Polymixia japonica 100 Polymixia lowei Anoplogaster cornuta Beryx splendens Periophthalmus magnuspinnatus 92 Kurtus gulliveri 95 Pholidichthys leucotaenia 86 Pomatomus saltatrix 100 Ruvettus pretiosus 100 89 Scomber scombrus 90 Thunnus orientalis Diplectrum formosum 96 Epinephelus akaara Notothenia coriiceps 100 96 Etheostoma radiosum 100 Perca flavescens 95 100 Sebastes elongatus 100 Anoplopoma fimbria 100 Aulorhynchus flavidus 100 Gasterosteus aculeatus Eugerres plumieri Cheilio inermis 98 Novaculichthys taeniourus 100 Xyrichtys novacula 100 Doratonotus megalepis 100 94 Thalassoma lunare 100 Coris gaimard 100 84 Halichoeres chrysus 100 Hemigymnus fasciatus 100 100 90 Labroides dimidiatus Haletta semifasciata 71 Cirrhilabrus punctatus 100 Pseudocheilinus hexataenia 71 Tautoga onitis 100 Tautogolabrus adspersus Scarus ghobban 94 100 100 Sparisoma viride 100 Epibulus insidiator 100 Oxycheilinus bimaculatus Terapon jarbua 100 Dichistius multifasciatus 100 Microcanthus strigatus 98 Cheilodactylus variegatus 100 Siniperca chuatsi 60 Elassoma evergladei 60 Lepomis macrochirus 86 100 Micropterus dolomieu Lateolabrax japonicus Platax orbicularis 91 Dicentrarchus labrax 81 100 Morone chrysops 86 100 Morone saxatilis Haemulon plumierii 99 Larimichthys crocea 100 Miichthys miiuy Holacanthus ciliaris 97 Scatophagus argus 89 Lutjanus campechanus 97 99 Monodactylus argenteus 100 Luvarus imperialis 100 Zanclus cornutus 100 Zebrasoma flavescens Antigonia capros 94 Capros aper Himantolophus albinares 94 98 Lophius americanus 93 Canthidermis maculata 100 Mola mola 100 Takifugu rubripes Caranx hippos 100 Coryphaena hippurus 100 Xiphias gladius 94 Lates calcarifer 98 Pseudopleuronectes yokohamae Ctenopoma acutirostre 100 Trichopodus trichopterus Ambassis interrupta 89 Monocirrhus polyacanthus 88 87 Crenimugil crenilabis 100 Mugil cephalus 100 Mugil curema Bedotia geayi 100 Melanotaenia parkinsoni Cololabis saira 99 99 Menidia menidia 88 99 Oryzias latipes 91 Kryptolebias marmoratus 100 Nothobranchius furzeri Cyprinodon variegatus 100 100 Fundulus heteroclitus 89 100 Poecilia reticulata 100 Xiphophorus maculatus Etroplus maculatus 100 Paretroplus maculatus Paratilapia polleni 100 Ptychochromis grandidieri 100 100 100 Ptychochromoides katria Crenicichla lepidota 100 100 Astronotus ocellatus Andinoacara rivulatus OVALENTARIA 99 100 Amphilophus citrinellus 100 100 Hypselecara temporalis Tylochromis pulcher 100 Oreochromis niloticus 100 Neolamprologus brichardi 100 Haplochromis burtoni 100 Tropheus duboisi Halidesmus scapularis 77 Plesiops coeruleolineatus 82 Pseudoplesiops revellei 96 Labracinus cyclophthalmus 86 100 Pseudochromis jamesi Gramma loreto 57 Lonchopisthus micrognathus 96 100 Opistognathus aurifrons 100 Opistognathus maxillosus 100 Acyrtops beryllinus Meiacanthus grammistes 100 100 Salarias fasciatus 99 Neoclinus blanchardi 100 Chaenopsis alepidota 100 Malacoctenus triangulatus Amphistichus rhodoterus Cymatogaster aggregata 100 100 Micrometrus minimus 99 Embiotoca jacksoni 92 Zalembius rosaceus 92 Brachyistius frenatus 100 Phanerodon furcatus Mecaenichthys immaculatus Parma victoriae 100 Parma oligolepis 97 100 Parma alboscapularis 100 Parma microlepis Microspathodon bairdii Microspathodon chrysurus 100 100 91 Microspathodon dorsalis 100 Nexilosus latifrons 99 Hypsypops rubicundus 100 Similiparma lurida 100 Similiparma hermani 100 Plectroglyphidodon phoenixensis 99 97 Plectroglyphidodon dickii 97 Plectroglyphidodon johnstonianus Plectroglyphidodon imparipennis 100 Plectroglyphidodon sagmarius 100 100 Plectroglyphidodon randalli 100 Plectroglyphidodon leucozonus 100 Plectroglyphidodon leucozonus 97 Plectroglyphidodon apicalis 100 Plectroglyphidodon obreptus Plectroglyphidodon fasciolatus 100 100 100 Plectroglyphidodon luteobrunneus 100 Plectroglyphidodon insularis 100 Plectroglyphidodon altus 97 100 Plectroglyphidodon aureus 97 Plectroglyphidodon marginatus 99 Plectroglyphidodon emeryi MICROSPATHODONTINAE 100 Plectroglyphidodon gascoynei Lepidozygus tapeinosoma 100 Lepidozygus tapeinosoma Stegastes pelicieri 100 Stegastes lacrymatus 100 Stegastes punctatus 100 Stegastes nigricans 90 100 Stegastes limbatus 100 Stegastes albifasciatus Stegastes beebei 97 Stegastes baldwini 81 99 Stegastes flavilatus Stegastes diencaeus 98 100 Stegastes adustus 98 Stegastes leucostictus 100 99 Stegastes variabilis 100 Stegastes xanthurus Stegastes otophorus Stegastes pictus 100 Stegastes partitus 93 Stegastes arcifrons Stegastes planifrons 99 Stegastes rectifraenum 99 100 Stegastes acapulcoensis 99 Stegastes rocasensis 96 Stegastes fuscus 100 100 Stegastes imbricatus Abudefduf declivifrons 100 Abudefduf taurus Abudefduf (Euschistodus) 100 Abudefduf concolor Abudefduf sordidus 100 POMACENTRIDAE 100 Abudefduf septemfasciatus Abudefduf (Abudefduf) 76 Abudefduf notatus 100 Abudefduf caudobimaculatus 100 Abudefduf sparoides 100 Abudefduf margariteus Abudefduf nigrimargo 95 100 Abudefduf bengalensis 66 Abudefduf whitleyi GLYPHISODONTINAE Abudefduf natalensis 64 Abudefduf conformis Abudefduf (Glyphisodon) 100 100 Abudefduf sexfasciatus 100 Abudefduf vaigiensis 100 Abudefduf lorenzi 100 Abudefduf abdominalis 100 Abudefduf troschelii 90 Abudefduf saxatilis 90 Abudefduf hoefleri Azurina elerae 100 Azurina lepidolepis 82 Azurina cyanea 67 Azurina brevirostris 81 Azurina hirundo 100 Azurina atrilobata 100 Azurina multilineata Dascyllus melanurus 100 Dascyllus aruanus 100 Dascyllus abudafur 100 Dascyllus marginatus Dascyllus flavicaudus 100 100 Dascyllus reticulatus Philippines 100 Dascyllus carneus 100 Dascyllus reticulatus Fiji 100 Dascyllus albisella 100 100 Dascyllus trimaculatus 100 Dascyllus strasburgi 100 Pycnochromis acares 96 Pycnochromis nigrurus 96 Pycnochromis vanderbilti 100 Pycnochromis alleni Pycnochromis bami Pycnochromis ovatiformis Pycnochromis amboinensis 90 93 99 Pycnochromis howsoni 86 Pycnochromis caudalis 100 99 Pycnochromis fatuhivae 88 Pycnochromis hanui Pycnochromis iomelas 95 93 Pycnochromis pacifica 51 Pycnochromis atripes Pycnochromis delta 73 98 Pycnochromis retrofasciatus 98 Pycnochromis leucurus Pycnochromis dimidiatus 100 Pycnochromis fieldi 100 Pycnochromis margaritifer 100 Pycnochromis abruptus Chromis atripectoralis 100 Chromis viridis 84 Chromis ternatensis Chromis (Hoplochromis) 100 Chromis flavaxilla Chromis nitida 100 Chromis fumea Chromis yamakawai 98 Chromis kennensis 97 100 Chromis ovalis CHROMINAE 97 Chromis notata 100 Chromis katoi 99 Chromis hypsilepis 84 99 Chromis dispila 99 Chromis tingting Chromis (Thrissochromis) Chromis okamurai 82 100 Chromis abyssicola 100 Chromis mamatapara 80 Chromis mirationis 99 Chromis pelloura 82 Chromis chrysura 81 Chromis randalli 100 100 Chromis pamae Chromis anadema 100 Chromis xanthura 100 Chromis opercularis 89 Chromis verater Chromis weberi 100 Chromis xanthopterygia 92 100 Chromis gunting 100 Chromis cinerascens 100 Chromis scotochiloptera 100 Chromis albicauda 100 99 Chromis analis 100 Chromis woodsi 100 99 Chromis flavapicis 100 Chromis hangganan 100 Chromis pembae Chromis limbata 100 Chromis chromis Chromis (Chromis) 100 Chromis cadenati 96 Chromis alpha 99 Chromis bowesi 100 Chromis earina 100 91 Chromis albomaculata Chromis degruyi 100 Chromis abyssus 100 Chromis circumaurea 97 Chromis crusma Chromis punctipinnis 100 Chromis alta 93 Chromis limbaughi 90 Chromis enchrysura 90 Chromis insolata 95 Chromis scotti “Chrysiptera” starcki 100 “Chrysiptera” galba 84 “Chrysiptera” rapanui 90 “Chrysiptera” glauca 100 “Chrysiptera” glauca 100 “Chrysiptera” unimaculata 100 “Chrysiptera” biocellata 100 “Chrysiptera” brownriggii 100 “Chrysiptera” leucopoma 100 “Chrysiptera” flavipinnis Dischistodus melanotus 100 Dischistodus pseudochrysopoecilus Dischistodus chrysopoecilus 100 Dischistodus perspicillatus 100 Dischistodus prosopotaenia 91 100 Dischistodus prosopotaenia CHEILOPRIONINI Pomachromis richardsoni 100 Pomachromis fuscidorsalis Cheiloprion labiatus Chrysiptera cyanea 100 Chrysiptera taupou 94 100 Chrysiptera rex 100 Chrysiptera caesifrons 100 Chrysiptera chrysocephala 97 Chrysiptera rollandi 97 Chrysiptera talboti 100 Chrysiptera traceyi 96 Chrysiptera hemicyanea 100 Chrysiptera parasema 100 Chrysiptera oxycephala 100 Chrysiptera springeri Hemiglyphidodon plagiometopon 100 Neoglyphidodon oxyodon Neoglyphidodon polyacanthus 100 Neoglyphidodon bonang 100 92 93 Neoglyphidodon melas Neoglyphidodon carlsoni 100 Neoglyphidodon nigroris 98 Neoglyphidodon thoracotaeniatus Acanthochromis polyacanthus 100 Altrichthys curatus 100 Altrichthys azurelineatus 100 80 Altrichthys alelia HEMIGLYPHIDODONTINI Amblyglyphidodon ternatensis Amblyglyphidodon batunaorum 100 Amblyglyphidodon aureus 98 Amblyglyphidodon leucogaster 100 Amblyglyphidodon flavilatus 97 78 Amblyglyphidodon indicus 77 Amblyglyphidodon orbicularis 50 Amblyglyphidodon silolona Amblyglyphidodon curacao 100 Amblyglyphidodon melanopterus Amphiprion biaculeatus 100 Amphiprion percula 100 100 Amphiprion ocellaris 100 Amphiprion ocellaris 100 Amphiprion latezonatus Amphiprion tricinctus 100 Amphiprion clarkii 100 91 Amphiprion clarkii Amphiprion akallopisos Amphiprion perideraion 100 100 100 Amphiprion sandaracinos 100 Amphiprion pacificus Amphiprion chrysopterus 97 100 Amphiprion leucokranos Amphiprion akindynos 100 Amphiprion mccullochi AMPHIPRIONINI 100 Amphiprion frenatus 91 91 Amphiprion rubrocinctus 100 Amphiprion barberi 100 Amphiprion ephippium 85 100 Amphiprion melanopus Amphiprion nigripes 100 100 Amphiprion chagosensis Amphiprion chrysogaster 85 96 Amphiprion allardi 100 Amphiprion latifasciatus 50 Amphiprion bicinctus 100 Amphiprion omanensis 60 Amphiprion polymnus 100 Amphiprion sebae POMACENTRINAE Amblypomacentrus annulatus Amblypomacentrus kuiteri 76 100 Amblypomacentrus tricinctus 100 Amblypomacentrus clarus 100 Amblypomacentrus breviceps Pristotis obtusirostris 100 Teixeirichthys jordani Neopomacentrus aquadulcis 98 Neopomacentrus bankieri 76 100 Neopomacentrus violascens 97 96 Neopomacentrus taeniurus 99 Neopomacentrus aktites 98 100 Neopomacentrus filamentosus Neopomacentrus fuliginosus 90 Neopomacentrus xanthurus Neopomacentrus miryae 100 Neopomacentrus sindensis Neopomacentrus cyanomos 100 Neopomacentrus nemurus 100 Neopomacentrus metallicus 100 Neopomacentrus azysron Neopomacentrus sororius Pomacentrus xanthosternus Pomacentrus leptus 100 Pomacentrus pavo 100 Pomacentrus similis 100 Pomacentrus alleni 100 Pomacentrus caeruleus 100 100 Pomacentrus micronesicus 100 Pomacentrus auriventris 100 Pomacentrus auriventris 100 Pomacentrus coelestis 99 Pomacentrus coelestis Pomacentrus sulfureus 81 87 Pomacentrus albicaudatus Pomacentrus aquilus Pomacentrus trichrourus 100 78 Pomacentrus vatosoa Pomacentrus baenschi 95 Pomacentrus trilineatus Pomacentrus grammorhynchus POMACENTRINI 100 Pomacentrus burroughi 78 100 74 Pomacentrus wardi Pomacentrus chrysurus 100 Pomacentrus vaiuli 98 Pomacentrus spilotoceps 100 Pomacentrus armillatus 100 Pomacentrus bankanensis Pomacentrus milleri 76 Pomacentrus amboinensis Pomacentrus maafu 100 100 100 Pomacentrus moluccensis Pomacentrus littoralis 98 70 Pomacentrus adelus 100 Pomacentrus adelus Pomacentrus melanochir 92 100 Pomacentrus bangladeshius 100 Pomacentrus tripunctatus 100 Pomacentrus taeniometopon Pomacentrus australis Pomacentrus flavioculus Pomacentrus callainus 100 100 Pomacentrus lepidogenys 82 Pomacentrus brachialis 100 100 Pomacentrus nigromarginatus 99 Pomacentrus reidi 100 Pomacentrus nagasakiensis 100 Pomacentrus microspilus 97 100 Pomacentrus cf. microspilus Tonga Pomacentrus stigma Pomacentrus aurifrons 100 Pomacentrus smithi 100 75 Pomacentrus nigromanus Pomacentrus alexanderae 99 Pomacentrus albiaxillaris Pomacentrus philippinus 89 98 Pomacentrus flavoaxillaris 84 Pomacentrus nigriradiatus 0.1 substitutions/site 91 Pomacentrus imitator 100 Pomacentrus magniseptus

Supplemental Fig. 1. The phylogenetic relationships of damselfishes (Teleostei: Pomacentridae) based on the maximum-likelihood topology with the best log likelihood score (ln L = −45,4518.728) recovered from 10 independent maximum-likelihood analyses of a data matrix composed of 462 taxa and 6,865 nucleotides. Bootstrap values from 1,000 ultrafast replicates are displayed for each node (values below 50% are not reported). Illustrations (not to scale) represent the following species, from top: Mecaenichthys immaculatus, Parma polylepis, Microspathodon chrysurus, Hypsypops rubicundus, Plectroglyphidodon dickii, Plectroglyphidodon imparipennis, Plectroglyphidodon leucozonus, Plectroglyphidodon fasciolatus, Plectroglyphidodon altus, Plectroglyphidodon gascoynei, Lepidozygus tapeinosoma, Stegastes lacrymatus, Stegastes nigricans, Stegastes beebei, Stegastes diencaeus, Stegastes xanthurus, Stegastes otophorus, Stegastes rectifraenum, Stegastes imbricatus, Abudefduf declivifrons, Abudefduf sordidus, Abudefduf bengalensis, Abudefduf natalensis, Abudefduf abdominalis, Abudefduf saxatilis, Azurina lepidolepis, Azurina cyanea, Azurina hirundo, Azurina multilineata, Dascyllus aruanus, Dascyllus albisella, Dascyllus trimaculatus, Pycnochromis nigrurus, Pycnochromis vanderbilti, Pycnochromis alleni, Pycnochromis ovatiformis, Pycnochromis hanui, Pycnochromis atripes, Pycnochromis fieldi, Pycnochromis margaritifer, Chromis viridis, Chromis ternatensis, Chromis fumea, Chromis notata, Chromis hypsilepis, Chromis okamurai, Chromis chrysura, Chromis randalli, Chromis opercularis, Chromis weberi, Chromis cinerascens, Chromis analis, Chromis pembae, Chromis chromis, Chromis alpha, Chromis abyssus, Chromis alta, Chromis insolata, “Chrysiptera” rapanui, “Chrysiptera” glauca, “Chrysiptera” biocellata, “Chrysiptera” brownriggii, Dischistodus chrysopoecilus, Dischistodus prosopotaenia, Pomachromis richardsoni, Cheiloprion labiatus, Chrysiptera cyanea, Chrysiptera rex, Chrysiptera traceyi, Chrysiptera oxycephala, Hemiglyphidodon plagiometopon, Neoglyphidodon polyacanthus, Neoglyphidodon nigroris, Acanthochromis polyacanthus, Altrichthys azurelineatus, Amblyglyphidodon aureus, Amblyglyphidodon curacao, Amblyglyphidodon orbicularis, Amphiprion ocellaris, Amphiprion latezonatus, Amphiprion clarkii, Amphiprion perideraion, Amphiprion chrysopterus, Amphiprion frenatus, Amphiprion ephippium, Amphiprion chrysogaster, Amphiprion bicinctus, Amphiprion polymnus, Amblypomacentrus tricinctus, Amblypomacentrus breviceps, Pristotis obtusirostris, Teixeirichthys jordani, Neopomacentrus bankieri, Neopomacentrus filamentosus, Neopomacentrus xanthurus, Neopomacentrus miryae, Neopomacentrus metallicus, Neopomacentrus azysron, Pomacentrus pavo, Pomacentrus caeruleus, Pomacentrus auriventris, Pomacentrus coelestis, Pomacentrus aquilus, Pomacentrus trilineatus, Pomacentrus chrysurus, Pomacentrus vaiuli, Pomacentrus bankanensis, Pomacentrus amboinensis, Pomacentrus moluccensis, Pomacentrus tripunctatus, Pomacentrus taeniometopon, Pomacentrus callainus, Pomacentrus brachialis, Pomacentrus nagasakiensis, Pomacentrus stigma, Pomacentrus nigromanus, Pomacentrus philippinus, Pomacentrus imitator.