Data from: Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish

Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated to lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated to inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated to inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat-stress and immune responses. Outcomes of gene-temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene-environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.

解析栖息于异质环境的种群长期适应背后的歧化选择基因组特征，是进化生物学的核心研究目标之一。本研究以加拿大魁北克省的31个湖红点鲑（*Salvelinus namaycush*）种群（总样本量n=673）为研究对象，利用7192个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）位点，对其中的中性、适应性与有害遗传变异展开分析。研究结果显示，种群平均遗传多样性水平偏低，且湖泊间的遗传共享程度较弱，同时与湖泊面积呈正相关，这表明湖泊隔离后遗传漂变在种群遗传结构塑造中发挥了主导作用。推定有害突变的平均频率低于其余SNP位点，且各群体内有害突变占总多态位点的比例与近交程度呈正相关，提示纯化选择的有效性与近交程度呈负相关，这一结果与理论预测一致。尽管存在显著的遗传漂变与近交现象，仍有多个离群位点与水温相关，且这些位点位于或邻近与热应激、免疫应答等关键生物学功能相关的基因。基因-水温关联的分析结果受高度近交种群的纳入影响显著，这类种群的等位基因频率与模型预测偏差最大。该结果凸显了在高遗传漂变与有限基因流场景下识别基因-环境关联的研究挑战，并提示近交程度较高的种群其适应能力受限。最后，我们讨论了本研究结果对于湖红点鲑种群及其他栖息于高度破碎化栖息地物种的保护与管理——尤其是放流与遗传拯救（genetic rescue）方面——的参考意义。