I would appreciate the opinions of anyone with experience running XPEHH. I have run this haplotype based selection test on phased whole genome SNP data to compare two recently split non-human populations. I am trying to detect regions of population specific selection.
I expected to see regions with a peak XPEHH score flanked by a decay in the score as the linkage breaks down. However occasionally I see very sharp peaks in the XPEHH score of only a MB in length (eg the peak at about 86Mb in the figure linked to below)
Do people have suggestions about how to interpret these sharp peaks? My first thought is that it is the result of some kind of error in the SNP calling. Maybe it is from a population specific recombination hotspot but the populations only split ~100 generations ago so this seems unlikely. Any thoughts or questions are welcome regarding how to interpret such a plot when looking for selection with XPEHH.
Thanks in advance for your help,