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      The Tree of Life and a New Classification of Bony Fishes


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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.

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          Author and article information

          PLoS Curr
          PLoS Curr
          PLoS Currents
          Public Library of Science (San Francisco, USA )
          18 April 2013
          : 5
          The George Washington University
          University of Oklahoma
          Biologist at The University of KansasUniversity of Kansas
          International Union for Conservation of NatureOld Dominion University
          University of Alaska MuseumUniversity of Alaska Fairbanks
          Shanghai Ocean University
          Johnson County Community College
          The George Washington University
          Old Dominion University
          University of Oklahoma
          Ph.D. studentUniversity of Oklahoma
          University of Alaska Fairbanks
          The George Washington University
          Research AssistantGeorge Washington University
          University of Nebraska-Lincoln
          Loyola University Chicago
          University of Nebraska-Omaha
          Florida A&M University
          University of Oklahoma
          University of Nebraska at Omaha
          Loyola University Chicago
          Courtesy Research Professor and Associated ResearcherUniversity of Kansas
          The George Washington University
          This work was supported by NSF awards DEB-0732988 (to REB), DEB-0732838, DEB-1019308 (to GO and CL), DEB-0732819 (EOW), DEB 0732589 (TG), DEB-0732894 (KC), DEB 0963767 (JAL), and DEB-0732969 (GL); GWU Selective Excellence in Diversity of Life program (to RBR); Leading Academic Discipline Project of Shanghai Municipal Education Commission, project number S30701 (CL). The Biodiversity Institute, University of Kansas, provided financial support for the collection used in this study.
          Tree of Life



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