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      Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals.

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          Abstract

          The relationships at the root of the animal tree have proven difficult to resolve, with the current debate focusing on whether sponges (phylum Porifera) or comb jellies (phylum Ctenophora) are the sister group of all other animals [1-5]. The choice of evolutionary models seems to be at the core of the problem because Porifera tends to emerge as the sister group of all other animals ("Porifera-sister") when site-specific amino acid differences are modeled (e.g., [6, 7]), whereas Ctenophora emerges as the sister group of all other animals ("Ctenophora-sister") when they are ignored (e.g., [8-11]). We show that two key phylogenomic datasets that previously supported Ctenophora-sister [10, 12] display strong heterogeneity in amino acid composition across sites and taxa and that no routinely used evolutionary model can adequately describe both forms of heterogeneity. We show that data-recoding methods [13-15] reduce compositional heterogeneity in these datasets and that models accommodating site-specific amino acid preferences can better describe the recoded datasets. Increased model adequacy is associated with significant topological changes in support of Porifera-sister. Because adequate modeling of the evolutionary process that generated the data is fundamental to recovering an accurate phylogeny [16-20], our results strongly support sponges as the sister group of all other animals and provide further evidence that Ctenophora-sister represents a tree reconstruction artifact. VIDEO ABSTRACT.

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          Author and article information

          Journal
          Curr. Biol.
          Current biology : CB
          Elsevier BV
          1879-0445
          0960-9822
          Dec 18 2017
          : 27
          : 24
          Affiliations
          [1 ] Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
          [2 ] Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.
          [3 ] Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
          [4 ] Centre de Théorisation et de Modélisation de la Biodiversité, Station d'Ecologie Théorique et Expérimentale, CNRS, UMR 5321, Moulis 09200, France; Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montréal, QC H3C 3J7, Canada.
          [5 ] Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy.
          [6 ] Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Lyon, France.
          [7 ] Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany; SNSB, Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany. Electronic address: woerheide@lmu.de.
          [8 ] School of Biological Sciences and School of Earth Sciences, University of Bristol, Bristol, UK. Electronic address: davide.pisani@bristol.ac.uk.
          Article
          S0960-9822(17)31453-7
          10.1016/j.cub.2017.11.008
          29199080
          6cb74cae-2ccd-4de9-9e5c-75f756bc8975
          History

          posterior predictive tests,compositional heterogeneity,data recoding,phylogenomics,Metazoa

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