Dataset from: High-recombining genomic regions affect demography inference based on ancestral recombination graphs

Multiple methods of demography inference are based on the ancestral recombination graph. This powerful approach uses observed mutations to model local genealogies changing along chromosomes by historical recombination events. However, inference of underlying genealogies is difficult in regions with high recombination rate relative to mutation rate due to the lack of mutations representing genealogies. Despite the prevalence of high-recombining genomic regions in some organisms, such as birds, its impact on demography inference based on ancestral recombination graphs has not been well studied. Here, we use population genomic simulations to investigate the impact of high-recombining regions on demography inference based on ancestral recombination graphs. We demonstrate that inference of effective population size and the time of population split events is systematically affected when high-recombining regions cover wide breadths of the chromosomes. Excluding high-recombining genomic regions can practically mitigate this impact, and population genomic inference of recombination maps is informative in defining such regions, yet the estimated values of local recombination rate may not be utilized for this decision. Finally, we confirm the relevance of our findings in empirical analysis by contrasting demography inferences applied for a bird species, the Eurasian blackcap (Sylvia atricapilla), using different parts of the genome with high and low recombination rates. Our results suggest that demography inference methods based on ancestral recombination graphs should be carried out with caution when applied in species whose genomes contain long stretches of high-recombining regions.

诸多种群历史推断方法均以祖先重组图（Ancestral Recombination Graph, ARG）为基础。这类高效研究手段借助观测到的突变位点，基于历史重组事件构建沿染色体动态演化的局部基因系谱模型。然而，当重组率相对于突变率较高时，由于缺乏能够反映基因系谱的突变位点，对底层基因系谱的推断会面临极大困难。尽管部分类群（如鸟类）的基因组中广泛存在高重组区域，但目前学界尚未对这类区域对基于祖先重组图的种群历史推断的影响开展充分研究。本研究通过种群基因组模拟，探究高重组区域对基于祖先重组图的种群历史推断的影响。研究结果表明，当高重组区域占据染色体大片段时，有效种群大小与种群分化时间的推断会受到系统性干扰。剔除高重组基因组区域可有效缓解该干扰，且通过种群基因组推断得到的重组图谱可用于界定这类区域，但局部重组率的估计值本身并不适用于该筛选决策。最后，本研究以欧亚黑顶林莺（Sylvia atricapilla）为研究对象，分别利用其基因组中高、低重组区域开展种群历史推断并对比结果，从而验证了本研究结论在实证分析中的适用性。本研究结果提示，在基因组中存在大片高重组区域的物种中应用基于祖先重组图的种群历史推断方法时，需保持谨慎。