New paper: An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives

Graphical Abstract

Congratulations to Peter Cowman and co-authors for a paper just accepted in Molecular Phylogenetics and Evolution.

The paper presents a molecular approach that has the potential to provide species level resolution with the Genus Acropora – the Holy Grail for Acropora taxonomy. The results of the phylogenomic analysis are profound (see quote below) and highlight the need for a systematic revision of the genus Acropora. In particular, the results suggests that there are up to 3-times more Acropora species than currently accepted due to lots of undescribed species and lots of incorrect synonymies. These are indeed exciting time to be a coral taxonomist!

“…over half the acroporid specimens (32) could not be linked to the type material of any of the 408 nominal species in the genus and are therefore likely to represent undescribed species. Furthermore, many of our specimens matched the type material of a number of nominal species that had previously been synonymised (e.g. A. bifurcata, A. convexa, A. orbicularis), suggesting that many of the synonymies were inappropriate. This suggests that the species richness of the genus is potentially much higher than indicated in the latest revision (Wallace et al. 2012)). A thorough taxonomic revision requires that all the nominal species be re-examined through the collection of topotypes and quantitative morphological comparisons with the relevant type material.”

Peter F. Cowman, Andrea M. Quattrini, Thomas C.L. Bridge, Gregory J. Watkins-Colwell, Nur Fadli, Mila Grinblat, Thomas E. Roberts, Catherine S. McFadden, David J. Miller, Andrew H. Baird. An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives. Mol Phylogen Evol


The Targeted enrichment of genomic DNA can profoundly increase the phylogenetic resolution of clades and inform taxonomy. Here, we redesign a custom bait set previously developed for the cnidarian class Anthozoa to more efficiently target and capture ultraconserved elements (UCEs) and exonic loci within the subclass Hexacorallia. We test this enhanced bait set (targeting 2,476 loci) on 99 specimens of scleractinian corals spanning both the “complex” (Acroporidae, Agariciidae) and “robust” (Fungiidae) clades. Focused sampling in the staghorn corals (genus Acropora) highlights the ability of sequence capture to inform the taxonomy of a clade previously deficient in molecular resolution. A mean of 1850 (± 298) loci were captured per taxon (955 UCEs, 894 exons), and a 75% complete concatenated alignment of 96 samples included 1792 loci (991 UCE, 801 exons) and ∼1.87 million base pairs. Maximum likelihood and Bayesian analyses recovered robust molecular relationships and revealed that species-level relationships within the Acropora are incongruent with traditional morphological groupings. Both UCE and exon datasets delineated six well-supported clades within Acropora. The enhanced bait set will facilitate investigations of the evolutionary history of many important groups of reef corals, particularly where previous molecular marker development has been unsuccessful.

Other literature cited

Wallace C.C., Done B.J., Muir P.R. (2012) Revision and catalogue of worldwide staghorn corals Acropora and Isopora (Scleractinia: Acroporidae) in the Museum of Tropical Queensland. Mem Queensl Mus 57:1-255

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