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

Mei Fang Lin,David John Miller,Sylvain Forêt,Chao Lun Allen Chen,Wen Hwa Chou,Marcelo V Kitahara

doi:10.7717/peerj.2463

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.

Highlights

Scleractinian corals are the subject of intense scientific, public and, media interest, because of the uncertain fate of coral reefs in the face of ever increasing anthropogenic challenges (Done, 1999; Hughes, 2003; Hughes et al, 2003)
Molecular clock estimates calibrated using the earliest fossils that can be unambiguously assigned to extant clades, and whose unique skeletal characters can be unequivocally recognized in fossil coralla, imply that the scleractinian corals originated from a non-skeletonized ancestor in the Ordovician (Stolarski et al, 2011)
The data matrix for the 15 taxa (Table S1) comprised 291 nuclear protein-coding genes, 263 of which have functional annotations, the other 28 coding for unknown proteins (Table S5) that probably correspond to cnidarian- or anthozoan-specific genes

Summary

Introduction

Scleractinian corals are the subject of intense scientific, public and, media interest, because of the uncertain fate of coral reefs in the face of ever increasing anthropogenic challenges (Done, 1999; Hughes, 2003; Hughes et al, 2003). Consistent with this hypothesis, the Scleractinia were paraphyletic in molecular phylogenetic analyses based on amino acid (aa) sequence data from mitochondrial protein-coding genes (Medina et al, 2006).

Results

Conclusion