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.