Figure 3.
The rate of linkage disequilibrium (LD) varies with the Glossina fuscipes fuscipes population. Pairwise LD between SNPs located in the same supercontig was estimated from all individuals of all populations using Vcftools v. 0.1.12 (Danecek et al. 2011) as r2. Each “dot” represents the mean LD for that set of binned SNP-pairs. The color of the dot illustrates the number of SNP-pairs contributing to the mean; the color scale is shown in the right vertical bar. The blue line is a loess regression line of best fit, and the purple line corresponds to r2max/2. (A) Masindi, MS; (B) Namutumba, NB; and (C) Otuboi, OT.