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，对于解析物种潜在适应其栖息环境的机制，以及开展科学合理的种群管理均具有核心意义。本研究以19个采样点的美洲龙虾为研究对象，结合种群分化（Population Differentiation, PD）方法与环境关联（Environmental Association, EA）分析，评估了空间分布、洋流及海表温度（Sea Surface Temperature, SST）对该物种潜在中性与适应性遗传变异模式的相对影响。

首先，采用PD方法（借助Bayescan、Arlequin与OutFLANK三款工具），共筛选出28个潜在受歧化选择的异常单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点，以及9770个共享的中性SNP位点。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共解释了31.7%的中性遗传分化，其中洋流对该关联的贡献最大（占比21.0%）。在去除空间分布的影响后，其余海表温度变量均未对潜在中性遗传变异产生显著影响，但年最低海表温度仍具有显著影响，其可解释8.1%的潜在适应性遗传变异。

其次，EA分析（采用皮尔逊相关检验、BayescanEnv与LFMM三种方法）共同筛选出7个与温度适应相关的候选SNP位点。借助空间多变量分析对这些SNP位点的协变模式进行评估，在控制空间分布的影响后，结果显示其与温度存在显著关联。在三种方法中至少一种检测到的505个候选SNP位点中，我们发现3个多态性位点位于此前被证实与温度适应相关的基因内。

本研究结果对美洲龙虾的种群管理具有重要指导价值，同时为预测该物种如何应对气候变化提供了坚实的理论基础。