Figure 3.

Select 50 kb windows of the genome with high divergence ($F_{ST}$) and either low normalized ${\theta }_{\pi }$ (A) or Zeng’s E (B and C) of almond (green) and peach (orange). Genes annotated in the peach reference genome are represented in the $F_{ST}$ plot by boxes colored by their location on the plus strand (blue) or minus strand (red). In the $F_{ST}$ plots, the gray lines indicate the upper 5% threshold, whereas in the ${\theta }_{\pi }$ and Zeng’s E panels the gray lines indicate the lower 5% thresholds of almond (dashed) and peach (dotted). Regions of interest, as described in the text, are boxed across adjacent panels and genes labeled. (A) S-locus divergence and diversity with S-locus genes, SFB (blue), and S-RNase (red), located on opposite sides of the central gap. Diversity in peach is drastically reduced immediately 3′ to SFB but only somewhat reduced 3′ to S-RNase, as might be expected for a linked locus. (B) and (C) Loci of interest on chromosome 3.