalus DB30 329876 Dendropicos griseocephalus Dendropicos abyssinicus DC15 Dendropicos gabonensis JF1513 Dendropicos lugubris DC04 Picumnus castelnau LSU7295 Dendropicos elliotii FMNH384843 Dendropicos elachus DC03 Dendropicos fuscescens FMNH384481 Dendropicos poecilolaemus JF507 Dendrocopos hyperythrus KU9939 Dendrocopos macei Z8 499952 Dendrocopos macei Dendrocopos atratus KU30742 Dendrocopos leucotos NRM996095 Dendrocopos noguchii YIO20090963 Dendrocopos himalayensis MNHNCG1939252 Indicator maculatus GB 552486 Indicator maculatus Picumnus subtilis LSU48206 Dendrocopos syriacus MNHN36H05 Dendrocopos assimilis MNHNCG1991156 Dendrocopos darjellensis AMNH5627 Dendrocopos major JF3892 Dendrocopos leucopterus ZMUC55700 Dryobates minor NR986593 Dryobates cathpharius MNHNCG1896719 Dryobates pubescens LSU40943 Dryobates nuttallii LSU49305 Dryobates scalaris LSU36938 Picumnus rufiventris LSU42916 Leuconotopicos borealis UWBM86645 Leuconotopicos villosus FMNH428786 733988 Picoides villosus Leuconotopicos villosus LSU19818 733988 Picoides villosus Leuconotopicos fumigatus LSU35763 Leuconotopicos albolarvatus LSU56661 Leuconotopicos arizonae MSB29802 Leuconotopicos stricklandi UWBM77746 Veniliornis affinis LSU11700 Veniliornis chocoensis Z26 876882 Veniliornis chocoensis Veniliornis spilogaster LSU25914 Picumnus squamatulus AMNH8879 Veniliornis lignarius LSU5693 Veniliornis mixtus LSU25793 Veniliornis cassini LSU20214 Veniliornis kirkii LSU46756 Veniliornis nigriceps LSU100051 Veniliornis dignus LSU8043 Veniliornis callonotus LSU44755 65431 Veniliornis callonotus Veniliornis callonotus Z25 65431 Veniliornis callonotus Veniliornis passerinus LSU43064 612926 Veniliornis passerinus Veniliornis sanguineus YPM137448 Picumnus exilis FMNH399173 130072 Picumnus exilis Veniliornis frontalis UWBM70727 Veniliornis passerinus LSU26094 612926 Veniliornis passerinus Indicator indicator 727823 Indicator indicator Indicator maculatus 552486 Indicator maculatus Indicator minor 494191 Indicator minor Jynx ruficollis 3600188 Jynx ruficollis Picumnus innominatus 802075 Picumnus innominatus Picumnus nebulosus 130075 Picumnus nebulosus Picumnus exilis Guy0302 130072 Picumnus exilis Picumnus pygmaeus 945043 Picumnus pygmaeus Picumnus varzeae 3600247 Picumnus varzeae Picumnus minutissimus 3600240 Picumnus minutissimus Picumnus spilogaster 130074 Picumnus spilogaster Picumnus temminckii 678452 Picumnus temminckii Picumnus steindachneri 3600250 Picumnus steindachneri Picumnus cirratus 839547 Picumnus cirratus Picumnus dorbignyanus 3600238 Picumnus dorbignyanus Picumnus lafresnayi LSU25473 945031 Picumnus lafresnayi Picumnus castelnau 3600242 Picumnus castelnau Picumnus subtilis 3600237 Picumnus subtilis Picumnus rufiventris 952672 Picumnus rufiventris Picumnus squamatulus 3600235 Picumnus squamulatus Picumnus pumilus 3600243 Picumnus pumilus Picumnus sclateri 3600249 Picumnus sclateri Picumnus olivaceus 3600244 Picumnus olivaceus Picumnus pumilus AMNH14190 Verreauxia africana 155286 Verreauxia africana Sasia abnormis 149822 Sasia abnormis Sasia ochracea 678453 Sasia ochracea Hemicircus canente 1025757 Hemicircus canente Hemicircus concretus 3600185 Hemicircus concretus Micropternus brachyurus 1076469 Micropternus brachyurus Picumnus sclateri LSU66121 Meiglyptes tukki 149819 Meiglyptes tukki Meiglyptes tristis 726782 Meiglyptes tristis Meiglyptes jugularis 3600184 Meiglyptes jugularis Gecinulus grantia 449214 Gecinulus grantia Dinopium rafflesii 3600186 Dinopium rafflesii Picumnus olivaceus LSU60837 Picus chlorolophus 1076474 Picus chlorolophus Picus puniceus 1031329 Picus puniceus Picus squamatus 3600218 Picus squamatus Picus xanthopygaeus 454978 Picus xanthopygaeus Picus rabieri 1031331 Picus rabieri Picus vittatus 1031343 Picus vittatus Picus viridanus 1031330 Picus viridanus Picus awokera 1086622 Picus awokera Picus canus 226445 Picus canus Picus erythropygius 1031332 Picus erythropygius Picumnus aurifrons LSU35376 706454 Picumnus aurifrons Picus vaillantii 282399 Picus vaillantii Picus sharpei 1031342 Picus sharpei Chrysophlegma miniaceum 724188 Chrysophlegma miniaceum Chrysophlegma mentale 738744 Chrysophlegma mentale Chrysophlegma flavinucha 968224 Chrysophlegma flavinucha Campethera caroli 952595 Campethera caroli Indicator minor GB 494191 Indicator minor Picumnus aurifrons LSU46136 706454 Picumnus aurifrons Campethera olivaceus 724169 Geocolaptes olivaceus Campethera tullbergi 3600210 Campethera tullbergi Campethera cailliautii 724180 Campethera cailliautii Campethera maculosa 3600217 Campethera maculosa Campethera nubica 3600213 Campethera nubica Campethera punctuligera 3600215 Campethera punctuligera Campethera scriptoricauda 5560013 Campethera scriptoricauda Campethera bennetti 3600212 Campethera bennettii Campethera notata 3600216 Campethera notata Campethera abingoni 3600211 Campethera abingoni Picumnus lafresnayi FMNH473979 945031 Picumnus lafresnayi Campethera mombasica 3600214 Campethera mombassica Mulleripicus fuliginosus 5925777 Mulleripicus fuliginosus Mulleripicus funebris 149816 Mulleripicus funebris Mulleripicus pulverulentus 3600183 Dryocopus pulverulentus Dryocopus martius 459335 Dryocopus martius Dryocopus pileatus 733984 Dryocopus pileatus Dryocopus lineatus 290738 Dryocopus lineatus Dryocopus schulzi 3600192 Dryocopus schulzi Verreauxia africana LSU27113 Celeus torquatus 724968 Celeus torquatus Celeus loricatus 704541 Celeus loricatus Celeus ochraceus 6520258 Celeus ochraceus Celeus flavescens 704537 Celeus flavescens Celeus elegans 724183 Celeus elegans Celeus lugubris 499951 Celeus lugubris Celeus galeatus 3600190 Celeus galeatus Celeus castaneus 724960 Celeus castaneus Celeus grammicus 499964 Celeus grammicus Celeus undatus 724966 Celeus undatus Sasia abnormis LSU36374 Celeus flavus 524497 Celeus flavus Celeus obrieni 724964 Celeus obrieni Celeus spectabilis 983476 Celeus spectabilis Colaptes aurulentus 3600209 Piculus aurulentus Piculus chrysochloros 149826 Piculus chrysochloros Piculus flavigula 876872 Piculus flavigula Piculus callopterus 3600207 Piculus callopterus Piculus leucolaemus 876874 Piculus leucolaemus Piculus litae 5560019 Piculus litae Colaptes auratus 733990 Colaptes auratus Sasia ochracea MNHNCG20052676 Colaptes chrysoides 3600175 Colaptes chrysoides Colaptes auricularis 838429 Colaptes auricularis Colaptes atricollis 290736 Colaptes atricollis Colaptes rubiginosus 210496 Colaptes rubiginosus Colaptes campestris 994349 Colaptes campestris Colaptes punctigula 923815 Colaptes punctigula Colaptes melanochloros 499950 Colaptes melanochloros Colaptes rivolii 290740 Colaptes rivolii Colaptes pitius 994333 Colaptes pitius Colaptes rupicola 1020134 Colaptes rupicola Nescotites micromegas 130077 Nesoctites micromegas Blythipicus pyrrhotis 534436 Blythipicus pyrrhotis Blythipicus rubiginosus 77828 Blythipicus rubiginosus Chrysocolaptes validus 1025755 Chrysocolaptes validus Chrysocolaptes lucidus 724186 Chrysocolaptes lucidus Chrysocolaptes erythrocephalus 6154937 Chrysocolaptes erythrocephalus Chrysocolaptes haematribon 5560014 Chrysocolaptes lucidus haematribon Campephilus haematogaster 706428 Campephilus haematogaster Campephilus imperialis 12995 Campephilus imperialis Campephilus principalis 78185 Campephilus principalis Campephilus magellanicus 64703 Campephilus magellanicus Hemicircus canente MNHNJF317 Campephilus leucopogon 499963 Campephilus leucopogon Campephilus robustus 3600233 Campephilus robustus Campephilus rubricollis 704536 Campephilus rubricollis Campephilus pollens 78216 Campephilus pollens Campephilus guatemalensis 704538 Campephilus guatemalensis Campephilus gayaquilensis 64702 Campephilus gayaquilensis Campephilus melanoleucos 724190 Campephilus melanoleucos Sphyrapicus thyroideus 90563 Sphyrapicus thyroideus Sphyrapicus varius 744570 Sphyrapicus varius Sphyrapicus nuchalis 90562 Sphyrapicus nuchalis Hemicircus concretus MNHNCG1960787 Sphyrapicus ruber 200801 Sphyrapicus ruber Melanerpes striatus 122919 Melanerpes striatus Melanerpes lewis 90564 Melanerpes lewis Melanerpes erythrocephalus 800693 Melanerpes erythrocephalus Melanerpes herminieri 925306 Melanerpes herminieri Melanerpes portoricensis 3600223 Melanerpes portoricensis Melanerpes cactorum 199362 Melanerpes cactorum Melanerpes candidus 90565 Melanerpes candidus Micropternus brachyurus USNM620445 Melanerpes chrysauchen 3600221 Melanerpes chrysauchen Melanerpes pucherani 199361 Melanerpes pucherani Melanerpes cruentatus 90567 Melanerpes cruentatus Melanerpes flavifrons 499949 Melanerpes flavifrons Melanerpes hypopolius 3600227 Melanerpes hypopolius Melanerpes pygmaeus 199360 Melanerpes pygmaeus Melanerpes chrysogenys 3600232 Melanerpes chrysogenys Melanerpes hoffmanni 3600222 Melanerpes hoffmannii Melanerpes rubricapillus 3600228 Melanerpes rubricapillus Melanerpes uropygialis 122918 Melanerpes uropygialis Meiglyptes tukki LSU57074 Melanerpes radiolatus 3600224 Melanerpes radiolatus Melanerpes superciliaris 3600225 Melanerpes superciliaris Melanerpes santacruzi 7068737 Melanerpes santacruzi Melanerpes aurifrons 425443 Melanerpes aurifrons Melanerpes carolinus 119082 Melanerpes carolinus Picoides arcticus 329874 Picoides arcticus Picoides dorsalis 183619 Picoides dorsalis Picoides tridactylus 178448 Picoides tridactylus Yungipicus canicapillus 701707 Dendrocopos canicapillus Jynx ruficollis DD62 Meiglyptes tristis LSU36352 Yungipicus maculatus 701712 Dendrocopos maculatus Yungipicus kizuki 7662877 Yungipicus kizuki Yungipicus temminckii 3600197 Picoides temminckii Leiopicus mahrattensis 1076483 Leiopicus mahrattensis Dendrocoptes auriceps 7662873 Dendrocoptes auriceps Dendrocoptes dorae 3600195 Dendrocopos dorae Dendropicos namaquus 3600169 Chloropicus namaquus Meiglyptes jugularis MNHNCG1939926 Dendropicos pyrrhogaster 499953 Chloropicus pyrrhogaster Dendropicos xantholophos 7658189 Dendropicus xantholophus Dendropicos obsoletus 3600170 Ipophilus obsoletus Dendropicos stierlingi 3600168 Dendropicos stierlingi Dendropicos goertae 704540 Dendropicos goertae Dendropicos spodocephalus 5560015 Dendropicos spodocephalus Dendropicos abyssinicus 3600172 Dendropicos abyssinicus Dendropicos gabonensis 123173 Dendropicos gabonensis Gecinulus grantia MNHN0516 Dendropicos lugubris 5560016 Dendropicos lugubris Dendropicos elliotii 499958 Dendropicos elliotii Dendropicos elachus 3600173 Dendropicos elachus Dendropicos fuscescens 329875 Dendropicos fuscescens Dendropicos poecilolaemus 3600174 Dendropicos poecilolaemus Dendrocopos hyperythrus 704539 Dendrocopos hyperythrus Dendrocopos macei 499952 Dendrocopos macei Dendrocopos atratus 3600205 Dendrocopos atratus Dendrocopos leucotos 309879 Dendrocopos leucotos Dendrocopos noguchii 534442 Dendrocopos noguchii Dinopium rafflesii LSU57083 Dendrocopos himalayensis 3600201 Dendrocopos himalayensis Dendrocopos syriacus 792919 Dendrocopos syriacus Dendrocopos assimilis 3600196 Dendrocopos assimilis Dendrocopos darjellensis 3600200 Dendrocopos darjellensis Dendrocopos major 348848 Dendrocopos major Dendrocopos leucopterus 744792 Dendrocopos leucopterus Dryobates minor 701710 Dendrocopos minor Dryobates cathpharius 3600202 Dendrocopos cathpharius Dryobates pubescens 873958 Picoides pubescens Dryobates nuttallii 701703 Picoides nuttallii Dinopium benghalense AMNH11104 3600187 Dinopium benghalense Dryobates scalaris 701702 Picoides scalaris Leuconotopicos borealis 701708 Picoides borealis Leuconotopicos fumigatus 876880 Picoides fumigatus Leuconotopicos albolarvatus 878373 Picoides albolarvatus Leuconotopicos arizonae 45511 Picoides arizonae Leuconotopicos stricklandi 178446 Picoides stricklandi Veniliornis affinis 860562 Veniliornis affinis Veniliornis chocoensis 876882 Veniliornis chocoensis Dinopium benghalense Z7 3600187 Dinopium benghalense Veniliornis spilogaster 302153 Veniliornis spilogaster Veniliornis lignarius 701705 Veniliornis lignarius Veniliornis mixtus 701709 Veniliornis mixtus Veniliornis cassini 860564 Veniliornis cassini Veniliornis kirkii 876870 Veniliornis kirkii Veniliornis nigriceps 65433 Veniliornis nigriceps Veniliornis dignus 876884 Veniliornis dignus Dinopium shorii 704547 Dinopium shorii Veniliornis sanguineus 454017 Veniliornis sanguineus Veniliornis frontalis 876878 Veniliornis frontalis Dinopium javanense LSU61522 1076468 Dinopium javanense Dinopium javanense M78 1076468 Dinopium javanense Picus chlorolophus USNM620432 Jynx torquilla DD33 467846 Jynx torquilla Picus puniceus N16 Picus squamatus ZMUC55689 Picus xanthopygaeus O99 454978 Picus xanthopygaeus Picus rabieri NRM23 Picus vittatus DD50 Picus viridanus M67 1031330 Picus viridanus Picus awokera L9 1086622 Picus awokera Picus canus NRM25 Picus erythropygius DD49 Picus vaillantii P148 Jynx torquilla MNHN1503 467846 Jynx torquilla Picus sharpei P214 Picus viridis JF3718 1010553 Picus viridis Picus viridis MNHNC38 1010553 Picus viridis Chrysophlegma miniaceum DB94 Chrysophlegma mentale LSU36478 Chrysophlegma flavinucha NRM22 Campethera caroli M38 952595 Campethera caroli Campethera nivosa MNHN0128 755098 Campethera nivosa Campethera nivosa JF3553 755098 Campethera nivosa Campethera olivaceus UWBM53192 Picumnus innominatus O76 802075 Picumnus innominatus Campethera tullbergi JP1443 Campethera cailliautii JF556 Campethera maculosa DC08 Campethera nubica JF786 Campethera punctuligera JP1444 Campethera scriptoricauda DB83 Campethera bennetti DNSM28947 Campethera notata MNHN1981 18 Campethera abingoni DA06 Campethera mombasica DC87 Picumnus nebulosus YPM100972 Mulleripicus fuliginosus KU18168 Mulleripicus funebris ZMUC114105 Mulleripicus pulverulentus KU12739 Dryocopus martius NRM20016156 Dryocopus javensis KU20897 3600191 Dryocopus javensis Dryocopus javensis W46 3600191 Dryocopus javensis Dryocopus pileatus CAS86173 Dryocopus lineatus NRM967106 Dryocopus schulzi LSU26113 Celeus torquatus LSU25574 Picumnus pygmaeus Z18 945043 Picumnus pygmaeus Celeus loricatus LSU11832 Celeus ochraceus FMNH63975 Celeus flavescens KU304 Celeus elegans LSU35528 Celeus lugubris NRM947231 Celeus galeatus UMMZ202091 Celeus castaneus LSU41627 Celeus grammicus LSU105252 Celeus undatus LSU48401 Celeus flavus LSU34957 ot:undefined node7 node1 false true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true