IRD, University of Montpellier, UMR DIADE BP 64501, Montpellier Cedex 5, France.
Department of Organismal Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.
Mol Ecol Resour. 2019 Jan;19(1):283-295. doi: 10.1111/1755-0998.12957. Epub 2018 Nov 22.
Inferring the mode and tempo of natural selection helps further our understanding of adaptation to past environmental changes. Here, we introduce McSwan, a method to detect and date past and recent natural selection events in the case of a hard sweep. The method is based on the comparison of site frequency spectra obtained under various demographic models that include selection. McSwan demonstrated high power (high sensitivity and specificity) in capturing hard selective sweep events without requiring haplotype phasing. It performed slightly better than SweeD when the recent effective population size was low and the genomic region was small. We then applied our method to a European (CEU) and an African (LWK) human re-sequencing data set. Most hard sweeps were detected in the CEU population (96%). Moreover, hard sweeps in the African population were estimated to have occurred further back in time (mode: 43,625 years BP) compared to those of Europeans (mode: 24,850 years BP). Most of the estimated ages of hard sweeps in Europeans were associated with the Last Glacial Maximum and were enriched in immunity-associated genes.
推断自然选择的模式和速度有助于我们进一步了解对过去环境变化的适应。在这里，我们引入了 McSwan 方法，该方法可在硬扫除的情况下检测和确定过去和最近的自然选择事件。该方法基于在包括选择在内的各种人口统计模型下获得的位点频率谱的比较。McSwan 表现出了很高的功效（高灵敏度和特异性），能够在不进行单倍型相位检测的情况下捕获硬选择性清扫事件。当最近的有效种群规模较低且基因组区域较小时，它的表现略优于 SweeD。然后，我们将我们的方法应用于欧洲（CEU）和非洲（LWK）人类重测序数据集。在 CEU 人群中检测到了大多数硬扫除（96％）。此外，与欧洲人（模式：24850 年 BP）相比，非洲人中硬扫除的发生时间更早（模式：43625 年前）。欧洲人中硬扫除的大多数估计年龄与末次冰期最大值有关，并且富集了与免疫相关的基因。
