Figure 3.

Patterns of sequence variation differ on marine and freshwater stickleback chromosomes. (A–C) Genome-wide sequence diversity (π) as a function of the distance from a RAD locus with reciprocal monophyly of marine and freshwater haplotypes. Diamonds show average sequence diversity among reciprocally monophyletic RAD loci. Density of RAD loci at x distance from the nearest reciprocally monophyletic locus with y level of diversity is shown in shades of gray. Bold lines are smoothed splines, dashed lines are genome-wide means. (A) Sequence diversity in the combined dataset [marine (RS) + freshwater (BT and BP)]. (B) Sequence diversity on chromosomes carrying marine haplotypes. (C) Sequence diversity on chromosomes carrying freshwater haplotypes. (D) Smoothed splines as in (A–C). (E) Splines as in (A–D) of Watterson’s θ. (F) θ_W of RAD loci within 0.5 Mbp of a reciprocally monophyletic RAD locus and on chromosomes not carrying a reciprocally monophyletic locus (“unlinked”). Data are means ± 1 SD ***P < 0.001.