Data from: Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus

Environmental factors can influence diversity and population structure in marine species and accurate understanding of this influence can both improve fisheries management and help predict responses to environmental change. We used 7163 SNPs derived from restriction site-associated DNA sequencing genotyped in 245 individuals of the economically important sea scallop, Placopecten magellanicus, to evaluate the correlations between oceanographic variation and a previously identified latitudinal genomic cline. Sea scallops span a broad latitudinal area (>10 degrees), and we hypothesized that climatic variation significantly drives clinal trends in allele frequency. Using a large environmental dataset, including temperature, salinity, chlorophyll a, and nutrient concentrations, we identified a suite of SNPs (285–621, depending on analysis and environmental dataset) potentially under selection through correlations with environmental variation. Principal components analysis of different outlier SNPs and environmental datasets revealed similar northern and southern clusters, with significant associations between the first axes of each (R2adj = .66–.79). Multivariate redundancy analysis of outlier SNPs and the environmental principal components indicated that environmental factors explained more than 32% of the variance. Similarly, multiple linear regressions and random-forest analysis identified winter average and minimum ocean temperatures as significant parameters in the link between genetic and environmental variation. This work indicates that oceanographic variation is associated with the observed genomic cline in this species and that seasonal periods of extreme cold may restrict gene flow along a latitudinal gradient in this marine benthic bivalve. Incorporating this finding into management may improve accuracy of management strategies and future predictions.

环境因子可影响海洋物种的多样性与种群结构，精准解析此类影响既能优化渔业管理，也有助于预测物种对环境变化的响应。本研究针对经济价值颇高的美洲海扇贝（*Placopecten magellanicus*）的245个个体进行基因分型，利用限制性酶切位点相关DNA测序（Restriction Site-Associated DNA sequencing, RADseq）获得的7163个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点，解析海洋环境变化与此前已报道的纬度梯度基因组渐变群之间的关联。该海扇贝的分布纬度跨度超过10°，本研究假设气候变异可显著驱动等位基因频率的渐变趋势。借助包含温度、盐度、叶绿素a及营养盐浓度在内的大型环境数据集，本研究通过与环境变异的相关性分析，筛选出285至621个（因分析方法与环境数据集而异）潜在受选择的SNP位点。对不同的异常SNP位点与环境数据集进行主成分分析后，得到了相似的南北聚类结果，且两者的第一主成分轴之间存在显著关联（校正R²=0.66~0.79）。针对异常SNP位点与环境主成分进行多变量冗余分析的结果显示，环境因子可解释超过32%的遗传变异。类似地，多元线性回归与随机森林分析均表明，冬季海水平均温度与最低温度是连接遗传变异与环境变异的关键参数。本研究结果证实，海洋环境变化与该物种已观测到的基因组渐变群存在关联，且季节性极端低温可能限制了这种海洋底栖双壳类物种沿纬度梯度的基因流。将该研究发现纳入渔业管理体系，可提升管理策略与未来预测的准确性。