Recently diverged taxa often exhibit heterogeneous landscapes of genomic differentiation, characterized by regions of elevated differentiation on an otherwise homogeneous background. While divergence peaks are generally interpreted as regions responsible for reproductive isolation, they can also arise due to background selection, selective sweeps unrelated to speciation, and variation in recombination and mutation rates. To investigate the association between patterns of recombination and landscapes of genomic differentiation during the early stages of speciation, we generated fine-scale recombination maps for six southern capuchino seedeaters (Sporophila) and two subspecies of White Wagtail (Motacilla alba), two recent avian radiations in which divergent selection on pigmentation genes has likely generated peaks of differentiation. We compared these recombination maps to those of Collared (Ficedula albicollis) and Pied Flycatchers (Ficedula hypoleuca), non-sister taxa characterized by moderate genomic divergence and a heterogenous landscape of genomic differentiation shaped in part by background selection. Although recombination landscapes were conserved within all three systems, we documented a weaker negative correlation between recombination rate and genomic differentiation in the recent radiations. All divergence peaks between capuchinos, wagtails, and flycatchers were located in regions with lower-than-average recombination rates, and most divergence peaks in capuchinos and flycatchers fell in regions of exceptionally reduced recombination. Thus, co-adapted allelic combinations in these regions may have been protected early in divergence, facilitating rapid diversification. Despite largely conserved recombination landscapes, divergence peaks are specific to each focal comparison in capuchinos, suggesting that regions of elevated differentiation have not been generated by variation in recombination rate alone.

中文翻译：

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尽管在物种形成早期有保守的重组景观，但选择的可变特征

最近分化的分类群通常表现出基因组分化的异质景观，其特征是在其他同质背景上分化升高的区域。虽然分歧峰通常被解释为负责生殖隔离的区域，但它们也可能由于背景选择、与物种形成无关的选择性扫描以及重组和突变率的变化而出现。为了研究在物种形成的早期阶段重组模式和基因组分化景观之间的关联，我们为六个南部卷尾猴 (Sporophila) 和两个白鹡鸰亚种 (Motacilla alba) 生成了精细比例的重组图，这是最近的两种鸟类辐射其中色素沉着基因的不同选择可能产生了分化峰。我们将这些重组图谱与 Collared (Ficedula albicollis) 和 Pied Flycatchers (Ficedula hypoleuca) 的重组图谱进行了比较，后者是非姐妹类群，其特征是中度基因组分歧和部分由背景选择形成的基因组分化异质景观。尽管在所有三个系统中都保存了重组景观，但我们记录了最近辐射中重组率和基因组分化之间较弱的负相关性。卷尾猴、鹡鸰和捕蝇器之间的所有分歧峰都位于重组率低于平均水平的区域，而卷尾猴和捕蝇器的大多数分歧峰都位于重组异常减少的区域。因此，这些区域中的共同适应等位基因组合可能在分化早期得到保护，促进快速多元化。尽管在很大程度上保守的重组景观，分歧峰是特定于卷尾猴的每个焦点比较，这表明分化升高的区域并不是由重组率的变化单独产生的。