Figure 1. Genome-wide distribution of variation.

Divergence (Dxy) between the D. pseudoobscura (Dpse) and each of D. persimilis (Dper, black line) and D. miranda (Dmir, blue line) is estimated in overlapping 500 kbp windows (100 kbp steps) across chromosome arms 2, 4, XL, and XR. All chromosome arms are presented from the telomere to centromere (left-to-right), though the sequence assemblies start well outside both the telomere and centromere in each case. Nucleotide diversity (Pxy) is estimated as the pairwise differences between genomic sequences of two strains of D. ps. pseudoobscura (red line). The breakpoints of the inversions distinguishing D. ps. pseudoobscura and D. persimilis are superimposed on each chromosome (rounded brown rectangle) and on the graph (vertical brown lines). The region where recombination is suppressed in hybrids is boxed in gray. Contigs from chromosomes are oriented and ordered according to previous studies. Each chromosomal increment is 5 Mbp. The positive control locus, Adh, is highlighted on chromosome 4 group 1.