Data from: Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments

Chilean mussel populations have been thought to be panmictic with limited genetic structure. Genotyping-by-sequencing approaches have enabled investigation of genome-wide variation that may better distinguish populations that have evolved in different environments. We investigated neutral and adaptive genetic variation in Mytilus from six locations in southern Chile with 1,240 SNP obtained with RAD-seq. Differentiation among locations with 891 neutral SNPs was low (FST = 0.005). Higher differentiation was obtained with a panel of 58 putative outlier SNPs (FST = 0.114) indicating the potential for local adaptation. This panel identified clusters of genetically related individuals and demonstrated that much of the differentiation (~92%) could be attributed to the three major regions and environments: extreme conditions in Patagonia, inner bay influenced by aquaculture (Reloncaví́), and outer bay (Chiloé Island). Patagonia samples were most distinct, but additional analysis carried out excluding this collection also revealed adaptive divergence between inner and outer bay samples. The four locations within Reloncaví́ area were most similar with all panels of markers, likely due to similar environments, high gene flow by aquaculture practices and low geographic distance. However, fine scale structure could be detected when analyses included only this zone. Our results and the SNP markers developed will be a powerful tool supporting management and programs of this harvested species.

智利贻贝种群长期以来被认为是泛交（panmictic）种群，仅存在有限的遗传结构。基于测序的基因分型技术（Genotyping-by-sequencing）得以让研究者探究全基因组变异，从而更精准地区分在不同环境下演化的种群。本研究利用限制性位点相关DNA测序（RAD-seq）获得的1240个单核苷酸多态性（SNP）标记，对智利南部6个采样点的贻贝属（Mytilus）物种的中性遗传变异与适应性遗传变异展开了分析。基于891个中性SNP标记计算得到的种群间分化程度较低（固定指数FST=0.005）。而采用包含58个候选异常位点SNP的标记组进行分析时，得到了更高的种群分化程度（FST=0.114），这表明该物种存在局部适应的潜力。该标记组成功鉴定出遗传亲缘关系相近的个体集群，并证实绝大多数种群分化（约92%）可归因于三大主要区域及其对应的环境特征：巴塔哥尼亚的极端环境、受水产养殖影响的内湾（Reloncaví）以及外湾（奇洛埃岛）。巴塔哥尼亚的采样样本分化程度最高，但在剔除该区域样本后开展的补充分析同样揭示了内湾与外湾样本间的适应性分化。Reloncaví区域内的4个采样点在所有标记组下的遗传相似性均最高，这可能源于其环境相似、水产养殖活动带来的高基因流以及地理距离较近。但当仅针对该区域开展分析时，仍可检测到精细的种群遗传结构。本研究的结果与开发的SNP标记将成为支持该经济贻贝物种管理与保护计划的有力工具。