The three-spined stickleback (Gasterosteus aculeatus) is an important model system for the study of parallel evolution in the wild, having repeatedly colonized and adapted to freshwater from the sea throughout the northern hemisphere. Previous studies identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine ecotypes but these had typically limited geographic sampling and mostly focused on the Eastern Pacific region. We analysed population genomic data from global samples of the three-spined stickleback marine and freshwater ecotypes to detect loci involved in parallel evolution at different geographic scales. Most signatures of parallel evolution were unique to the Eastern Pacific and trans-oceanic marine–freshwater differentiation was restricted to a limited number of shared genomic regions, including three chromosomal inversions. On the basis of simulations and empirical data, we demonstrate that this could result from the stochastic loss of freshwater-adapted alleles during the invasion of the Atlantic basin and selection against freshwater-adapted variants in the sea, both of which can reduce standing genetic variation available for freshwater adaptation outside the Eastern Pacific region. Moreover, the elevated linkage disequilibrium associated with marine–freshwater differentiation in the Eastern Pacific is consistent with secondary contact between marine and freshwater populations that evolved in isolation from each other during past glacial periods. Thus, contrary to what earlier studies from the Eastern Pacific region have led us to believe, parallel marine–freshwater differentiation in sticklebacks is far less prevalent and pronounced in all other parts of the species global distribution range.

三刺棘鱼 ( Gasterosteus aculeatus) 是研究野外平行进化的重要模型系统，在整个北半球反复殖民并适应来自海洋的淡水。以前的研究确定了许多基因组区域，显示淡水和海洋生态型之间的遗传差异一致，但这些区域的地理采样通常有限，并且主要集中在东太平洋地区。我们分析了来自三刺棘鱼海洋和淡水生态型全球样本的种群基因组数据，以检测参与不同地理尺度平行进化的基因座。大多数平行进化的特征是东太平洋独有的，跨洋海洋 - 淡水分化仅限于有限数量的共享基因组区域，包括三个染色体倒位。在模拟和经验数据的基础上，我们证明这可能是由于在大西洋盆地入侵期间淡水适应等位基因的随机损失和对海洋中淡水适应变体的选择，这两者都可以减少常设遗传变异可用于东太平洋地区以外的淡水适应。此外，与东太平洋海洋 - 淡水分化相关的升高的连锁不平衡与过去冰期相互隔离进化的海洋和淡水种群之间的二次接触是一致的。因此，与东太平洋地区早期的研究使我们相信的相反，