FIGURE 3
FIGURE 3 Loci important to acidic adaptation, and their allele frequencies and haplotypes across samples. The lower panels in (a) show three exemplary genome regions exhibiting strong differentiation between the acidic and basic stickleback pools. The dots connected by lines represent individual SNPs, and the horizontal blue line indicates genome-wide median differentiation. The markers exhibiting the highest differentiation in these regions are marked by orange triangles and were included in the panel of adaptive SNPs (AFD => 0.85). The adaptive SNP on chromosome VII is the most strongly differentiated marker in our study, while the locus on chromosome IX showed the strongest acidic-basic differentiation in a previous genome scan (Figure 3A in Haenel et al. 2019) (the width of the visualized chromosome window is 100 kb for these two loci). The locus on chromosome XI is an inversion (window width is 600 kb). The panels above indicate for each freshwater and marine stickleback pool the frequency of the allele predominant in the acidic pool (acidic allele) at all SNPs within a 5 kb window centered at the three adaptive SNPs. Each SNP is a separate column. The NU pool combines marine individuals from the North Uist sites ARDH and OBSM. (b) Haplotype genealogies based on phased genotypes derived from individual sequencing at SNPs across the same 5 kb windows. Pies represent unique haplotypes and edges connecting pies or nodes indicate one inferred mutational step. Within each panel, sample size is given for one pie per size class. Note that the acidic populations generally share haplotypes highly distinct from those prevailing in the marine samples and in the basic populations.