Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4.
Institute of Ecology and Evolution, Department of Biology, University of Bern, 3012 Bern, Switzerland.
G3 (Bethesda). 2024 Nov 6;14(11). doi: 10.1093/g3journal/jkae225.
The amount of standing variation present within populations is a fundamental quantity of interest in population genetics, commonly represented by calculating the average number of differences between pairs of nucleotide sequences (nucleotide diversity, π). It is well understood that both background and positive selection can cause reductions in nucleotide diversity, but less clear how local adaptation affects it. Depending on the assumptions and parameters, some theoretical studies have emphasized how local adaptation can reduce nucleotide diversity, while others have shown that it can increase it. Here, we explore how local adaptation shapes genome-wide patterns in within-population nucleotide diversity, extending previous work to study the effects of polygenic adaptation, genotypic redundancy, and population structure. We show that local adaptation produces two very different patterns depending on the relative strengths of migration and selection, either markedly decreasing or increasing within-population diversity at linked sites at equilibrium. At low migration, regions of depleted diversity can extend large distances from the causal locus, with substantially more diversity eroded than expected with background selection. With higher migration, peaks occur over much smaller genomic distances but with much larger magnitude changes in diversity. Across spatially extended environmental gradients, both patterns can be found within a single species, with increases in diversity at the center of the range and decreases towards the periphery. Our results demonstrate that there is no universal diagnostic signature of local adaptation based on within-population nucleotide diversity, so it will not be broadly useful for explaining increased FST. However, given that neither background nor positive selection inflate diversity, when peaks are found they suggest local adaptation may be acting on a causal allele in the region.
群体内的遗传多态性是群体遗传学中一个基本的研究课题，通常用计算核苷酸序列（核苷酸多样性，π）之间成对差异的平均值来表示。背景选择和正选择都能导致核苷酸多样性降低是众所周知的，但是局部适应如何影响核苷酸多样性则不太清楚。根据假设和参数的不同，一些理论研究强调了局部适应如何降低核苷酸多样性，而另一些研究则表明它可以增加核苷酸多样性。在这里，我们探讨了局部适应如何塑造群体内核苷酸多样性的全基因组模式，将以前的工作扩展到研究多基因适应、基因型冗余和群体结构的影响。我们表明，局部适应会产生两种截然不同的模式，具体取决于迁移和选择的相对强度，在平衡时，连锁位点的群体内多样性要么明显降低，要么明显增加。在低迁移的情况下，多样性耗竭区域可以从因果基因座延伸很远的距离，与背景选择导致的多样性耗损相比，耗损的多样性要多得多。随着迁移率的增加，多样性的峰值出现在更小的基因组距离上，但多样性的变化幅度要大得多。在空间上扩展的环境梯度中，同一物种内可以同时存在这两种模式，多样性的增加发生在范围的中心，而在边缘则减少。我们的研究结果表明，基于群体内核苷酸多样性，不存在局部适应的普遍诊断特征，因此它不会广泛用于解释增加的 FST。然而，由于背景选择和正选择都不会增加多样性，因此当发现多样性峰值时，它们表明局部适应可能正在该区域的因果等位基因上起作用。
