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, 10 (10), e0139068
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Phylogenomic Analyses Support Traditional Relationships Within Cnidaria

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Phylogenomic Analyses Support Traditional Relationships Within Cnidaria

Felipe Zapata et al. PLoS One.

Abstract

Cnidaria, the sister group to Bilateria, is a highly diverse group of animals in terms of morphology, lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. Phylogenetic analyses using different partition schemes and models of molecular evolution, as well as topology tests for alternative phylogenetic relationships, support the monophyly of Medusozoa, Anthozoa, Octocorallia, Hydrozoa, and a clade consisting of Staurozoa, Cubozoa, and Scyphozoa. Support for the monophyly of Hexacorallia is weak due to the equivocal position of Ceriantharia. Taken together, these results further resolve deep cnidarian relationships, largely support traditional phylogenetic views on relationships, and provide a historical framework for studying the evolutionary processes involved in one of the most ancient animal radiations.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Photographs of cnidarian representatives.
The color of the boxes corresponds to the color of clades in the results and supplemental figures. (A) Scyphozoa, Pelagiidae: Chrysaora quinquecirrha. (B) Scyphozoa, Cepheidae: Cephea cephea. (C) Scyphozoa, Pelagiidae: Pelagia noctiluca. (D) Hydrozoa, Trachylinae: Crossota millsae. (E) Hydrozoa, Siphonophora: Physalia physalis. (F) Hydrozoa, Filifera: Podocoryna carnea. (G) Hydrozoa, Filifera: Hydractinia. (H) Cubozoa: Copula sivickisi. (I) Staurozoa: Haliclystus californiensis. (J) Octocorallia, Clavulariidae: Clavularia sp. (K) Octocorallia, Pennatulidae: Pennatula sp. (L) Octocorallia, Gorgoniidae: Gorgonia ventalina. (M) Hexacorallia, Poritidae: Porites sp. (N) Hexacorallia, Dendrophylliidae: Tubastrea faulkneri. (O) Hexacorallia, Stichodactylidae: Heteractis magnifica. Photo credits: S. Siebert (A-D), P. Cartwright (F), A. Collins (H-I), and C. Dunn (E, G, J-N).
Fig 2
Fig 2. Alternative hypotheses for internal relationships within Cnidaria.
(A) Traditional classification and relationships within Cnidaria. (B) Anthozoa paraphyletic with Octocorallia sister to Medusozoa [8]. (C) Hexacorallia paraphyletic with Ceriantharia sister to Hexacorallia + Octocorallia clade [17]. (D) Staurozoa as the sister taxon to the rest of Medusozoa [7]. The color of the branches corresponds to the color of clades in the results and supplemental figures.
Fig 3
Fig 3. The 50% gene occupancy matrix.
Black indicates sampled genes for each of the 41 taxa. Genes and species are sorted by sampling, with the best sampled in the upper left. The last three taxa, Calibelemnon francei, Craspedacusta sowerbii, and Obelia longissima, had less than 5% gene occupancy and were excluded from further analyses to produce matrix 1.
Fig 4
Fig 4. Rooted phylogram of the maximum likelihood (ML) analysis.
Branch support values correspond to percent ML-bootstrap values/percent Bayesian posterior probabilities. No values are shown for branches with 100/100 support. The areas of the lollipops, at the branch tips, are proportional to the number of genes sampled. Illustrations (by F. Goetz) are provided for select species, as indicated by lead lines.

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Publication types

Grant support

This project was supported by the National Science Foundation (http://www.nsf.gov) Cnidarian Tree of Life Project (DEB 05-31799 to PC and AGC), National Science Foundation DEB-0953571 to PC and the National Science Foundation Alan T Waterman Award to CWD. Sequencing at the Brown Genomics Core facility was supported in part by National Institutes of Health (http://www.nih.gov) P30RR031153 and National Science Foundation EPSCoR EPS-1004057. Data transfer was supported by National Science Foundation RII-C2 EPS-1005789. Analyses were conducted with computational resources and services at the Center for Computation and Visualization at Brown University, supported in part by the National Science Foundation EPSCoR EPS-1004057 and the State of Rhode Island. Cubozoan samples were collected by CLA thanks to research funds from a Smithsonian Peter Buck Fellowship and Iridian Genomes Inc. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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