I have a large RADseq database of wild-caught samples (~200) that are haplodiploid, though i only have female (diploid) samples. These samples are from 4 locations and comprise 3 species located at each site. I have called SNPs for them with the intention of now identifying if there are any loci with signatures of selection within species or between sites.
I will use a couple of packages to do this (bayescan, SelEstim, Arlequin) but i'm unsure about weather or not i should filter loci based on Hardy-Weinberg Equilibrium. I was originally told to only use loci that fall within the HWE. but wont this just leave me with loci that are showing only neutral selection? surely i should either not filter by HWE at all, or select just those that do not fall within the HWE?
I have run bayescan with just loci within the HWE and non go beyond the FDR threshold.
What are peoples thoughts? is it reasonable to look at those outside HWE
fyi, i use genepop to identify HWE where p>0.05 are in HWE