Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias
- Wellcome Trust Sanger Institute, United Kingdom
- Max Planck Institute for Marine Microbiology, Germany
- University of Hawaii at Manoa, United States
- University of California, Santa Cruz, United States
- The Natural History Museum, United Kingdom
- 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.
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Data from: Placozoa and Cnidaria are sister taxaDOI: https://doi.org/10.5061/dryad.6cm1166.
Article and author information
Author details
Christopher E Laumer
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
- Antonis Rokas, Vanderbilt University, United States
Version history
- Received: February 27, 2018
- Accepted: October 11, 2018
- Accepted Manuscript published: October 30, 2018 (version 1)
- 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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Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias
eLife 7:e36278.
https://doi.org/10.7554/eLife.36278
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