Data from: Contemporary ancestor? Adaptive divergence from standing genetic variation in Pacific marine threespine stickleback

Background: Populations that have repeatedly colonized novel environments are useful for studying the role of ecology in adaptive divergence - particularly if some individuals persist in the ancestral habitat. Such "contemporary ancestors" can be used to demonstrate the effects of selection by comparing phenotypic and genetic divergence between the derived population and their extant ancestors. However, evolution and demography in these "contemporary ancestors" can complicate inferences about the source (standing genetic variation, de novo mutation) and pace of adaptive divergence. Marine threespine stickleback (Gasterosteus aculeatus) have colonized freshwater environments along the Pacific coast of North America, but have also persisted in the marine environment. To what extent are marine stickleback good proxies of the ancestral condition?
Results: We sequenced >5800 variant loci in over 250 marine stickleback from eight locations extending from Alaska to California, and phenotyped them for platedness and body shape. Pairwise FST varied from 0.02 to 0.18. Stickleback were divided into five genetic clusters, with a single cluster comprising stickleback from Washington to Alaska. Plate number, Eda, body shape, and candidate loci showed evidence of being under selection in the marine environment. Comparisons to a freshwater population demonstrated that candidate loci for freshwater adaptation varied depending on the choice of marine populations.
Conclusions: Marine stickleback are structured into phenotypically and genetically distinct populations that have been evolving as freshwater stickleback evolved. This variation complicates their usefulness as proxies of the ancestors of freshwater populations. Lessons from stickleback may be applied to other "contemporary ancestor"-derived population studies.

研究背景：反复拓殖新生境的种群是研究生态在适应性分化中作用的理想研究体系——若部分个体仍留存于祖先栖息地，则尤为如此。这类‘当代祖先种群（contemporary ancestors）’可通过比较衍生种群与其现存祖先种群之间的表型与遗传分化，验证选择作用的效应。然而，这类当代祖先种群自身的演化与种群动态，会干扰对适应性分化的来源（现存遗传变异、新发突变）及速率的推断。海洋三棘刺鱼（Gasterosteus aculeatus）不仅已拓殖北美太平洋沿岸的淡水生境，同时也留存于海洋环境中。那么海洋刺鱼在多大程度上可作为祖先状态的有效替代种群？
研究结果：我们对从阿拉斯加到加利福尼亚的8个采样点的250余尾海洋刺鱼进行测序，共获得超过5800个变异位点，并对其骨板数与体型开展表型分型。两两群体间的群体遗传分化系数（FST）介于0.02至0.18之间。刺鱼可划分为5个遗传簇，其中一个簇涵盖了从华盛顿州到阿拉斯加的所有采样个体。骨板数、Eda基因、体型及候选位点均显示出在海洋环境中受到选择的信号。与淡水种群的对比分析表明，淡水适应性相关的候选位点会因所选用的海洋种群不同而存在差异。
研究结论：海洋刺鱼已分化为表型与遗传均存在显著差异的种群，且其演化进程与淡水刺鱼同步。这种种群分化使得海洋刺鱼作为淡水种群祖先替代种群的应用价值受到限制。刺鱼研究所得的经验，可推广至其他基于当代祖先种群的衍生种群研究中。