Detecting selection using extended haplotype homozygosity (EHH)-based statistics in unphased or unpolarized data

Analysis of population genetic data often includes the search for genomic
regions with signs of recent positive selection. One of the approaches
involves the concept of Extended Haplotype Homozygosity (EHH) and its
associated statistics. These statistics typically need phased haplotypes
and, some of them, polarized variants. Here, we unify and extend
previously proposed modifications to loosen these requirements. We compare
the modified versions with the original ones by measuring the False
Discovery Rate in simulated whole-genome scans and quantifying the overlap
of inferred candidate regions in empirical data. We find that phasing
information is indispensable for the accurate estimation of
within-population statistics for all but very large samples and of
cross-population statistics for small samples. Ancestry information, in
contrast, is of lesser importance for both. Our publicly available R
package rehh incorporates the modified statistics presented here.