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.