title: Corallimorpharians are not "naked corals": insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses.
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.
authors.affiliation: Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia; Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, Australia.
authors.forename: Mei Fang
authors.initials: MF
authors.lastname: Lin
authors.affiliation: Biodiversity Research Center, Academia Sinica , Taipei , Taiwan.
authors.forename: Wen Hwa
authors.initials: WH
authors.lastname: Chou
authors.affiliation: Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil; Centro de Biologia Marinha, Universidade Federal de São Paulo, São Sebastião, São Paulo, Brazil.
authors.forename: Marcelo V
authors.initials: MV
authors.lastname: Kitahara
authors.affiliation: Biodiversity Research Center, Academia Sinica , Taipei , Taiwan.
authors.forename: Chao Lun Allen
authors.initials: CL
authors.lastname: Chen
authors.affiliation: Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia; Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, Australia.
authors.forename: David John
authors.initials: DJ
authors.lastname: Miller
authors.affiliation: Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia; Research School of Biology, Australian National University, Canberra, ACT, Australia.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Forêt
keywords: Anthozoa; Corallimorpharia; Corals; Phylogenomics; Scleractinia