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 the 1000 Genomes Project and examine haplotype frequency spectrum patterns at the LCT and MHC loci. We also apply it to a data set of brown rats sampled in NYC and identify genes related to olfactory perception. To facilitate use of this method, we have implemented it in user-friendly open source software.Author summary: Identifying regions of the genome that contain adaptive variation is of fundamental interest in evolutionary biology, providing insight into an organism’s history and biology. When positive selection is recent or ongoing, we expect to find genomic patterns such as high frequency haplotypes and low genetic diversity in the vicinity of the adaptive locus. Here we develop a statistic to identify these regions based on distortions of the haplotype frequency spectrum from a background distribution. We evaluate the performance of this statistic under numerous realistic settings of interest to empiricists and demonstrate its superior performance relative to other haplotype-based selection statistics. We also apply this statistic to real population-genetic data. As a positive control, we explore two well-studied loci, LCT and MHC, in a European and an African human population that show strong evidence for selection. We also apply this statistic to the genomes of an urban brown rat population, where we uncover evidence for adaptation in olfactory perception genes. We release user-friendly software implementing this statistic.