looking for SNP under selection - is Hardy-Weinberg Equilibrium important?
0
0
Entering edit mode
4.1 years ago
peter • 0

Hello,

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

HWE bayescan RADseq SNP Outlier • 1.7k views
ADD COMMENT

Login before adding your answer.

Traffic: 2088 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6