Data from: Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds

Recombination rate is heterogeneous across the genome of various species, and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium (LD) across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200-kb, but we also identified differences in the local rate of recombination despite their recent divergence (<1 million years). Genetic diversity and differentiation were associated with recombination rate in a lineage-specific manner, indicating differences in the extent of linked selection between species. We detected 400-3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands (CGIs), regardless of whether CGIs were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements (TEs), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGIs are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TEs and fine-scale variation in recombination rate may be associated with the evolution of the epigenetic landscape.

多种物种的基因组中重组率存在异质性，受连锁选择（linked selection）影响，遗传多样性与分化亦呈现相应的异质性。但目前学界对调控重组的潜在分子机制仍缺乏清晰认知。本研究基于两种近缘姬鹟属（Ficedula）鸟类——白领姬鹟（Ficedula albicollis）与斑姬鹟（Ficedula hypoleuca）——多个种群的基因组连锁不平衡（linkage disequilibrium, LD）模式，估算了精细尺度的种群重组率。结果显示，在200千碱基（kb）尺度下，这两个物种的重组景观整体保守；但尽管二者分化时间较近（不足100万年），其局部重组率仍存在差异。遗传多样性与分化水平与重组率呈现谱系特异性关联，表明两物种间连锁选择的作用程度存在差异。本研究在每个种群中均可检测到400至3085个重组热点（recombination hotspots）；热点的位置在物种间保守，但热点的活性强度在物种间存在差异。重组热点主要与CpG岛（CpG islands, CGIs）相关联，无论这些CGIs位于启动子区域还是基因间隔区域。重组热点亦与特定转座因子（transposable elements, TEs）相关，但这种关联可能是间接的——转座机制与重组机制均偏好开放的可及染色质区域，二者存在共同的偏好性。本研究结果表明，CGIs是决定重组热点定位的主要因素；我们推测，转座因子的分布以及重组率的精细尺度变异，或均与表观遗传景观的演化相关联。