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

Cowman, Peter F., Quattrini, Andrea M., Bridge, Tom C.L., Watkins-Colwell, Gregory J., Fadli, Nur, Grinblat, Mila, Roberts, T. Edward, McFadden, Catherine S., Miller, David J., and Baird, Andrew H. (2020) An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives. Molecular Phylogenetics and Evolution, 153. 106944.

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Abstract

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 2476 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 Glade 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 similar to 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.

Item ID: 64944
Item Type: Article (Research - C1)
ISSN: 1095-9513
Keywords: Scleractinia, Targeted enrichment, Ultraconserved elements, UCEs, Exon, Phylogenetics
Copyright Information: © 2020 Elsevier Inc. All rights reserved.
Funders: Australian Research Council (ARC) Discovery Early Career Researcher Award (DECRA), National Science Foundation (NSF)
Projects and Grants: ARC DECRA Fellowship DE170100516, ARC DECRA Fellowship DE180100746, ARC Centre of Excellence Programme CE140100020, NSF-DEB #1457817
Date Deposited: 04 Nov 2020 07:36
FoR Codes: 31 BIOLOGICAL SCIENCES > 3103 Ecology > 310305 Marine and estuarine ecology (incl. marine ichthyology) @ 100%
SEO Codes: 18 ENVIRONMENTAL MANAGEMENT > 1805 Marine systems and management > 180504 Marine biodiversity @ 100%
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