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. 23 Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the 24 evolutionary relationship between these two groups is key to understanding the evolution of 25 calcification in the coral lineage. One pivotal question is whether scleractinians are a 26 monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals 27 that have lost their ability to calcify, as is implied by the "naked-coral" hypothesis. Despite 28 major efforts, relationships between scleractinians and corallimorpharians remain equivocal and 29 controversial. Although the complete mitochondrial genomes of a range of scleractinians and 30 corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates 31 means that mitochondrial sequences are insufficient to understand the relationship between these 32 two groups. To overcome these limitations, transcriptome data were generated for three 33 representative corallimorpharians. These were used in combination with sequences available for 34 a representative range of scleractinians to identify 291 orthologous single copy protein-coding 35 nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any 50 group. This lack of understanding limits our ability to predict how corals, and therefore the 51 diverse habitats that they support, will respond to climate change and oce...

Universal target‐enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long‐standing problems

“…The “naked coral hypothesis” was thus proposed, suggesting that corallimorpharians arose from a scleractinian ancestor that had undergone skeletal loss during paleoclimate conditions when the oceans experienced increased CO 2 concentrations (Medina et al., ). Since that study, other studies based on transcriptomic data (Lin et al., ), rDNA (Fukami et al., ), and mitochondrial data (Fukami et al., ; Kayal et al., ; Kitahara et al., ; Park et al., ) recovered a monophyletic Scleractinia with corallimorpharians as the sister clade. Our results also recovered a monophyletic Scleractinia, thus supporting the conclusions of others that corallimorpharians are not naked corals.…”

“…Our results demonstrate the utility of the target‐capture enrichment approach for inferring phylogenomic relationships in the class Anthozoa. To date, a few studies based on transcriptomic data have recovered well‐supported phylogenomic relationships within Anthozoa, but these studies were based on only a handful (≤15) of taxa (Lin et al., ; Pratlong et al., ; Zapata et al., ) and were limited in scope. In general, phylogenomic studies based on transcriptomic data have provided well‐supported and well‐resolved phylogenies based on 100s to 1,000s of orthologs (Dunn et al., ; Kocot et al., ; Zapata et al., ).…”