Dataset from: Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure

Genetic variation of the entire genome represents population structure, yet individual loci can show distinct patterns. Such deviations identified through genome scans have often been attributed to effects of selection instead of randomness. This interpretation assumes that long enough genomic intervals average out randomness in underlying genealogies, which represent local genetic ancestries. However, an alternative explanation to distinct patterns has not been fully addressed: too few genealogies to average out the effect of randomness. Specifically, distinct patterns of genetic variation may be due to reduced local recombination rate, whichreduces the number of genealogies in a genomic window. Here, we associate distinct patterns of local genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using genome sequences and recombination maps. We find that distinct patterns of local genetic variation reflect haplotype structure at low-recombining regions either shared in most populations or found only in a few populations. At the former species-wide low-recombining regions, genetic variation depicts conspicuous haplotypes segregating in multiple populations. At the latter population-specific low-recombining regions, genetic variation represents variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns of haplotype structure evolve dueto reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolution of reduced local recombination rate. Recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.全基因组的遗传变异可反映种群结构，但单个基因座却往往呈现迥异的模式。通过基因组扫描鉴定出的这类偏差，常被归因于选择作用而非随机过程。该解释的前提是，足够长的基因组区间可抵消其下代表局部遗传祖先的基因谱系所带来的随机性。然而，另一种针对这些差异模式的解释尚未得到充分探讨：即用于抵消随机效应的基因谱系数量不足。具体而言，遗传变异的差异模式可能源于局部重组率降低，这会减少基因组窗口内的基因谱系数量。本研究以鸣禽欧亚黑顶林莺（Sylvia atricapilla）为研究对象，借助基因组序列与重组图谱，将局部遗传变异的差异模式与低重组率相关联。我们发现，遗传变异的差异模式对应两类低重组区域的单倍型结构：一类是多数种群共有的低重组区域，另一类则仅存在于少数种群中。在前者这类全物种共有的低重组区域中，遗传变异呈现出在多个种群中分离的显著单倍型；而在后者这类种群特异性低重组区域中，遗传变异则体现为低重组种群内部隐蔽单倍型间的差异。通过模拟实验，我们证实这类单倍型结构的差异模式是由重组率降低演化而来，选择作用可叠加于这一过程之上。本研究结果表明，遗传变异的差异模式可通过局部重组率降低的演化过程产生。因此，作为一种可演化性状的重组景观，在决定基因组上遗传变异的异质性分布中发挥着重要作用。