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Near et al. 10.1073/pnas.1304661110 SI Text and SD of 0.8 to set 57.0 Ma as the minimal age offset and 65.3 Ma as the 95% soft upper bound. Calibration Age Priors † Here we provide, for each fossil calibration prior, the identity of Calibration 7. Trichophanes foliarum, calibration 13 in Near et al. the calibrated node in the phylogeny, the taxa that rep- (1). Prior setting: a lognormal prior with the mean of 1.899 and resent the first occurrence of the lineage in the fossil record, SD of 0.8 to set 34.1 Ma as the minimal age offset and 59.0 Ma as a description of the character states that justify the phylogenetic the 95% soft upper bound. placement of the fossil taxon, information on the stratigraphy of Calibration 8. †Turkmene finitimus, calibration 16 in Near et al. the rock formations bearing the fossil, and the absolute age es- (1). Prior setting: a lognormal prior with the mean of 2.006 and timate for the fossil; outline the prior age setting used in the SD of 0.8 to set 55.8 Ma as the minimal age offset and 83.5 Ma as BEAST relaxed clock analysis; and provide any additional notes the 95% soft upper bound. on the calibration. Less detailed information is provided for 26 of the calibrations used in a previous study of actinopterygian di- Calibration 9. †Cretazeus rinaldii, calibration 14 in Near et al. (1). vergence times, as all the information and prior settings for these Prior setting: a lognormal prior with the mean of 1.016 and SD of calibrations is found in the work of Near et al. (1). Each cali- 0.8 to set 70.6 Ma as the minimal age offset and 80.9 Ma as the bration is numbered, and the phylogenetic placement of the 95% soft upper bound. calibration is highlighted in Fig. S2. Calibration 10. †Zenopsis clarus †Zenopsis tyleri and †Zenopsis † , , Calibration 1. Rubiesichthys gregalis, calibration 6 in Near et al. hoernesi, calibration 15 in Near et al. (1). Prior setting: a log- (1). Prior setting: a lognormal prior with the mean of 1.51 and normal prior with the mean of 0.231 and SD of 0.8 to set 32.0 Ma SD of 0.8 to set 133.9 Ma as the minimal age offset and 150.8 Ma as the minimal age offset and 36.7 Ma as the 95% soft upper as the 95% soft upper bound. bound. † Calibration 2. Estesesox foxi, calibration 9 in Near et al. (1). Prior Calibration 11. †Hoplopteryx simus and †Hoplopteryx lewesiensis, setting: a lognormal prior with the mean of 1.091 and SD of 0.8 calibration 17 in Near et al. (1). Prior setting: a lognormal prior to set 76.4 Ma as the minimal age offset and 87.5 Ma as the 95% with the mean of 0.479 and SD of 0.8 to set 93.6 Ma as the soft upper bound. minimal age offset and 105.8 Ma as the 95% soft upper bound. † Calibration 3. Eosalmo driftwoodensis, calibration 10 in Near Calibration 12. †Gephyroberyx robustus,calibration19inNear et al. (1). Prior setting: a lognormal prior with the mean of 1.618 et al. (1). Prior setting: a lognormal prior with the mean of and SD of 0.8 to set 51.8 Ma as the minimal age offset and 76.4 0.231 and SD of 0.8 to set 32.0 Ma as the minimal age offset Ma as the 95% soft upper bound. and 36.7 Ma as the 95% soft upper bound.

Calibration 4. Node: stem lineage Alepisauroidei, dating the most Calibration 13. †Eoholocentrum macrocephalum, †Berybolcensis recent common ancestor (MRCA) of Bathypterois and all other leptacanthus,and†Tenuicentrum pattersoni,calibration18in † sampled . First occurrence: zimapan- Near et al. (1). Prior setting: a lognormal prior with the mean ensis La Negra horizon, El Doctor Formation, Muhi quarry, of 0.672 and SD of 0.8 to set 50.0 Ma as the minimal age offset Zimapán, Hidalgo, Mexico (2), Enchodus brevis Ein-Yabrud, and 57.3 Ma as the 95% soft upper bound. Jerusalem, Israel (3), Enchodus venator Jebel Tselfat, Morocco (4), Enchodus marchesettii Hakel and Hadjula, Lebanon (5), and Calibration 14. †Gasterorhamphosus zuppichinii, calibration 20 in Enchodus mecoanalis Namoura, Lebanon (6). Resolution in Near et al. (1). Prior setting: a lognormal prior with the mean of phylogenetic analyses: maximum parsimony analysis of 87 mor- 1.016 and SD of 0.8 to set 70.6 Ma as the minimal age offset and phological characters resolve Synodus as the sister lineage of all 80.9 Ma as the 95% soft upper bound. other sampled Aulopiformes including †Enchodus (figure 1 of ref. 7). Character states: pharyngeal toothplates bearing large Calibration 15. †“Syngnathus” heckeli and †Prosolenostomus lessi- teeth, known from congeneric Enchodus longidens from the nii, calibration 22 in Near et al. (1). Prior setting: a lognormal Santonian of Sahel Alma, Lebanon (figure 68 of ref. 8); slender prior with the mean of 0.672 and SD of 0.8 to set 50.0 Ma as the maxilla; palatine dominant tooth-bearing bone of upper jaw; first minimal age offset and 57.3 Ma as the 95% soft upper bound. epipleural originates on first centrum (8–10). Stratigraphy: lower . Absolute age estimate: 99.6 Ma (11). Prior setting: Calibration 16. †Paramphisile weileri and †Paraeoliscus robinetae, an exponential prior with the mean of 2.86 to set 99.6 Ma as the calibration 21 in Near et al. (1). Prior setting: a lognormal prior minimal age offset and 108.2 Ma as the 95% soft upper bound. with the mean of 0.672 and SD of 0.8 to set 50.0 Ma as the The upper bound is based on the calculation of fossil age (FA)95 minimal age offset and 57.3 Ma as the 95% soft upper bound. following Marshall (12). Calibration 17. Node: crown lineage Exocetoidei, dating the MRCA of Calibration 5. †Homonotichthys dorsalis, calibration 11 in Near Arrhamphus and Dermogenys. First occurrence: †Rhamphexocoetus et al. (1). Prior setting: a lognormal prior with the mean of 0.476 volans Pesciara beds of “Calcari nummulitici,” Bolca, Italy (13). and SD of 0.8 to set 93.6 Ma as the minimal age offset and 99.6 Resolution in phylogenetic analyses: none. Character states: Ma as the 95% soft upper bound. lower jaw symphysis extended; ventral lobe of caudal fin enlarged relative to dorsal lobe; pectoral fins greatly expanded (14–16). Calibration 6. †Massamorichthys wilsoni, calibration 12 in Near Stratigraphy: upper [ calcareous nannofossil et al. (1). Prior setting: a lognormal prior with the mean of 0.525 zone (NP)14] (17). Absolute age estimate: 50 Ma (17). Prior set-

Near et al. www.pnas.org/cgi/content/short/1304661110 1of20 ting: a lognormal prior with the mean of 0.672 and the SD of 0.8 to the minimal age offset and 63.9 Ma as the 95% soft upper set 50.0 Ma as the minimal age offset and 57.3 Ma as the 95% soft bound. The upper bound is based on the calculation of FA95 upper bound. The upper bound is based on the calculation of FA95 following Marshall (12). following Marshall (12). Calibration 26. †Archoplites clarki, calibration 36 in Near et al. (1). Calibration 18. †Eobothus minimus, calibration 27 in Near et al. Prior setting: a lognormal prior with the mean of 0.1 and SD of (1). Prior setting: a lognormal prior with the mean of 0.672 and 0.5 to set 15.5 Ma as the minimal age offset and 17.8 Ma as the SD of 0.8 to set 50.0 Ma as the minimal age offset and 57.3 Ma as 95% soft upper bound. the 95% soft upper bound. Calibration 27. †Euleiognathus tottori, calibration 32 in Near et al. Calibration 19. †Oligobothus pristinus, calibration 29 in Near et al. (1). Prior setting: a lognormal prior with the mean of 1.602 and (1). Prior setting: a lognormal prior with the mean of 0.165 and SD of 0.8 to set 11.6 Ma as the minimal age offset and 23.1 Ma as SD of 0.8 to set 30.0 Ma as the minimal age offset and 34.4 Ma as the 95% soft upper bound. the 95% soft upper bound. Calibration 28. Chaetodontidae cf. Chaetodon (tholichthys-stage † † Calibration 20. Eobuglossus and Turahbuglossus, calibration 28 larvae), calibration 30 in Near et al. (1). Prior setting: a lognormal in Near et al. (1). Prior setting: a lognormal prior with the mean prior with the mean of 0.165 and SD of 0.8 to set 30.1 Ma as the of 0.946 and SD of 0.8 to set 40.4 Ma as the minimal age offset minimal age offset and 34.5 Ma as the 95% soft upper bound. and 50 Ma as the 95% soft upper bound. Calibration 29. †Avitoluvarus dianae, †Avitoluvarus mariannae, † Calibration 21. oblongus, calibration 23 in Near et al. †Kushlukia permira,and†Luvarus necopinatus, calibration 25 in (1). Prior setting: a lognormal prior with the mean of 0.776 and Near et al. (1). Prior setting: a lognormal prior with the mean of SD of 0.8 to set 55.8 Ma as the minimal age offset and 63.9 Ma as 0.776 and SD of 0.8 to set 55.8 Ma as the minimal age offset the 95% soft upper bound. and 63.9 Ma as the 95% soft upper bound. Calibration 22. Node: stem lineage , dating the MRCA Calibration 30. Node: stem lineage , dating the MRCA of , , and . First occurrence: †Eastmanalepes of Acanthurinae and Nasinae. First occurrence: †Proacanthurus primaevus, Pesciara beds of Calcari nummulitici, Bolca, Italy tenius, Pesciara beds of Calcari nummulitici, Bolca, Italy. Reso- (18). Resolution in phylogenetic analyses: none. Character states: lution in phylogenetic analyses: none. Character states: caudal lateral line scales modified as thick scutes (19). Stratigraphy: up- per Ypresian [NP14] (17). Absolute age estimate: 50 Ma (17). peduncle bears folding spine. Stratigraphy: upper Ypresian Prior setting: a lognormal prior with the mean of 0.672 and the SD [NP14] (17). Absolute age estimate: 50 Ma (17). Prior setting: of 0.8 to set 50.0 Ma as the minimal age offset and 57.3 Ma as the a lognormal prior with the mean of 0.672 and the SD of 0.8 to set 95% soft upper bound. The upper bound is based on the calcu- 50.0 Ma as the minimal age offset and 57.3 Ma as the 95% soft upper bound. The upper bound is based on the calculation of lation of FA95 following Marshall (12). FA95 following Marshall (12). Calibration 23. †Opisthomyzon glaronensis and an unnamed echeneid, calibration 24 in Near et al. (1); misreported as †Uropteryx Calibration 31. Node: Stem lineage Siganidae, dating the MRCA of glaronensis there. Prior setting: a lognormal prior with the mean of Siganidae and Scatophagidae. First occurrence: †Siganopygaeus 0.165 and SD of 0.8 to set 30.1 Ma as the minimal age offset and rarus, Danatinsk Suite, Uylya-Kushlyuk locality, Turkmenistan 34.5 Ma as the 95% soft upper bound. (25). Resolution in phylogenetic analyses: maximum parsimony analysis of 12 morphological characters resolve †Siganopygaeus Calibration 24. Node: stem lineage Sphyraenidae, dating the MRCA as the sister lineage of a clade containing †Protosiganus and Si- of Sphyraena and Centropomus. First occurrence: †Sphyraena ganus (figure 20 of ref. 25). Character states: two pelvic fin bolcensis, Pesciara beds of Calcari nummulitici, Bolca, Italy. Res- spines; seven or more anal fin spines; 10 or fewer anal rays (25). olution in phylogenetic analyses: none. Character states: three Stratigraphy: uppermost –lowermost Ypresian (22). T-shaped, sutured predorsals or spineless pterygiophores (20); Absolute age estimate: 55.8 Ma (11). Prior setting: a lognormal elongate gape; upper jaw nonprotrusible; enlarged fangs on prior with the mean of 0.776 and the SD of 0.8 to set 55.8 Ma as dentary, premaxilla, and palatine. Stratigraphy: upper Ypresian the minimal age offset and 63.9 Ma as the 95% soft upper [NP14] (17). Absolute age estimate: 50.0 Ma (17). Prior setting: bound. The upper bound is based on the calculation of FA a lognormal prior with the mean of 0.672 and the SD of 0.8 to set 95 following Marshall (12). 50.0 Ma as the minimal age offset and 57.3 Ma as the 95% soft upper bound. The upper bound is based on the calculation of Calibration 32. Node: stem lineage Antennarioidei, dating the FA95 following Marshall (12). MRCA of Antennarioidei and a clade containing Ogocepha- lioidei and Ceratioidei. First occurrence: †Eophryne bartutii, Calibration 25. Node: stem lineage Menidae, dating the MRCA of † “ Pesciara beds of Calcari nummulitici, Bolca, Italy (26). Resolu- and Xiphioidei. First occurrence: Mene purdyi, Mancora † Formation,” Peru (21); †Mene triangulum, Danatinsk Suite, tion in phylogenetic analyses: none. Eophryne was hypothesized Uylya-Kushlyuk locality, Turkmenistan (22, 23); and †Mene sp., to share common ancestry with Antennariidae based on overall “Stolle Klint clay,” Ølst Formation, Denmark (24). Resolution in morphological similarity (26). The phylogenetic placement used phylogenetic analyses: none. Character states: frontal vault; many for this calibration is conservatively applied to the more inclusive small infraorbitals; all anal fin rays short, with anteriormost rays Antennarioidei. Character states: triradiate ectopterygoid; spat- plate like; anal fin spines absent; postcleithrum broad and con- ulate postmaxillary process of premaxilla (26–28). Stratigraphy: tacts first anal fin pterygiophore; disk-like body with deep ventral upper Ypresian [NP14] (17). Absolute age estimate: 50 Ma (17). keel; greatly elongated second anal fin ray (21). Stratigraphy: Prior setting: a lognormal prior with the mean of 0.672 and the uppermost Thanetian–lowermost Ypresian [NP14] (21, 22, 24). SD of 0.8 to set 50.0 Ma as the minimal age offset and 57.3 Ma as Absolute age estimate: 55.8 Ma (11). Prior setting: a lognormal the 95% soft upper bound. The upper bound is based on the prior with the mean of 0.776 and the SD of 0.8 to set 55.8 Ma as calculation of FA95 following Marshall (12).

Near et al. www.pnas.org/cgi/content/short/1304661110 2of20 Calibration 33. †Prodiodon tenuispinus, †Prodiodon erinaceus, currence: †Austromola angerhoferi, Ebelsberg Formation, Pucking, †Heptadiodon echinus,and†Zignodon fornasieroae,calibra- Austria (32). Resolution in phylogenetic analyses: parsimony tion 33 in Near et al. (1). Prior setting: a lognormal prior with analysis of 57 morphological characters resolves †Austromola as themeanof0.672andSDof0.8toset50.0Maastheminimal the sister lineage of a clade containing Mola and Masturus (figure age offset and 57.3 Ma as the 95% soft upper bound. 9 of ref. 32). Character states: basal pterygiophores of dorsal and anal fins expanded proximally; first basal pterygiophore of anal fin Calibration 34. †Gornylistes prodigiosus, calibration 35 in Near concave and encloses distal end of haemal spines of first two et al. (1). Prior setting: a lognormal prior with the mean of 0.37 caudal vertebrae; posteriormost dorsal and anal fin pterygiophores and SD of 0.8 to set 37.2 Ma as the minimal age offset and 42.6 inserted approximately normal to body axis; pectoral finwith Ma as the 95% soft upper bound. rounded outline; deep body; bone spongy and weakly ossified (32, 33). Stratigraphy: Aquitanian, upper Egerian regional stage (32). Calibration 35. Node: stem lineage Molidae, dating the MRCA of Absolute age estimate: 22 Ma (32). Prior setting: a lognormal Molidae and Triacanthus. First occurrence: †Eomola bimaxil- prior with the mean of 1.4055 and the SD of 0.8 to set 22.0 Ma as laria, Kuma Horizon, Krasnodar Region, Caucasus (29). Res- the minimal age offset and 37.2 Ma as the 95% soft upper bound. olution in phylogenetic analyses: parsimony analysis of 219 The upper bound is based on the age of †Eomola bimaxillaria morphological characters resolves †Eomola as the sister lineage (Calibration 35). of a clade containing Mola and Ranzania (figure 4 of ref. 30). Character states: striated bone surface; laterally elongate tritu- Calibration 37. Node: crown lineage Gasterosteus, dating the ration teeth; individual fused teeth in parrot-like beak indis- MRCA of Gasterosteus aculeatus and Gasterosteus wheatlandi. tinguishable (29, 30). Stratigraphy: Bartonian [NP17], Kumian First occurrence: Gasterosteus cf. aculeatus, Monterey Forma- regional stage (31). Absolute age estimate: 37.2 Ma (11). Prior tion, California (34). Resolution in phylogenetic analyses: none. setting: a lognormal prior with the mean of 0.37 and the SD of 0.8 Character states: two elongate, free dorsal fin spines, complete to set 37.2 Ma as the minimal age offset and 42.6 Ma as the 95% series of lateral plates (34). Stratigraphy: Serravallian, lowermost soft upper bound. The upper bound is based on the calculation of Mohnian regional stage (34). Absolute age estimate: 13 Ma (34). FA95 following Marshall (12). Prior setting: an exponential prior with the mean of 1.17 to set 13.0 Ma as the minimal age offset and 16.5 Ma as the 95% soft Calibration 36. Node: Crown lineage Molidae, dating the MRCA of upper bound. The upper bound is based on the calculation of Ranzania and a clade containing Mola and Masturus. First oc- FA95 following Marshall (12).

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Near et al. www.pnas.org/cgi/content/short/1304661110 3of20 A Ameiurus natalis = 100% bootstrap replicates Ostariophysi Opsariichthys uncirostris Gonorynchus abbreviatus = 99-90% bootstrap replicates Gonorynchus greyi Chanos chanos = 89-70% bootstrap replicates Cromeria nilotica Phractolaemus ansorgii Argentina silus Thymallus brevirostris Salvelinus alpinus Parahucho perryi Umbra limi Novumbra hubbsi Esox americanus Osmerus mordax Hypomesus pretiosus Osmeridae Polymetme sp. Neonesthes capensis Astronesthes leucopogon Euteleostei Chauliodus sloani Chauliodus macouni Gonostoma elongatum Cyclothone microdon Polyipnus spinifer Sternoptyx sp. Argyropelecus gigas Argyropelecus affinis Ateleopus japonicus Ateleopodidae Ijimaia loppei Synodus variegatus Synodus foetens Bathypterois atricolor Benthalbella infans Aulopiformes Notolepis coatsi Magnisudis prionosa Anotopterus pharao Neoteleostei Alepisaurus ferox Neoscopelus macrolepidotus Neoscopelus microchir Scopelengys sp. Scopelengys tristis Notoscopelus resplendens Lampanyctus jordani Eurypterygii Stenobrachius leucopsarus Ceratoscopelus maderensis Gymnoscopelus nicholsi Gymnoscopelus opisthopterus Gymnoscopelus braueri Diaphus sp. Diaphus rafinesquii Electrona antarctica Protomyctophum choriodon Krefftichthys anderssoni Hygophum proximum Symbolophorus evermanni Tarletonbeania crenularis Ctenosquamata japonica Polymixia lowei Percopsis omiscomaycus Chologaster cornuta Aphredoderus sayanus Cyttomimus affinis Cyttopsis rosea Zeus faber Zenopsis conchifera Stylephorus chordatus Coryphaenoides rupestris Acanthomorpha Coryphaenoides armatus Nezumia bairdii Macrourus sp. Muraenolepis microps Lota lota Gadus morhua Lampris guttatus Trachipterus arcticus Trachipterus trachypterus Regalecus russelii Regalecus glesne

To Figure S1B 0.05 substitutuions per site

Fig. S1. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 4of20 B To Figure S1A = 100% bootstrap replicates Neoniphon vexillarium = 99-90% bootstrap replicates Sargocentron cornutum Myripristis murdjan = 89-70% bootstrap replicates Myripristis violacea Diretmichthys parini Diretmus argenteus Monocentris japonica Anomalops katoptron Gephyroberyx darwini Hoplostethus atlanticus Anoplogaster cornuta Paratrachichthys sajademalensis Aulotrachichthys prosthemius Rondeletia loricata Acanthochaenus luetkenii Barbourisia rufa Gyrinomimus sp. Cetostoma regani Centroberyx druzhinini Beryx decadactylus Melamphaes polylepis Scopelogadus beanii Poromitra crassiceps Scopeloberyx sp. Brosmophycis marginata Diplacanthopoma brunnea Cataetyx lepidogenys Barathronus maculatus Brotula multibarbata Lamprogrammus niger Carapus bermudensis Pyramodon ventralis Onuxodon parvibrachium Porichthys plectrodon Porichthys notatus Batrachoides pacifici Opsanus pardus Opsanus beta Scomberomorus maculatus Sarda sarda Thunnus albacares Auxis rochei Scomber scombrus Peprilus triacanthus Cubiceps baxteri Psenes maculatus Icosteus aenigmaticus Ruvettus pretiosus Pomatomus saltatrix Icichthys lockingtoni Scombriformes Platyberyx opalescens Caristius macropus Chiasmodon sp. Kali kerberti Trichiurus lepturus Assurger anzac Paradiplospinus gracilis Pteraclis aesticola Brama japonica Taractes asper Upeneus parvus Mulloidichthys flavolineatus Pseudupeneus maculatus Parupeneus trifasciatus Mullidae Parupeneus barberinus Eurypegasus draconis Dactyloptena peterseni Dactyloptena orientalis Dactyloptena gilberti Synchiropus splendidus Neosynchiropus ocellatus Synchiropus agassizi Callionymus bairdi Foetorepus sp. Aeoliscus strigatus Macroramphosus scolopax Aulostomus chinensis Aulostomus maculatus Fistularia petimba Fistularia commersonii Hippocampus erectus Syngnathus leptorhynchus Syngnathus fuscus To Figure S1C 0.05 substitutuions per site

Fig. S1. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 5of20 C = 100% bootstrap replicates = 99-90% bootstrap replicates To Figure S1B Kurtus gulliveri = 89-70% bootstrap replicates Kurtus indicus Astrapogon stellatus Phaeoptyx pigmentaria Sphaeramia orbicularis Apogonidae Cheilodipterus quinquelineatus Ostorhinchus lateralis Odontobutis potamophila Odontobutidae Percottus glenii Eleotris pisonis Dormitator maculatus Eleotridae Ophiocara porocephala Butidae Oxyeleotris selheimi Lepidogobius lepidus Gobionellidae Stonogobiops nematodes Gobiidae Nemateleotris magnifica Ptereleotridae Ptereleotris evides Macrognathus siamensis Mastacembelus niger Mastacembelus brachyrhinus Mastacembelus cunningtoni Monopterus albus Indostomus paradoxus Indostomus crocodilus fasciata Pristolepis sp. Dario dario Badis pyema Nandus nebulosus Nandus andrewi Nandus nandus Channa lucius Channa melasoma Channa striata kingsleyae Microctenopoma nanum Helostoma temminckii Trichopodus pectoralis Betta splendens Polydactylus sextarius Eleutheronema rhadinum Polynemidae Lates niloticus Psettodes erumei Citharoides macrolepis Gymnachirus melas Achirus lineatus Samariscus latus Citharoides macrolepidotus Symphurus atricaudus Aseraggodes kobensis Heteromycteris japonicus Pleuronectiformes* Scophthalmus aquosus Bothus lunatus Pleuronectes platessa Pseudopleuronectes americanus Lepidopsetta bilineata Paralichthys dentatus Citharichthys sordidus saurus Trachinotus carolinus Seriola dumerili Carangidae Caranx crysos naucrates Rachycentron canadum Echeneoidea hippurus Tetrapturus angustirostris Xiphias gladius Xiphioidei Toxotes jaculatrix Nematistius pectoralis Centropomus undecimalis Centropomus armatus Sphyraena japonica Sphyraena barracuda Sphyraena jello To Figure S1D

To Figure S1E 0.05 substitutuions per site

Fig. S1. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 6of20 D = 100% bootstrap replicates Labidesthes sicculus = 99-90% bootstrap replicates Menidia peninsulae = 89-70% bootstrap replicates Poblana ferdebueni Menidia beryllina To Figure S1C Atherinomorus lacunosus Melanotaenia sp. Rheocles wrightae Iso sp. Phenacostethus smithi Pseudomugil signifer Pseudomugil gertrudae Pachypanchax playfairii Cyprinodon variegatus Jordanella floridae Atherinomorpha Fundulus heteroclitus Lucania goodei Poeciliopsis elongata Gambusia affinis Oryzias latipes Arrhamphus sclerolepis Cheilopogon melanurus Cheilopogon pinnatibarbatus Dermogenys collettei Xenentodon cancila Scomberesox saurus Strongylura marina Platybelone argala Polycentropsis abbreviata Monocirrhus polyacanthus schomburgkii Pholidichthys leucotaenia Paretroplus maculatus Etroplus maculatus Paratilapia polleni Ptychochromis grandidieri Heterochromis multidens Cichlidae Oreochromis niloticus Cichla temensis Heros efasciatus Herichthys cyanoguttatus Ambassis urotaenia Pseudambassis ranga Mugil curema Mugil cephalus Mugilidae Cymatogaster aggregata Embiotocidae Phanerodon furcatus Rhacochilus vacca Congrogadus subducens Congrogadidae Plesiops coeruleolineatus Plesiopidae Chromis cyanea Abudefduf saxatilis Stegastes leucostictus Pomacentridae Microspathodon bairdii Pseudochromis fridmani Pholidochromis cerasina Ogilbyina novaehollandiae Pseudochromidae Labracinus cyclophthalmus Gramma loreto Grammatidae Opistognathus aurifrons Opistognathidae Diademichthys lineatus Gobiesox maeandricus Arcos sp. Helcogramma ellioti Tripterygiidae Enneanectes boehlkei Gibbonsia metzi Clinidae Labrisomus multiporosus Labrisomidae Gillellus semicinctus Dactyloscopidae Chaenopsis alepidota Chaenopsidae Blennioidei Ophioblennius atlanticus Salarias fasciatus Entomacrodus nigricans Hypsoblennius hentz Blenniidae Meiacanthus grammistes Enchelyurus flavipes 0.05 substitutuions per site

Fig. S1. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 7of20 E Lachnolaimus maximus = 100% bootstrap replicates = 99-90% bootstrap replicates To Figure S1C Haletta semifasciata Bodianus rufus = 89-70% bootstrap replicates Clepticus parrae Xyrichtys martinicensis Coris gaimard Halichoeres bivittatus Oxyjulis californica Gomphosus varius Halichoeres margaritaceus Coris batuensis Labrichthys unilineatus Labropsis australis Labridae Diproctacanthus xanthurus Pteragogus enneacanthus Tautoga onitis Tautogolabrus adspersus Oxycheilinus celebicus Epibulus brevis Epibulus insidiator Calotomus carolinus Cryptotomus roseus Cetoscarus bicolor Chlorurus sordidus Scarus globiceps Scarus niger Ulaema lefroyi Eugerres plumieri Gerreidae Centrogenys vaigiensis Astroscopus y-graecum Uranoscopidae Kathetostoma averruncus Cheimarrichthys fosteri Parapercis clathrata Pinguipedidae Parapercis hexophtalma Ammodytes dubius Ammodytidae Ammodytes hexapterus Girella mezina Girellidae punctatus Kyphosus elegans Kyphosidae Kyphosus cinerascens Kuhlia rupestris Kuhlia marginata Terapon jarbua Hephaestus fuliginosus Scortum barcoo Percalates novemaculeata Percichthyidae* Percalates colonorum Enoplosus armatus Maccullochella peelii Gadopsis marmoratus ambigua Percichthyidae* Nannoperca australis irwini pixi Cheilodactylus variegatus Cheilodactylidae Chirodactylus brachydactylus Paracirrhites arcatus Amblycirrhitus pinos Cirrhitichthys falco Neocirrhites armatus Siniperca chuasti Elassoma okefenokee Elassoma zonatum Lepomis cyanellus Micropterus salmoides Archoplites interruptus Ambloplites rupestris

0.05 substitutuions per site To Figure S1GTo Figure S1F

Fig. S1. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 8of20 F = 100% bootstrap replicates To Figure S1E Acropoma japonica * = 99-90% bootstrap replicates Ostracoberyx dorygenys Howella zina = 89-70% bootstrap replicates Champsodon snyderi Limnichthys sp. Creediidae Acanthaphritis unoorum Glaucosoma buergeri Glaucosoma hebraicum Pempheris schwenkii Pempheris schomburgkii Pempheridae Stereolepis gigas Polyprionidae Malakichthys elegans Acropomatidae* Banjos banjos Histiopterus typus Pseudopentaceros pectoralis Pentaceros japonicus Pseudopentaceros wheeleri Hypoplectrus puella Serranus tigrinus Serranidae Paralabrax nebulifer Rypticus saponaceus Grammistes sexlineatus Cephalopholis argus Epinephelidae Mycteroperca microlepis Hemanthias aureorubens Pseudanthias pascalus Anthiidae Niphon spinosus Perca flavescens Etheostoma atripinne Percidae Percina caprodes Bovichtus diacanthus Eleginops maclovinus Chionobathyscus dewitti Notothenioidei Dissostichus eleginoides Hoplichthys gilberti Hoplichthys langsdorfii Rogadius asper Platycephalidae Platycephalus indicus Parabembras curtus Bembras japonicus Bembridae Sebastolobus alascanus Sebastes ruberrimus Sebastidae Sebastes fasciatus gobioides Bembropidae evolans hemisticta Anoplopoma fimbria Anoplopomatidae Hexagrammos otakii Hexagrammidae Trichodon trichodon Trichodontidae Eumicrotremus orbis Cyclopterus lumpus Cyclopteridae Paraliparis meganchus Liparis mucosus Liparidae Cottus carolinae Leptocottus armatus Cottidae* Aspidophoroides monopterygius Stellerina xyosterna Agonidae Scorpaenichthys marmoratus Artediellus uncinatus Cottidae* Hypoptychus dybowskii Aulorhynchus flavidus japonicus Apeltes quadracus Gasterosteidae Gasterosteus wheatlandi Gasterosteus aculeatus Rathbunella hypoplecta Bathymasteridae* Bathymaster signatus Cebidichthys violaceus Stichaeidae Pholis ornatus Pholis crassispina Pholidae Cryptacanthodes maculatus Anarhichas lupus Anarhichadidae Allolepis hollandi Lycodes terraenovae Zoarcidae Lycodes diapterus 0.05 substitutuions per site

Fig. S1. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 9of20 G To Figure S1E Morone saxatilis = 100% bootstrap replicates Morone mississippiensis Moronidae = 99-90% bootstrap replicates = 89-70% bootstrap replicates Morone chrysops Chaetodipterus faber Ephippidae orbicularus Siganus spinus Siganus vulpinus Selenotoca multifasciata Scatophagus argus Scatophagidae Sphenanthias tosaensis Cepolidae Cepola schlegelii Pristigenys alta Priacanthus arenatus Priacanthidae Priacanthus cruentatus Capros aper Antigonia rubescens Antigonia capros Lophius gastrophysus Lophiidae Lophius americanus Ogcocephalus nasutus Ogcocephalidae Halieutichthys aculeatus Antennarius striatus Antennariidae Histiophryne cryptacanthus Chaunax sp. Lophiiformes Chaunax suttkusi Chaunacidae Chaunax stigmaeus Himantolophus sagamius Cryptopsaras couesi Ceratiidae Ceratias holboelli Gigantactis sp. Gigantactinidae Gigantactis vanhoeffeni Chilomycterus schoepfii Diodontidae Diodon holocanthus Canthigaster jactator Sphoeroides nephelus Arothron nigropunctatus Tetraodontidae Tetraodon miurus Triodon macropterus Aracana aurita Rhinesomus triqueter Ostracion cubicus Ostraciidae Halimochirurgus alcocki Triacanthodidae Triacanthodes anomalus Triacanthus biaculeatus Triacanthidae Ranzania laevis Masturus lanceolatus Molidae Mola mola Tetraodontiformes Cantherhines pullus Paraluteres prionurus Pervagor nigrolineatus Acreichthys tomentosus Monacanthidae Pervagor janthinosoma Stephanolepis hispidus Sufflamen chrysopterum Balistapus undulatus Xanthichthys ringens Pseudobalistes flavimarginatus To Figure S1H Rhinecanthus verrucosus Balistidae Abalistes stellatus Balistes vetula Balistes capriscus 0.05 substitutuions per site

Fig. S1. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 10 of 20 H = 100% bootstrap replicates To Figure S1G = 99-90% bootstrap replicates Luvarus imperialis = 89-70% bootstrap replicates Zanclus cornutus Naso brevirostris Naso lituratus Acanthuroidei rostratum Acanthurus nigricans Acanthurus bahianus Ctenochaetus strigosus surinamensis Lobotidae Menticirrhus littoralis Cynoscion regalis Leiostomus xanthurus Sciaenidae Aplodinotus grunniens Micropogonias undulatus Sciaenops ocellatus Monodactylus sebae Monodactylidae Leiognathus equulus Leiognathidae Gazza minuta Prognathodes aculeatus Chaetodon ornatissimus Chaetodon striatus Chelmon rostratus Chaetodontidae Forcipiger flavissimus Hemitaurichthys polylepis Johnrandallia nigrirostris Erythrocles scintillans Emmelichthyidae Erythrocles schlegelii Grammatonotus surugaensis Callanthiidae Sillago chondropus Sillaginidae Sillago sihama Chaetodontoplus melanosoma Holacanthus passer Pomacanthidae Pomacanthus zonipectus Pentapodus caninus Scolopsis margaritifer Nemipteridae Scolopsis bilineata Monotaxis grandoculis Lethrinus erythropterus Lethrinidae Lethrinus erythracanthus Pagrus pagrus Calamus calamus Sparidae Stenotomus chrysops Lagodon rhomboides Caulolatilus princeps Malacanthidae Malacanthus plumieri Orthopristis chrysoptera Anisotremus surinamensis Haemulon plumierii Haemulidae Haemulon sciurus Haemulon vittatum Haemulon aurolineatum Caesio cuning Caesionidae Pterocaesio pisang Lutjanus griseus Lutjanus biguttatus Ocyurus chrysurus Lutjanidae Rhomboplites aurorubens Lutjanus mahogoni 0.05 substitutuions per site

Fig. S1. Phylogeny of 579 teleost species, including 520 acanthomorphs, inferred from a partitioned maximum-likelihood analysis of DNA sequences from 10 nuclear genes. Filled black circles identify clades supported with a bootstrap score of 100%, filled gray circles identify clades with a bootstrap score between 99 and 90%, and unfilled white circles identify clades supported with a bootstrap score between 89% and 70%. The shaded portion of the phylogeny along the side of the figure indicates placement of clades in the full phylogeny. Where space permits, polytypic and polygeneric higher-level taxonomic groups are labeled and paraphyletic named groups are denoted with an asterisk. The phylogeny is presented in eight parts, labeled A–H.

Near et al. www.pnas.org/cgi/content/short/1304661110 11 of 20 Ameiurus natalis A Ostariophysi Opsariichthys uncirostris Gonorynchus abbreviatus Gonorynchus greyi Chanos chanos 1 Cromeria nilotica Phractolaemus ansorgii Argentina silus Thymallus brevirostris 3 Salvelinus alpinus Parahucho perryi Umbra limi Novumbra hubbsi 2 Esox americanus Osmerus mordax Hypomesus pretiosus Polymetme sp. Neonesthes capensis Astronesthes leucopogon Euteleostei Chauliodus sloani Chauliodus macouni Gonostoma elongatum Cyclothone microdon Polyipnus spinifer Sternoptyx sp. Argyropelecus gigas Argyropelecus affinis Ateleopus japonicus Ijimaia loppei Synodus variegatus Synodus foetens Bathypterois atricolor 4 Benthalbella infans Notolepis coatsi Magnisudis prionosa Alepisaurus ferox Anotopterus pharao Neoteleostei Neoscopelus macrolepidotus Neoscopelus microchir Scopelengys sp. Scopelengys tristis Ceratoscopelus maderensis Lampanyctus jordani Stenobrachius leucopsarus Eurypterygii Diaphus sp. Diaphus rafinesquii Notoscopelus resplendens Gymnoscopelus nicholsi Gymnoscopelus opisthopterus Gymnoscopelus braueri Electrona antarctica Protomyctophum choriodon Krefftichthys anderssoni Hygophum proximum Tarletonbeania crenularis Ctenosquamata Symbolophorus evermanni Polymixia japonica Polymixia lowei 5 Percopsis omiscomaycus 6 Chologaster cornuta 7 Aphredoderus sayanus Cyttomimus affinis Cyttopsis rosea 10 Zeus faber 9 Zenopsis conchifera Stylephorus chordatus Muraenolepis microps Lota lota Gadus morhua Acanthomorpha Macrourus sp. Nezumia bairdii Coryphaenoides rupestris Coryphaenoides armatus Lampris guttatus 8 Trachipterus arcticus Trachipterus trachypterus Regalecus russelii Regalecus glesne

To Figure S2B 300 250 200 150 100 50 millions of years ago

Fig. S2. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 12 of 20 B Anoplogaster cornuta Diretmichthys parini Diretmus argenteus Monocentris japonica Anomalops katoptron Hoplostethus atlanticus 12 Gephyroberyx darwini Beryciformes Aulotrachichthys prosthemius 11 Paratrachichthys sajademalensis Sargocentron cornutum To Figure S2A Neoniphon vexillarium 13 Myripristis violacea Myripristis murdjan Rondeletia loricata Cetostoma regani Gyrinomimus sp. Acanthochaenus luetkenii Barbourisia rufa Beryx decadactylus Centroberyx druzhinini Poromitra crassiceps Scopeloberyx sp. Melamphaes polylepis Scopelogadus beanii Brosmophycis marginata Diplacanthopoma brunnea Cataetyx lepidogenys Barathronus maculatus Acanthopterygii Brotula multibarbata Lamprogrammus niger Carapus bermudensis Pyramodon ventralis Onuxodon parvibrachium Porichthys notatus Porichthys plectrodon Batrachoides pacifici Opsanus pardus Opsanus beta Upeneus parvus Mulloidichthys flavolineatus Pseudupeneus maculatus Parupeneus trifasciatus Parupeneus barberinus Eurypegasus draconis Dactyloptena peterseni Dactyloptena orientalis Dactyloptena gilberti Synchiropus splendidus Percomorpha Neosynchiropus ocellatus Synchiropus agassizi Callionymus bairdi Foetorepus sp. Aeoliscus strigatus 16 Macroramphosus scolopax 14 Aulostomus chinensis Aulostomus maculatus Fistularia petimba Fistularia commersonii 15 Hippocampus erectus Syngnathus leptorhynchus Syngnathus fuscus Scomber scombrus Scomberomorus maculatus Sarda sarda Thunnus albacares Auxis rochei Peprilus triacanthus Psenes maculatus Cubiceps baxteri Icosteus aenigmaticus Caristius macropus Platyberyx opalescens Icichthys lockingtoni Pomatomus saltatrix Ruvettus pretiosus Chiasmodon sp. Kali kerberti Assurger anzac Trichiurus lepturus To Figure S2C Paradiplospinus gracilis Pteraclis aesticola Brama japonica Taractes asper 150 100 50 millions of years ago

Fig. S2. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 13 of 20 C To Figure S2B Kurtus gulliveri Kurtus indicus Astrapogon stellatus Phaeoptyx pigmentaria Sphaeramia orbicularis Cheilodipterus quinquelineatus Ostorhinchus lateralis Odontobutis potamophila Percottus glenii Lepidogobius lepidus Stonogobiops nematodes Ptereleotris evides Nemateleotris magnifica Eleotris pisonis Dormitator maculatus Oxyeleotris selheimi Ophiocara porocephala Monopterus albus Indostomus paradoxus Indostomus crocodilus Macrognathus siamensis Mastacembelus niger Mastacembelus brachyrhinus Mastacembelus cunningtoni Pristolepis fasciata Pristolepis sp. Dario dario Badis pyema Nandus nebulosus Nandus andrewi Nandus nandus Channa lucius Channa melasoma Channa striata Ctenopoma kingsleyae Microctenopoma nanum Helostoma temminckii Trichopodus pectoralis Betta splendens Polydactylus sextarius Eleutheronema rhadinum Lates niloticus Psettodes erumei Citharoides macrolepis Scophthalmus aquosus Bothus lunatus 18 Citharichthys sordidus 19 Paralichthys dentatus Pseudopleuronectes americanus Lepidopsetta bilineata Pleuronectes platessa Gymnachirus melas Achirus lineatus Samariscus latus 20 Citharoides macrolepidotus Symphurus atricaudus Aseraggodes kobensis Heteromycteris japonicus Seriola dumerili 22 Caranx crysos Selene setapinnis 21 Echeneis naucrates 23 Coryphaena hippurus Rachycentron canadum Oligoplites saurus Trachinotus carolinus Trachinotus ovatus Toxotes jaculatrix Mene maculata 25 Tetrapturus angustirostris Xiphias gladius Nematistius pectoralis Centropomus undecimalis Centropomus armatus 24 Sphyraena japonica Sphyraena barracuda To Figure S2D Sphyraena jello To Figure S2E

100 50 millions of years ago

Fig. S2. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 14 of 20 D Polycentropsis abbreviata Monocirrhus polyacanthus To Figure S2C Labidesthes sicculus Menidia peninsulae Poblana ferdebueni Menidia beryllina Atherinomorus lacunosus Rheocles wrightae Melanotaenia sp. Iso sp. Phenacostethus smithi Pseudomugil gertrudae Pseudomugil signifer Ovalentaria Pachypanchax playfairii Cyprinodon variegatus Jordanella floridae Poeciliopsis elongata Gambusia affinis Fundulus heteroclitus Lucania goodei Oryzias latipes Arrhamphus sclerolepis Cheilopogon melanurus 17 Cheilopogon pinnatibarbatus Dermogenys collettei Xenentodon cancila Scomberesox saurus Strongylura marina Platybelone argala Pholidichthys leucotaenia Paretroplus maculatus Etroplus maculatus Paratilapia polleni Ptychochromis grandidieri Heterochromis multidens Oreochromis niloticus Cichla temensis Heros efasciatus Herichthys cyanoguttatus Congrogadus subducens Pseudambassis ranga Ambassis urotaenia Mugil curema Mugil cephalus Hyperprosopon argenteum Cymatogaster aggregata Phanerodon furcatus Rhacochilus vacca Embiotoca lateralis Embiotoca jacksoni Plesiops coeruleolineatus Chromis cyanea Abudefduf saxatilis Stegastes leucostictus Microspathodon bairdii Labracinus cyclophthalmus Ogilbyina novaehollandiae Pholidochromis cerasina Pseudochromis fridmani Gramma loreto Opistognathus aurifrons Diademichthys lineatus Gobiesox maeandricus Arcos sp. Enneanectes boehlkei Helcogramma ellioti Gibbonsia metzi Labrisomus multiporosus Gillellus semicinctus Chaenopsis alepidota Hypsoblennius hentz Meiacanthus grammistes Enchelyurus flavipes Ophioblennius atlanticus Entomacrodus nigricans Salarias fasciatus 100 50 millions of years ago

Fig. S2. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 15 of 20 Champsodon snyderi E To Figure S2C Ulaema lefroyi Eugerres plumieri Lachnolaimus maximus Haletta semifasciata Clepticus parrae Bodianus rufus Pteragogus enneacanthus Xyrichtys martinicensis Coris gaimard Gomphosus varius Halichoeres bivittatus Oxyjulis californica Coris batuensis Halichoeres margaritaceus Labrichthys unilineatus Labropsis australis Diproctacanthus xanthurus Tautogolabrus adspersus Tautoga onitis Oxycheilinus celebicus Epibulus brevis Epibulus insidiator Calotomus carolinus Cryptotomus roseus Cetoscarus bicolor Chlorurus sordidus Scarus globiceps Scarus niger Centrogenys vaigiensis Cheimarrichthys fosteri Parapercis clathrata Parapercis hexophtalma Ammodytes dubius Ammodytes hexapterus Kathetostoma averruncus Astroscopus y-graecum Girella mezina Oplegnathus punctatus Kyphosus elegans Kyphosus cinerascens Kuhlia rupestris Kuhlia marginata Terapon jarbua Hephaestus fuliginosus Scortum barcoo Percalates novemaculeata Percalates colonorum Enoplosus armatus Maccullochella peelii Gadopsis marmoratus Macquaria ambigua Nannoperca australis Percilia irwini Siniperca chuasti Elassoma okefenokee Elassoma zonatum Lepomis cyanellus Micropterus salmoides Archoplites interruptus 26 Ambloplites rupestris Cheilodactylus pixi Cheilodactylus variegatus Chirodactylus brachydactylus Paracirrhites arcatus Neocirrhites armatus Cirrhitichthys falco Amblycirrhitus pinos Limnichthys sp. Acanthaphritis unoorum Pempheris schwenkii Pempheris schomburgkii Glaucosoma buergeri Glaucosoma hebraicum Howella zina Acropoma japonica Ostracoberyx dorygenys Stereolepis gigas Malakichthys elegans Banjos banjos Histiopterus typus Pseudopentaceros pectoralis To Figure S2G Pentaceros japonicus To Figure S2F Pseudopentaceros wheeleri

100 millions of years ago 50

Fig. S2. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 16 of 20 F Cephalopholis argus To Figure S2E Mycteroperca microlepis Grammistes sexlineatus Rypticus saponaceus Bovichtus diacanthus Eleginops maclovinus Chionobathyscus dewitti Dissostichus eleginoides Niphon spinosus Perca flavescens Etheostoma atripinne Percina caprodes Bembrops anatirostris Hypoplectrus puella Serranus tigrinus Paralabrax nebulifer Pseudanthias pascalus Hemanthias aureorubens Rogadius asper Platycephalus indicus Parabembras curtus Bembras japonicus Hoplichthys gilberti Hoplichthys langsdorfii Pterygotrigla hemisticta Sebastolobus alascanus Sebastes ruberrimus Sebastes fasciatus Anoplopoma fimbria Hexagrammos otakii Trichodon trichodon Eumicrotremus orbis Cyclopterus lumpus Paraliparis meganchus Liparis mucosus Leptocottus armatus Cottus carolinae Aspidophoroides monopterygius Stellerina xyosterna Artediellus uncinatus Scorpaenichthys marmoratus Hypoptychus dybowskii Aulorhynchus flavidus Aulichthys japonicus Apeltes quadracus Gasterosteus aculeatus 37 Gasterosteus wheatlandi Rathbunella hypoplecta Bathymaster signatus Cebidichthys violaceus Cryptacanthodes maculatus Pholis ornatus Pholis crassispina Anarhichas lupus Allolepis hollandi Lycodes terraenovae Lycodes diapterus

50 millions of years ago

Fig. S2. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 17 of 20 G

To Figure S2E Morone saxatilis Morone mississippiensis Morone chrysops Drepane punctata Chaetodipterus faber Platax orbicularus Grammatonotus surugaensis Erythrocles scintillans Erythrocles schlegelii Sillago chondropus Sillago sihama Pagrus pagrus Calamus calamus Stenotomus chrysops Lagodon rhomboides Monotaxis grandoculis Lethrinus erythropterus Lethrinus erythracanthus Pentapodus caninus Scolopsis margaritifer Scolopsis bilineata Caulolatilus princeps Malacanthus plumieri Chaetodontoplus melanosoma Holacanthus passer Pomacanthus zonipectus Orthopristis chrysoptera Anisotremus surinamensis Haemulon vittatum Haemulon aurolineatum Haemulon sciurus Haemulon plumierii Pterocaesio pisang Caesio cuning Lutjanus biguttatus Lutjanus griseus Ocyurus chrysurus Lutjanus mahogoni Rhomboplites aurorubens Lobotes surinamensis Datnioides microlepis Cynoscion regalis Menticirrhus littoralis Leiostomus xanthurus Aplodinotus grunniens Micropogonias undulatus Sciaenops ocellatus Monodactylus sebae Gazza minuta 27 Leiognathus equulus 28 Prognathodes aculeatus Chaetodon ornatissimus Chaetodon striatus Chelmon rostratus To Figure S2H Forcipiger flavissimus Johnrandallia nigrirostris Hemitaurichthys polylepis

50 millions of years ago

Fig. S2. (Continued)

Near et al. www.pnas.org/cgi/content/short/1304661110 18 of 20 H To Figure S2G Luvarus imperialis 29 Zanclus cornutus Naso brevirostris Naso lituratus 30 Zebrasoma rostratum Acanthurus nigricans Ctenochaetus strigosus Acanthurus bahianus Siganus spinus Siganus vulpinus 31 Selenotoca multifasciata Scatophagus argus Cepola schlegelii Sphenanthias tosaensis Pristigenys alta Priacanthus arenatus Priacanthus cruentatus Capros aper Antigonia rubescens Antigonia capros Lophius gastrophysus Lophius americanus Halieutichthys aculeatus Ogcocephalus nasutus Antennarius striatus 32 Histiophryne cryptacanthus Chaunax sp. Chaunax suttkusi Chaunax stigmaeus Gigantactis sp. Gigantactis vanhoeffeni Himantolophus sagamius Cryptopsaras couesi Ceratias holboelli Diodon holocanthus Chilomycterus schoepfii 33 Canthigaster jactator Sphoeroides nephelus Tetraodon miurus Arothron nigropunctatus Triodon macropterus Aracana aurita Ostracion cubicus Rhinesomus triqueter Halimochirurgus alcocki Triacanthodes anomalus Triacanthus biaculeatus 35 Ranzania laevis 36 Mola mola Masturus lanceolatus Cantherhines pullus Paraluteres prionurus Pervagor nigrolineatus Stephanolepis hispidus Pervagor janthinosoma 34 Acreichthys tomentosus Balistapus undulatus Xanthichthys ringens Pseudobalistes flavimarginatus Sufflamen chrysopterum Balistes capriscus Balistes vetula Abalistes stellatus Rhinecanthus verrucosus 50 millions of years ago

Fig. S2. Time-calibrated maximum clade credibility Bayesian inferred phylogeny of 579 teleost species, including 520 acanthomorphs, based on 10 nuclear genes and 37 fossil age constraints. Bars represent the posterior distribution of divergence time estimates. Gray bars identify nodes supported with Bayesian posterior probabilities ≥0.95, and white bars mark nodes with Bayesian posterior probabilities <0.95. Nodes with age priors taken from the fossil record are numbered, and specific information on calibrations are provided in SI Text. Calibration labels are placed on the branch leading to the node if it would completely obscure the bar depicting the posterior distribution. The time-calibrated tree is scaled to the geological time scale, with absolute time given in millions of years. The shaded portion of the phylogeny along the side of the figure indicates placement of clades in the full phylogeny. The time-calibrated phylogeny is presented in eight parts, labeled A–H.

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Table S1 (DOC) Table S2 (DOC) Table S3 (DOC) Table S4 (DOC) Table S5 (DOC)

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