Detecting selection using Extended Haplotype Homozygosity-based
statistics on 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 on simulated whole-genome scans and quantifying the
overlap of inferred candidate regions on 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.