Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias

  1. Christopher E Laumer  Is a corresponding author
  2. Harald Gruber-Vodicka
  3. Michael G Hadfield
  4. Vicki B Pearse
  5. Ana Riesgo
  6. John C Marioni
  7. Gonzalo Giribet
  1. Wellcome Trust Sanger Institute, United Kingdom
  2. Max Planck Institute for Marine Microbiology, Germany
  3. University of Hawaii at Manoa, United States
  4. University of California, Santa Cruz, United States
  5. The Natural History Museum, United Kingdom
  6. Harvard University, United States

Abstract

The phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria as seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that support for the Cnidaria+Bilateria clade can be assigned to this source of systematic error. In interpreting these results, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution.

Data availability

SRA accession codes, where used, and all alternative sources for sequence data (e.g. individually hosted websites, personal communications), are listed above in the Materials and Methods section. A DataDryad accession is available at https://doi.org/10.5061/dryad.6cm1166, which makes available all helper scripts, orthogroups, multiple sequence alignments, phylogenetic program output, and raw host proteomes inputted to OrthoFinder. Metagenomic bins containing placozoan host contigs and raw RNA reads used to derive gene annotations from H4, H6 and H11 isolates are also provided in this accession. PhyloBayes .chain files, due to their large size, are separately accessioned at in Zenodo at https://doi.org/10.5281/zenodo.1197272.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Christopher E Laumer

    Wellcome Trust Sanger Institute, Hinxton, United Kingdom
    For correspondence
    claumer@ebi.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8097-8516
  2. Harald Gruber-Vodicka

    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Michael G Hadfield

    Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Vicki B Pearse

    Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Ana Riesgo

    Life Sciences, Invertebrate Division, The Natural History Museum, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. John C Marioni

    Wellcome Trust Sanger Institute, Hinxton, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9092-0852
  7. Gonzalo Giribet

    Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.

Funding

Max-Planck-Institute fuer Marine Microbiologie

  • Harald Gruber-Vodicka

EMBL-European Bioinformatics Institute

  • John C Marioni

Harvard University Faculty of Arts and Sciences

  • Gonzalo Giribet

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Antonis Rokas, Vanderbilt University, United States

Version history

  1. Received: February 27, 2018
  2. Accepted: October 11, 2018
  3. Accepted Manuscript published: October 30, 2018 (version 1)
  4. Version of Record published: December 3, 2018 (version 2)

Copyright

© 2018, Laumer et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Christopher E Laumer
  2. Harald Gruber-Vodicka
  3. Michael G Hadfield
  4. Vicki B Pearse
  5. Ana Riesgo
  6. John C Marioni
  7. Gonzalo Giribet
(2018)
Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias
eLife 7:e36278.
https://doi.org/10.7554/eLife.36278

Share this article

https://doi.org/10.7554/eLife.36278

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