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The Tree of Life and a New Classification of Bony Fishes
PLoS Curr. 2013 April 18; 5: ecurrents.tol.53ba26640df0ccaee75bb165c8c26288. doi: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288 Tree of Life
The Tree of Life and a New Classification of Bony Fishes
Ricardo Betancur-R., Richard E. Broughton, Edward O. Wiley, Kent Carpenter, J. Andrés López, Chenhong Li,* Nancy I. Holcroft, Dahiana Arcila, Millicent Sanciangco, James C Cureton II, Feifei Zhang, Thaddaeus Buser, Matthew A. Campbell, Jesus A Ballesteros, Adela Roa-Varon, Stuart Willis, W. Calvin Borden, Thaine Rowley, Paulette C. Reneau, Daniel J. Hough,* Guoqing Lu, Terry Grande,* Gloria Arratia,* and Guillermo Ortí
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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.
“…With the variety of both primitive and advanced teleosts living today, we are most emphatically of the opinion that approaches other than morphological ones would be exceedingly fruitful in the investigation of teleostean interrelationships..." Greenwood et al. (1966)1 Our view of the phylogeny and classification of bony fishes is rapidly changing under the influence of molecular phylogenetic studies based on larger and more taxonomically comprehensive datasets. Classification schemes displayed in widely used text books on fish biodiversity (e.g.,2, 3) have been based on loosely formulated syntheses (supertrees) and community consensus views of largely disconnected studies. The phylogenetic structure underpinning such classifications has many areas that are notably unresolved and poorly known, providing weak or no justification for many groups that, although formally recognized, are implicitly known to be polyphyletic (e.g. percoids, perciforms, scorpaeniforms). A comprehensive phylogenetic tree for all major groups of fishes has been elusive because explicit analyses including representatives across their diversity have never been accomplished. Detailed morphological cladistic investigations of fish relationships have typically focused on lower taxonomic scales and few attempts to synthesize morphology at higher taxonomic levels proved to be challenging and met limited success (e.g.,4).
The Tree of Life and a New Classification of Bony Fishes
A recent effort to systematically collect morphological synapomorphies from published records for all currently recognized groups resulted in the first teleost classification based on monophyletic groups5. This effort, however, did not produce a global phylogenetic hypothesis. Similarly, molecular analyses have been limited and many times conflicting in terms of genetic coverage and taxonomic sampling. As predicted by Greenwood et al.1, development of molecular markers, especially sequences of mitochondrial DNA (mtDNA) genes or complete mitochondrial genomes, catalyzed new views of bony fish relationships by providing a common yardstick of phylogenetic information across vast taxonomic scales6, 7 , 8. Studies based on mitogenomic data proliferated to methodically probe conflicting hypotheses of relationship for several groups at diverse taxonomic levels, many times proposing alternative arrangements supporting new clades unsuspected by previous classifications10, 11 , 12, 13. In spite of their new powerful insights, mitogenomic hypotheses were not universally embraced because they represent information from a single locus, prompting corroboration from additional genomic regions. Several nuclear DNA markers were subsequently developed and applied to infer bony fish relationships. The most popular ones include 28S ribosomal subunit14 , 15, 16, tmo4c4 17 , 18, rhodopsin19, 20, rag1 and rag221 , 22, mll20, irbp23, and rnf21324. Using a systematic approach to scan genomic databases, a larger set of nuclear markers became available in 2007 25, opening a new window to obtaining large multilocus datasets25, 26, 27 , 28, 66. Recent studies using between 10 and 20 of these nuclear markers for a few hundred taxa27 , 28, 29, 30, 31 , 66, have shown improved resolution of phylogenetic relationship at higher and lower taxonomic levels. Many but not all of the mitogenomic hypotheses received support from nuclear gene data, but the discovery of new clades continued with increasing taxonomic sampling. Initially identified by letters (e.g., clades A, B, C, etc.19, 23, 32), new names were recently proposed for many groupings supported by molecular evidence, such as Stiassnyiformes, Zeiogadiformes, Carangimorpha, Cottimorpha, Ovalentaria, Gobiiformes etc.24 , 31 , 33. Validation of these groups (and their proposed names) is pending until a comprehensive study including all taxa is produced. Proliferation of new names is useful for identification of the newly discovered groups, but may create confusion if not systematically organized into a global classification. Molecular phylogenetic methods (e.g., BEAST34) in combination with fossil evidence also opened a new temporal window to understand bony fish diversification. Attempts to estimate divergence dates among crowgroup lineages using this approach (e.g., 35, 36, 37) frequently produced conflicting views with the paleontological literature38, 39, 40, sometimes implying large gaps in the fossil record. The discrepancy is larger when divergence estimates for crown teleost lineages have been based on mitogenomic data (e.g.,37 , 41 , 115). Nucleotide saturation, compressing basal branch lengths for mtDNA, and the specific approaches used to apply fossils constraints to calibrate the molecular phylogeny may explain this discordance43. Other studies based on several nuclear genes and larger sets of fossil calibration points produced divergence dates more consistent with the fossil record29, 66, but a comprehensive time-tree for osteichthyan diversification is not yet available. The shape of the bony fish tree of life is currently better resolved for the early-branching lineages than for the more apical acanthomorph groups, in particular the percomorphs, a large and diverse group of spiny-finned fishes with uncertain affinities that came to be known as “bush at the top”44. Few basal branching events among osteichthyans remain problematic, for example, the relationships among lungfishes, coelacanths, and tetrapods45, 46, 47 , 66. In contrast, the basal branching pattern for early extant actinopterygians (involving polypteriforms, chondrosteans, lepisosteids, Amia and teleosts) have been resolved with confidence based on morphological and DNA sequence evidence66. Similarly, recent molecular studies based on several nuclear genes25 consistently support relationships among major teleost groups: Elopomorpha, Osteoglossomorpha and Euteleostei29, 66. The deeper nodes among euteleosts and percomorphs also could be resolved with confidence with this new set of nuclear markers, but a comprehensive phylogeny including all groups is lacking. In this study we report phylogenetic results based on a taxonomically comprehensive dataset with DNA sequences for 21 nuclear genes. A dataset with 1416 taxa was assembled, including four tetrapod and two chondrichthyan outgroups. Bony fish diversity is represented by 1093 genera (of ca. 4300), 369 families (of 502), and all traditionally recognized orders5, making this the most comprehensive dataset ever compiled in systematic ichthyology. Phylogenetic results corroborate many previously established hypotheses, but also provide unprecedented resolution among percomorphs. The uncertain relationships involving most of the extant diversity of percomorphs is resolved into several well-supported groups and, for the first time, we offer a monophyletic definition for Perciformes. Using a set of 60 calibrations, we also provide the most
tbr1b (=tbr1 ). as identified using bootstrap trees obtained with RAxML v7.nih. DNA extraction. including EToL markers (enc1 . The PCR amplicons obtained were submitted for purification and sequencing in both directions to High Throughput Sequencing Solutions (HTSeq. and zic1 ) and three additional markers. 96). 28. Our taxonomic sampling emphasizes representation of percomorph groups. *1st and 2nd are primers for the first and nested/seminested (optional) rounds of PCR.g. Table 1.gov/pmc/articles/PMC3644299/ 3/28 . 25. gtdc2 (=glyt). 369 families (of 502. ficd. A total of 1184 bony fish taxa were initially targeted for this study and samples were primarily obtained from the tissue repository of the Ichthyology Collection at University of Kansas (1129 samples) or other collections. A complete list of material examined is given in Table S1. Considering the new clades obtained in this study and previously published well-supported clades. 26. or other genomic databases. 66. 4300). we vetted the data by visually inspecting individual gene trees estimated with the Geneious Tree Builder algorithm in Geneious. 27 . Sequencher v4 (Gene Codes Corporation). 3100051) plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). some sequences retrieved from public databases were combined as genus-level composite taxa (52 taxa). Fish diversity is represented in the phylogenetic data matrix by a sample of 1410 bony fish species (of ca. were generated for our previous studies (e.nlm. 25. 25. Because nested PCR is highly prone to cross-contamination. All scientific names were checked against the Catalog of Fishes51. 26. Sequence alignment and phylogenetic analyses Contigs were assembled from forward and reverse sequences using CodonCode Aligner v3. were newly developed for this study using the same approach.5). rag2. Our final sampling thus included 1081 taxa and sequence data from 335 additional taxa were obtained from previous EToL studies (e. Of the initial list.ncbi. To qualitatively assess gene-tree congruence. A total of 21 molecular markers with a genome-wide distribution were examined. and gpr85 (=sreb2)) or markers developed by others (16S mtDNA. Primer sequences and optimized PCR conditions used for the three new markers is presented in Table 1. 27 . Our hope is that this explicit proposal will facilitate communication among ichthyologists attempting to chart the rapidly changing landscape of phylogeny and classification of fishes.5/22/13 The Tree of Life and a New Classification of Bony Fishes comprehensive hypothesis to date about the tempo of osteichthyan diversification. amplification protocols via nested PCR. with 1037 (of >15000) species in 201 families. plagl2.g.g. ptchd4 (=ptr).4 (CodonCode Corporation). samples for 18 taxa either failed to amplify or belonged to duplicate species that were ultimately combined or discarded.5 (Biomatters Ltd.g.. and all traditionally recognized orders (e. Sixty taxa that produced sequence data for one or two genes only were also discarded. Sequence data from seven additional markers. sidkey .. snx33 (=sh3px3). we propose a new classification for bony fishes based on the nomenclatural scheme recently proposed by Wiley and Johnson5. 28.349 and the RogueNaRok server50. Materials and Methods Molecular data and taxonomic sampling Go to: This study is the main product of the Euteleost Tree of Life Project (EToL). panx2. 28. and rh ).953 using 1000 iterations and the genafpair algorithm. the final gene alignments were analyzed under maximum www. and vcpip). 26. 27 . the majority of which were developed by EToL using a genomic screen pipeline25. and primers followed previous studies (e. 66.). 96) or public databases (Table S1). see below). including one intron (hoxc6a) and two exons (svep1 . Exons markers were sequenced from 11 nuclear genes previously published by our group (kiaa1239. respectively. or Geneious Pro v4.. 96) or obtained from NCBI. 66.5. myh6.. rag1 . In order to minimize missing data. Twenty-five additional taxa were excluded from the final matrix because they had low genetic coverage and highly variable phylogenetic placement in preliminary analyses. Exon markers were aligned individually based on their underlying reading frame in TranslatorX52 using the MAFFT aligner53. ripk4. The hoxc6a and 16S sequences were aligned with MAFFT v6. Ensembl. The taxonomic sampling of bony fishes consists of 1093 genera (of ca.org) or other core facilities. This pipeline compared the Danio rerio and Takifugu rubripes genomes to identify single-copy genes with long exons (>800 bp) and divergence levels suggesting they evolve at rates appropriate for phylogenetic resolution among distantly related taxa. Primers used for new markers developed and optimized PCR conditions.
The 7+ dataset was analyzed with the 24-partition scheme only.7167 using the RAxML tree.858 or Geneious. 65. Five replicates of the Markov chain Monte Carlo (MCMC) analyses were each run for 200 million generations. sectorial searches and tree fusion. To make the PartitionFinder analysis scalable.nih. with the topology constrained to that recovered in the phylogenetic analyses of the 3+ dataset (pruned for taxa not included in the subset). 1. one including all 1416 taxa with sequence data from three genes or more (3+ dataset) and a subset including 1020 taxa with sequence data from seven genes or more (7+ dataset). Sixty calibration points were selected as priors for divergence time estimates.6. A strict consensus of nine equally optimal trees (length 407187 steps. we selected a subset of 202 taxa for 18 genes that had representation of: (i) all major bony fish lineages. 56.1. The complete tree with 1416 taxa was time-calibrated under penalized likelihood (PL67) with treePL69. A starting chronogram that satisfied all priors (e. Tree files from the five runs were combined in LogCombiner v1. Appendix 1). were also excluded). and the collection of sample trees was used to draw the bibartition frequencies on the optimal tree. All RAxML analyses were conducted in the CIPRES portal v3.168. the actual BEAST analysis conducted for this study included 59 calibrations only (see details under calibration 60.0 and death rate = 0. Divergence times were estimated in BEAST v1. (ii) lineages encompassing the nodes in which the assignment of fossil calibrations is most informative. the final searches implemented tree-bisection-reconnection (TBR). 57) could not be applied to this dataset due to high proportion of missing data (see Results).. bootstrap bipartition frequencies were drawn on the consensus tree.gov/pmc/articles/PMC3644299/ 4/28 .7 using the uncorrelated log-normal (UCLN) clock-model34. The optimal tree search and bootstrap trees were set to run independently. A relatively mild value of k (20) was chosen arbitrarily due to computational limitations to explore sensitivity of the nodes to other weighting functions. However.568 and mixing was considered complete if the effective sample size of each parameter was >20034 . of which 58 are based on previous studies29.7. Analyses of the 3+ dataset were performed under maximum likelihood (ML) using two partitioning schemes. Nodal support was assessed using the rapid bootstrapping algorithm of RAxML with 1000 replicates estimated under the GTRCAT model60. The PL model. was estimated with TreeAnnotator v1. For comparison purposes. the 3+ dataset was also analyzed under implied-weighted parsimony61. drift. The substitution model was GTR+G with 4 rate classes and the data were partitioned into 4 categories with independent parameter estimation: three codon positions across exons of protein-coding genes plus 16S. saving only one tree per replicate (1000 replicates).5/22/13 The Tree of Life and a New Classification of Bony Fishes likelihood (ML) in RAxML using ten independent runs for each. mean highest www. 66 and two (calibrations 45 and 60) are proposed here (Appendix 1). (iii) taxa with the highest genetic coverage to minimize missing data in the data matrix (the markers vcpip. 68. has been shown to perform poorly in simulation studies resulting in high stochastic error of divergence time estimates70. To model branching rates on the tree.54 . a simple one determined arbitrarily with 5 data partitions (3 codon positions across all exons plus 16S and hoxc6a). Post-run analysis of MCMC log files was assessed using Tracer v.ncbi. Bootstrap search strategies were relaxed to ten random addition sequences and TBR. including a high proportion of missing data. The exhaustiveness of the search parameters was self-adjusted every 2 hits of the current best score. a representative subset of 201 taxa was run under the Bayesian Information Criterion59. Thus. with means and 95% highest posterior density of divergence times.nlm. To maximize tree-space exploration. a birth-death process was used for the tree prior with initial birth rate = 1.7. svep1 . Clock and tree priors were linked across partitions. and a more complex scheme with 24 partitions (a combination of codon positions and individual genes plus 16S and hoxc6a) indicated by PartitionFinder59.g.19) was computed.468 with the first 10% of trees from each run discarded as burn-in. exon alignments were partitioned by codon position. monophyly and initial divergence times) was generated under penalized likelihood in r8s v1. 55. Two datasets were assembled and analyzed separately. To ameliorate this problem.163 using a driven-search strategy combining the following tree-search algorithms: ratchet. Analyses for both datasets and partition schemes were conducted in RAxML using 30 independent replicates under the GTRGAMMA model. Tree searches were performed in TNT 1.. fit 7309. Gaps were treated as missing characters and all parsimony uninformative characters were ignored. 64 . Divergence time estimates Time-tree estimation in a Bayesian framework using the complete dataset was computationally infeasible.g. Individual genes were concatenated using SequenceMatrix v1. hoxc6a. Alternative approaches to analyze combined data based on species-tree methods that account for gene-tree heterogeneity due to lineage sorting (e. The maximum clade credibility tree.5. which assumes rate autocorrelation.
Because our results corroborate these hypotheses (e.gov/pmc/articles/PMC3644299/ 5/28 . The rate smoothing parameter was set to 10 based on the cross-validation procedure and the χ 2 test in treePL (four smoothing values between 1 and 1000 were compared). Table 2. Figs. S1) we propose a new classification for ordinal and subordinal groups of bony fishes and subsequently discuss some of the most significant findings. including data presence. Fig. 11).g. 74). The time-calibrated (BEAST) tree for the subset (202 taxa and 18 genes) and 59 calibration points are shown in Fig. The phylogenetic tree was estimated in RAxML using the 3+ dataset (1416 taxa) and 24 partitions with divergence times estimated under PL using 126 fixed secondary calibrations from the BEAST analysis (see Fig.. branching order of elopomorphs and osteoglossomorphs. we find the nonmonophyly of Beryciformes (including Stephanoberyciformes) and a sister-group relationship between holocentrids and percomorphs. in particular the unprecedented resolution among percomorphs. 1. The most significant new results involve crown acanthomorph lineages. We also provide for the first time a monophyletic definition of Perciformes.c4d3j). Gasterosteiformes. Based on the topology obtained (Figs. and sequence variation for each marker is given in Table 2 (see also Table S1).. but challenged by Johnson and Patterson4. 1). The sequence alignment (nexus format). 12 compares the results of divergence times estimated for major groups with those obtained by other recent multi-locus studies. 66. The proverbial “bush at the top” is now disambiguated into several well-supported clades at the ordinal or supraordinal level.nlm. Results and Discussion Go to: The final concatenated alignments included 21 markers with 20853 sites for 1416 taxa in the 3+ dataset and 1020 taxa in the 7+ dataset. Terminal clades are either orders or . Among the euacanthomorphs. 2 provides measures of congruence among alternative analyses (concatenation and gene trees) for all major clades and provides discrete tests for traditional hypotheses in ichthyology. 1). including the ages obtained for all major groups in the tree as well as the nodes near which primary calibrations were defined.ncbi. 3–10 provide more detail on the relationships within selected percomorph clades based on the tree in Fig. rather than using primary calibrations with minimum and maximum age constrains. Fig.0% for the 3+ dataset and 48. 3+ dataset. Fig. sinking into this clade components of Scorpaeniformes. Main phylogenetic hypothesis of bony fish groups collapsed to depict higher-level clades.5/22/13 The Tree of Life and a New Classification of Bony Fishes posterior density estimates of clade ages obtained with the subset in BEAST were imposed as fixed secondary calibrations for the PL analysis. Characterization of molecular markers examined. represented in this study by 1037 species in 201 families. and Table S1 are available from the Dryad repository (DOI:10. A summary of dataset features. 1-10. first recognized by Stiassny and Moore75 and Moore76. with well-resolved relationships amongst them (Fig. time-calibrated under PL). The new sequences have been deposited in GenBank under accession numbers KC825360-KC831391. The main phylogenetic hypothesis is summarized in Fig. alignment length. The average presence of data (number of sequences per taxon) across the alignments was 41. albeit with reduced taxonomic sampling. and Cottiformes (Fig. The basal nodes of the tree and relationships among early branching groups of bony fishes have been well established and thoroughly discussed by recent molecular systematic studies based on similar sets of genes29. S1 as a cladogram and can also be visualized online as a time-tree using a fractal explorer and zooming interface at OneZoom73 (also posted at DeepFin).5061/dryad. The complete phylogeny with bootstrap values and taxonomic annotations is depicted in Fig. we refer the reader to those papers for discussion on relationships among lineages from the root of the tree up to the Euteleosteomorpha. ML tree (newick format). 10.nih. A total of 126 secondary calibrations were used for this analysis. see also16.2% for the 7+ dataset. *New markers developed here www. 1 (24-partition RAxML tree. 11 (see also Appendix 1). monophyly of Actinopterygii and Holostei.
1. Spariformes is a Bleeker name and Centrarchiformes is a Webber and de Beaufort name.gov/pmc/articles/PMC3644299/ 6/28 . three of which are new (Holocentriformes. Horabagridae (following Sullivan et al. as long as the incongruence is not supported by strong bootstrap values. but most can be found in the literature at various hierarchical levels. Percentages in parentheses following www. Also. 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. Zanclorhynchidae. et al.ncbi. Our list is not intended as a comprehensive revision of valid family names. Unlike Eschmeyer and Fong89 and van der Laan et al. A total of 502 families are recognized here. Some ordinal or subordinal names may appear to be new.nih.90 for authorship of family names and Wiley and Johnson5 for authorship of ordinal and subordinal names.g.” New infraorders are named in Suborder Cottioidei to circumscribe well-corroborated clades and may conserve the rank of superfamily in subsequent revisions. and Pempheriformes). Istiophoriformes. Ovalentariae.94).96). Munroe99.5%) were examined.28).. monophyletic groups . even if bootstrap support is low (e. 92). of which 369 (73. In some cases. the aulopiform Bathysauropsidae and Sudidae (following Davis91). listed in Eschmeyer and Fong89 and van der Laan et al.90. 146 families included only one representative (39.5/22/13 The Tree of Life and a New Classification of Bony Fishes Sensitivity analyses for selected clades obtained in this study (shown in Figs.nlm. and 15 are resurrected or validated under a new circumscription. we recognize the following families.6%) and 40 (17. Osteoglossocephalai sensu Arratia79 with only 38% bootstrap).9%) of the remaining 223 were rendered non-monophyletic in our analysis (non-monophyletic families are indicated below). apparently omitted by Eschmeyer and Fong89).. As examples. Consult van der Laan et al. adjustments are made to recognize new well-supported molecular clades.e.90. we have not made a thorough attempt to establish first use. and Percomorpharia remains uncertain (i. we do not recognize the family status of Anotopteridae. Examples include the suborder Blennioidei (not monophyletic here but monophyletic in Wainwright et al. it is simply an adaptation of their list based on published studies that we know validate or synonymize family groups using explicit phylogenetic evidence.incertae sedis) due to poor phylogenetic resolution.93). Omosudidae (synonyms of Alepisauridae91) or Latidae (synonym of Centropomidae27 . Diplophidae (following Nelson2.. instead.31) and the order Pleuronectiformes (not monophyletic here but monophyletic in Betancur-R. Sinipercidae (following Li et al.. 3-10) and for selected alternative hypotheses. A total of 66 orders are classified. et al. Of these. Because priority is not applied to names above the family level. and the pleuronectiform Paralichthodidae. Order-level or supraordinal taxa are erected (new) or resurrected on the basis of well-supported clades only (>90% bootstrap values). Betancur-R. Steindachneriidae (following Roa-Varon and Ortí98). The ordinal status of 50 percomorph families examined (as well as many others unexamined) belonging to Carangimorphariae. with minor modifications. For some gene trees. 90 as synonyms or subfamilies of other families: Botiidae (following Chen et al. However. Only those three for which no reference could be found are listed as “new. Revised Classification for Bony Fishes The nomenclatural arrangement presented in Appendix 2 builds on the existing classification by Wiley and Johnson5 and intends to preserve names and taxonomic composition of groups whenever possible. many of which also have been obtained by previous molecular studies (several examples discussed below). Family names for bony fishes are based on Eschmeyer and Fong89 and van der Laan et al. The list of unexamined families is also intended as a resource that may help fish systematists to direct future sequencing efforts. and Rhombosoleidae (following Chapleau97. we assess support from individual gene trees (indicating whether the group was obtained) or from the concatenated data sets (indicating whether the group was obtained and showing boostrap support). Poecilopsettidae.28). For each case. Current taxon names supported by previous molecular or morphological studies are retained if congruent with our results. ordinal or subordinal taxa that were not monophyletic in our analysis are also validated.
nlm. is the hypothesis that alepocephalid fishes (slickheads) have affinities within Otomorpha. More explicit tests of new and alternative phylogenetic hypotheses based on multiple analyses of our dataset are presented in Fig. Paracanthomorphacea: mitogenomics dixit (Fig. and Lampridiformes (removal of Stylephorus).ncbi. first proposed by López et al.g. For example. with some being grossly polyphyletic in our tree. Of 123 clades recognized by them.gov/pmc/articles/PMC3644299/ 7/28 .9%) are congruent with bootstrap values >95% obtained in this study.nih. Appendix 2). with the exclusion of Gobiesociformes2. sedis mutabilis. 41 .7%) are monotypic. 1). Second. More recently. Otomorpha (inclusion of Alepocephaliformes). seven additional clades (5. Gobiesociformes. Examples include Stomiatii (inclusion of Osmeriformes sensu stricto). For example. is the sister group relationship of Osmeriformes and Stomiatiformes (=Stomiiformes). as any other hypothesis.g. We do not attempt to provide a complete account of all taxonomic issues. this is also true within many of the major clades (e. Another six clades (4.” Although our results fall short of resolving with confidence circumscription and relationships among taxa in this group (hence Protacathopterygii is a sedis mutabilis taxon in our proposed classification). There is considerable consensus between morphology and the interrelationships of major clades. But there is also incongruence. The complete phylogenetic tree with annotated classification is illustrated in Fig. relationships within Elopomorpha). Finally. some relationships are well supported and consistent with previous studies (Fig. the major cohorts of living teleosts and their interrelationships are congruent with the listing convention employed by Wiley and Johnson5. 5 relative to the composition of “protacanthopterygians. Comparison of classifications Our results (Appendix 2) invite comparison to the recent classification of Wiley and Johnson5 based on morphological evidence gleamed from many investigators. instead of Argentiformes. 24 . For the most updated version visit DeepFin. First.1) to refer to a large group of spiny-finned fishes that included Batrachoidiformes. but to give some perspective and contrast to discuss the evidence supporting novel and established taxa. 29 and supported by our data (see also Fig. 101 and recently corroborated with a subset of the nuclear markers used in this study29. Johnson and Patterson4) with lampridiforms.21 based on mtDNA and rag1 sequence data. 2). a result also obtained with nuclear genes 19. 1) Our analyses support several recent hypotheses based on molecular data that contradict the consensus based on morphology2. mitogenomic data7 . The new classification scheme presented here should be considered a work in progress (version 1. 2. percopsiforms. the position of Lepidogalaxias at the base of the euteleosts rendering Galaxiidae non-monophyletic also was proposed previously102. especially in reference to well-established relationships and newly found clades among the euteleosts. Gadiformes (with Ophioidei and Zoarcoidei). the name Zeioigadiformes24 was coined for this new www. Novel Clades of Teleost Fishes The following sections highlight some of the salient features of this global phylogeny and classification of bony fishes. Updates should be forthcoming as new evidence become available and feedback from experts help refine it. but a conservative stance persisted in classifications supporting the original circumscription. zeiforms and gadiforms branching off basally relative to polymixiiforms. Smegmamorpharia. Early euteleost lineages: tenuous relationships (Fig. This result was first proposed on the basis of mitogenomic data10. as proposed by Johnson and Patterson4. 1) This name was first introduced as superorder Paracanthopterygii (sensu Greenwood et al.5%) are incongruent. and incertae sedis taxa. It is likely to include involuntary errors and omissions in addition to the many unexamined. and Labriformes.. Others are incongruent based on exclusion of subclades and are rendered monophyletic in our classification by the addition or removal of smaller clades.5/22/13 The Tree of Life and a New Classification of Bony Fishes names indicate bootstrap support (no bootstrap values shown for redundant groups or monotypic taxa). relationships among early-branching acanthomorph groups differ considerably from previous morphological hypotheses (e. 100. Many other taxa were added and also removed on the basis of conflicting evidence ever since Paracanthopterygii was conceived. Forty clades (32. and Percopsiformes. Notable examples are Protacanthopterygii. Five of these 70 clades are included in our sample by only one family and thus their monophyly is not critically tested. 8 discovered a sister-group relationship between Zeiformes and Gadiformes. 70 (56. Neoteleostei (removal of Stomiatiformes). S1.9%) are congruent but are supported by lower bootstrap values. 103. Lophiiformes.
20. Carangimorphariae. for the first time recovered from a vast taxonomic sample. halfbeaks. the remaining seven supraordinal clades (four Series and three Subseries) have never been discovered by examination of anatomical features. Our results place the sticklebacks. 7. Molecular data (mitogenomic and smaller subsets of nuclear genes). 5. Fig. percopsids and crown acanthomorphs in their Euacanthopterygii. 2. 6. and Percomorpharia (Figs. 12. 1). 9). increased phylogenetic resolution within Percomorpharia allowed the definition of a monophyletic Perciformes (Figs. Furthermore. Our results. however.nlm. in one form or another. 2). Fig. suborders Synbranchoidei and Mastacembeloidei) are placed with confidence in Anabantomorphariae (Fig.. Fig. and based on diverse genetic markers. We adopt the name but modify the circumscription to recognize a well-supported clade (99% bootstrap) that includes beryciforms. 30. one of the 11 families previously included in the order Gasterosteiformes. gadiforms. Fig. together with armored sticklebacks (Indostomidae).ncbi. 107). 10) and the rest of the families previously assigned to the suborder Syngnathoidei were relocated to our newly defined order Syngnathiformes within the Scombrimorpharia (Fig. A review of published morphological characters by Borden et al. 1. Elements included in this supraordinal taxon are now scattered throughout the molecular phylogeny. Most classifications2. Percopsiformes. 8. 4 accept separate orders Stephanoberyciformes and Beryciformes. 9). holocentrids and percomorphs. The polyphyly of Gasterosteiformes (another large clade assigned to Smegmamorpha) was first pointed out by mitogenomic evidence12. by previous molecular studies (e. With the exception of the cusk-eels (Ophidiimorpharia) and the toadfishes (Batrachoidimorpharia). Analysis of four nuclear markers in addition to mtDNA confirmed this result103. in agreement with our results (Fig. 8). the pygmy sunfishes (Elassoma) are back with the other sunfishes (centrarchids). 28.nih. 4. 31 . 2).7 . 32. supporting a monophyletic taxon Paracanthopterygii that includes percopsiforms. For example. needlefishes. 3). but see 106. 29. Gadiformes. guppies and allies) are placed within Ovalentariae (Fig. Fig. Scombrimorpharia (Figs. Stylephorus (placed in its own order Stylephoriformes) and zeiforms. placed within many of the newly found clades with high bootstrap support. 33). 4 and 5). 2). tubesnouts and sand eels (previously assigned to Gasterosteoidei) in our newly defined Perciformes (suborder Cottioidei. several of these clades have been obtained.g. 11 . Centrarchids plus elassomatids are placed here in the resurrected order Centrarchiformes (within Percomorpharia.gov/pmc/articles/PMC3644299/ 8/28 . Batrachoidimorpharia. Fig. Fig. Our new circumscription of Beryciformes is also most similar to that of the order Trachichthyiformes described by Moore76. which was unexpectedly found to form the sister group of Gadiformes. whose monophyly has been recognized in most classifications (i. however. Fig. 19.11 redefined the Paracanthopterygii to include Polymixiidae. The swamp eels and spiny eels (order Synbranchiformes. a result first obtained by Stiassny and Moore75 and Moore 76 but subsequently challenged by Johnson and Patterson4. in contrast. proportionally more individual gene trees support this relationship (47%) relative to the alternative molecular hypothesis uniting holocentrids with the remaining beryciform groups (20%.e. each monophyletic and placed as successive sister-groups of the percomorphs. as suggested by earlier classifications and recently confirmed by molecules30.. 27 . www. and Zeioidei and subsequently Miya et al. 8). have supported the inclusion of Stephanoberyciformes in the same clade as Beryciformes8.5/22/13 The Tree of Life and a New Classification of Bony Fishes grouping. Percomorphaceae: no longer an unresolved bush (Figs. Appendix 2): Ophidiimorpharia. Miya et al. Holocentriformes) that is sister to percomorphs (Fig. see below). 1. A corollary of the increased resolution of percomorph relationships is the demise of the Smegmamorpharia sensu Johnson and Patterson4 (see also Wiley and Johnson5. reject this hypothesis in favor of recognizing a separate holocentrid clade (proposed here as a new order. 29 and consistently include holocentrids within this clade. Mugiliforms (mullets) and atherinomorphs (silversides. 9 and 10). The main issue at this level is delimitation of Beryciformes and relationships of its proposed components to Percomorphaceae. 1-10) A major contribution from our study has been the disambiguation of the percomorph bush into nine wellsupported supraordinal groups (six Series and three Subseries. Despite relatively low support for our holocentrid-percomorph clade (57-69% bootstrap). Carangimorpharia (with three Subseries: Anabantomorphariae. Euacanthomorphacea: holocentrids sister to percomorphs (Fig.105 also found significant congruence between this arrangement and morphological character-state distributions for many of the proposed relationships. and Ovalentariae. 24 .13 added to this group the lampridiform genus Stylephorus. Gobiomorpharia (Fig. except that the latter excludes the berycids. a taxon not classified by Wiley and Johnson5. 5). 1) Johnson and Patterson4 included polymixiids. Under different combinations of taxa.
Carangimorphariae. Thacker33 resurrected the order Gobiiformes. Icosteiformes (Icosteidae). 4) and Scombriformes (Fig. and Apogonoidei (including apogonids and pempherids). 1). together with Glaucosomatidae). Despite the disparate morphology among members of Scombriformes.ncbi. and Percomorpharia may be challenging to recover given the rapid radiation and diversification of these clades. 10). the new hypothesis implies that endothermy has evolved at least twice independently in teleosts111 . stromateids. kurtids and. and Perciformes (Bramidae. 6) www. A major difference is that our hypothesis segregates the family Pempheridae (sweepers) to its own order (Pempheriformes. Because billfishes and tunas are not closely related as previously suggested by anatomical studies83 (Fig. 7) together with disparate taxa such as remoras (Echeneidae). such as Stromateiformes (Centrolophidae. and others (see below). 5). 1). Recent molecular studies have emphasized the non-monophyly of Scorpaeniformes74.gov/pmc/articles/PMC3644299/ 9/28 . 5) includes most of the families previously grouped in the perciform suborder Scombroidei2 or the order Scombriformes5. 112. Nomeidae. 3. grouping such disparate fishes as seahorses and tunas. Previous molecular studies have shown affinities between gobioids. dactylopterids. we provide a restricted definition for Perciformes that includes many scorpaeniform taxa (Fig. however. except for the barracudas (Sphyraenidae) and the billfishes and swordfishes (here placed in their own order. 11 .nlm. and Caristiidae). The Syngnathiformes. will require additional study. Kurtidoidei (nurseryfish). apogonids. scombrids. Not surprisingly. Sphyraenidae and Istiophoriformes are now firmly placed within Carangimorphariae (Fig. mullids. a close relationship among taxa contained within this group. to accommodate three suborders: Gobioidei (gobies and sleepers). Detailed relationships among families of Syngnathiformes (see also Fig. as defined here (Fig. traditionally placed in three distinct percomorph orders.5/22/13 The Tree of Life and a New Classification of Bony Fishes Phylogenetic resolution within five newly discovered clades. comprises mostly tropical marine reef-dwellers. There is also morphological evidence supporting a close relationship between gobids and apogonids108. We have noted above the dissolution of Gasterosteiformes12 and. Values in parentheses indicate number of genera examined Our new order Scombriformes (Fig. Pomatomidae. Detailed relationships among orders and families of Gobiomorpharia (see also Fig. Values in parentheses indicate number of genera examined. to some extent. Relationships within Syngnathiformes. jacks (Carangidae). including Gasterosteiformes (syngnathids). 3) Based on a phylogeny estimated with four mitochondrial markers. Detailed relationships among families of Scombriformes (see also Fig. an others. callionymids. has never been proposed on morphological grounds. flatfishes (Pleuronectiformes). 4 and 5) One of the most unanticipated new percomorph clades is the Scombrimorpharia. 1. Ovalentariae. most are offshore fishes that inhabit pelagic and/or deep-sea waters. This new circumscription of Scombriformes also comprises families belonging to multiple orders in previous classifications. Gobiomorpharia: sweepers are out (Fig. archer fishes (Toxotidae). 109 as well as between kurtids and apogonids110. 4). Scombrimorpharia: sea horses and tunas are close relatives (Figs. “Perciformes” (mullids and callionymids) and “Scorpaeniformes” (dactylopterids). Istiophoriformes). Stromateidae). Anabantomorphariae: freshwater and air breathing (Fig. Scombriformes. 2). Values in parentheses indicate number of genera examined. Our results provide partial support for the Gobiiformes sensu Thacker33 but we treat it here as a supraordinal group (Gobiomorpharia). 1. Trachiniformes (Chiasmodontidae). This clade includes the newly circumscribed orders Syngnathiformes (Fig.nih. 9). including syngnathids. within Percomorpharia (Figs. 1). Ariommatidae. 16. as discussed below. pempherids and dactylopterids8.
This clade was first found on the basis of mitogenomic evidence8.g. Carangimorphariae. www. A remarkable condition shared by members of this novel grouping is their mostly freshwater origin and restriction to Africa and South East Asia (although some members in the family Synbranchidae occur in Mexico. jawfishes and basslets). 112.24 (see also27 . This higherlevel group has been referred to as ‘‘clade L’’ sensu Chen et al. has evolved multiple times in percomorphs31. beloniforms. and Anabantiformes (gouramis) (Fig. some of these characters are symplesiomorphies while others are absent in the remaining carangimorph groups. Our results suggest that this group can be divided into four subgroups (superorders). 31. and atherinomorphs (atheriniforms. Hemiramphidae). including more than 5000 species in some 44 families. Species in Anabantomorphariae include representatives placed in three separate orders by Wiley and Johnson5: Synbranchiformes (swamp eels). Pomacentridae. 11 .g. grouping seemingly distinct groups such as cichlids. blennies. 1). 6). Embiotocidae and Pseudochromidae). 19.nlm. 28. 1). Many families in Ovalentariae. remain incertae sedis (e. billfishes. however. 7) A close affinity between other seemingly disparate groups.. swordfishes.28). Carangimorphariae: flatfishes and unlikely relatives (Fig. and carangids.. Two different studies have coined a name for this group. Detailed relationships among orders and families of Anabantomorphariae (see also Fig.5/22/13 The Tree of Life and a New Classification of Bony Fishes Another major percomorph group proposed here is the series Carangimorpharia. Most are able to occupy marginal. and lack supraneurals. and Ovalentariae (Fig. 5. An interesting implication of this phylogenetic hypothesis is that the pharyngeal jaw apparatus (pharyngognathy). flatfishes. including three subseries: Anabantomorphariae. 26. Values in parentheses indicate number of genera examined. 28. Detailed relationships among orders and families of Carangimorphariae (see also Fig. 27 . The monophyly of Anabantomorphariae has also been supported on the basis of mitogenomics8. stagnant waters due to their capacity to tolerate anoxia and to obtain oxygen directly from the air. 112 (Fig. Ovalentaria by Wainwright et al. whereas the opposite is true for pleuronectiforms28. including barracudas. 28). It thus seems paradoxical that despite the apparent lack of morphological synapomorphies for carangimorphs there is a strong molecular signal supporting their monophyly. 24 . Anabantiforms have a suprabranchial organ and synbranchids have suprabranchial pouches with respiratory function. 12 and later confirmed with nuclear sequence data23. according to Friedman113. present in many members of this clade (e. However. 7). two of which already existed (Atherninomorphae and Mugilomorphae) and two that are new: (i) Cichlomorphae (Cichlidae plus Pholidichthyidae) and (ii) Blennimorphae (blennioids plus clingfishes. 24 . 113. has been well established by recent molecular studies10. For additional insights and discussion on Carangimorphariae we refer the reader to recent studies24 . and Central and South America). Values in parentheses indicate number of genera examined (see also Betancur-R. We refer the reader to Wainwright et al. 16.gov/pmc/articles/PMC3644299/ 10/28 . first Stiassnyiformes by Li et al.31 for additional discussion on Ovalentariae. et al. more recently.112 found that most taxa share a relatively low number of vertebrae. 8) Ovalentariae is one of the most spectacular percomorph radiations. While the first two orders belonged to the Smegmamorpharia4 . have multiple dorsal pterygiophores inserting before the second neural spine.ncbi.31 for their characteristic demersal.24 and. and others. 27 . the armored stickleback). among others. Cichlidae. the Anabantiformes were placed as incertae sedis in Percomorphacea5. Ovalentariae: sticky eggs (Fig.19 or Carangimorpha by Li et al. and cyprinodontiforms). 1). mullets. Little et al. adhesive eggs with chorionic filaments (lost secondarily in some groups). 12 and nuclear markers28. jacks. Gasterosteiformes (Indostomus. In looking for possible anatomical synapomorphies uniting flatfishes.nih.
Our definition indicates unambiguous membership for 38 families and uncertain membership for an additional 42 that were not examined in our study but that have been assigned to either “Perciformes” (10). 9) Percomorpharia is by far the largest percomorph clade. in each terminal order. The largest group within Percomorpharia is the order Perciformes. Nelson’s classification2 included 160 families in Perciformes. 116. and Scorpaenidae)2. Although most family-level and ordinal groups within Percomorpharia receive high bootstrap support. caproids.g. Pempheriformes). 1). Cottiformes (8). 114 . 16. but with far more limited sampling (e. More than one third (514) of the species in our bony fish phylogeny are placed in this clade. the new bush at the top. by several authors16. Previous molecular studies obtained monophyletic groups with a combination of taxa here assigned to Percomorpharia. 74).. Ephippiformes.. including three of the top ten most diverse families of fishes (i.g. a monophyletic definition of Perciformes can be recovered from phylogenetic analysis of a comprehensive taxon sampling. 10). Labridae. Lophiiformes. 5. including 11 orders with some of the most prominent ones such as Perciformes. searobins (Triglidae). Perciformes: no longer a taxonomic waste basket (Fig. and places them close to tetraodontiforms. All of these taxa are included in our definition of Perciformes (Fig. At least 151 families (105 examined) belong in Percomorpharia.. 10 for expanded relationships on perciform groups. Several of these groups are newly proposed or resurrected orders under new circumscription (e.nlm. perches (Percidae). “Scorpaeniformes” (14). pomacanthids. 19. icefishes (Notothenioidei). 31). The new circumscription of Perciformes reduces significantly the number of included taxa. chaetodontids. while retaining remarkable diversity that can be organized into several suborders and infraorders.nih. Uranoscopiformes. and in different combinations.5/22/13 The Tree of Life and a New Classification of Bony Fishes Detailed relationships among orders and families of Ovalentariae (see also Fig. sculpins (Cottoidei). eelpouts (Zoarcoidei) and scorpionfishes (Scorpaenoidei) have been obtained in one form or another. ephippids and others (see also 87 . Serranidae.e. as was suggested by previous classifications78. Labriformes. respectively. Many clades lacking taxonomic annotations on nodes are incertae sedis taxa (for details.ncbi. Percomorpharia: the new bush at the top (Fig. Values in parentheses indicate number of genera examined in each terminal family or number of families and genera. the maximum possible number of families in the newly defined Perciformes is reduced to 71. 115). www. Earlier molecular studies lacked sufficient sampling to resolve phylogenetic questions among “percoids. 23. Hence.. 5 with ‘‘percoids’’ scattered throughout Percomorpha and no clear phylogenetic distinction among Percoidei. acanthuriforms.” but close relationships among groupers (Serranidae).. and Tetraodontiformes. see classification). Our new arrangement removes anglerfishes (Lophiiformes) from Paracanthomorphacea. sticklebacks (Gasterosteidae). This number is closer to the 90 families proposed by Wiley and Johnson5 for their Perciformes. Detailed relationships among orders and families of Percomorpharia (the new bush at the top.gov/pmc/articles/PMC3644299/ 11/28 . see also Fig. Many clades lacking taxonomic annotations . For a long time. 8. interrelationships among them are largely unresolved (hence. Fig. 29. Values in parentheses indicate number of genera examined (see also Wainwright et al. 74 . 1). and Percomorpha74. 10) For the first time. 20. 24 . or Trachiniformes (1) in previous classifications2. Perciformes. making it the largest order of all vertebrates. Perciformes has been regarded as a “taxonomic waste basket”2. but with a very different composition. 11 . 9). See also Fig.
. Additional taxon sampling and more data are needed to resolve interrelationships among these taxa. albeit they support a close relationship of Percophidae with notothenioids and divide platycephaloids into three groups. Harpagiferidae. and several unexamined families remain unclassified.g. 66.5/22/13 The Tree of Life and a New Classification of Bony Fishes Within Perciformes. suggesting that the current trend to analyze larger data sets with well established fossil constraints will result in robust time trees in the future. given that Percidae is included and serranids have historically been considered a family within Perciformes. Smith and Craig74). Time-calibrated BEAST phylogeny based on a subset of 202 taxa. 120. including the families Nototheniidae sensu stricto. 118. *Nototheniidae sensu lato. We refer the reader to this paper. Bars represent the 95% highest posterior credibility intervals of divergence times. A New Timescale of Bony Fish Evolution In addition to the novel insights regarding the interrelationships of teleost fishes. The time-calibrated phylogeny for bony fishes provided here should stimulate macroevolutionary studies of fishes using phylogenetic comparative methods (PCMs). www. Detailed relationships among families of Perciformes (see also Figs. Smith and Wheeler16. Scorpaenoidei. 41. Bathydraconidae. 1 and 9). the same team of researchers (Lautredou et al. molecular markers. 37 . we tentatively propose suborders (Notothenioidei.24. and Channichthyidae. indicating the placement for the 59 calibrations used. Values in parentheses indicate number of genera examined. suggesting that development of better statistical methods and best practice approaches should decrease disparity among estimated ages of clades43. our study provides the most comprehensively sampled time-tree of bony fish evolution based on 60 calibrations points (Figs. 121 . Recent studies that estimated divergence times using multi-locus nuclear approaches had more restricted taxonomic focus and implemented fewer (<36) fossil calibrations29. Four suborders/infraorders were recognized as separate orders by Wiley and Johnson5: Percoidei. but two incertae sedis (Percophidae and Platycephalidae). 36. 12). Calibration (60) was not included for this analysis (see Appendix 1).gov/pmc/articles/PMC3644299/ 12/28 . estimates based on multi-locus data and denser taxonomic sampling tend to converge (Fig. and fossil constraints have been discussed extensively by several authors. 119.116) presented a detailed analysis of this clade using seven nuclear markers and obtained phylogenetic relationships that are generally congruent with our results (Fig. 11). Most recently. This choice of name is misleading. Compared to earlier studies reporting divergence times among teleost lineages35.nih. 11). Cottoidei) for clades with high support that also represent some well-established groups. Artedidraconidae. Trigloidei. for more details on taxonomic issues.nlm. and Gasterosteales (an infraorder of Cottioidei). The composition of Perciformes obtained from our phylogeny is remarkably similar to a group named “Serraniformes” by Li et al. Cottioidei. 1. 65.ncbi. Our estimates of mean divergence dates for early actinopterygian lineages tend to be younger and the divergence of neoteleosts and subtending clades are substantially older relative to those in Near et al. Sensitivity of molecular calibrations to different combinations of taxa. 10). as well as others (e.29 (although 95% probability distributions overlap in many cases). Although our approach for calibrating the molecular phylogeny is based on a set of common fossil constraints used by the cited studies and others64 . Scorpaenoidei. some differences in the results are evident (Fig. Adoption of Serraniformes would obliterate the long ichthyological tradition of defining higher taxa with the prefix “perco” for hierarchical groups that contain perciforms (preserved in our classification).
efficient non-stationary approaches to analyze large and heterogeneous multi-locus data sets such as the one presented here currently are not available. Pleuronectiformes. which resulted in extinction of up to 96% of all marine species of that time123. two sister taxa with little or no genetic overlapping may not be resolved as closely related. or have dubious resolution due to the combination of missing data. Gymnotiformes.nih. Recent work suggested that a major burst of teleost diversification. Batrachoidiformes.5/22/13 The Tree of Life and a New Classification of Bony Fishes Comparison of mean (triangle) and 95% highest posterior credibility intervals (horizontal bars) of divergence dates for selected clades (see also Figs 1. Lophiiformes. have low bootstrap support. The date estimates presented herein (Figs 1. but explicit analyses using robust PCMs would be necessary to assess rate shifts of lineage diversification through time. revealing an explosive morphological diversification of percomorphs in the aftermath of the end-Cretaceous extinction125. According to our estimates. 66.g. Another major factor that may severely compromise phylogenetic inference is compositional heterogeneity (non-stationarity). as suggested by a recent study that examined a fraction of the taxa and markers included here28. Scombrimorpharia. lungfishes and tetrapods46.66 Absent lines imply that the particular date estimation was not performed in the corresponding study. with the sarcopterygian crown group evolving in the Early Devonian (409 Ma) and the actinopterygian crown group evolving at the Middle-Late boundary of the Devonian (383 Ma).gov/pmc/articles/PMC3644299/ 13/28 . Appearance of the three major teleost lineages (Elopomorpha. Osteoglossomorpha and Clupeocephala) took place in a narrow temporal window of 13 million years during this period. Although the oldest teleost fossils are from the late Triassic (e. predominantly within Otophysa and Percomorphacea. Unfortunately. and the OneZoom tree) confirm the notion that divergences of major ray-finned fish lineages are considerably older than the oldest known fossils for their respective groups29. Patterns in the fossil record corroborate this idea. Several parts of the fish tree that require additional study include (i) resolution of the relationships among coelacanths. 124. the major lineages within Percomorphaceae (Ophidiiformes. Our estimate of 425 Ma for divergence of crown Osteichthyes places the origin of Sarcopterygii and Actinopterygii in the Middle Silurian. www. (ii) the basal divergence of euteleosteomorph groups and circumscription of Protacanthopterygii. are often poorly resolved. Percomorpharia and Perciformes) originated between 132 Ma and 82 Ma.ncbi. The relatively high proportion of missing data in the 3+ dataset (59%) is likely to have a stronger topological impact at the fine scale (towards the tips). Paleoecological conditions surrounding the end Permian mass extinction. in particular interrelationships of argentiniforms. however. took place in a relatively short time span between the late Mesozoic and early Cenozoic29. Gobiomorpharia. Carangimorpharia.. Black lines and mean dates are from this study. Carangiformes. Fish orders with dubious internal relationships include the Characiformes. both of which correspond to the “Age of Fishes”. Remaining Challenges and Unresolved Issues The new shape of the tree of life of bony fishes and the classification reflecting this structure offered by this study leaves many questions unanswered and suggests several directions for future sequencing efforts. galaxiiforms. 2-11. might have shaped the evolutionary history of early teleosts. and or other sources of systematic error. 11).29 and green are from Broughton et al. the molecular hypothesis suggests that the initial divergence of crown group Teleostei occurred long before in the Early Permian (283 Ma).nlm. such as those within the rapid percomorph radiations. The same is true for the diversification of many lineages within each of these groups. †Pholidophorus latiusculus. in particular for gene trees. Norian122). taxon sampling. 47 . blue are from Near et al. Many families not included in the present analysis are listed in the classification and many groups defined as incertae sedis or sedis mutabilis clearly deserve additional study. among others. 66. e. before the end of the Cretaceous. Relationships for many terminal taxa.g..
MRCA: Leucoraja.06 (crown calibration). CL. Bentley (Biodiversity Institute. Appendix 1 Go to: Calibration points and age prior settings This section provides details on calibrations and prior settings used for divergence time estimates. JAL. MS. Danio. We predict that these difficult challenges in ichthyology will find renewed sources of evidence with the advent of next generation sequencing approaches and phylogenomics (e. RBR and GO wrote the paper and RB. mean= 6. KC.ncbi. and Perciformes.0 Ma. CL. Additionally. and others. molecular and morphological systematics. For calibration details. Nichols and T. One geological calibration uses a normal distribution with soft minimum and maximum bounds (calibration 37). . the Gibbs Jr. RBR and DA downloaded sequences from NCBI. A. Reinterpretation of morphology and new studies of developmental patterns will be necessary to reconcile the molecular phylogenetic hypothesis with existing and expanding phenotypic data sets (e. Author contributions Go to: CL and GO designed the molecular markers. Eschmeyer and J.. REB made the figures.15. JC. RBR and EOW proposed the new classification and NIH. Harris. RBR. Coates made insightful comments on earlier versions of the manuscript. Ovalentariae. vertebrate development. I am the editor-in-chief of Mesozoic Fishes volumes. EOW. Analyst. refer to the original studies cited under each. DJH. Go to: Biographies • Dr Chenhong Li is a professor at Shanghai Ocean University.L. SW. and molecuiar evidence of extant fishes. especially teleostean fishes based on fossils and morphological. and assembled the datasets.g. KL. many of them monographs. I am the recipient of numerous awards including the Humboldt Prize for Contributions to Sciences. research interests: Ichthyology.gov/pmc/articles/PMC3644299/ 14/28 . studying molecular phylogeny and ecology in fishes. Fong provided access to their Catalog of Fishes database. MC. Department of Biology. GO and GA took care of the final editing. and TL digitized the EToL database. University of Kansas) and W. A.= 0.5/22/13 The Tree of Life and a New Classification of Bony Fishes osmeriforms. FZ. A. Percomorpharia. Oklahoma Biological Survey • Professor. vetted all the sequences compiled. RBR. and the editor of seven books.nlm. Makinen for providing laboratory assistance. Member of the Academy of Sciences of Chile. C. St. Honorary Member of ASIH. Mullaney. Dev. 126.nih. (iii) interrelationships among components within Scombrimorpharia. all authors contributed to the writing. GO. Carangimorphariae. ARV. and DA made insightful additions. Award for my publication record in ichthyology (American Society of Ichthyologists and Herpetologists). rather than mid-point of age range [see 1]. TG. Smith (Field Museum of Natural History) provided tissue samples.g. I am part of the advisory board of a few journals. Hard lower bounds or minimum age reflect the youngest possible age interpretation of fossils. Calibration source: Broughton et al. My publication record includes over 130 papers. 95% soft maximum age: 519. REB.. stomiatiforms and neoteleosts. 128. the Artedi Lecturer Award for my contributions to the knowledge of Nature and Sciences (Swedish Academy of Sciences and FishBase). DA. GA. H. (1) Gnathostomata. and DA designed the taxonomic sampling. NIH. DA. www.T. GO. and M. I am interested in the origin and phylogenetic relationships of actinopterygians. López-Fernández. • I. developmental. RBR and JAB performed phylogenetic analyses. RBR and GA selected the fossil calibrations and RBR estimated divergence times. • I am a biologist specialized in ichthyology and ichthyopaleontology. TB. Acknowledgments Go to: We are grateful to K. prior distributions and settings for some calibrations were adapted for this study. and (iv) the ordinal status of 55 percomorph families examined (as well as many others unexamined) that remain with uncertain ordinal affiliation (incertae sedis). Loyola University Chicago. and WCB generated sequence data via PCR and edited chromatograms. RBR. soft upper bounds or maximum age indicate the oldest possible fossil age. salmoniforms. Acero.N. Prior setting: Lognormal distribution. Hard minimum age: 426. 127). esociforms. TG. GL.0 Ma. 129). W.
Calibration source: Broughton et al.0 Ma. MRCA: Lepisosteus.nlm. Prior setting: Exponential distribution.0 Ma. (8) Actinopterygii (total group).40 (crown calibration).0 Ma.0 Ma. MRCA: Xenopus. Calibration source: Broughton et al. Danio. . (9) Polypteriformes. MRCA: Albula. mean= 4. Prior setting: Exponential distribution.0 Ma.0 Ma. 95% soft maximum age: 139. Calibration source: Broughton et al. mean= 4. Calibration source: Broughton et al. Calibration source: Broughton et al.0 Ma.0 Ma. mean= 38. Amia. (16) Osteoglossomorpha. Halosauropsis. Polypterus. Calibration source: Broughton et al.70 (crown calibration). Hard minimum age: 136. Protopterus. Prior setting: Exponential distribution. Prior setting: Exponential distribution. MRCA: Hiodon.0 Ma.0 Ma. .0 Ma. Calibration source: Broughton et al. Hard minimum age: 62. MRCA: Lepidosiren. mean= 8. Prior setting: Uniform distribution (crown calibration). Heterotis.0 Ma. Danio. Hard minimum age: 375. Hard minimum age: 124. (14) Elopomorpha. . mean= 34. . mean= 26.0 Ma.nih. mean= 13. 95% soft maximum age: 260. Hard minimum age: 70. .73 (crown calibration). (6) Metatheria. Hard minimum age: 100. . Prior setting: Exponential distribution. Calibration source: Broughton et al.66 (crown calibration). Prior setting: Exponential distribution. Homo. mean= 12. Prior setting: Exponential distribution. .70 (crown calibration).0 Ma. Prior setting: Uniform distribution (crown calibration). MRCA: Scaphirhynchus. (11) Chondrostei.69 (crown calibration). 95% soft maximum age: 216. Prior setting: Exponential distribution. Homo. MRCA: Gymnarchus. Hard minimum age: 5. Danio. . mean= 40. Benton and Donoghue . (5) Tetrapoda. . Hard minimum age: 246. Calibration source: Broughton et al. Danio. Lepidosiren.0 Ma.5 Ma. MRCA: Elops. 95% soft maximum age: 386.0 Ma.0 Ma.0 Ma. (4) Lepidosirenoidei. Xenomystus.00 (crown calibration). 95% soft maximum age: 423.5 Ma. MRCA: Monodelphis. (7) Human-Mouse. MRCA: Lepisosteus. 95% soft maximum age: 416.0 Ma. MRCA: Arapaima. mean= 6. Calibration source: Broughton et al.5/22/13 The Tree of Life and a New Classification of Bony Fishes (2) Osteichthyes. Calibration source: Broughton et al. Prior setting: Exponential distribution. MRCA: Mus. 95% soft maximum age: 260. Hard minimum age: 407. (17) Notopteridae (total group). (15) Albuliformes + Anguilliformes. Hard minimum age: 130. Hard minimum age: 260. . 95% soft maximum age: 438. . Calibration source: Broughton et al. Prior setting: Exponential distribution.34 (stem calibration). (12) Neopterygii.0 Ma. . MRCA: Erpetoichthys. (18) Arapaimidae. Hard minimum age: 330. 95% soft maximum age: 246. Polyodon. 95% soft maximum age: 415. 95% soft maximum age: 419. 95% soft maximum age: www.0 Ma. MRCA: Latimeria. Benton and Donoghue . Calibration source: Broughton et al. . Halosauropsis. Prior setting: Exponential distribution. Benton and Donoghue . .35 (stem calibration).84 (crown calibration). Calibration source: Broughton et al. MRCA: Latimeria.0 Ma. mean= 6. Calibration source: Broughton et al. (13) Holostei.0 Ma.0 Ma. Prior setting: Uniform distribution (crown calibration).0 Ma.ncbi. Hard minimum age: 65. 95% soft maximum age: 101. Hard minimum age: 149. (3) Sarcopterygii.0 Ma. MRCA: Polypterus.0 Ma. Prior setting: Uniform distribution (crown calibration). 95% soft maximum age: 350. Hard minimum age: 418. 95% soft maximum age: 216. 95% soft maximum age: 99. Prior setting: Uniform distribution (crown calibration).0 Ma. . Hard minimum age: 398. Hard minimum age: 125. Calibration source: Broughton et al. 95% soft maximum age: 350.gov/pmc/articles/PMC3644299/ 15/28 . (10) Actinopteri (total group).0 Ma.0 Ma. MRCA: Scaphirhynchus.50 (crown calibration). Arapaima. . Homo.0 Ma.
MRCA: Ictalurus. 95% soft maximum age: 216.= 0. Prior setting: Exponential distribution. mean= 0. (20) Cobitoidea. Hard minimum age: 61.  (prior setting adapted for this study). mean= 23. Dev. stem ostariophysan †Tischlingerichthys viohli (see calibration 20 above). Late Jurassic. Calibration source: Saitoh et al. Hard minimum age: 34. mean= 1.nih. 95% soft maximum age: 146. mean= 1. MRCA: Percopsis. Hard minimum age: 65.5 Ma. MRCA: Callichthys. MRCA: Danio. Chologaster.0 Ma. Hard minimum age: 34.0 Ma. stem ostariophysan †Tischlingerichthys viohli (see calibration 20 above). Germany . Takifugu. (19) Chanidae.55 (crown calibration). Hard minimum age: 139. Cromeria. Calibration source: Near et al. Ictalurus.  (prior setting adapted for this study).0 Ma.  (prior setting adapted for this study).0 Ma. 95% soft maximum age: 76. mean= 27. (24) Ictaluridae + Cranoglanidae. .  (prior setting adapted for this study). Hard minimum age: 76.8 (crown calibration). Dev.05 (crown calibration). . . Hard minimum age: 149 Ma. Novumbra.0 Ma.5 Ma. . modified to include the MRCA of Chanidae plus Kneriidae.62. Ariopsis. (29) Salmonidae.20 (crown calibration). MRCA: Pygocentrus.= 0. 95% soft maximum age: 36. mean= 25.8 (crown calibration). Corydoras. Hard minimum age: 63.70 (crown calibration). 95% soft maximum age: 146.02 (crown calibration). MRCA: Aphredoderus. Prior setting: Exponential distribution. Prior setting: Lognormal distribution.70 (crown calibration). Aphredoderus.0 Ma.= 0. 95% soft maximum age: 63.0 Ma. Calibration source: Near et al.8 (stem calibration). (25) Ictaluridae.5-145.gov/pmc/articles/PMC3644299/ 16/28 . mean= 32. MRCA: Gogo. Calibration source: Broughton et al.nlm. Calibration source: Near et al.5 Ma.5/22/13 The Tree of Life and a New Classification of Bony Fishes 136. Zeus. www. Prior setting: Exponential distribution.5 Ma. mean= 0. Calibration source: Broughton et al. St. Prior setting: Lognormal distribution. Hard minimum age: 32 Ma. Calibration source: Saitoh et al. .ncbi. (27) Euteleostei. Calibration source: Broughton et al. .0 Ma.53. Prior setting: Exponential distribution. . mean= 27.  (prior setting adapted for this study).8 Ma. MRCA: Zenopsis. . .= 0. MRCA: Esox. 95% soft maximum age: 97. mean= 29.0 Ma. (28) Esocidae + Umbridae. Notemigonus. 95% soft maximum age: 65. Late Jurassic.5 Ma. Prior setting: Exponential distribution. Prior setting: Lognormal distribution. Prior setting: Exponential distribution.0 Ma. Oncorhynchus. .8 (stem calibration). MRCA: Coregonus.5 Ma. (21) Cyprinidae. Dev. stem ostariophysan †Tischlingerichthys viohli.5-145. mean= 12.53 (crown calibration). Hard minimum age: 48. Calibration source: Lundberg et al. Dev. St. Dev. MRCA: Lepidogalaxias. mean= 10.0 Ma. (22) Serrasalmidae + Hemiodontidae. MRCA: Hypentelium. (30) Percopsidae. Calibration source: Broughton et al.01 (crown calibration). 95% soft maximum age: 59. Calibration source: Lundberg et al. 95% soft maximum age: 260 Ma. Prior setting: Lognormal distribution. Calibration source: Broughton et al. Hard minimum age: 51.90.8 (stem calibration). Comments: Kneriidae is not represented in the taxonomic sampling of Broughton et al. . mean= 1. 95% soft maximum age: 146. mean= 27.4 Ma. Calibration source: Near et al.0 Ma.23. St. stem ostariophysan †Tischlingerichthys viohli (see calibration 20 above). stem ostariophysan †Tischlingerichthys viohli. Prior setting: Exponential distribution. (26) Arioidea.= 0. (31) Aphredoderidae. Germany.0 Ma. Calibration source: Near et al. 95% soft maximum age: 87. Hard minimum age: 57. Calibration source: Lundberg et al.5 Ma.5-145. 95% soft maximum age: 146.87 (crown calibration). St. Prior setting: Uniform distribution (crown calibration).5 Ma. MRCA: Chanos. Prior setting: Exponential distribution. 95% soft maximum age: 146.5 Ma.5 Ma. Prior setting: Exponential distribution. St. MRCA: Ameiurus. Cranoglanis.5145. (32) Zenopsis + Zeus. Hard minimum age: 60. Barbatula. Hemiodus. (23) Callichthyidae.09.5 Ma. Hard minimum age: 58. Prior setting: Lognormal distribution.
95% soft maximum age: 3. Prior setting: Lognormal distribution.8 (crown calibration). we place it in the stem Centriscidae because the position of this group is unstable. Dev.= 0. maculatus. 95% soft maximum age: 83. it should be the crown.67. . 95% soft maximum age: 57. St. Prior setting: Lognormal distribution. 5% soft minimum age: 2.5 Ma.5/22/13 The Tree of Life and a New Classification of Bony Fishes (33) Lampridiformes. chinensis.8 (stem calibration).5 Ma. Prior setting: Lognormal distribution. Comments: Near et al. www. Prior setting: Lognormal distribution.15. Echeneis. Hard minimum age: 32 Ma. mean= 3. 95% soft maximum age: 34. their figure S2 shows the calibration placed in the stem of Holocentridae.Panama Isthmus. (35) Trachichthyidae.  noted that there is no phylogenetic resolution for †“Syngnathus” heckeli and †Prosolenostomus lessinii among syngnathids and assigned these fossils as stem calibration points for the MRCA of Fistularia and Syngnathus.= 0.17. mean= 0. MRCA: Caranx. St. Comments: Near et al.8 (crown calibration). MRCA: A. 95% soft maximum age: 57. Dev. Calibration source: Near et al. St. Dev.ncbi.= 0. MRCA: Myripristis. (34) Holocentridae. mean= 0.01. St.5 Ma.8 (crown calibration). Dev.5 Ma. Dev. Hard minimum age: 50 Ma. 95% soft maximum age: 81 Ma. We are not convinced that the state in this fossil can be meaningfully distinguished from the condition found in cynoglossids. mean= 0. MRCA: Gephyroberyx. (44) Bothidae (total group). Calibration source: Near et al. MRCA: Lophotus.8 (stem calibration).67. St. Prior setting: Lognormal distribution. Hard minimum age: 56 Ma. Dev.nih.= 0. . However. .8 (crown calibration). Prior setting: Lognormal distribution. Heteromycteris." A placement †Eobuglossus in the Soleidae + Cynoglossidae crown reconciles both opinions. 95% soft maximum age: 34. Prior setting: Lognormal distribution.67. Dev. mean= 2. Hard minimum age: 50 Ma. . St.5 Ma. Calibration source: Near et al.02. (42) Pleuronectoidei. . because Fistularia is not a syngnathid (i. 95% soft maximum age: 57.78. Prior setting: Lognormal distribution. MRCA: Asterorhombus. Calibration source: Near et al.8 (crown calibration). 95% soft maximum age: 64 Ma. Instead. Prior setting: Normal distribution.95. Callionymus. Dev. .= 0. A.= 0. Calibration source: Near et al. Dev.8 (stem calibration). Dev. Calibration source: Bowen et al.= 0.= 0. Monocentris. . Echeneis.. lacks body plates). St.67. Hard minimum age: 30 Ma. .5 Ma.  report the fossil as a stem lineage of Myripristinae and assigns it to the divergence of Myripristinae + Holocentrinae. Comments: Near et al. St.5 Ma. 95% soft maximum age: 57. (43) Soleidae + Cynoglossidae.= 0. . . Hard minimum age: 70. Macroramphosus. modified to include the MRCA of Lophotus and Lampris. Hard minimum age: 40.8 (crown calibration).nlm. St.gov/pmc/articles/PMC3644299/ 17/28 . Sargocentron. St. mean= 0. Comments: Lophotus was not examined by Near et al.5 Ma. Hard minimum age: 56 Ma.= 0. MRCA: Lepidoblepharon. . (39) Syngnathidae (total group). Calibration source: Near et al. Calibration source: Near et al. MRCA: Syngnathus. Symphurus. Laeops. (38) Centriscidae (total group).  placed the calibration one node below (Samaridae + Soleidae + Cynoglossidae) arguing that "Chanet (1994) argues that †Eobuglossus can be identified as a soleid on the basis of the geometry of the ascending process of the blind side premaxilla.23.5 Ma.8 Ma. mean= 0. mean= 0. Prior setting: Lognormal distribution.5 Ma. Comments: Near et al. Prior setting: Lognormal distribution.8 (stem calibration). Hard minimum age: 50 Ma.8 (crown calibration). (37) Aulostomus .212 (crown calibration). (41) Echeneidae + Coryphaenidae + Rachycentridae.  used this as crown calibration one node below (with Aulostomus). (40) Carangiformes. Comments: Near et al. MRCA: Aulostomus. Prior setting: Lognormal distribution. Doryrhamphus. However. it is likely a stem bothid . mean= 1. Dev. Hard minimum age: 30 Ma.5 Ma. a more appropriate placement for these two fossils (both of which have body plates) is the stem Syngnathidae. Calibration source: Near et al. MRCA: Heteromycteris. Calibration source: Near et al. Calibration source: Near et al. St. (36) Syngnathiformes (sensu lato). Hard minimum age: 50 Ma. .17. Calibration source: Near et al. 95% soft maximum age: 50 Ma. 95% soft maximum age: 36. mean= 0. St.  assigned the fossil †Oligobothus to the divergence of Bothidae + Pleuronectidae. MRCA: Coryphaena.= 0.= 0.e. mean= 0. Lampris. Dev. . MRCA: Aeoliscus. mean= 0.
8 (crown calibration). St. mean= 0. . Takifugu. Leiognathus. mean= 0. Hard minimum age: 7. (51) Cichlidae . Because our taxonomic sampling lacks Archoplites.= 0. 95% soft maximum age: 64 Ma. 95% soft maximum age: 50 Ma. Prior setting: Exponential distribution. Diagnosis and phylogenetic placement: placement of †Eolates gracilis in Latinae is supported by the presence of posterior pad in infraorbital 1 and by having 10+14 vertebrae. .5 Ma. Comments: a stem calibration is required because our taxonomic sampling lacks earlybranching heroins. .17. 95% soft maximum age: 122 Ma.10. Pomoxis. mean= 6. Calibration source: Near et al.5/22/13 The Tree of Life and a New Classification of Bony Fishes (45) Centropomidae (new crown calibration).gov/pmc/articles/PMC3644299/ 18/28 .= 0. MRCA: Gazza.5 Ma. mean= 0. it should be the crown. . (54) Tetraodontiformes (total group). MRCA: Ambloplytes. (48) Leiognathidae.. MRCA: Chaetodon.5 (crown calibration).40 (stem calibration). based on the FA95 (Marshall . we assign it to the MRCA of Ambloplytes + Pomoxis. (47) Chaetodon + Prognathodes. . Prior setting: Lognormal distribution. these results should be taken cautiously until explicit evidence challenging the traditional placement of †Plectocretacicus (e. following Collar et al. mean= 0. Alfaro et al. upper Y presian. Tetraodon. MRCA: Crenichichla. argenteus. MRCA: Diodon.e. Lates.01 (crown calibration). Hard minimum age: 32 Ma.10. 95% soft maximum age: 143 Ma. Prior setting: Lognormal distribution. Comments: Near et al.= 0. vulpinus. Calibration source: LópezFernández et al. Dev.. Dev. Prior setting: Lognormal distribution.g. Dev. . St. Dev. Alfaro et al. . mean= 11. Dev. Calibration source: Near et al. Hard minimum age: 49 Ma. Comments: The fossils used by Near et al. .5 Ma. 95% soft upper bound: 57.nih. S. mean= 0. unpublished) casts doubt on their phylogenetic affinities.67. mean= 0. their figure S2 shows the calibration placed in the stem of this clade. (56) Diodontidae + Tetraodontidae. Prior setting: Lognormal distribution. 95% soft maximum age: 34.8 (crown calibration).ncbi. ). Hard minimum age: 85 Ma.  are stem diodontids. Calibration source: Near et al. (52) Cichlidae . Hard minimum age: 56 Ma.  argue: "The oldest taxon assigned to this clade is the stem tetraodontiform †Cretatriacanthus guidottii from the Santonian of Nardo (Italy). Hard minimum age: 50 Ma. MRCA: Takifugu. MRCA: Luvarus. MRCA: Chaetodon. MRCA: Centropomus. Absolute age estimate: 50 Ma .= 0. (55) Tetraodontidae.12. St.= 0. ) becomes available.= 0. Prior setting: Lognormal distribution.78. following Near et al. Prognathodes. St.e. mean= 31.. Dev.  assign †Archoplites to the divergence of Archoplites + Ambloplytes. (50) Siganidae (total group). 95% soft maximum age: 143 Ma. Stratigraphic horizon and locality: early Eocene. Prior setting: Lognormal distribution.1 Ma. mean= 1. Prior setting: Exponential distribution. St.= 0. . Comments: Alfaro et al.69 (stem calibration). Leiognathus. Calibration source: Alfaro et al. Dev. Hard minimum age: 15. Hard minimum age: 56 Ma.5 Ma. 95% soft maximum age: 23 Ma. MRCA: Triacanthodes. Calibration source: Near et al.8 (crown calibration).40 (terminal-branch calibration).52 (crown www.8. 95% soft maximum age: 18 Ma. .78. St. stem tetraodontiformes because preliminary reexamination of the relationships of extant and fossil tetraodontiforms (Santini. Calibration source: López-Fernández et al." Although we adopt Santini’s interpretation here. Calibration source: Near et al. Prior setting: Exponential distribution. Acanthurus.  (i. Hard minimum age: 11. 95% soft maximum age: 9 Ma.Heroini. MRCA: Heros. While they argue that their assignment is one node below (i. .  and Santini et al. Herichthys. Prior setting: Lognormal distribution. Hard minimum age: †Eolates gracilis  and †Centropomus . Prior setting: Exponential distribution. 95% soft maximum age: 64 Ma. Calibration source: Alfaro et al. Monte Bolca. (53) Ambloplytes + Pomoxis. 95% soft maximum age: 85 Ma (stem †Cretatriacanthus).3 (crown calibration). . Calibration source: Near et al. St. We chose this taxon to date the minimum age rather than other. Pomoxis + Archoplites + Ambloplytes). Tetraodon. Italy. mean= 11. Hard minimum age: 30 Ma. Prior setting: Exponential distribution. older [†Plectocretacicus clarae]. Hard minimum age: 49 Ma. (46) Chaetodontidae (total group). divergence of Tetraodontidae + Diodontidae). mean= 31. †Eolates gracilis is the earliest branching lineage of Latiinae . MRCA: S.nlm. (49) Luvaridae.Geophagini.8 (stem calibration).
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