Data from: A genomic island linked to ecotype divergence in Atlantic cod

The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome-wide or localized in “genomic mosaics” during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or “genomic island”, as potentially associated with ecological divergence and suggest a selective sweep involved in ecological divergence. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although underlying mechanisms are still unknown, the results suggest that “genomic mosaics” of differentiation may even be found under high levels of gene flow, and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence.

对于绝大多数生物而言，介导伴随基因流（gene flow）的生态分化与生态物种形成的基因组架构，目前仍在很大程度上未被阐明。核心问题之一在于：在基因流仍显著的早期分化阶段，基因组分化究竟是全基因组范围的，还是局限于所谓的"基因组镶嵌格局（genomic mosaics）"之中？迄今为止，相关实证研究较为匮乏，基因流与自然选择对基因组格局的相对影响尚未得到充分探究。本研究以大西洋鳕鱼（Atlantic cod）的生态型为研究对象，在一个以高基因流与大有效种群大小为特征的自然系统中，探究其基因组多样性格局与种群分化情况——理论上，这类特征可能会限制局部基因组区域的分化。我们在两处不同采样点的洄游型与定居型大西洋鳕鱼生态型配对样本中，鉴定出一段长度约20厘摩（cM）、存在显著种群分化的基因组区域。此外，该区域在洄游型生态型样本中表现出显著降低的遗传多样性水平。研究结果凸显出该基因组区域（或"基因组岛（genomic island）"）与生态分化存在潜在关联，并暗示生态分化过程中可能涉及选择性清除（selective sweep）。最后，本研究还验证了此前的研究发现：东大西洋种群间分化相关的另外3个连锁群（linkage groups）中存在局部基因组分化。因此，尽管其背后的分子机制仍未明确，但研究结果表明：即便在高水平基因流的条件下，也可能存在分化的"基因组镶嵌格局"；同时，海洋鱼类或许可为研究并鉴定生态分化过程中选择的初始靶点提供极具启发性的模式系统。