Figure 4: Population genetic variation for inversion and standard groups.

a,b, Nucleotide diversity (π, a) and Tajima’s D (b) of the inverted genomic region (yellow), block D of chromosome 1 (red), and chromosomes 2–7 (blue) in the inversion (INV) and standard (STD) genotypes. Block D (south end of LG1) is treated separately because it has unusually high polymorphism in related species. In these box plots, the median is shown by a horizontal line, while the bottom and top of each box represents the first and third quartiles. The whiskers extend to 1.5 times the interquartile range. Outliers are represented by black dots. c, Distribution of population genetic statistics along chromosome 1. Nucleotide diversity (π) in INV (red) and STD (blue) genotypes, with genome-wide averages shown as dashed horizontal lines. Linkage disequilibrium (r²) between the inversion and SNPs is shown for all INV and STD genotypes from the inversion zone, and the relationship between physical and linkage maps. The dashed vertical lines mark the inverted (gold) and block D (light blue) regions. N = 122 genotypes, except for the LD (r²) analysis where four admixed individuals were excluded. LD for 10 comparator SNPs with derived allele frequencies similar to Bsi1-inv is shown in Supplementary Figure 8b.