The following supporting information is available for this article:

Figure S1. Capture specificity.

Figure S2. Capture uniformity.

Figure S3. FST distributions.

Figure S4. Distribution of FST by position on scaffolds.

Figure S5. Correlation between FST values at different SNPs against the distance between SNPs.

Figure S6. Comparison of the ratio πa/πs between host races and the ratio πa/πs within host races.

Figure S7. Neutrality index (NI) for outlier and nonoutlier genes.

Table S1. Target genes.

Table S2. Number and type of genes under study: from initial to analyzed targets.

Table S3. Read numbers and mapping.

Table S4. All SNPs.

Table S5A. Outlier SNPs—global analysis.

Table S6. Outlier genes probability &equals; Poisson probability of the observed or a greater number of SNP outliers given the number of SNPs in the gene and the overall proportion of outliers in red: P < 0.05 in gray shade: genes with three or more outlier SNPs in their sequence.

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