Fig. 2: Divergent regions on chromosome 1, 3, and 5 in the southern assembly.
From: Inversions maintain differences between migratory phenotypes of a songbird
The top panel shows genetic differentiation (FST) between 11 resequenced samples from each subspecies for variants with a minor allele frequency (MAF) ≥ 0.1, with blue lines representing a weighted average for MAF ≥ 0.1 bi-allelic SNPs in 10 kb non-overlapping windows. Below, scaffolds or chromosomes (chr) in each assembly matching the divergent regions are shown as light green rectangles (with ID and plotted orientation) and predicted upstream and downstream scaffolds as light blue and light purple rectangles, respectively. Blue segments on scaffolds show the location of large tandem arrays at the ends or breakpoint regions, black segments represent gaps and gray segments the location of 31 kb duplicated intervals in the chromosome 5 region on the northern assembly. Yellow lines above scaffolds represent 1:1 alignment intervals (≥2 kb) to scaffolds in the southern assembly. For chromosome 5, the second inversion interval has been highlighted in orange to improve visibility. The zebra finch genome shows the same major structural differences as seen in the flycatcher genome and has, therefore, not been included.
