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，伴随基因流的生态分化与生态成种作用背后的基因组架构，目前仍在很大程度上未被阐明。其中一个核心问题是：在基因流仍显著的早期分化阶段，种群分化是全基因组范围的，还是以“基因组镶嵌体（genomic mosaic）”的形式局域化存在？迄今为止相关实证研究仍较为匮乏，基因流与自然选择对基因组模式的相对影响尚未得到充分探究。
本研究以大西洋鳕（Atlantic cod）的生态型为研究材料，在一个兼具高基因流与大有效种群大小特征的自然系统中，探究基因组多样性模式与种群分化特征——这类系统属性在理论上可能会对局域基因组区域的分化产生限制作用。我们在两个不同采样点的洄游型与定居型大西洋鳕生态型配对样本中，鉴定出一个跨度约20 cM的强种群分化基因组区域。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。
本研究结果凸显出这一或可称为“基因组岛（genomic island）”的区域与生态分化存在潜在关联，并提示生态分化过程中可能伴随了一次选择性清除（selective sweep）。最后，本研究还验证了此前的研究发现：与东大西洋种群分化相关的另外3个连锁群（linkage group）中存在局域基因组分化。
综上，尽管其背后的分子机制仍有待阐明，但本研究结果表明，即便在高基因流水平下，种群分化也可能以“基因组镶嵌体”的形式存在；同时，海洋鱼类或可成为研究并鉴定生态分化过程中初始选择靶点的理想模型系统。