Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
Mol Biol Evol. 2024 Sep 4;41(9). doi: 10.1093/molbev/msae191.
The heterogeneous landscape of genomic variation has been well documented in population genomic studies. However, disentangling the intricate interplay of evolutionary forces influencing the genetic variation landscape over time remains challenging. In this study, we assembled a chromosome-level genome for Castanopsis eyrei and sequenced the whole genomes of 276 individuals from 12 Castanopsis species, spanning a broad divergence continuum. We found highly correlated genomic variation landscapes across these species. Furthermore, variations in genetic diversity and differentiation along the genome were strongly associated with recombination rates and gene density. These results suggest that long-term linked selection and conserved genomic features have contributed to the formation of a common genomic variation landscape. By examining how correlations between population summary statistics change throughout the species divergence continuum, we determined that background selection alone does not fully explain the observed patterns of genomic variation; the effects of recurrent selective sweeps must be considered. We further revealed that extensive gene flow has significantly influenced patterns of genomic variation in Castanopsis species. The estimated admixture proportion correlated positively with recombination rate and negatively with gene density, supporting a scenario of selection against gene flow. Additionally, putative introgression regions exhibited strong signals of positive selection, an enrichment of functional genes, and reduced genetic burdens, indicating that adaptive introgression has played a role in shaping the genomes of hybridizing species. This study provides insights into how different evolutionary forces have interacted in driving the evolution of the genomic variation landscape.
基因组变异的异质景观在群体基因组研究中得到了很好的记录。然而，要理清随时间影响遗传变异景观的复杂进化力量之间的相互作用仍然具有挑战性。在这项研究中，我们为锥栗组装了一个染色体水平的基因组，并对来自 12 个锥栗物种的 276 个个体的全基因组进行了测序，这些物种跨越了广泛的分化连续体。我们发现这些物种之间存在高度相关的基因组变异景观。此外，基因组上遗传多样性和分化的变化与重组率和基因密度强烈相关。这些结果表明，长期的连锁选择和保守的基因组特征促成了共同的基因组变异景观的形成。通过研究群体综合统计数据之间的相关性如何随物种分化连续体而变化，我们确定背景选择本身并不能完全解释观察到的基因组变异模式；必须考虑到反复出现的选择清扫的影响。我们进一步揭示了广泛的基因流对锥栗物种基因组变异模式有重大影响。估计的杂种比例与重组率呈正相关，与基因密度呈负相关，支持选择反对基因流的情景。此外，假定的渐渗区域表现出强烈的正选择信号、功能基因的富集和遗传负担的减少，表明适应性渐渗在塑造杂交种的基因组方面发挥了作用。这项研究提供了有关不同进化力量如何相互作用推动基因组变异景观进化的见解。
