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

Feuda, Roberto and Dohrmann, Martin and Pett, Walker and Philippe, Hervé and Rota-Stabelli, Omar and Lartillot, Nicolas and Wörheide, Gert and Pisani, Davide (2017) Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals. Current Biology, 27 (24). pp. 3864-3870. ISSN 0960-9822. http://resolver.caltech.edu/CaltechAUTHORS:20171201-151524053

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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; 2; 3; 4 ; 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; 9; 10 ; 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; 14 ; 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; 17; 18; 19 ; 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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1016/j.cub.2017.11.008DOIArticle
http://www.sciencedirect.com/science/article/pii/S0960982217314537PublisherArticle
Additional Information:© 2017 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Received 21 June 2017, Revised 19 September 2017, Accepted 2 November 2017, Available online 30 November 2017. Published: November 30, 2017. We would like to thank the University of Bristol ACRC (Advanced Computing Research Center) and Leibniz-Rechenzentrum der Bayerischen Akademie der Wissenschaften for providing access to supercomputing infrastructure. This work was supported by a NERC grant (NE/P013643/1) and a Templeton Foundation grant (ID 60579) to D.P. H.P. acknowledges the French Laboratory of Excellence project “TULIP” (ANR-10-LABX-41 and ANR-11-IDEX-0002-02). N.L. acknowledges French National Research Agency grant no. ANR-10-BINF-01-01 “Ancestrome.” G.W. acknowledges funding by LMU Munich’s Institutional Strategy LMU excellent within the framework of the German Excellence Initiative and German Research Foundation (DFG) grant no. Wo896/15-1. The authors would like to thank the reviewers for their helpful suggestions. Author Contributions: Conceptualization, D.P., G.W., R.F., and O.R.-S.; Methodology, D.P., O.R.-S., W.P., N.L., and H.P.; Software, W.P. and N.L.; Validation, W.P., R.F., M.D., D.P., and G.W.; Investigation, R.F., D.P., G.W., and H.P.; Writing – Original Draft, R.F., M.D., D.P., and G.W.; Writing – Review & Editing, M.D., R.F., D.P., G.W., W.P., N.L., H.P., and O.R.-S.; Visualization, R.F.; Supervision, D.P. and G.W.; Funding Acquisition, D.P., G.W., N.L., and H.P.
Funders:
Funding AgencyGrant Number
Natural Environment Research Council (NERC)NE/P013643/1
Templeton Foundation60579
Agence Nationale pour la Recherche (ANR)ANR-10-LABX-41
Agence Nationale pour la Recherche (ANR)ANR-11-IDEX-0002-02
Agence Nationale pour la Recherche (ANR)ANR-10-BINF-01-01
Deutsche Forschungsgemeinschaft (DFG)Wo896/15-1
Subject Keywords:Metazoa; phylogenomics; compositional heterogeneity; data recoding; posterior predictive tests
Record Number:CaltechAUTHORS:20171201-151524053
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20171201-151524053
Official Citation:Roberto Feuda, Martin Dohrmann, Walker Pett, Hervé Philippe, Omar Rota-Stabelli, Nicolas Lartillot, Gert Wörheide, Davide Pisani, Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals, Current Biology, Volume 27, Issue 24, 18 December 2017, Pages 3864-3870.e4, ISSN 0960-9822, https://doi.org/10.1016/j.cub.2017.11.008. (https://www.sciencedirect.com/science/article/pii/S0960982217314537)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:83635
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:02 Dec 2017 04:45
Last Modified:04 Jan 2018 18:50

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