Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu, China.
Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden.
Mol Ecol. 2020 Mar;29(6):1120-1136. doi: 10.1111/mec.15388. Epub 2020 Mar 9.
Increasing our understanding of how evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, genome-wide patterns of within- and between- species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories and investigate patterns of diversity and divergence within and between species. Using Populus trichocarpa as an outgroup species, we further infer the genealogical relationships and estimate the extent of ancient introgression among the three aspen species (Populus tremula, Populus davidiana and Populus tremuloides) throughout the genome. Our results show substantial variation in these patterns along the genomes with this variation being strongly predicted by local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection have also been crucial components in shaping patterns of genome-wide variation during the speciation process.
增加我们对进化过程如何驱动变异的基因组景观的理解，对于更好地理解物种形成的基因组后果至关重要。然而，尽管大多数森林树种具有全球生态和经济重要性，但在大多数情况下，它们的种内和种间变异的全基因组模式尚未得到充分研究。在这里，我们使用跨越物种形成连续体的四个杨树物种的全基因组重测序数据来重建它们的种群历史，并研究种内和种间多样性和分化的模式。使用 Populus trichocarpa 作为外群物种，我们进一步推断了三个白杨物种（Populus tremula、Populus davidiana 和 Populus tremuloides）的系统发育关系，并估计了整个基因组中古老基因渗入的程度。我们的结果表明，这些模式在基因组上存在很大的差异，这种差异强烈地受到局部重组率和功能元件密度的预测。这意味着，在很长一段时间内，反复选择和内在基因组特征之间的相互作用极大地塑造了基因组景观。此外，我们的研究结果表明，除了背景选择之外，近期的正选择和长期的平衡选择也是在物种形成过程中塑造全基因组变异模式的关键因素。
