Screening for selective sweeps
The pairwise F ST revealed by the snx 33 gene indicated significant genetic differentiation among different S. schlegeli populations (SCS vs. YS, F ST = 0.057,p < 0.001; SCS vs. ECS, F ST = 0.058, p < 0.05) (Table S6). We calculated the genome-wide nucleotide diversity (Pi) and population-differentiation statistic (F ST) for each population using a 50kb sliding window with a 10kb step size. Selected genomic regions invariably show specific patterns of variation, such as high population-differentiation statistic (F ST) and lower levels of nucleotide diversity (Pi) (Ellegren & Sheldon 2008; Sabeti et al. 2006; Wang et al.2015). We calculated the distribution of π ratio and F STvalues to identify the selected regions for the north (YS-ECS) and SCS populations, and we inferred the selected genome regions from high π log-ratios and an extreme divergence of allele frequencies (Figure 3a,b). Most of the genome regions shows a low level of differentiation (Figure 3b), and the differentiated genome regions harbored 143 annotated protein-coding genes, including cold shock domain-containing protein E1 (csde1 ), paired box protein 7 (pax7 ), eyes shut homolog gene (eys ), retinal structural protein (rx3 ), and retinal guanylate cyclase (retgc-2 ), et al (Table S7), which we assumed to be subject to selection. The Gene Ontology annotations on these genes were conducted to further understand their regulatory functions (Figure 3c). The selection sweep analysis of the candidate gene eys revealed high Pi value difference and an extreme divergence of allele frequencies. (Figure 3d).