The repeated occurrence of similar phenotypes in independent lineages (i.e., parallel evolution) in response to similar ecological conditions can provide compelling insights into the process of adaptive evolution. An intriguing question is to what extent repeated phenotypic changes are underlain by repeated changes at the genomic level and whether patterns of genomic divergence differ with the geographic context in which populations evolve. Here, we combined genomic, morphological and ecological data sets to investigate the genomic signatures of divergence across populations of threespine stickleback (Gasterosteus aculeatus) that adapted to contrasting ecological niches (benthic or limnetic) in either sympatry or allopatry. We found that genome‐wide differentiation (F_ST) was an order of magnitude higher and substantially more repeatable for sympatric benthic and limnetic specialists compared to allopatric populations with similar levels of ecological divergence. We identified genomic regions consistently differentiated between sympatric ecotypes that were also differentiated between or associated with benthic vs. limnetic niche in allopatric populations. These candidate regions were enriched on three chromosomes known to be involved in the benthic‐limnetic divergence of threespine stickleback. Some candidate regions overlapped with QTL for body shape and trophic traits such as gill raker number, traits that strongly differ between benthic and limnetic ecotypes. In summary, our study shows that magnitude and repeatability of genomic signatures of ecological divergence in threespine stickleback highly depend on the geographic context. The identified candidate regions provide starting points to identify functionally important genes for the adaptation to benthic and limnetic niches.

中文翻译：

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在同种异体和同伴三脊背棘中沿底-lim轴线的生态发散的基因组特征

响应相似的生态条件，在独立谱系中重复出现相似的表型（即平行进化）可以为适应性进化的过程提供令人信服的见解。一个有趣的问题是，在多大程度上重复的表型变化是由基因组水平上的重复变化所决定的，以及基因组差异的模式是否随种群演化的地理环境而变化。在这里，我们结合了基因组学，形态学和生态学数据集，研究了三脊背棘背（（Gasterosteus aculeatus）种群间差异发散的基因组特征，该三脊背棘背背甲适应于自然生态系统（底栖动物或立足动物）中的对比生态位（底栖或边缘）。我们发现全基因组分化（F _ST与同等生态散布水平的异特异种群相比，同栖底栖生物和边缘生物专家的数量级要高得多，并且可重复性要高得多。我们确定了同域生态型之间始终存在差异的基因组区域，同生型生态型在同种异体种群的底栖生态位与边缘生物位之间也存在差异或相关。这些候选区域富集在三个已知与三脊棘背底下-地幔发散有关的染色体上。一些候选区域的身体形状和营养特性（如g耙数量）与底栖生物和Qlim重叠，这些特性在底栖生态系统和边缘生态型之间有很大差异。综上所述，我们的研究表明，三脊刺背le生态多样性的基因组特征的数量和可重复性高度依赖于地理环境。鉴定出的候选区域提供了起点，以鉴定功能重要的基因以适应底栖生物和边缘生物。