School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, UK.
Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK.
Mol Ecol Resour. 2024 Jul;24(5):e13969. doi: 10.1111/1755-0998.13969. Epub 2024 May 15.
A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (F), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.
进化生物学的一个主要目标是理解为什么基因组多样性的模式在分类群和空间内存在差异。对广泛分布物种的大规模基因组研究有助于研究环境和人口统计学如何塑造基因组分歧的模式。在这里，我们描述了迄今为止对野生脊椎动物进行的最具地理综合性的基因组变异调查之一；大山雀（Parus major）HapMap 项目。我们在来自 29 个种群的 647 个个体中筛选了约 50 万个 SNP 标记，覆盖了约 30 度的纬度和 40 度的经度-几乎是欧洲亚种的整个地理范围。全基因组的变异与从东南欧避难所向欧洲的最近一次殖民化一致，在岛屿种群中存在瓶颈和遗传多样性降低。基因组水平上的分化高度不均匀，存在明显的“分化岛屿”，即使在全基因组分化水平非常低的种群中也是如此。低局部重组率是高局部基因组分化（F）的强烈预测因子，特别是在岛屿和外围大陆种群中，这表明遗传漂变和重组之间的相互作用导致了高度不均匀的分化景观。我们还检测到了局限于一个或多个外围大山雀种群的基因组异常区域，这可能是由于物种分布边缘的近期定向选择。基于单倍型的选择度量与重组率有关，尽管不太强烈，但强调了种群特异性的扫荡，这可能是由于正选择所致。我们的研究强调了对野生生物全基因组变异进行全面筛选如何能够为时空进化动态提供独特的见解。
