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Fig. S1 Qualitative comparisons of FST between populations in similar environments (left panels) and different environments (right panels). These results are for the last iteration of each simulation with the smaller population size (100). See Fig. 3 caption for an explanation of the boxplot conventions.

Fig. S2 Results of statistical analyses (100 bootstrap comparisons of 95% confidence intervals) for when FST comparisons reveal the expected signature of ecological speciation. The y-axis shows the fraction of simulations in which FST was significantly greater between populations in different environments than between population in similar environments. These results are cumulative for the last 100 iterations of each simulation with the smaller population size (100). See Fig. 3 caption for an explanation of the boxplot conventions.

Fig. S3 Comparisons of confidence limits obtained with 100 versus 10000 bootstraps (larger minus smaller bootstraps, y-axis) relative to the estimated FST with 10000 bootstraps (x-axis) for populations in different (top panel) or similar (bottom panel) environments. The key observation is that the two bootstrap levels show consistent upper confidence limits for similar environment and consistent lower confidence limits for different environments. The result is no bias when using 100 bootstrap confidence limits to infer the expected signature of ecological speciation.

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