Data from: Ecological factors and morphological traits are associated with repeated genomic differentiation between lake and stream stickleback

The repeated evolution of similar phenotypes in independent populations (i.e. parallel or convergent evolution) provides an opportunity to identify genetic and ecological factors that influence the process of adaptation. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model for such studies, as they have repeatedly adapted to divergent habitats across the Northern hemisphere. Here, we use genomic, ecological and morphological data from 16 independent pairs of stickleback populations adapted to divergent lake and stream habitats. We combine a population genomic approach to identify regions of the genome that are likely under selection in these divergent habitats with an association mapping approach to identify regions of the genome that underlie variation in ecological factors and morphological traits. Over 37% of genomic windows are repeatedly differentiated across lake–stream pairs. Similarly, many genomic windows are associated with variation in abiotic factors, diet items and morphological phenotypes. Both the highly differentiated windows and candidate trait windows are non-randomly distributed across the genome and show some overlap. However, the overlap is not significant on a genome-wide scale. Together, our data suggest that adaptation to divergent food resources and predation regimes are drivers of differentiation in lake–stream stickleback, but that additional ecological factors are also important.

独立种群中相似表型的反复演化（即平行演化或趋同演化（parallel or convergent evolution））为识别影响适应过程的遗传与生态因子提供了绝佳契机。三刺棘鱼（Gasterosteus aculeatus）是此类研究的极佳模型类群，因其在北半球多次适应了迥异的生境。本研究利用了16对独立棘鱼种群的基因组、生态及形态学数据，这些种群均已适应湖泊与溪流两类截然不同的生境。我们结合群体基因组学方法与关联作图（association mapping）方法：前者用于鉴定这些分歧生境中受选择作用的基因组窗口（genomic windows），后者则用于识别驱动生态因子与形态性状变异的基因组区域。超过37%的基因组窗口在湖泊-溪流种群对中呈现反复分化特征。同样，诸多基因组窗口与非生物因子、食物类群及形态表型的变异相关联。高度分化的基因组窗口与候选性状相关基因组窗口均在全基因组范围内呈非随机分布，且存在一定重叠，但在全基因组尺度下，该重叠并不具备统计学显著性。综合来看，我们的数据表明，针对不同食物资源与捕食模式的适应是驱动湖泊-溪流棘鱼种群分化的关键因素，但其他生态因子同样具有重要作用。