The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.

BackgroundFish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson’s volumes of Fishes of the World and W. Eschmeyer’s Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny (www.deepfin.org). We here update the first version of that classification by incorporating the most recent phylogenetic results.ResultsThe updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified.ConclusionsThis version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0958-3) contains supplementary material, which is available to authorized users.

A vertebral column consisting of a persistent notochord and ossified arcocentra is the primitive condition for Gnathostomata; it still persists in primitive actinopterygians and sarcopterygians. Advanced actinopterygians and sarcopterygians develop numerous types of centra that include, among others, the presence of holocentrum, chordacentrum, and autocentrum. The chordacentrum, a mineralization or calcification of the fibrous sheath of the notochord, is only found in actinopterygians, whereas an autocentrum is a synapomorphy of teleosts above Leptolepis coryphaenoides. The chordacentrum, formed by migration of cartilaginous cells from the arches into the fibrous sheath of the notochord and usually covered by a thin calcification, is a unique feature of chondrichthyans. The actinopterygian chordacentrum and the chondrichthyan chordacentrum are not homologous. The postcaudal cartilaginous centrum is only known in postcaudal vertebrae of living dipnoans. The holocentrum is present in certain fossil dipnoans and actinopterygians, where it has been independently acquired. It is formed by proliferation of cartilage cells around the elastica externa of the notochord. These cells later ossify, forming a compact centrum. A vertebral column formed by a persistent notochord without vertebral centra is the primitive pattern for all vertebrates. The formation of centra, which is not homologous among vertebrate groups, is acquired independently in some lineages of placoderms, most advanced actinopterygians, and some dipnoans and rhipidistians. Several series of structures are associated with the vertebral column such as the supraneurals, interhaemals, radials, and ribs. In living dipnoans median neural spine, "supraneural," and dorsal radial result from growth and distal differentiation of one median cartilage into two or three median bones during ontogeny. The median neural spine articulates with the neural arch and fuses with it in the caudal vertebrae early in ontogeny. Two bones differentiate in the anterior abdominal vertebrae, i.e., the proximal neural spine and the distal "supraneural." Three bones differentiate in front of the dorsal fin, i.e., the proximal neural spine, the middle "supraneural", and the distal radial; the same pattern is observed in front of the anal fin (the proximal haemal spine, the middle interhaemal, and the distal radial). Considering that the three dorsal (and also the three ventral) bones originate from growth of only one cartilage, they cannot be serial homologs of the neural spines, or "supraneural." They are linear homologs of the median neural cartilage in living dipnoans. The development of these elements differs within osteichthyans from sarcopterygians to actinopterygians, in which the neural spine originates as a continuation of the basidorsal arcualia and in which the supraneural and radial originate from independent cartilages that appear at different times during early ontogeny. The ribs of living dipnoans are unique in that they are not articulated with parapophyses, like in primi...

Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a full sample of all bony fishes. Here we conducted a comprehensive phylogenetic study on a broad taxonomic sample of 61 actinopterygian and sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular data set of 21 independent loci. These data yielded a resolved phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally monophyletic Sarcopterygii and Actinopterygii, as currently understood, with polypteriforms as the first diverging lineage within Actinopterygii; 2) a monophyletic group containing gars and bowfin (= Holostei) as sister group to teleosts; and 3) the earliest diverging lineage among teleosts being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating analysis employing a set of 24 newly applied fossil calibrations reveals divergence times that are more consistent with paleontological estimates than previous studies. Establishing a new phylogenetic pattern with accurate divergence dates for bony fishes illustrates several areas where the fossil record is incomplete and provides critical new insights on diversification of this important vertebrate group.

The ontogenetic development of caudal vertebrae and associated skeletal elements of salmonids provides information about sequence of ossification and origin of bones that can be considered as a model for other teleosts. The ossification of elements forming the caudal skeleton follows the same sequence, independent of size and age at first appearance. Dermal bones like principal caudal rays ossify earlier than chondral bones; among dermal bones, the middle principal caudal rays ossify before the ventral and dorsal ones. Among chondral bones, the ventral hypural 1 and parhypural ossify first, followed by hypural 2 and by the ventral spine of preural centrum 2. The ossification of the dorsal chondral elements starts later than that of ventral ones. Three elements participate in the formation of a caudal vertebra: paired basidorsal and basiventral arcocentra, chordacentrum, and autocentrum; appearance of cartilaginous arcocentra precedes that of the mineralized basiventral chordacentrum, and that of the perichordal ossification of the autocentrum. Each ural centrum is mainly formed by arcocentral and chordacentrum. The autocentrum is irregularly present or absent. Some ural centra are formed only by a chordacentrum. This pattern of vertebral formation characterizes basal teleosts and primitive extant teleosts such as elopomorphs, osteoglossomorphs, and salmonids. The diural caudal skeleton is redefined as having two independent ural chordacentra plus their arcocentra, or two ural chordacentra plus their autocentra and arococentra, or only two ural chordacentra. A polyural caudal skeleton is identified by more than two ural centra, variably formed as given for the diural condition. The two ural centra of primitive teleosts may result from early fusion of ural centra 1 and 2 and of ural centra 3 and 4, or 3, 4, and 5 (e.g., elopomorphs), respectively. The two centra may corespond to ural centrum 2 and 4 only (e.g., salmonids). Additionally, ural centra 1 and 3 may be lost during the evolution of teleosts. Additional ural centra form late in ontogeny in advanced salmonids, resulting in a secondary polyural caudal skeleton. The hypural, which is a haemal spine of a ural centrum, results by growth and ossification of a single basiventral ural arococentrum and its haemal spine. The proximal part of the hypural always includes part of the ventral ural arcocentrum. The uroneural is a modification of a ural neural arch, which is demonstrated by a cartilaginous precursor. The stegural of salmonids and esocids originates from only one paired cartilaginous dorsal arcocentrum that grows anteriorly by a perichondral basal ossification and an anterodorsal membranous ossification. The true epurals of teleosts are detached neural spines of preural and ural neural arches as shown by developmental series; they are homologous to the neural spines of anterior vertebrae. Free epurals without any indication of connection with the dorsal arococentra are considered herein as an advanced state of the epural. Caudal distal radials originate fr...

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The palatoquadrate and associated dermal bones have significant evolutionary transformations among teleostomes and provide numerous features that characterize teleostomian subgroups. The palatoquadrate forms the upper part of the mandibular arch and is present as a single cartilaginous element in the early ontogeny of teleostomes, except for some advanced teleosts such as siluroids where it is divided into pars autopalatina and pars pterygoquadrata. During ontogeny, the palatoquadrate may ossify as a unit, with a pars autopalatina (absent in Acanthodii), pars quadrata, and pars metapterygoidea in teleostomes (e.g., primitive acanthodians and actinopterygians, onychodonts, and rhipidistians). However, the palatoquadrate may remain cartilaginous (e.g., chondrosteans) or it may ossify as separate elements (e.g., autopalatine, metapterygoid, and quadrate) as occurs in advanced acanthodians, Polypterus and advanced actinopterygians, and advanced actinistians. From the single-unit pattern, separate autopalatine, metapterygoid, and quadrate evolve in parallel in the three teleostomian subgroups. Therefore, it is necessary to distinguish between actinopterygian and actinistian autopalatines and among acanthodian, actinopterygian, and actinistian metapterygoids and quadrates. A palatoquadrate fused with the neurocranium occurs in parallel in dipnoans. There are differences in the timing of ossification of the autopalatine, metapterygoid, and quadrate. The autopalatine ossifies late in ontogeny in Polypterus, Amia, and primitive teleosts (absent in lepisosteids and osteoglossmorphs), whereas both metapterygoid and quadrate ossify early in ontogeny. The early ossification of the autopalatine is characteristic of clupeocephalan teleosts. During ontogeny, tooth plates (not forming a separate dermometapterygoid) fuse with the metapterygoid in actinopterygians. Pars autopalatina, pars metapterygoidea, and pars quadrata are regions at the three corners of the single-unit palatoquadrate present in primitive teleostomes; there are no clear limits among these regions, but they may be identified by their processes, articular facets, and topographical relationships with surrounding bones and the orbit. Autopalatine, metapterygoid, and quadrate are chondral bones, perichondrally ossified. Dermal elements such as dermopalatine(s), entopterygoid, ectopterygoid, and tooth plates may cover the palatoquadrate medially. The predermopalatine that originates in front of pars autopalatina in Cladistia and the "dermopalatine" that lies medial to the ectopterygoid in Ginglymodi are specializations of these groups. A dermopalatine fused with the autopalatine is characteristic of clupeocephalan teleosts. Highly specialized tendon bone pterygoids are found in some teleosts (e.g., siluroids). The presence of both maxilla and lacrimal lateral to the pars autopalatina is synapomorphous of osteichthyans. The eye supported by the bony palatoquadrate is a teleostomian synapomorphy. Dermal elements support the eye in actinopterygians, the entopterygoid in...

The diural caudal skeleton of teleostean actinopterygians develops phylogenetically and ontogenetically from a polyural skeleton. The reduction of the polyural anlage to f w r , three, two or fewer centra in thc adult caudal skeleton takes different pathways in different genera (e.g. compare Elops and Albula) and groups o f teleosts. As a result, ural centra are not homologous throughout the teleosts. By numbering the ural centra in a homocercal tail in polyural fashion, one can demonstrate these and the following differences. The ventral elements (hypurals) always occur in sequential series, whereas the dorsal elements (epurals and uroneurals) may alter like the ural centra. The number of epurals, five or four in fossil primitive teleosts, is reduced in other primitive and advanrrd teleosts, but the same epurals are not zlways lost. The number of uroneurals, seven in fossil teleosts, is reduced in living teleosts, but it has not been demonstrated that the first uroneural is always derived from the neural arch of the same ural centrum. The landmark in the homoccrcal tail is the preural centrum 1 which can be identified by (1) bifurcation of the caudal artery and vein in its ventral element, the parhypural, (2) its position directly caudal to the preural centrum (PU2) which supports the lowermost principal caudal ray with its haemal spine, (3) carrying the third hypaxial element ventral to the course of arteria and vena pinnalis, and (4) by carrying the first haemal spine (parhypural) below the dorsal end of the ventral cartilage plate. The study of the drvelopment of the vertebral column reveals that teleosts have different patterns of centrum formation. A vertebral centrum is a complete or partial ring of mineralized, cartilaginous or bony material surrounding at least the lateral sides of the notochord. A vertebral centrum may be formed by arcocentrum alone, or arcocentral arcualia and chordacentrum, or arco-, chorda-and autocentrum, or arcocentral arcualia and autocentrum. This preliminary research demonstrates that a detailed ontogenetic .interpretation of the vertebral centra and of the caudal skeleton of different teleosts may be useful tools for further interpretations of teleostean interrelationships.