Table S1 Sequences of primers used for classical AFLPs, profile reduction analyses and candidate gene sequencing.

Table S2 Demographic history of the Aedes aegypti Bti-resistant strain.

Table S3 Blast results and outlier location in the Ae. aegypti genome.

Table S4 DNA variation and divergence at sequenced loci.

Fig. S1 A, plot of Fst values against heterozygosity estimates obtained with Dfdist. Each dot indicates an AFLP marker and lines represent the 95% confidence interval. B, plot of Fst values against logit of posterior probabilities obtained with BayeScan. C, plot of logit of posterior probabilities from BayeScan against logit of empirical p-values from Dfdist. Outliers are indicated in red.

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