Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

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1 James Cook University, Australian Research Council Centre of Excellence for Coral Reef Studies, Townsville 4810, QLD, Australia
2 Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
3 Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil
4 Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
5 James Cook University, Australian Research Council Centre of Excellence for Coral Reef Studies, Townsville 4811, QLD, Australia
6 Research School of Biology, Australian National University, Canberra 2601, ACT, Australia
DOI
10.7287/peerj.preprints.2151v1
Published
Accepted
Subject Areas
Evolutionary Studies, Taxonomy, Zoology
Keywords
Anthozoa, Corallimorpharia, Phylogenomics, Scleractinia, Corals
Copyright
© 2016 Lin et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Lin MF, Chou WH, Kitahara MV, Chen CLA, Miller DJ, Foret S. 2016. Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses. PeerJ Preprints 4:e2151v1

Abstract

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

Annotations of the protein coding genes used in this study

DOI: 10.7287/peerj.preprints.2151v1/supp-1

Best fitting amino-acid substitution models for the partitions

Best fitting amino-acid substitution models for the partitions inferred by partition finder.

DOI: 10.7287/peerj.preprints.2151v1/supp-2