Rehmann Clara T, Small Scott T, Ralph Peter L, Kern Andrew D
Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA.
Department of Biology, University of Oregon, Eugene, OR, USA.
Mol Biol Evol. 2025 Jun 4;42(6). doi: 10.1093/molbev/msaf141.
As organisms adapt to environmental changes, natural selection modifies the frequency of nonneutral alleles. For beneficial mutations, the outcome of this process may be a selective sweep, in which an allele rapidly increases in frequency and perhaps reaches fixation within a population. Selective sweeps have well-studied effects on patterns of local genetic variation in panmictic populations, but much less is known about the dynamics of sweeps in continuous space. In particular, because limited movement across a landscape leads to unique patterns of population structure, spatial dynamics may influence the trajectory of selected mutations. Here, we use forward-in-time, individual-based simulations in continuous space to study the impact of space on beneficial mutations as they sweep through a population. In particular, we show that selection changes the joint distribution of allele frequency and geographic range occupied by a focal allele and demonstrate that this signal can be used to identify selective sweeps. We then leverage this signal to identify in-progress selective sweeps within the malaria vector Anopheles gambiae, a species under strong selection pressure from vector control measures. By considering space, we identify multiple previously undescribed variants with potential phenotypic consequences, including mutations impacting known IR-associated genes and altering protein structure and properties. Our results demonstrate a novel signal for detecting selection in spatial population genetic data that may have implications for genomic surveillance and understanding geographic patterns of genetic variation.
随着生物体适应环境变化，自然选择会改变非中性等位基因的频率。对于有益突变，这一过程的结果可能是选择性清除，即一个等位基因的频率迅速增加，并可能在种群中达到固定状态。选择性清除对随机交配种群中局部遗传变异模式的影响已得到充分研究，但对于连续空间中清除的动态过程了解较少。特别是，由于在景观中有限的移动会导致独特的种群结构模式，空间动态可能会影响被选择突变的轨迹。在这里，我们使用连续空间中基于个体的时间向前模拟，来研究空间对有益突变在种群中扩散时的影响。特别是，我们表明选择会改变焦点等位基因的频率和所占据地理范围的联合分布，并证明这一信号可用于识别选择性清除。然后，我们利用这一信号在冈比亚按蚊（一种受到媒介控制措施强大选择压力的物种）中识别正在进行的选择性清除。通过考虑空间因素，我们识别出多个先前未描述的具有潜在表型后果的变异，包括影响已知与杀虫剂抗性相关基因并改变蛋白质结构和特性的突变。我们的结果展示了一种用于检测空间种群遗传数据中选择的新信号，这可能对基因组监测和理解遗传变异的地理模式具有重要意义。
