Recombination is responsible for breaking up haplotypes, influencing genetic variability, and the efficacy of selection. Bird genomes lack the protein PR domain-containing protein 9, a key determinant of recombination dynamics in most metazoans. Historical recombination maps in birds show an apparent stasis in positioning recombination events. This highly conserved recombination pattern over long timescales may constrain the evolution of recombination in birds. At the same time, extensive variation in recombination rate is observed across the genome and between different species of birds. Here, we characterize the fine-scale historical recombination map of an iconic migratory songbird, the Eurasian blackcap (Sylvia atricapilla), using a linkage disequilibrium–based approach that accounts for population demography. Our results reveal variable recombination rates among and within chromosomes, which associate positively with nucleotide diversity and GC content and negatively with chromosome size. Recombination rates increased significantly at regulatory regions but not necessarily at gene bodies. CpG islands are associated strongly with recombination rates, though their specific position and local DNA methylation patterns likely influence this relationship. The association with retrotransposons varied according to specific family and location. Our results also provide evidence of heterogeneous intrachromosomal conservation of recombination maps between the blackcap and its closest sister taxon, the garden warbler. These findings highlight the considerable variability of recombination rates at different scales and the role of specific genomic features in shaping this variation. This study opens the possibility of further investigating the impact of recombination on specific population-genomic features.

中文翻译：

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精细尺度图谱揭示了与欧亚黑帽基因组特征相关的高度可变的重组率

重组负责破坏单倍型、影响遗传变异和选择的功效。鸟类基因组缺乏含有 PR 结构域的蛋白 9，这是大多数后生动物重组动态的关键决定因素。鸟类的历史重组图显示重组事件定位明显停滞。这种长时间尺度上高度保守的重组模式可能会限制鸟类重组的进化。与此同时，在不同鸟类的基因组中和不同物种之间观察到重组率存在巨大差异。在这里，我们使用基于连锁不平衡的方法来解释人口统计，描绘了标志性迁徙鸣禽欧亚黑帽（Sylvia atricapilla）的精细历史重组图。我们的结果揭示了染色体之间和染色体内的可变重组率，这与核苷酸多样性和GC含量呈正相关，与染色体大小呈负相关。调控区域的重组率显着增加，但基因体的重组率不一定增加。CpG 岛与重组率密切相关，尽管它们的特定位置和局部 DNA 甲基化模式可能会影响这种关系。与逆转录转座子的关联因特定家族和地点而异。我们的结果还提供了黑帽与其最接近的姊妹类群花园莺之间重组图谱的异质染色体内保守性的证据。这些发现强调了不同规模重组率的相当大的变异性以及特定基因组特征在形成这种变异中的作用。这项研究为进一步研究重组对特定群体基因组特征的影响提供了可能性。