Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
University of the Chinese Academy of Sciences, Beijing, China.
Genome Biol Evol. 2022 Apr 10;14(4). doi: 10.1093/gbe/evac043.
The strength of selection varies among populations and across the genome, but the determinants of efficacy of selection remain unclear. In this study, we used whole-genome sequencing data from 467 Boechera stricta accessions to quantify the strength of selection and characterize the pattern of local adaptation. We found low genetic diversity on 0-fold degenerate sites and conserved non-coding sites, indicating functional constraints on these regions. The estimated distribution of fitness effects and the proportion of fixed substitutions suggest relaxed negative and positive selection in B. stricta. Among the four population groups, the NOR and WES groups have smaller effective population size (Ne), higher proportions of effectively neutral sites, and lower rates of adaptive evolution compared with UTA and COL groups, reflecting the effect of Ne on the efficacy of natural selection. We also found weaker selection on GC-biased sites compared with GC-conservative (unbiased) sites, suggested that GC-biased gene conversion has affected the strength of selection in B. stricta. We found mixed evidence for the role of the recombination rate on the efficacy of selection. The positive and negative selection was stronger in high-recombination regions compared with low-recombination regions in COL but not in other groups. By scanning the genome, we found different subsets of selected genes suggesting differential adaptation among B. stricta groups. These results show that differences in effective population size, nucleotide composition, and recombination rate are important determinants of the efficacy of selection. This study enriches our understanding of the roles of natural selection and local adaptation in shaping genomic variation.
选择的力度在不同种群和整个基因组中有所差异，但选择有效性的决定因素仍不清楚。在这项研究中，我们使用了 467 个 Boechera stricta 个体的全基因组测序数据，来量化选择的力度，并描述局部适应的模式。我们发现 0 倍简并位点和保守非编码区的遗传多样性较低，表明这些区域受到功能限制。适应性效应的估计分布和固定替换比例表明，B. stricta 中存在松弛的负选择和正选择。在四个群体中，NOR 和 WES 群体的有效种群大小（Ne）较小，有效中性位点的比例较高，适应进化的速度较低，与 UTA 和 COL 群体相比，这反映了 Ne 对自然选择有效性的影响。我们还发现，GC 偏向性位点的选择力度弱于 GC 保守性（非偏向性）位点，表明 GC 偏向性基因转换影响了 B. stricta 中的选择力度。我们发现，重组率对选择有效性的作用存在混合证据。在 COL 群体中，高重组区域的正选择和负选择比低重组区域更强，但在其他群体中则没有。通过扫描基因组，我们发现了不同的选择基因子集，表明 B. stricta 群体之间存在差异适应。这些结果表明，有效种群大小、核苷酸组成和重组率的差异是选择有效性的重要决定因素。本研究丰富了我们对自然选择和局部适应在塑造基因组变异中的作用的理解。
