Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age
Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age
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DOI：
10.1111/mec.16841
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发表时间：
2022-02
期刊：
影响因子：
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通讯作者：
L. R. Moreira;J. Klicka;B. Smith
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文献类型：
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作者：
L. R. Moreira;J. Klicka;B. Smith
更新世的冰期旋回对物种的进化具有全球性的影响。虽然遗传漂变对种群遗传动态的影响已被很好地理解，但在这些剧烈的气候变化中，选择在形成基因组变异模式中的作用尚不清楚。我们使用全基因组重测序数据来研究人口统计学和自然选择之间的相互作用及其对绒毛啄木鸟和毛啄木鸟基因组景观的影响，这些物种共同分布在以前冰川覆盖的北美。研究结果揭示了该种群的瓶颈期和扩张期反复循环的动态历史，以及与冰川避难有关的遗传结构。绒毛啄木鸟和毛啄木鸟基因组的核苷酸多样性水平差异很大，但这种差异在两个物种之间高度相关，表明存在保守的基因组特征。两种物种的核苷酸多样性均与重组率呈正相关，与基因密度负相关，表明连锁选择在低重组和选择目标高密度区域发挥了降低多样性的作用。尽管Ne的时间波动很大，但我们的人口统计分析表明，绒毛啄木鸟和毛啄木鸟能够在冰期保持相对较大的有效种群规模，这可能有利于自然选择。连锁选择的影响程度似乎被种群和物种的个体人口统计轨迹所调节，因此，由于毛啄木鸟的长期Ne较大，净化选择在去除有害等位基因方面更有效。这些结果强调，虽然漂移捕获了气候扰动期间人口收缩和扩张的预期特征，但多个过程的相互作用产生了可预测的高度异质的基因组景观。
The glacial cycles of the Pleistocene had a global impact on the evolution of species. Although the influence of genetic drift on population genetic dynamics is well understood, the role of selection in shaping patterns of genomic variation during these dramatic climatic changes is less clear. We used whole genome resequencing data to investigate the interplay between demography and natural selection and their influence on the genomic landscape of Downy and Hairy Woodpecker, species co-distributed in previously glaciated North America. Our results revealed a dynamic population history with repeated cycles of bottleneck and expansion, and genetic structure associated with glacial refugia. Levels of nucleotide diversity varied substantially along the genomes of Downy and Hairy Woodpecker, but this variation was highly correlated between the two species, suggesting the presence of conserved genomic features. Nucleotide diversity in both species was positively correlated with recombination rate and negatively correlated with gene density, suggesting that linked selection played a role in reducing diversity in regions of low recombination and high density of targets of selection. Despite strong temporal fluctuations in Ne, our demographic analyses indicate that Downy and Hairy Woodpecker were able to maintain relatively large effective population sizes during glaciations, which might have favored natural selection. The magnitude of the effect of linked selection seems to have been modulated by the individual demographic trajectory of populations and species, such that purifying selection has been more efficient in removing deleterious alleles in Hairy Woodpecker owing to its larger long-term Ne. These results highlight that while drift captures the expected signature of contracting and expanding populations during climatic perturbations, the interaction of multiple processes produces a predictable and highly heterogeneous genomic landscape.