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).