2.8 | Recent nature selection analysis
Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score
(iHS) methods were used for detecting SNPs under recently positive
selection of three roundworm populations (Mathieu & Renaud, 2012). We
use SNPs with an iHS score of top 0.5% and the distance between
adjacent SNPs < 50 kb as candidate SNPs (Akagi, Hanada,
Yaegaki, Gradziel, & Tao, 2016). We searched for genes in the 5-kb
flanking region from both sides of candidate SNPs, and calculate the
accumulated iHS scores by adding all iHS scores of candidate genes.
Next, to uncover genetic variants under strong positive selection in
each host population, we used XP-extended haplotype homozygosity
(XP-EHH) method on each pair of combination (horse roundworm (PEc) vs
zebra roundworm (PEz), horse roundworm (PEc) vs donkey roundworm (PEa)
and PEz vs PEa) to find population-specific SNPs under strong positive
selection. XP-EHH we used in this study was from the R package rehh
(v3.1.2;
https://cran.r-project.org/web/packages/rehh/vignettes/rehh.html).
The regions with P values < 0.01 were considered
significant signals in the population of interest.