PT  - JOURNAL ARTICLE
AU  - Alexandre M. Harris
AU  - Nandita R. Garud
AU  - Michael DeGiorgio
TI  - Detection and classification of hard and soft sweeps from unphased genotypes by multilocus genotype identity
AID  - 10.1101/281063
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 281063
4099  - http://biorxiv.org/content/early/2018/03/12/281063.short
4100  - http://biorxiv.org/content/early/2018/03/12/281063.full
AB  - Positive natural selection can lead to a decrease in genomic diversity at the selected site and at linked sites, producing a characteristic signature of elevated expected haplotype homozygosity. These selective sweeps can be hard or soft. In the case of a hard selective sweep, a single adaptive haplotype rises to high population frequency, whereas in a soft selective sweep, multiple adaptive haplotypes sweep through the population simultaneously, producing distinct patterns of genetic variation in the vicinity of the selected site. Measures of expected haplotype homozygosity have previously been used to detect sweeps in a number of study systems. However, these methods are formulated for phased haplotype data, which is typically unavailable for nonmodel organisms, and may have reduced power to detect soft sweeps due to their increased genetic diversity relative to hard sweeps. To address these limitations, we applied the H12 and H2/H1 statistics of Garud et al. [2015] to unphased multilocus genotypes, denoting them as G12 and G2/G1. G12 (as well as the more direct expected homozygosity analogue to H12, denoted G123) has comparable power to H12 for detecting both hard and soft sweeps. G2/G1 can be used to classify hard and soft sweeps analogously to H2/H1, conditional on a genomic region having high G12 or G123 values. The reason for this power is that under random mating, the most frequent haplotypes will yield the most frequent multilocus genotypes. Simulations based on human parameters suggest that methods are best suited for detecting recent sweeps, and increase in power under recent population expansions. Finally, we find candidates for selective sweeps within the 1000 Genomes CEU, YRI, GIH, and CHB populations, which corroborate and complement existing studies.