Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oyster (Crassostrea gigas) populations revealed by genome-wide SNP data

Cultivated bivalves are hugely important not only because of their economic value, but also due to their impacts on natural ecosystems. The Pacific oyster (Crassostrea gigas) is the world's most heavily cultivated shellfish species and has been introduced to all continents except Antarctica for aquaculture. We therefore used a medium density single nucleotide polymorphism (SNP) array to investigate the genetic structure of this species in Europe, where it was introduced during the 1960s and has since become a prolific invader of coastal ecosystems across the continent. We analyzed 21,499 polymorphic SNPs in 232 individuals from 23 localities spanning a latitudinal cline from Portugal to Norway and including the source populations of Japan and Canada. We confirmed the results of previous studies by finding clear support for a southern and a northern group, with the former being indistinguishable from the source populations indicating the absence of a pronounced founder effect. We furthermore conducted a large-scale comparison of wild and hatchery populations to reveal substantial genetic differences including significantly higher levels of inbreeding in some but not all of the hatchery populations. These findings were confirmed by a smaller but representative SNP dataset generated using restriction site associated DNA sequencing. We therefore conclude that genomic approaches can generate increasingly detailed insights into the genetics of invasive populations, while also providing a novel window on how hatchery propagation may influence inbreeding, with important economic and management implications.

养殖双壳类不仅具有极高的经济价值，同时对自然生态系统也有着重要影响。太平洋牡蛎（Crassostrea gigas）是全球养殖规模最大的贝类物种，已被引入除南极洲以外的所有大陆用于水产养殖。该物种于20世纪60年代被引入欧洲，随后已成为欧洲沿岸生态系统中极具入侵性的物种，为此我们采用中等密度单核苷酸多态性（SNP）芯片，对该物种在欧洲的遗传结构展开研究。我们对覆盖从葡萄牙到挪威的纬度梯度、共23个采样点的232个个体进行了分析，共检测到21499个多态性SNP位点，同时纳入了日本和加拿大的源种群作为对照。我们的研究结果验证了既往研究结论：明确存在南部和北部两个类群，其中南部类群与源种群无显著遗传分化，表明该物种未出现显著的奠基者效应。此外，我们还对野生种群与孵化场种群开展了大规模比对，揭示了二者间显著的遗传差异：部分（而非全部）孵化场种群的近交水平显著更高。通过采用限制性酶切位点相关DNA测序技术生成的小型但具有代表性的SNP数据集，我们进一步验证了上述研究结果。综上，我们认为基因组学方法能够为入侵种群的遗传学研究提供愈发精细的认知，同时也为解析孵化繁育如何影响近交水平提供了新视角，该研究具有重要的经济与管理应用价值。