Data from: Widespread hybridisation and bi-directional introgression in sympatric species of coral reef fish

Coral reefs are highly diverse ecosystems, where numerous closely related species often co-exist. How new species arise and are maintained in these high gene flow environments have been long-standing conundrums. Hybridisation and patterns of introgression between sympatric species provides a unique insight into the mechanisms of speciation and the maintenance of species boundaries. In this study, we investigate the extent of hybridisation between two closely related species of coral reef fish: the common coral trout (Plectropomus leopardus) and the bar-cheek coral trout (Plectropomus maculatus). Using a complementary set of 25 microsatellite loci, we distinguish pure genotype classes from first- and later-generation hybrids. We provide the first evidence of extensive hybridisation between two co-occurring coral reef species within their common geographic range, identifying 124 interspecific hybrids from a collection of almost three thousand coral trout sampled in the southern Great Barrier Reef. Hybrid individuals were ubiquitous among reefs, fertile and spanned multiple generations. To explore the extent of genomic introgression, we constructed a ddRAD library of pure and hybrid classes, which recovered 2,271 SNP loci. An analysis of genomic clines indicates that genome-wide introgression has occurred with selection favouring both pure and hybrid genotypes. Our results show that hybridisation can occur among closely related species with common geographic ranges, and not just at biogeographic boundaries. We suggest that both evolutionary and ecological processes may act to maintain species barriers despite on-going introgression.

珊瑚礁（Coral reefs）是一类高度多样的生态系统，诸多近缘物种常在此共生。在这类高基因流环境中，新物种如何形成并得以维持，长期以来都是悬而未决的科学难题。同域物种间的杂交（Hybridisation）与基因渐渗（introgression）模式，为解析物种形成机制及物种边界的维持机制提供了独特研究视角。本研究针对两种近缘珊瑚礁鱼类——普通珊瑚鳟（Plectropomus leopardus）与颊斑珊瑚鳟（Plectropomus maculatus）的杂交程度展开探究。研究人员采用一套互补的25个微卫星位点（microsatellite loci），可准确区分纯合基因型类群与第一代及后续世代的杂交个体。本研究首次证实，在两种同域分布珊瑚礁物种的共同分布区内存在广泛的种间杂交：在大堡礁南部采集的近3000尾珊瑚鳟样本中，共鉴定出124尾种间杂交个体。杂交个体广泛分布于各珊瑚礁中，且可育并覆盖多个世代。为探究基因组水平的基因渐渗程度，研究人员构建了纯合类群与杂交类群的双酶切简化基因组文库（ddRAD library），最终获得2271个单核苷酸多态性位点（SNP loci）。基因组梯度分析结果显示，全基因组水平的基因渐渗已发生，且选择同时青睐纯合基因型与杂交基因型。本研究结果表明，近缘物种间的杂交可发生在具有共同分布范围的类群之间，而非仅局限于生物地理交界区域。我们提出，尽管存在持续的基因渐渗，进化与生态过程仍可共同维持物种间的生殖隔离屏障。