Extended Data Figure 9 |. Population genomic structure and QTL analysis of Ae. aegypti strains.

a, Chromosomal patterns of nucleotide diversity (π) in four strains of Ae. aegypti measured in 100 kb non-overlapping windows and presented as a LOESS-smoothed curve (Extended Data Fig. 9a-b). b, Mean nucleotide diversity in four colonized strains of Ae. aegypti, with standard deviation indicated in parentheses. Nucleotide diversity (π) was measured in non-overlapping 100 kb windows. The Liverpool and Costa Rica colonies maintain extensive diversity despite being colonized in the laboratory more than a decade ago, but show reduced genome-wide diversity (on the order of 30–40%) relative to the more recently laboratory colonized Innisfail and Clovis c, Pairwise linkage disequilibrium (LD) between SNPs located within the same chromosome estimated from 28 wild-caught individuals from the indicated populations. Each point represents the mean LD for that set of binned SNP-pairs. Solid lines are LOESS-smoothed curves, and dashed lines correspond to r ² _max /2 (Extended Data Fig. 9a-b). Inclusion of additional individuals available from the Amacuzac population (up to 137) had a minimal effect on the LD estimations (ΔR² < 0.017; data not shown). d, Table of linkage disequilibrium (r²) values along the Ae. aegypti AaegL5 genome assembly based on pairwise SNP comparisons. Data were obtained from the average r² of SNPs in 1 kb bins.