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      Phylogenetic classification of bony fishes

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          Abstract

          Background

          Fish 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.

          Results

          The 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.

          Conclusions

          This 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 material

          The online version of this article (doi:10.1186/s12862-017-0958-3) contains supplementary material, which is available to authorized users.

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          Most cited references 317

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          Fishes of the World

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            Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

            Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
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              AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS

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                Author and article information

                Contributors
                betanri@fishphylogeny.org
                ewiley@suddenlink.net
                garratia@ku.edu
                aacerop@unal.edu.co
                nbailly@hcmr.gr
                miya@chiba-muse.or.jp
                lecointre@noos.fr
                gorti@gwu.edu
                Journal
                BMC Evol Biol
                BMC Evol. Biol
                BMC Evolutionary Biology
                BioMed Central (London )
                1471-2148
                6 July 2017
                6 July 2017
                2017
                : 17
                Affiliations
                [1 ]Department of Biology, University of Puerto Rico, Río Piedras, P.O. Box 23360, San Juan, PR 00931 USA
                [2 ]ISNI 0000 0000 8716 3312, GRID grid.1214.6, Department of Vertebrate Zoology, National Museum of Natural History, , Smithsonian Institution, ; Washington, DC USA
                [3 ]ISNI 0000 0001 2106 0692, GRID grid.266515.3, Biodiversity Institute and Department of Ecology & Evolutionary Biology, , University of Kansas, ; Lawrence, KS USA
                [4 ]ISNI 0000 0001 2291 1903, GRID grid.263046.5, Sam Houston State Natural History Collections, , Sam Houston State University, ; Huntsville, Texas USA
                [5 ]Universidad Nacional de Colombia sede Caribe, Cecimar, El Rodadero, Santa Marta, Magdalena Colombia
                [6 ]GRID grid.424367.0, , FishBase Information and Research Group, ; Los Baños, Philippines
                [7 ]GRID grid.471892.1, Department Ecology and Environmental Sciences, , Natural History Museum and Institute, ; Chiba, Japan
                [8 ]ISNI 0000 0001 2174 9334, GRID grid.410350.3, , Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, ; Paris, France
                [9 ]ISNI 0000 0004 1936 9510, GRID grid.253615.6, Department of Biology, , The George Washington University, ; Washington, DC USA
                Article
                958
                10.1186/s12862-017-0958-3
                5501477
                28683774
                © The Author(s). 2017

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: DEB-147184
                Award ID: DEB-1541491
                Award ID: NSF DEB-0732819
                Award ID: DEB-1457426
                Award ID: DEB-1541554
                Award Recipient :
                Funded by: JSPS/MEXT JSPS KAKENHI
                Award ID: 22370035
                Award ID: 26291083
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2017

                Evolutionary Biology

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