Fig. 1.

Ruff male phenotypes and inversion haplotypes. a) Left: 3 male ruff phenotypes: independent, faeder, and satellite (illustrations reproduced with permission of Lynx Edicions). Chromosome 11 alignments between satellite and independent assemblies with the 4.3-Mb inversion highlighted in red. Right: a graphical representation of the ancestral independent chromosome 11, inverted faeder chromosome, and the recombined satellite chromosome. Satellites and faeders are heterozygous for inversion haplotypes and Independents are homozygous for the noninverted haplotype. b) Genetic divergence estimated by F_ST in 15-kb rolling windows between all 3 chromosomal arrangements across chromosome 11. The 4.3-Mb inverted region is highlighted by a red box marking the 5.55- and 9.89-Mb breakpoints. Blue boxes mark the recombinant regions in the satellite haplotype. c) Local phylogenetic trees for the nonrecombinant (high F_ST between independents and satellites) and recombinant regions (low F_ST between independents and satellites) based on 16 independents, a single satellite and a single faeder individual. The background colors used for the high and low F_ST trees are the same as used to highlight these regions in Fig. 1b.