Classification v.2

New and Revised Classification of Bony Fishes

Based on Molecular Data — Version 2

Version Date: 27 November 2013 -- this version has been superseded by version 3 on 31 July 2014

Contributors to this version: Ricardo Betancur-R, Ed Wiley, Masaki Miya, Guillaume Lecointre, Nicolas Bailly & Guillermo Ortí

Citing this classification:

Betancur-R, R., E. Wiley, M. Miya, G. Lecointre, N. Bailly, and G. Ortí. 2013. New and Revised Classification of Bony Fishes Version 2 (http://www.deepfin.org/Classification_v2.htm).

Betancur-R., R., R.E. Broughton, E.O. Wiley, K. Carpenter, J.A. Lopez, C. Li, N.I. Holcroft, D. Arcila, M. Sanciangco, J. Cureton, F. Zhang, T. Buser, M. Campbell, T. Rowley, J.A. Ballesteros, G. Lu, T. Grande, G. Arratia & G. Ortí. 2013. The tree of life and a new classification of bony fishes. PLoS Currents Tree of Life. 2013 Apr 18.

This classification is an update of version 1 (18 April 2013) published by Betancur-R. et al. (2013a) . It is based on new analyses of a molecular data set with 1591 taxa that adds 165 new taxa and ca. 25 families not examined in version 1. The new data set combines evidence published by Betancur-R. et al. (2013a) and Near et al. (2013). Methods used for phylogenetic inference were as described by Betancur-R. et al. (2013a), based on maximum likelihood analyses with RAxML using a 24-partition scheme and 1000 bootstrap replicates to assess clade support. The complete phylogenetic tree (pdf, unpublished results), a pretty figure with all the major groups, and a spreadsheet with the classification scheme can be downloaded at the bottom of this page. Families in the classification are linked to FishBase family pages (Froese and Pauly (2013); except for the differences noted in the spreadsheet).

A major change in version 2 is that the nine well-supported percomorph clades are now recognized as a separate series to facilitate communication. These are: Ophidiimorpharia, Batrachoidimorpharia, Gobiomorpharia, Syngnathimorpharia, Pelagimorpharia (Scombriformes in version1), Anabantomorpharia, Carangimorpharia, Ovalentaria, and Percomorpharia (Fig. 1). A complete list of changes from version 1 can be found here.

Figure 1. Phylogeny of the nine major percomorph (Percomorphaceae) clades (from Betancur-R. et al. (2013a) and new results). Each major clade is now recognized as a separate series. Values in parentheses indicate total number of orders, total number of families, and the number of families included in each series that cannot be placed in any order at this time (insertae sedis families).

This classification (version 2), building on Wiley and Johnson (2010) and Betancur-R. et al. (2013a), intends to preserve names and taxonomic composition of groups as much as possible. However, adjustments have been made to recognize well-supported molecular clades, many of which also have been obtained by previous molecular studies (several examples discussed below). Order-level or supraordinal taxa have been erected (listed as new) or resurrected on the basis of well-supported clades only (>90% bootstrap values). Current taxon names supported by previous molecular or morphological studies have been retained if congruent with our results, even if bootstrap support is low (e.g., Osteoglossocephalai sensu Arratia (1999) with only 38% bootstrap). In some cases, ordinal or subordinal taxa that were not monophyletic in our analysis are also validated, as long as the incongruence is not supported by strong bootstrap values. Examples include the suborder Blennioidei (not monophyletic here but monophyletic in Wainwright et al., 2012) and the order Pleuronectiformes (not monophyletic here but monophyletic in Betancur-R. et al., 2013b).

A total of 68 orders are classified, of which two are new for version 2 (Lobotiformes and Terapontiformes). Three orders were new in the version 1 (Holocentriformes, Istiophoriformes, and Pempheriformes). The ordinal status of several percomorph families examined (as well as many others unexamined) belonging to the Series Carangimorpharia, Ovalentaria, and Percomorpharia remains uncertain (incertae sedis) due to poor phylogenetic resolution. We therefore list these families as incertae sedis within each of these groups (Carangimorpharia, Ovalentaria, and Percomorpharia) awaiting new phylogenetic evidence to clarify their ordinal status.

Family names for bony fishes are based on Eschmeyer and Fong (2013) and van der Laan et al. (2013), with minor modifications. Van der Laan et al. (2013) and Eschmeyer (2013) should be consulted for authorship of family names and Wiley and Johnson (2010) for authorship of ordinal and subordinal names. Our list is not intended as a comprehensive revision of valid family names. Instead, it is simply an adaptation of their lists based on published studies that we know validate or synonymize family groups using explicit phylogenetic evidence. Following this criterion, we do not recognize the family status of Phractolaemidae (synonym of Kneriidae; Davis et al., 2013), Anotopteridae, Omosudidae (synonym of Alepisauridae; Davis, 2010), or Latidae (synonym of Centropomidae; Greenwood, 1976; Li et al., 2011). Also, we recognize the following families, listed in Eschmeyer and Fong (2013) and van der Laan et al. (2013) as synonyms or subfamilies of other families: Botiidae (Chen et al., 2009), Diplophidae (Nelson, 2006 apparently ommited by ; Eschmeyer and Fong, 2013), Horabagridae (Sullivan et al., 2006), Niphonidae (Smith and Craig, 2007), Sinipercidae (Li et al., 2010), Steindachneriidae (Roa-Varon and Orti, 2009), Sudidae (Davis, 2010), Bembropidae (Near et al., 2013), and the pleuronectiform Paralichthodidae, Poecilopsettidae, and Rhombosoleidae (Chapleau, 1993; Munroe, 2005).

A total of 504 families of bony fishes are now recognized (excluding tetrapods), of which 396 (78.6%) were examined. Among the examined families, 41 (8.1 %) were rendered non-monophyletic in our analysis (indicated below). For each order/suborder we list all families examined as well as the unexamined families whose taxonomic affinity is expected on the basis of traditional taxonomy or phylogenetic evidence. The list of 108 unexamined families can be easily obtained from the spreadsheet that also contains the complete classification (bottom of this page), and is intended as a resource to help fish systematists direct future sequencing efforts.

The new classification scheme presented here should still be considered work in progress (version 2), as any other hypothesis. It is likely to include involuntary errors and omissions in addition to the many unexamined, sedis mutabilis, and incertae sedis taxa. Updates should be forthcoming as new evidence becomes available and feedback from experts help refine it. Please send comments or concerns to guilleorti@gmail.com. For the most updated version always visit DeepFin.

Classification for Bony Fishes (version 2)

Megaclass Osteichthyes (=Euteleostomi, =Euosteichthyes)

Superclass Actinopterygii (100%)

Class Cladistia (100%)

Order Polypteriformes

Polypteridae

Class Actinopteri (100%)

Subclass Chondrostei, (100%)

Order Acipenseriformes

Acipenseridae

Polyodontidae

Subclass Neopterygii (100%)

Infraclass Holostei (100%)

Order Amiiformes

Amiidae

Order Lepisosteiformes (100%)

Lepisosteidae

Infraclass Teleostei(100%)

Megacohort Elopocephalai sensu Arratia (1999) (100%)

Supercohort Elopocephala (100%)

Cohort Elopomorpha (100%)

Order Elopiformes (100%)

Elopidae

Megalopidae

Order Albuliformes (100%)

Albulidae

Order Notacanthiformes (100%)

Halosauridae

Notacanthidae

Order Anguilliformes (100%)

Not examined: Chlopsidae, Colocongridae, Cyematidae, Derichthyidae, Heterenchelyidae, Monognathidae, Moringuidae, Myrocongridae, Nettastomatidae, Protanguillidae, Synaphobranchidae.

Comment: Suborders recognized in Wiley and Johnson (2010) based on previous work cited therein are significantly incongruent with the clades obtained in this analysis; thus, no subordinal classification is proposed.

Megacohort Osteoglossocephalai sensu Arratia (1999) (38%)

Supercohort Osteoglossocephala sensu Arratia (1999) (99%)

Cohort Osteoglossomorpha

Order Hiodontiformes (100%)

Hiodontidae

Order Osteoglossiformes (100%)

Supercohort Clupeocephala sensu Arratia (2010) (100%)

Cohort Otomorpha (=Otocephala, Ostarioclupeomorpha) (100%)

Subcohort Clupei (87%)

Order Clupeiformes

Suborder Denticipitoidei

Denticipitidae

Suborder Clupeoidei (100%)

Chirocentridae

Clupeidae (not monophyletic)

Engraulidae

Pristigasteridae

Not examined: Dussumieriidae, Sundasalangidae.

Comment: family-level groupings may require major revision; Pristigasteridae, Chirocentridae and Engraulidae are supported by other molecular studies, but not Clupeidae (Li and Ortí, 2007; Lavoué et al., 2013) ; five well-supported lineages identified by Lavoué et al., (2013) could become new families.

Subcohort Alepocephali (100%)

Order Alepocephaliformes

Alepocephalidae (not monophyletic)

Platytroctidae

Not examined: Leptochilichthyidae.

Subcohort Ostariophysi (100%)

Section Anotophysa (97%)

Order Gonorynchiformes

Suborder Gonorynchoidei

Gonorynchidae

Suborder Chanoidei

Chanidae

Suborder Knerioidei (100%)

Kneriidae

Section Otophysa (100%)

Superorder Cypriniphysae (100%)

Order Cypriniformes

Not examined: Balitoridae, Barbuccidae, Ellopostomatidae, Psilorhynchidae, Serpenticobitidae, Vaillantellidae.

Superorder Characiphysae (100%)

Order Gymnotiformes (100%)

Suborder Gymnotoidei (not monophyletic)

Gymnotidae (not monophyletic)

Suborder Sternopygoidei (not monophyletic)

Apteronotidae

Rhamphichthyidae

Sternopygidae (not monophyletic)

Not examined: Hypopomidae.

Comment: Although not monophyletic here, the monophyly gymnotiform suborders is corroborated by Albert and Crampton (2005).

Order Characiformes (100%)

Suborder Citharinoidei (not monophyletic)

Citharinidae

Distichodontidae

Suborder Characoidei (not monophyletic)

Not examined: Anostomidae, Curimatidae, Iguanodectidae.

Comment: Although not monophyletic in this analysis, the monophyly of characiform suborders has been corroborated by other molecular studies (Calcagnotto et al., 2005).

Order Siluriformes (100%)

Suborder Loricaroidei (93%)

Suborder Diplomystoidei

Diplomystidae

Suborder Siluroidei (100%)

Not examined: Aspredinidae, Austroglanididae, Erethistidae, Lacantuniidae, Olyridae, Scoloplacidae.

Supercohort Clupeocephala (cont.)

Cohort Euteleosteomorpha (100%)

Subcohort Lepidogalaxii

Order Lepidogalaxiiformes

Lepidogalaxiidae

Subcohort Protacanthopterygii sedis mutabilis (37%)

Order Galaxiiformes (100%)

Galaxiidae

Order Argentiniformes (100%)

Order Salmoniformes (100%)

Salmonidae

Order Esociformes (100%)

Esocidae

Umbridae

Subcohort Stomiatii (73%)

Order Stomiatiformes (=Stomiiformes) (100%)

Diplophidae

Gonostomatidae

Phosichthyidae (not monophyletic)

Sternoptychidae

Stomiidae

Order Osmeriformes (100%)

Subcohort Neoteleostei (100%)

Infracohort Ateleopodia (100%)

Order Ateleopodiformes

Ateleopodidae

Infracohort Eurypterygia (96%)

Section Aulopa (100%)

Order Aulopiformes

Suborder Aulopoidei (not monophyletic)

Aulopidae

Pseudotrichonotidae

Synodontidae (not monophyletic)

Suborder Paraulopoidei

Paraulopidae

Suborder Alepisauroidei (not monophyletic)

Alepisauridae

Bathysauridae

Chlorophthalmidae (not monophyletic)

Evermannellidae

Giganturidae

Ipnopidae (not monophyletic)

Notosudidae

Paralepididae (not monophyletic)

Scopelarchidae (not monophyletic)

Sudidae

Not examined: Bathysauroididae, Bathysauropsidae.

Comment: Suborders and families listed are as in (2010). Although not monophyletic herein, the monophyly aulopiform suborders is supported by Davis (2010).

Section Ctenosquamata (97%)

Subsection Myctophata (100%)

Order Myctophiformes

Myctophidae

Neoscopelidae

Subsection Acanthomorphata (97%)

Division Lampridacea (100%)

Order Lampridiformes

Not examined: Radiicephalidae, Veliferidae.

Division Paracanthomorphacea sensu Grande et al. (2013) (93%)

Series Percopsaria (100%)

Order Percopsiformes

Amblyopsidae

Aphredoderidae

Percopsidae

Series Zeiogadaria(=Zeiogadiformes sensu Li et al., 2009) (98%)

Subseries Zeariae (100%)

Order Zeiformes

Parazenidae

Zeidae

Zenionidae

Not examined: Cyttidae, Grammicolepididae, Oreosomatidae.

Subseries Gadariae (100%)

Order Stylephoriformes (sensu Miya et al., 2007)

Stylephoridae

Order Gadiformes (100%)

Suborder Macrouroidei

Macrouridae (not monophyletic)

Steindachneriidae

Suborder Gadoidei (not monophyletic)

Gadidae

Lotidae (not monophyletic)

Merlucciidae

Moridae

Phycidae

Not examined: Bregmacerotidae, Euclichthyidae, Melanonidae.

Suborder Muraenolepidoidei

Muraenolepididae

Comment: The subordinal classification follows Roa-Varón and Orti (2009): fig. 6.

Division Polymixiacea (100%)

Order Polymixiiformes

Polymixiidae

Division Euacanthomorphacea sensu Johnson and Patterson (1993) (99%)

Subdivision Berycimorphaceae (87%)

Order Beryciformes (similar to Trachichthyiformes sensu Moore, 1993)

Trachichthyidae (not monophyletic)

Not examined: Gibberichthyidae, Hispidoberycidae (expected affinity following Moore, 1993).

Subdivision Holocentrimorphaceae (100%)

Order Holocentriformes

Holocentridae

Comment: Moore (1993) and Stiassny and Moore (1992) provide morphological evidence supporting a sister-group relationship between holocentrids and percomorphs, which further guarantees placement of this family in its own order.

Subdivision Percomorphaceae (="Percomorpha" sensu Miya et al. (2003) and Miya et al. (2005)).

Subdivision Percomorphaceae (cont.)

Series Ophidiimorpharia (100%)

Order Ophidiiformes

Suborder Ophidioidei

Carapidae (not monophyletic)

Ophidiidae

Suborder Bythitoidei

Aphyonidae

Bythitidae (not monophyletic)

Not examined: Parabrotulidae

Series Batrachoidimorpharia (100%)

Order Batrachoidiformes

Batrachoididae

Series Gobiomorpharia (see also Thacker, 2009; Chakrabarty et al., 2012) (100%)

Comment: In addition to the well-supported molecular circumscription of this group, kurtids, apogonids and gobioids are characterized by the presence of sensory papillae rows on the head and body (Thacker, 2009).

Order Kurtiformes (98%)

Suborder Kurtoidei

Kurtidae

Suborder Apogonoidei

Apogonidae

Comment: Johnson (1993) noted that the configuration of the dorsal gill-arch elements may be homologous in Kurtus and apogonids.

Order Gobiiformes (100%)

Suborder Odontobutoidei (100%)

Odontobutidae

Suborder Eleotroidei (97%)

Eleotridae

Suborder Gobioidei (100%)

Gobiidae (not monophyletic)

Microdesmidae

Not examined: Kraemeriidae, Rhyacichthyidae, Schindleriidae, Thalasseleotrididae, Xenisthmidae.

Series Syngnathimorpharia, new (96%)

Order Syngnathiformes

Suborder-level incertae sedis in Syngnathiformes

Aulostomidae

Centriscidae

Fistulariidae

Suborder Syngnathoidei (92%)

Syngnathidae

Pegasidae

Not examined: Solenostomidae (assumed affinity with Syngnathidae)

Suborder Dactylopteroidei (100%)

Dactylopteridae

Suborder Callionymoidei (100%)

Callionymidae

Not examined: Draconettidae (assumed affinity with Callionymidae).

Suborder Mulloidei (92%)

Mullidae

Series Pelagimorpharia, new name and circumscription (=Stromateoidei sensu Li et al. (2009); = Pelagia sensu Miya et al. (2013)) (100%)

Order Scombriformes

Ariommatidae

Arripidae (not examined, included here following Yagishita et al., 2009; Miya et al., 2013)

Gempylidae (not monophyletic)

Icosteidae

Nomeidae

Pomatomidae

Scombridae (not monophyletic)

Scombrolabracidae

Stromateidae

Tetragonuridae (not examined, included here following Miya et al., 2013)

Trichiuridae

Other “Stromateoid” families not examined: Amarsipidae, Scombropidae (Doiuchi et al., 2004; Miya et al., 2013)

Comment: interfamilial resolution in Scombriformes is tenuous; circumscription of scombriform families into suborders (e.g., Scombroidei, Stromateoidei, Icostoidei) or new orders requires further work.

Series Anabantomorpharia (=Anabantiformes sensu Li et al., 2009) (99%)

Order Synbranchiformes (98%)

Suborder Indostomoidei

Indostomidae

Suborder Synbranchoidei

Synbranchidae

Suborder Mastacembeloidei

Mastacembelidae

Not examined: Chaudhuriidae.

Order Anabantiformes (=Labyrinthici) (100%)

Suborder Anabantoidei (95%)

Suborder Channoidei (85%)

Channidae

Nandidae

Series Carangimorpharia (=Carangimorpha sensu Li et al. (2009)) (100%)

Order-level incertae sedis in Carangimorpharia

Centropomidae (sensu Greenwood)

Not examined: Lactariidae (included in Carangimorphariae according to Campbell et al., 2013)

Order Istiophoriformes (100%)

Istiophoridae

Xiphiidae

Order Carangiformes sedis mutabilis (not monophyletic)

Comment: Monophyly of Carangiformes is not significantly rejected by the data (see Betancur-R. et al., 2013b).

Order Pleuronectiformes sedis mutabilis (not monophyletic)

Suborder Psettodoidei (100%)

Psettodidae

Suborder Pleuronectoidei (100%)

Paralichthyidae (not monophyletic)

Pleuronectidae

Poecilopsettidae

Rhombosoleidae (not monophyletic)

Samaridae

Scophthalmidae

Soleidae

Not examined: Paralichthodidae.

Comment: Although Psettodidae is not recovered as the sister group of pleuronectoids in the present analysis, the order was resolved as monophyletic by a recent study (Betancur-R. et al., 2013b).

Series Ovalentaria (sensu Smith & Near in Wainwright et al. (2012); =Stiassnyiformes sensu Li et al. (2009)) (100%)

Order-level incertae sedis in Ovalentaria

Ambassidae

Embiotocidae

Grammatidae (not monophyletic)

Plesiopidae

Polycentridae

Pomacentridae

Pseudochromidae (not monophyletic)

Opistognathidae

Superorder Cichlomorphae (93%)

Order Cichliformes

Cichlidae

Order Pholidichthyiformes

Pholidichthyidae

Superoder Atherinomorphae (100%)

Order Atheriniformes (100%)

Not examined: Dentatherinidae, Notocheiridae.

Order Beloniformes (32%)

Suborder Adrianichthyoidei

Adrianichthyidae

Suborder Exocoetoidei (100%)

Belonidae (not monophyletic)

Exocoetidae

Hemiramphidae (not monophyletic)

Scomberesocidae

Zenarchopteridae (not monophyletic)

Order Cyprinodontiformes (57%)

Suborder Aplocheiloidei

Aplocheilidae

Suborder Cyprinodontoidei (100%)

Cyprinodontidae

Fundulidae

Poeciliidae

Not examined: Anablepidae, Goodeidae, Nothobranchiidae, Profundulidae, Rivulidae, Valenciidae.

Superorder Mugilomorphae (100%)

Order Mugiliformes

Mugilidae

Superorder Blenniimorphae (80%)

Order Blenniiformes (100%) sensu Li et al. (2009)

Suborder Gobiesocoidei

Gobiesocidae

Suborder Blennioidei (not monophyletic; = Blenniiformes sensu Lin and Hastings (2013))

Blenniidae

Chaenopsidae (not monophyletic)

Clinidae

Dactyloscopidae

Labrisomidae (not monophyletic)

Tripterygiidae

Comment: While blennioids are not monophyletic in the megatree, we note that preliminary analyses resulted in the reciprocal monophyly of gobiesocoids and blennioids, which is congruent with molecular (Wainwright et al., 2012; Lin and Hastings, 2013) and morphological (Springer and Orrell, 2004) evidence. Monophyly of gobiesocoids and blennioids (as separate orders/suborders) is further supported by both morphological (Wiley and Johnson, 2010) and molecular evidence.

Series Percomorpharia (99%)

Order-level incertae sedis in Percomorpharia

Lutjanidae (not monophyletic)

Malacanthidae

Monodactylidae

Moronidae

Percichthyidae (not monophyletic)

Not examined: Dinolestidae, Dinopercidae (see Smith and Craig, 2007). Six families traditionally placed in “Perciformes” are also provisionally listed here are: Bathyclupeidae, Dichistiidae, Hapalogenyidae, Parascorpididae, Symphysanodontidae, Trichonotidae; these are not placed in the recently circumscribed Perciformes given the long history of phylogenetic indistinctiveness between Percoidei, Perciformes, and Percomorpha (e.g., Smith and Craig, 2007).

Order Uranoscopiformes (=Paratrachinoidei sensu Li et al. (2009)) (95%)

Order Labriformes sensu stricto (100%)

Labridae (not monophyletic)

Odacidae

Scaridae

Order Lobotiformes (100%)

Lobotidae

Datnioididae

Order Ephippiformes (100%)

Drepaneidae

Ephippidae

Comment: Greenwood et al. (1966) hypothesized a close affinity between Drepane and ephippids.

Order Spariformes sensu Akazaki (1962) and Johnson (1981) (94%)

Lethrinidae

Sparidae

Possibly included (examined): Nemipteridae

Not examined but assumed affinity (Johnson, 1981): Centracanthidae

Comment: Akazaki (1962) proposed that Lethrinidae, Sparidae, and Nemipteridae were closely related based on specializations of the suspensorium and other features (Johnson, 1993). Johnson (1981) supported the monophyly of Akazaki's spariforms with the addition of Centracanthidae.

Order Lophiiformes (100%). This order is the sister group of Tetraodontiformes (55% bootstrap); also supported by anatomical evidence (Chanet et al. (2013), larval characters (Baldwin (2013)), and previous molecular studies (e.g. Dettaï and Lecointre (2008), Miya et al. (2003), Miya et al. (2010)).

Suborder Lophioidei (100%)

Lophiidae

Suborder Antennarioidei (100%).

Antennariidae

Not examined: Brachionichthyidae, Lophichthyidae, Tetrabrachiidae.

Suborder Chaunacoidei (100%)

Chaunacidae

Suborder Ogcocephaloidei (100%)

Suborder Ceratioidei

Not examined: Caulophrynidae, Centrophrynidae, Diceratiidae, Linophrynidae, Neoceratiidae, Thaumatichthyidae.

Order Tetraodontiformes (100%). This order is the sister group of Lophiiformes (55% bootstrap); also supported by anatomical evidence (Chanet et al. (2013), larval characters (Baldwin (2013)), and previous molecular studies (e.g. Dettaï and Lecointre (2008), Miya et al. (2003), Miya et al., (2010)).

Suborder Triacanthodoidei (100%)

Triacanthodidae

Suborder Triacanthoidei

Triacanthidae

Suborder Tetraodontoidei (100%)

Diodontidae

Tetraodontidae

Suborder Moloidei (100%)

Molidae

Suborder Balistoidei (100%)

Balistidae

Monacanthidae

Suborder Ostracioidei (100%)

Aracanidae

Ostraciidae

Suborder Triodontoidei, new

Triodontidae

Comment: This subordinal classification differs from that proposed by Santini and Tyler (2003).

Order Acanthuriformes, restricted circumscription (see also Holcroft and Wiley, 2008) (100%)

Acanthuridae

Luvaridae

Zanclidae

Order Terapontiformes, new (95%)

Order Pempheriformes sedis mutabilis, new circumscription (44%)

Acropomatidae (not monophyletic)

Polyprionidae (not monophyletic)

Not examined: Leptoscopidae (assumed affinity with Creediidae according to Odani and Imamura, 2011)

Comment: Tominaga (1986) suggested that features of the cranium and swimbladder may be homologous in Pempheris and Glaucosoma. Although support for Pempheriformes is only 44%, this clade is often recovered in different analyses.

Order Cirrhitiformes (similar to Cirrhithoidea sensu Greenwood (1995) and Burridge and Smolenski (2004)) (91%)

Cheilodactylidae

Cirrhitidae

Not examined but expected affinity (Burridge and Smolenski, 2004; Greenwood, 1995): Aplodactylidae, Chironemidae, Latridae.

Order Centrarchiformes (100%)

Centrarchidae

Elassomatidae

Order Perciformes (=Serraniformes sensu Lautredou et al. (2013); Li et al. (2009)) (99%)

Not examined (12 families traditionally placed in Scorpaeniformes): Apistidae, Aploactinidae, Congiopodidae, Cottocomephoridae, Eschmeyeridae, Gnathanacanthidae, Neosebastidae, Pataecidae, Perryenidae, Plectrogeniidae, Zanclorhynchidae.

Suborder-level incertae sedis in Perciformes

Bembropidae

Hoplichthyidae

Platycephalidae.

Suborder Serranoidei sedis mutabilis (19%)

Serranidae

Suborder Percoidei, restricted circumscription (99%)

Niphonidae

Percidae

Not examined: Trachinidae.

Comment: Lautredou et al. (2013) using seven nuclear markers obtained a clade uniting Percidae and Trachinidae with full support.

Suborder Notothenioidei (100%)

Pseudaphritidae

Eleginopsidae

Nototheniidae (not monophyletic)

Artedidraconidae

Harpagiferidae

Bathydraconidae (not monophyletic)

Channichthyidae

Bovichtidae

Suborder Scorpaenoidei (83%)

Scorpaenidae (not monophyletic)

Suborder Bembroidei (96%)

Bembridae

Parabembridae

Suborder Triglioidei sensu Jordan (1923) (100%)

Triglidae

Peristediidae

Suborder Cottioidei (=Cottimorpha sensu Li et al. (2009)) (100%)

Comment: We have chosen to recognize clades within this suborder as infraorders, adopting the ending –ales for this rank. Gasterosteales and Zoarcales are most probably sister-groups; they are have been grouped as Zoarciformes by Li et al. (2009)

Infraorder Anoplopomatales

Anoplopomatidae

Infraorder Gasterosteales (100%)

Aulorhynchidae

Gasterosteidae

Hypoptychidae

Infraorder Zoarcales (100%)

Anarhichadidae

Bathymasteridae (not monophyletic)

Cryptacanthodidae

Stichaeidae (not monophyletic)

Pholidae

Zaproridae

Zoarcidae

Not examined: Ptilichthyidae, Scytalinidae.

Infraorder Cottales (96%)

Agonidae (not monophyletic)

Cyclopteridae

Cottidae (not monophyletic)

Hexagrammidae (not monophyletic)

Liparidae

Psychrolutidae

Trichodontidae

Not examined: 7 families traditionally placed in Cottoidei: Abyssocottidae, Bathylutichthyidae, Comephoridae, Ereuniidae, Hemitripteridae, Normanichthyidae, Rhamphocottidae.

Superclass Sarcopterygii (96%)

Class Coelacanthimorpha (=Actinistia)

Order Coelacanthiformes

Latimeriidae

Class Dipnotetrapodomorpha sedis mutabilis (65%)

Subclass Dipnomorpha (100%)

Superorder Ceratodontae

Order Ceratodontiformes

Suborder Ceratodontoidei

Neoceratodontidae

Suborder Lepidosirenoidei (100%)

Lepidosirenidae

Protopteridae

Subclass Tetrapodomorpha (100%)

List of all changes from version 1 to version 2

Changes based on new taxa examined:

Phractolaemidae: now examined but no longer recognized as a family; now listed as subfamily of Kneriidae following Davis et al. (2013) .

Niphonidae: newly validated family, following Smith and Craig (2007); placed in the suborder Percoidei in Perciformes.

Pegasidae: removed from “not examined” in Callionymoidei to examined in Syngnathoidei.

Zenionidae: now examined; same placement.

Carapidae: now examined; same placement.

Muraenolepididae: now examined; same placement.

Callanthiidae: now examined; listed as incertae sedis in Percomorpharia.

Cepolidae: now examined; listed as incertae sedis in Percomorpharia.

Badidae: now examined; same placement.

Hoplichthyidae: now examined; listed as incertae sedis in Perciformes.

Pentacerotidae: now examined; listed in the newly circumscribed Pempheriformes.

Banjosidae: now examined; listed in the newly circumscribed Pempheriformes.

Ostracoberycidae: now examined; listed in the newly circumscribed Pempheriformes.

Stephanoberycidae: now examined; same placement.

Champsodontidae: now examined; listed as incertae sedis in Percomorpharia.

Aphyonidae: now examined; same placement.

Bembridae: now examined in Perciformes; placed in the newly classified suborder Bembroidei.

Parabembridae: now examined in Perciformes; placed in the newly classified suborder Bembroidei.

Cheimarrichthyidae: now examined; same placement.

Perciliidae: now examined; listed as incertae sedis in Percomorpharia (note that validation of this family results in the paraphyly of Percichthyidae).

Pristolepididae: now examined, same placement.

Trichodontidae: now examined in Perciformes, infraorder Cottales.

Triodontidae: now examined; placed in the newly classified suborder Triodontoidei.

Anomalopidae: now examined; same placement.

Datnioididae: now examined, placed in the newly classified order Lobotiformes (with Lobotidae).

Phallostethidae: now examined; same placement.

Other Changes:

Creediidae is removed from Syngnathiformes and placed in Pempheriformes (Percomorpharia). This is the major topological change in the new tree. The previous version had only four gene sequences for Limnichthys (two of which were likely contaminated) and this species is now represented in eight markers. The new placement is consistent with that obtained by Near et al. (2013) .

The order Pempheriformes has a broader circumscription, including the families Acropomatidae, Banjosidae, Creediidae, Epigonidae, Glaucosomatidae, Howellidae, Lateolabracidae, Leptoscopidae, Ostracoberycidae, Pempheridae, Pentacerotidae, Percophidae, and Polyprionidae.

Bembrops is now placed in Bembropidae, following Near et al. (2013) . Percophidae, as traditionally recognized (including Bembropinae), is polyphyletic in the new tree (as well as in Near et al., 2013) , with Acanthaphristis and Bembrops falling in different places.

Girella is now recognized in its own family, Girellidae, following Carpenter (2001) . Inclusion of Girella in Kyphosidae renders this family non-monophyletic.

The families Girellidae, Kuhliidae, Kyphosidae, Oplegnathidae, and Terapontidae are classified in the new order Terapontiformes in Percomorpharia.

Solenostomidae is removed from “not examined” in Callionymoidei and listed as “not examined” in Syngnathoidei, following Johnson and Patterson (1993) and Nelson (2006) .

Fistulariidae is removed from “possibly included” in Syngnathoidei and listed as incertae sedis in Syngnathiformes.

Leptoscopidae is removed from “not examined” in Syngnathiformes (Syngnathimorpharia) and listed in the newly circumscribed Pempheriformes (Percomorpharia).

Pelagimorpharia was adopted to replace Scombrimorpharia, following Miya et al. (2013). Pelagia was not adopted because it is already in use for a genus of scyphozoan jellyfish (Fam Pelagiidae).

Lactariidae is removed from“not examined” in Percomorphaceae and listed as “not examined” in Carangimorphariae (based on new evidence by Campbell et al., 2013) .

Six families traditionally placed in “Perciformes”, and previously listed as incertae sedis in Percomorphaceae, are provisionally listed in Percomorpharia: Bathyclupeidae, Dichistiidae, Hapalogenyidae, Parascorpididae, Symphysanodontidae, Trichonotidae.

The superorder “Cyprinae” was changed to “Cypriniphysae” following Nelson (2006).

The monophyly of both Ceratioidei and Ceratiidae was challenged in version 1 due to misplacement of Cryptosaras. This is no longer the case in the phylogeny supporting version 2, where Cryptosaras and Ceratias are resolved as sister taxa with 98% bootstrap support.

References

Akazaki, M. 1962. Studies on the spariform fishes-anatomy - phylogeny, ecology, and taxonomy. Kosugi Co. Ltd., Osaka, Japan.

Albert, J. S., and W. G. R. Crampton. 2005. Diversity and Phylogeny of Neotropical Electric Fishes (Gymnotiformes), p. 360–409. In: Electroreception. C. D. Bullock, A. N. Hopkins, and R. R. Fay (eds.). Springer, New York.

Arratia, G. 1999. The monophyly of Teleostei and stem-group teleosts. Consensus and disagreements, p. 265-334. In: Mesozoic Fishes 2 – Systematics and Fossil Record. G. Arratia and H. P. Schultze (eds.). Verlag Dr. F. Pfeil, München.

Arratia, G. 2010. The Clupeocephala re-visited: Analysis of characters and homologies. Revista de Biologia Marina & Oceanografia. 45:635-657.

Baldwin, C.C. 2013. The phylogenetic significance of colour patterns in marine teleost larvae. Zool. J. Linn. Soc. 168:496-563.

Betancur-R., R., R. E. Broughton, E. O. Wiley, K. Carpenter, J. A. Lopez, C. Li, N. I. Holcroft, D. Arcila, M. Sanciangco, J. Cureton, F. Zhang, T. Buser, M. Campbell, T. Rowley, J. A. Ballesteros, G. Lu, T. Grande, G. Arratia, and G. Ortí. 2013a. The tree of life and a new classification of bony fishes. PLoS Currents Tree of Life. 2013 Apr 18.