Data from: Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals.

Discrepancies between morphology-based taxonomy and phylogenetic
systematics are common in Scleractinian corals. In Pocillopora corals,
nine recently identified genetic lineages disagree fundamentally with the
17 recognized Pocillopora species, including 5 major Indo-Pacific
reef-builders. Pocillopora corals hybridize in the Tropical Eastern
Pacific, so it is possible that some of the disagreement between the
genetics and taxonomy may be due to introgressive hybridization. Here we
used 6769 genome-wide SNPs from Restriction-site Associated DNA sequencing
(RAD-Seq) to conduct phylogenomic comparisons among three common,
Indo-Pacific Pocillopora species - P.'damicornis, P. eydouxi and P.
elegans - within and between populations in the Tropical Eastern Pacific
(TEP) and the Central Pacific. Genome-wide RAD-Seq comparisons of Central
and TEP Pocillopora confirm that the morphospecies P.'damicornis, P.
eydouxi and P. elegans are not monophyletic, but instead fall into three
distinct genetic groups. However, hybrid samples shared fixed alleles with
their respective parental species and, even without strict monophyly, P.
damicornis share a common set of 33 species- specific alleles across the
Pacific. RAD-Seq data confirm the pattern of one-way introgressive
hybridization among TEP Pocillopora, suggesting that introgression may
play a role in generating shared, polyphyletic lineages among currently
recognized Pocillopora species. Levels of population differentiation
within genetic lineages indicate significantly higher levels of population
differentiation in the Tropical Eastern Pacific than in the Central West
Pacific.