This PDF file includes:

• fig. S1. Genotype frequencies of SNP outliers for A. fragilis.
  
• fig. S2. Genome-wide pairwise differentiation (F_ST) of populations.
  
• fig. S3. Genetic structuring of S. intersepta populations based on most divergent SNPs.
  
• table S1. Details of the sampled A. fragilis and S. intersepta populations.
• table S2. Estimators of the number of STRUCTURE clusters for A. fragilis and S. intersepta.
  
• table S3. Genome-wide pairwise differentiation (F_ST) of populations.

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