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.