title: Genomic data do not support comb jellies as the sister group to all other animals.
abstract: Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the "Ctenophora-sister" hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data.
authors.affiliation: School of Earth Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom; School of Biological Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom; davide.pisani@bristol.ac.uk woerheide@lmu.de.
authors.forename: Davide
authors.initials: D
authors.lastname: Pisani
authors.affiliation: Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, 69622 Villeurbanne cedex, France;
authors.forename: Walker
authors.initials: W
authors.lastname: Pett
authors.affiliation: Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany;
authors.forename: Martin
authors.initials: M
authors.lastname: Dohrmann
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;
authors.forename: Roberto
authors.initials: R
authors.lastname: Feuda
authors.affiliation: Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige 38010, Italy;
authors.forename: Omar
authors.initials: O
authors.lastname: Rota-Stabelli
authors.affiliation: Centre for Biodiversity Theory and Modelling, USR CNRS 2936, Station d'Ecologie Expérimentale du CNRS, Moulis 09200, France; Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montreal, QC, Canada H3C 3J7;
authors.forename: Hervé
authors.initials: H
authors.lastname: Philippe
authors.affiliation: Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, 69622 Villeurbanne cedex, France;
authors.forename: Nicolas
authors.initials: N
authors.lastname: Lartillot
authors.affiliation: Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany; Bayerische Staatssammlung für Paläontologie und Geologie, Munich 80333, Germany davide.pisani@bristol.ac.uk woerheide@lmu.de.
authors.forename: Gert
authors.initials: G
authors.lastname: Wörheide
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D015982:Bias; D037302:Ctenophora / Q000145:classification* / Q000235:genetics*; D030541:Databases, Genetic; D016678:Genome; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D015203:Reproducibility of Results; D012641:Selection, Genetic
keywords: Ctenophora; Metazoa; Porifera; evolution; phylogenomics