2.10 | Recent natural selection analysis
Extended Haplotype Homozygosity (EHH) and iHS methods were used for detecting SNPs under strong positive selection of the captive and wild population, respectively (Mathieu & Renaud, 2012). We use the data2haplohh (), scan_hh () and ihhh2ihs () functions of the R package rehh (v3.1.2) to calculate the iHS scores (Mathieu & Renaud, 2012). We took the Top 0.5% iHS score as the loci with strong positive selection. We added accumulated iHS scores at intervals of genes. The XP-EHH method was used to detect selective sweeps using the rehh (v3.1.2). 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 Pvalues less than 0.01 were considered significant signals in the population of interest.