Identifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced‐representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyika's two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, where L. miodon was introduced in 1959. Our results reveal differentiation within both S. tanganicae and L. miodon that is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex‐specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large chromosomal rearrangement in L. miodon, creating two homokaryotypes and one heterokaryotype. We found all karyotypes throughout Lake Tanganyika, but the frequencies vary along a north–south gradient and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation by distance, even over the hundreds of kilometres covered by our sampling, but we do find shallow population structure.

中文翻译：

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结构基因组变异导致坦any尼喀湖沙丁鱼的遗传分化。

识别遗传结构的模式和生态适应的遗传基础是进化生物学的核心目标，可以为易受气候变化加剧的种群减少影响的物种的管理和保护提供信息。我们使用减少表示形式的基因组测序方法来更好地了解坦any尼喀湖的两个沙丁鱼物种Limnothrissa miodon和Stolothrissa tanganicae种群之间及其内部的遗传结构。从坦any尼喀湖的整个长度以及附近的基伍湖（Lake miodon于1959年引入）附近收集了这些具有生态和经济意义的物种的样本。和L. miodon不是由地理解释。相反，这种遗传分化是由于两个物种的基因组中都存在较大的性别特定区域，但每个物种都涉及不同的多态性位点。因此，我们的结果表明了这两个物种中XY性别确定的迅速发展。此外，我们发现了L. miodon中染色体重排较大的证据，创建两个同核型和一个异核型。我们在坦any尼喀湖发现了所有核型，但频率沿南北梯度变化，并且在引入的基伍湖种群中有很大差异。我们没有找到证据证明即使在采样覆盖的数百公里内，也存在距离隔离的问题，但是我们确实发现了浅层的人口结构。