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.

The New Systematics of Scleractinia: Integrating Molecular and Morphological Evidence

“…The 28S rDNA (Chen et al 1995;Cuif et al 2003), 16S rDNA Palumbi 1996, 1997;Le Goff-Vitry et al 2004;Kitahara et al 2010a), 12S rDNA (Chen et al 2002), combined 16S rDNA and 28S rDNA (Romano and Cairns 2000), combined cytochrome b and COI, as well as β-tubulin (Fukami et al 2008) all support the split between the "complex" and "robust" clades. The sister relationship between the "basal" clade and the rest of Scleractinia has been recovered by 12S rDNA, COI, 28S rDNA (Kitahara et al 2010b;Stolarski et al 2011), and most other mitochondrial loci (Huang 2012;Huang andRoy 2013, 2015;Kitahara et al 2014;Lin et al 2014). To date, no morphological characters associated with the hard skeleton have been found to correlate directly with the molecular splits.…”

“…Like its new confamilials, Alveopora possesses synapticulothecal walls (Wallace 2012). Its exact phylogenetic placement is unstable to date, although evidence has pointed to a close relationship with Astreopora (Fukami et al 2008;Kitahara et al 2010bKitahara et al , 2014Huang and Roy 2015;Kitano et al 2014; Fig. 4.1).…”

“…Stony corals belonging to the order Scleractinia (Anthozoa: Hexacorallia) are a clade of cnidarians that build a calcium carbonate skeleton in the form of aragonite, and are sister group to the non-stony corallimorpharians (Daly et al 2003;Fukami et al 2008;Kitahara et al 2014;Lin et al 2014). At present, Scleractinia contains 31 families, about 240 genera, and over 1,500 species (Cairns 1999(Cairns , 2009Appeltans et al 2012;Huang and Roy 2015), including both zooxanthellate-hosting the symbiotic dinoflagallate Symbiodiniumand azooxanthellate corals.…”

Mitochondrial Genome Rearrangements in the Scleractinia/Corallimorpharia Complex: Implications for Coral Phylogeny

“…1.—Alternative phylogenetic hypotheses for relationships between Scleractinia and Corallimorpharia based on mt genome nucleotide sequences ( A ) or the amino acid sequences of the proteins that they encode ( B ). The trees were modified from Kitahara et al (2014). Note that, for both ( A ) and ( B ) scenarios, support for the node separating Corallimorpharia from Scleractinia (the root of the gray part of the tree) was over 97% under both maximum-likelihood analysis and Bayesian inference.…”

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

“…Fukami & Knowlton 2005; Kitahara et al 2014). However, no such compositional biases appear 232 to hold for nuclear protein-coding genes, implying that these nuclear sequences are more 233 appropriate sources of phylogenetic information than mitochondrial data ).…”