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.