Tajima’s D was calculated using the program Variscan [35]. After an exploratory data analysis of window size, we used a sliding window size of 1000 bp, and window increments of 100 bp for the analysis. Smaller window sizes resulted in too few SNPs in a window to calculate Tajima’s D, while larger windows made it much harder to narrow down specific SNPs that may be the ultimate target of selection. Variscan outputs a file giving the Tajima’s D value for every window of the specified bp size on the sliding scale [35]. These values were then superimposed onto graphs of the regions.
