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ResolvingthePhylogeneticPositionofCoelacanth:TheClosest RelativeIsNotAlwaystheMostAppropriateOutgroup Takezaki N,NishiharaH.2016.GenomeBiol Evol 8:1208-1221. Abstract Determiningthephylogeneticrelationshipoftwoextantlineagesoflobe-finnedfish,coelacanths andlungfishes,andtetrapods isimportantforunderstandingtheoriginoftetrapods.Weanalyzed datasetsfromtwopreviousstudiesalongwithanewlycollecteddataset,eachofwhichhad varyingnumbersofspeciesandgenesandvaryingextentofmissingsites.Wefoundthatinallthe datasetsthesisterrelationshipoflungfishandtetrapods wasconstructedwiththeuseof cartilaginousfishastheoutgroupwithahighdegreeofstatisticalsupport.Incontrast,whenrayfinnedfishwereusedastheoutgroup,whichistaxonomicallyanimmediateoutgroupoflobefinnedfishandtetrapods,thesisterrelationshipofcoelacanthandtetrapods wassupportedmost strongly,althoughthestatisticalsupportwasweaker.Eventhoughitisgenerallyacceptedthatthe closestrelativeisanappropriateoutgroup,ouranalysissuggestedthatthelargedivergenceofthe ray-finnedfishasindicatedbytheirlongbranchlengthsanddifferentaminoacidfrequenciesmade themlesssuitableasanoutgroupthancartilaginousfish. a) Lobe-finned vertebrate Bony vertebrates Ray-finned fish Cartilaginous fish b) Tree 1 Tetrapod Lungfish Coelacanth Ray-finned fish Tetrapod Tree 2 Coelacanth Lungfish Ray-finned fish Tetrapod Tree 3 Coelacanth Lungfish Ray-finned fish Fig.1.—Thephylogeneticrelationshipofthemajorlineagesinjawedvertebratesandlobe-finned vertebrates.(a)Therelationshipofmajorlineagesinjawedvertebrates.(b)Threepossible relationshipsforthethreeextantlineagesoflobe-finnedvertebrates:sisterrelationshipsoflungfishes andtetrapods (Tree1),coelacanthsandtetrapods (Tree2)andlungfishesandcoelacanths(Tree3). Table1 DatasetsAnalyzedinThisStudy Note.—IndatasetI,onlyconcatenatedsequencewasavailable,andtwosharkspecieswere missing.IndatasetIIgeneswith<50aminoacidsiteswereexcluded. Missingsites Dataset Source I Amemiyaetal. II Liangetal. III Thisstudy Genes Aminoacidsites (%) Species 251 112,212 20 14.2 1,288 618,946 10 6.5 831 242,475 25 0 a) Human Mouse 54 0.05 Dog 100 Armadillo 100 Elephant Tammar wallaby 100 100 Opossum Platypus 100 100 Chicken 100 Turkey 100 Zebra finch 100 Lizard Western clawed frog 100 Chinese brown frog Lungfish Coelacanth Tilapia 100 Pufferfish 100 Zebrafish Little skate 99 99 87 97 b) Human Chicken 100 100 100 100 Western clawed frog Lungfish Coelacanth Pufferfish 100 100 100 d) Human Mouse Dog Armadillo 100 Elephant Tammar wallaby 100 100 Opossum Platypus 100 100 Chicken 100 Turkey Zebra finch 100 Lizard Western clawed frog 100 Chinese brown frog Coelacanth Lungfish Tilapia 100 Pufferfish 100 Zebrafish 99 99 59 100 0.05 100 54 e) 100 100 0.05 Human Chicken 95 Western clawed frog Coelacanth Lungfish Zebrafish Spotted catshark Little skate Pufferfish 100 Zebrafish Elephant shark 0.05 Human Mouse Dog Elephant 100 77 Armadillo 0.05 Tasmanian devil 100 Opossum 100 Chicken 100 100 Turkey 100 Duck 100 100 Flycatcher Turtle 100 100 Lizard Western clawed frog 100 Lungfish Coelacanth Platyfish 100 100 Medaka Tilapia 100 Stickleback 100 Pufferfish 79 Cod 100 Zebrafish Spotted catshark 100 Little skate 100 Elephant shark c) 100 100 100 f) Human Mouse Dog 100 Elephant 100 Armadillo 73 Tasmanian devil 100 Opossum 100 100 Chicken 100 Turkey 100 Duck 100 Flycatcher Turtle 100 Lizard Western clawed frog Coelacanth Lungfish 100 Platyfish 100 Medaka 100 Tilapia Stickleback 100 95 Pufferfish Cod Zebrafish 100 100 0.05 100 52 100 Fig. 2.—Maximum likelihood trees constructed for concatenated sequences of the three datasets. (a)– (c): CF and RF were used as the outgroup. (d)–(f): RF were used as the outgroup. (a), (d): Dataset I from Amemiya et al. (2013). (b), (e): Dataset II from Liang et al. (2013). (c), (f): Dataset III collected in this study. The numbers on the branches are BPs from 500 replications. The trees were constructed with the JTTFG4 setting by PhyML.