2.13 | Recent nature selection analysis
Extended Haplotype Homozygosity (EHH) and iHS methods was used for detecting SNPs under strong positive selection of Captive and wild population, respectively(Mathieu & Renaud, 2012). We searched for genes in the 5-kb flanking region from both sides of candidate SNPs, and calculate the accumulated iHS scores by adding each iHS score of the top 0.5% SNPs. Next, to uncover genetic variants involved in adaptation of different environments, we performed comparisons between Captive and wild population. The XP-EHH method was used to detect selective sweeps using the R package rehh (v3.1.2;https://cran.r-project.org/web/packages/rehh/vignettes/rehh.html). We then split the genome into non-overlapping segments of 50 kb to use the maximum (positive) XP-EHH score of all SNPs. The regions with P values less than 0.01 were considered significant signals in the population of interest.