The "naked coral" hypothesis revisited: evidence for and against Scleractinian monophyly

Kitahara, Marcelo V., Lin, Mei-Fang, Forêt, Sylvain, Huttley, Gavin, Miller, David J., and Chen, Chaolun Allen (2014) The "naked coral" hypothesis revisited: evidence for and against Scleractinian monophyly. PLoS One, 9 (4). e94774. pp. 1-13.

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Abstract

The relationship between Scleractinia and Corallimorpharia, Orders within Anthozoa distinguished by the presence of an aragonite skeleton in the former, is controversial. Although classically considered distinct groups, some phylogenetic analyses have placed the Corallimorpharia within a larger Scleractinia/Corallimorpharia clade, leading to the suggestion that the Corallimorpharia are "naked corals" that arose via skeleton loss during the Cretaceous from a Scleractinian ancestor. Scleractinian paraphyly is, however, contradicted by a number of recent phylogenetic studies based on mt nucleotide (nt) sequence data. Whereas the "naked coral" hypothesis was based on analysis of the sequences of proteins encoded by a relatively small number of mt genomes, here a much-expanded dataset was used to reinvestigate hexacorallian phylogeny. The initial observation was that, whereas analyses based on nt data support scleractinian monophyly, those based on amino acid (aa) data support the "naked coral" hypothesis, irrespective of the method and with very strong support. To better understand the bases of these contrasting results, the effects of systematic errors were examined. Compared to other hexacorallians, the mt genomes of "Robust" corals have a higher (A+T) content, codon usage is far more constrained, and the proteins that they encode have a markedly higher phenylalanine content, leading us to suggest that mt DNA repair may be impaired in this lineage. Thus the "naked coral" topology could be caused by high levels of saturation in these mitochondrial sequences, long-branch effects or model violations. The equivocal results of these extensive analyses highlight the fundamental problems of basing coral phylogeny on mitochondrial sequence data.

Item ID: 34121
Item Type: Article (Research - C1)
ISSN: 1932-6203
Additional Information:

© 2014 Kitahara et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funders: National Science Council (NSC), Academia Sinica, Australian Research Council (ARC), São Paulo Funding Agency (FAPESP)
Projects and Grants: NSC Thematic grants 2005-2010, FAPESP grant 2012/21583-1
Date Deposited: 16 Jul 2014 09:12
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060499 Genetics not elsewhere classified @ 25%
06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060399 Evolutionary Biology not elsewhere classified @ 25%
06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060309 Phylogeny and Comparative Analysis @ 50%
SEO Codes: 97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 100%
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