Nucleotide Variation Pattern and Selected Analysis
Nucleotide diversity (π) was calculated for the four groups using a 100
kb nonoverlapping sliding window and VCFtools (Danecek et al., 2011).
Additionally, the fixation index (Fst) between each of the four groups
was calculated by VCFtools (Danecek et al., 2011) using SNPs. PopLDdecay
(C. Zhang, Dong, Xu, He, & Yang, 2019) software was applied to compute
linkage disequilibrium (LD) decay among different groups and chromosomes
separately. To avoid the influence of LD on subsequent association and
selection analysis, we employed PLINK v.1.9 (Purcell et al., 2007) to
filter SNPs with the following parameters: –indep-pairwise 50 10 0.2.
The filtered data with 151,577 SNPs were phased using Beagle v.3.3.2
(Browning & Browning, 2007). To explore the effect of local adaptation
on 12 quantitative traits, we used the single-phenotype Qst-Fst test
with the R package ‘QstFstComp’ (Gilbert & Whitlock, 2015). If Qst
> Fst, the differentiation of traits is the major effect of
divergent selection and shows local adaptation. We used the half-sib dam
model and 10000 resampling steps for each QstFstComp analysis. To
identify candidate loci under natural selection from 151,577 SNPs, we
used BayeScan v.2.1 (Foll & Gaggiotti, 2008) software with default
parameters, and PGDSpider (Lischer & Excoffier, 2012) was used to
produce an input file for BayeScan. SNPs with a q value lower than 0.05
were considered potentially selected loci.