title: The "naked coral" hypothesis revisited--evidence for and against scleractinian monophyly.
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.
authors.affiliation: Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil; Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo, São Sebastião, São Paulo, Brazil.
authors.forename: Marcelo V
authors.initials: MV
authors.lastname: Kitahara
authors.affiliation: School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia; Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.
authors.forename: Mei-Fang
authors.initials: MF
authors.lastname: Lin
authors.affiliation: ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia; Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Forêt
authors.affiliation: John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.
authors.forename: Gavin
authors.initials: G
authors.lastname: Huttley
authors.affiliation: School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.
authors.forename: David J
authors.initials: DJ
authors.lastname: Miller
authors.affiliation: Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan; Institute of Oceanography, National Taiwan University, Taipei, Taiwan; Taiwan International Graduate Program (TIGP)-Biodiversity, Academia Sinica, Taipei, Taiwan.
authors.forename: Chaolun Allen
authors.initials: CA
authors.lastname: Chen
mesh_terms: D000596:Amino Acids / Q000235:genetics; D000818:Animals; D037421:Anthozoa / Q000145:classification / Q000235:genetics*; D001482:Base Composition / Q000235:genetics; D003062:Codon / Q000235:genetics; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics*; D024101:Mitochondrial Proteins / Q000235:genetics*; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012358:RNA, Transfer, Met / Q000235:genetics; D012364:RNA, Transfer, Trp / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D000596:Amino Acids; D003062:Codon; D004272:DNA, Mitochondrial; D024101:Mitochondrial Proteins; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012358:RNA, Transfer, Met; D012364:RNA, Transfer, Trp; C075526:RNA, ribosomal, 12S
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