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，精准解析该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。本研究以245尾具有重要经济价值的海扇贝（*Placopecten magellanicus*）为对象，对其进行基因分型后，通过限制性酶切位点相关DNA测序（restriction site-associated DNA sequencing, RADseq）获得7163个单核苷酸多态性位点（Single Nucleotide Polymorphism, SNP，后文简称SNPs），以此探究海洋环境变化与此前已报道的纬度梯度基因组渐变之间的相关性。海扇贝的分布纬度跨度超过10°，本研究推测气候变异可显著驱动等位基因频率的渐变趋势。借助涵盖温度、盐度、叶绿素a及营养盐浓度的大型环境数据集，本研究筛选出285~621个（因分析方法与环境数据集而异）与环境变异显著相关、可能受选择作用的SNPs。对不同离群SNPs与环境数据集开展主成分分析（Principal Components Analysis, PCA），结果显示南北聚类模式高度一致，且二者的第一主成分轴间存在显著关联（校正决定系数adjusted R-squared=0.66~0.79）。对离群SNPs与环境主成分开展多变量冗余分析，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，冬季海洋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。本研究证实，海洋环境变化与该物种已观测到的基因组渐变存在关联，且季节性极端低温可能限制这类海洋底栖双壳类物种沿纬度梯度的基因流。将该研究发现纳入管理体系，可提升渔业管理策略与未来预测的准确性。