Figure legend
Figure 1 (a) Map of sampling locations. Annual sea surface temperature
is indicated. (b) Genome-wide distribution of nucleotide diversity in 40
kb non-overlapping windows.
(c) Admixture analysis of the five Sillago japonica populations.
The length of each colored segment represents the proportion of the
individual genome inferred from ancestral populations (K = 2–6).
(d) Principal components 1 and 2 for the 49 Sillago japonicaindividuals. (e) Neighbor-Joining tree constructed using p-distances
among the 49 Sillago japonica individuals.
Figure 2 Plot of pairwise estimates of F ST/ (1 −F ST) versus two types of geographic distances
(coastal distance and oceanic distance) between the populations.
Figure 3 Demographic history for each population inferred from PSMC
analysis.
Figure 4 Pattern of population splits and mixture between the fiveSillago japonica populations. The drift parameter is proportional
to Ne generations, where Ne is the effective population size. Scale bar
shows the average standard error of the estimated entries in the sample
covariance matrix.
Figure 5 Genomic regions with strong selective signals in populations ofSillago japonica. (a) Distribution of
log2(θ πratios) andF ST values calculated in 40 kb sliding windows
with 20 kb increments between the RS/ZS populations (ZS as control
group). The data points in red (corresponding to the top 5% of
empirical log2[θ π ratios]
ratio distribution with values of >0.1204 and the top 5%
of F ST distribution with values
of >0.0904) are genomic regions under selection in the RS
population. (b) Overlap candidate genes of the RS/ZS and RS/ST pairs
based on a Venn diagram. (c) Overlap candidate genes of the ST/ZS and
ST/RS pairs based on a Venn diagram. (d) Overlap candidate genes of the
ZS/RS and Japan/RS pairs based on a Venn diagram. (e) Allele frequency
of one SNP within the cold-temperature adaptation genePicalm across the five S. japonica populations. (f) Allele
frequency of one SNP within the high-temperature adaptation geneARHGAP42 across the five S. japonica populations. (g)
Allele frequencies of one SNP within the warm-temperature adaptation
gene SORCS3 across the five S. japonica populations.
Figure 6 PCA based on the SNPs located in the candidate genes (a,
cold-temperature adaptation genes; b, high-temperature adaptation genes;
c, warm-temperature adaptation genes).
Figure 7 Top 20 KEGG pathway enrichment statistics for the candidate
genes.
Figure 8 The predicted potential distribution (a, b), changes in habitat
suitability (c) of China group under RCP45 scenarios and (d) response
curves of predicted occurrence probability of China group against
temperature.
Figure 9 The predicted potential distribution (a, b), changes in habitat
suitability (c) of Japan group under RCP45 scenarios and (d) response
curves of predicted occurrence probability of Japan group against
temperature.