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.基于形态学的分类系统与系统发育分类学之间的分歧在石珊瑚（Scleractinian corals）中颇为常见。 在杯形珊瑚属（Pocillopora）珊瑚中，新近鉴定出的9个遗传支系与目前公认的17个杯形珊瑚属物种存在根本性冲突，其中涵盖5个主要的印度-太平洋造礁物种。 杯形珊瑚在东热带太平洋（Tropical Eastern Pacific, TEP）区域存在杂交现象，因此遗传学与分类学之间的部分分歧可能源于渐渗杂交（introgressive hybridization）。 本研究利用来自限制性酶切位点相关DNA测序（Restriction-site Associated DNA sequencing, RAD-Seq）的6769个全基因组单核苷酸多态性（genome-wide SNPs）位点，针对东热带太平洋与中太平洋区域内的种群以及两大区域间种群中的3种常见印度-太平洋杯形珊瑚物种——P. damicornis、P. eydouxi和P. elegans——开展系统基因组学比较。 对中太平洋与东热带太平洋杯形珊瑚的全基因组RAD-Seq比较结果证实，形态种P. damicornis、P. eydouxi和P. elegans并非单系类群，而是分别归入3个独立的遗传支系。 不过，杂交样本携带与其各自亲本物种共有的固定等位基因；即便不满足严格的单系性要求，P. damicornis仍在整个太平洋范围内共享一套包含33个物种特异性等位基因的基因集。 RAD-Seq数据证实了东热带太平洋杯形珊瑚间存在单向渐渗杂交模式，这表明渐渗作用可能是导致当前公认的杯形珊瑚物种出现共享多系支系的关键诱因之一。 遗传支系内的种群分化水平分析显示，东热带太平洋的种群分化程度显著高于中西太平洋区域。