A spatially aware likelihood test to detect sweeps from haplotype distributions

The inference of positive selection in genomes is a problem of great interest in evolutionary genomics. By identifying putative regions of the genome that contain adaptive mutations, we are able to learn about the biology of organisms and their evolutionary history. Here we introduce a composite likelihood method that identifies recently completed or ongoing positive selection by searching for extreme distortions in the spatial distribution of the haplotype frequency spectrum along the genome relative to the genome-wide expectation taken as neutrality. Furthermore, the method simultaneously infers two parameters of the sweep: the number of sweeping haplotypes and the “width” of the sweep, which is related to the strength and timing of selection. We demonstrate that this method outperforms the leading haplotype-based selection statistics, though strong signals in low-recombination regions merit extra scrutiny. As a positive control, we apply it to two well-studied human populations from ...基因组中正选择（positive selection）的推断是进化基因组学领域广受关注的研究课题。通过识别基因组中携带适应性突变的推定区域，我们能够深入解析生物体的生物学特性及其演化历程。本文提出一种复合似然法（composite likelihood method），通过搜索基因组上单倍型频率谱（haplotype frequency spectrum）的空间分布相较于以全基因组中性预期为基准的极端偏离，来识别新近完成或正在进行的正选择事件。此外，该方法可同时推断选择性清扫（selective sweep）的两项参数：受选择清扫的单倍型数量，以及与选择强度和发生时机相关的清扫‘宽度’。我们证明，该方法优于当前主流的基于单倍型的选择统计工具，不过低重组区域中出现的强选择信号仍需额外审慎核查。作为阳性对照，我们将其应用于两个已被深入研究的人类群体……