Signatures of selection detection
Two complementary methods (CLR and iHS) that were found to have
power > 70% to detect selection signatures were applied
(Ma et al., 2015). CLR values based on the variation in the
site-frequency spectrum along the chromosome were computed at 1000 grids
(-grid 1000) using the SweeD program version 4.0.0 (Pavlidis et al.,
2013) at each SNP. To generate phased haplotypes, SHAPEIT version 2.r900
(Delaneau et al., 2013) was used to perform haplotype phasing with
default settings. The ratio of extended haplotype homozygosities (EHH)
associated with each allele was calculated into standardized iHS
(|iHS|) values using the function “ihh2ihs”in rehh version 3.2.1 R package (Gautier et al., 2017). The iHS
analysis was conducted using unpolarized alleles, which is ideal for
non-model organisms that lack representative studies to allow for the
correct designation of ‘ancestral’ or ‘derived’ alleles (Santos et al.,
2021).