New approaches to species delimitation and population structure of corals: two case studies using ultraconserved elements and exons

BioRxiv : the Preprint Server for Biology
K. L. EricksonC. S. McFadden


As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological variation and slowly evolving molecular markers confound species identification. New approaches to species delimitation in corals are needed to overcome these challenges. Here, we test whether target enrichment of ultraconserved elements (UCEs) and exons can be used for delimiting species boundaries and population structure within species of corals by focusing on two octocoral genera, Alcyonium and Sinularia, as exemplary case studies. We designed an updated bait set (29,363 baits) to target-capture 3,040 UCE and exon loci, recovering a mean of 1,910 +/- 168 SD per sample with a mean length of 1,055 +/- 208 bp. Similar numbers of loci were recovered from Sinularia (1,946 +/- 227 SD) and Alcyonium (1,863 +/- 177 SD). Species-level phylogenies were highly supported for both genera. Clustering methods based on filtered SNPs delimited species and populations that are congruent with previous allozyme, DNA barcoding, reproduc...Continue Reading

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