Data from: Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus)

Investigating how environmental features shape the genetic structure of populations is crucial for understanding how they are potentially adapted to their habitats, as well as for sound management. In this study, we assessed the relative importance of spatial distribution, ocean currents and sea surface temperature (SST) on patterns of putatively neutral and adaptive genetic variation among American lobster from 19 locations using population differentiation (PD) approaches combined with environmental association (EA) analyses. First, PD approaches (using bayescan, arlequin and outflank) found 28 outlier SNPs putatively under divergent selection and 9770 neutral SNPs in common. Redundancy analysis revealed that spatial distribution, ocean current-mediated larval connectivity and SST explained 31.7% of the neutral genetic differentiation, with ocean currents driving the majority of this relationship (21.0%). After removing the influence of spatial distribution, no SST were significant for putatively neutral genetic variation whereas minimum annual SST still had a significant impact and explained 8.1% of the putatively adaptive genetic variation. Second, EA analyses (using Pearson correlation tests, bayescenv and lfmm) jointly identified seven SNPs as candidates for thermal adaptation. Covariation at these SNPs was assessed with a spatial multivariate analysis that highlighted a significant temperature association, after accounting for the influence of spatial distribution. Among the 505 candidate SNPs detected by at least one of the three approaches, we discovered three polymorphisms located in genes previously shown to play a role in thermal adaptation. Our results have implications for the management of the American lobster and provide a foundation on which to predict how this species will cope with climate change.

探究环境特征如何塑造种群遗传结构，对于理解物种潜在的栖息地适应机制，以及开展科学合理的资源管理均至关重要。本研究结合种群分化（population differentiation, PD）分析与环境关联（environmental association, EA）方法，评估了空间分布、洋流与海表温度（sea surface temperature, SST）对19个采样位点美洲龙虾种群间假定中性与适应性遗传变异模式的相对影响。首先，通过bayescan、arlequin与outflank三种种群分化分析工具，共筛选出28个处于潜在歧化选择下的候选单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs），以及9770个共有中性SNPs。冗余分析结果显示，空间分布、洋流介导的幼体连通性与海表温度可解释31.7%的中性遗传分化，其中洋流贡献了该关联的大部分（21.0%）。在去除空间分布的影响后，海表温度整体对假定中性遗传变异不再具有显著影响，但年最低海表温度仍对假定适应性遗传变异存在显著影响，可解释8.1%的该类变异。其次，通过皮尔逊相关性检验、bayescenv与lfmm三种环境关联分析方法，共联合鉴定出7个温度适应性候选SNPs。通过空间多变量分析对这些SNPs的协同变异进行评估，结果显示在控制空间分布影响后，仍存在显著的温度关联。在至少一种分析方法鉴定出的505个候选SNPs中，我们发现了3个位于此前被证实参与温度适应过程的基因内的多态性位点。本研究结果对美洲龙虾的资源管理具有指导意义，并为预测该物种如何应对气候变化提供了理论基础。