Fig. S1 Plots of (a) π, (b) θ and (c) Tajima's D, across the genome based on sliding windows analysis, with nonoverlapping windows of 100 Kb. The orange line represents the Winters population, and the blue line is the estimate for Raleigh.

Fig. S2 Plots of θST between Winters and Raleigh populations for nonsynonymous positions for all chromosome arms except 3L (Fig. 2). Red lines represent the 0.1% quantile.

mec12468-sup-0001-TabS1-5.docWord document133K

Table S1 Mean estimates of π, θ and Tajima's D for all chromosome arms and the X chromosome for all site categories.

Table S2 List of highly differentiated genomic regions spanning <50 Kb.

Table S3 List of genes with highly divergent nonsynonymous changes between Raleigh and Winters. ‘NSYN’ indicates the total number of nonsynonymous changes and θST is the mean θST value across the nonsynonymous positions.

Table S4 Linkage disequilibrium analysis for the highly differentiated region in chromosome 3L (20 190 000–20 240 000) between Winters and Raleigh.

Table S5 Pairwise FST analysis for the gene Obst-F (FBgn0036947) between Winters, Raleigh, and two sets of samples from the southeastern United States (SEUS) and several Caribbean locations.

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