Data from: Genetic subdivision and candidate genes under selection in North American gray wolves

Previous genetic studies of the highly mobile gray wolf (Canis lupus) found population structure that coincides with habitat and phenotype differences. We hypothesized that these ecologically distinct populations (ecotypes) should exhibit signatures of selection in genes related to morphology, coat color, and metabolism. To test these predictions, we quantified population structure related to habitat using a genotyping array to assess variation in 42,036 SNPs in 111 North American gray wolves. Using these SNP data and individual-level measurements of 12 environmental variables, we identified six ecotypes: West Forest, Boreal Forest, Arctic, High Arctic, British Columbia, and Atlantic Forest. Next, we explored signals of selection across these wolf ecotypes through the use of three complementary methods to detect selection: FST/XP-EHH bivariate percentile, BayeScan, and environmentally correlated directional selection with Bayenv. Across all methods, we found consistent signals of selection on genes related to morphology, coat coloration, metabolism, as predicted, as well as vision and hearing. In several high-ranking candidate genes, including LEPR, TYR, and SLC14A2, we found marked clines in allele frequencies that follow environmental changes in temperature and precipitation, a result that is consistent with local adaptation rather than genetic drift. Our findings show that local adaptation can occur despite gene flow in a highly mobile species and can be detected through a moderately dense genomic scan. These patterns of local adaptation revealed by SNP genotyping likely reflect high fidelity to natal habitats of dispersing wolves, strong ecological divergence among habitats, and moderate levels of linkage in the wolf genome.

此前针对高流动性灰狼（Canis lupus）的遗传学研究发现，其种群结构与栖息地及表型差异相契合。我们据此推测，这些生态特征迥异的种群（生态型，ecotypes）应在与形态、毛色及代谢相关的基因中呈现选择信号。为验证上述推测，我们通过基因分型芯片对111只北美灰狼的42036个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）位点变异进行检测，以此量化与栖息地相关的种群结构。结合上述SNP数据与12项环境变量的个体水平测量值，我们共鉴定出6类灰狼生态型：西部森林（West Forest）、北方森林（Boreal Forest）、北极（Arctic）、高北极（High Arctic）、不列颠哥伦比亚（British Columbia）与大西洋森林（Atlantic Forest）。随后，我们采用三种互补的选择检测方法，对这些灰狼生态型的选择信号展开分析：FST/XP-EHH双变量百分位法、BayeScan软件，以及基于Bayenv的环境关联定向选择分析。经所有方法检测，我们发现与形态、毛色、代谢相关的基因均呈现出预期的一致性选择信号，此外与视觉和听觉相关的基因亦存在此类信号。在多个排名靠前的候选基因（如LEPR、TYR与SLC14A2）中，我们发现等位基因频率存在显著的梯度变化，且该变化与温度和降水的环境变化相契合，这一结果符合局部适应而非遗传漂变的特征。本研究结果表明，即便在具有高流动性的物种种群中，局部适应仍可在基因流存在的情况下发生，且可通过中等密度的基因组扫描予以检测。本次通过SNP基因分型揭示的局部适应模式，大概率反映了扩散灰狼对出生地栖息地的高度忠实性、不同栖息地间强烈的生态分化，以及灰狼基因组中中等程度的连锁水平。