Fig. S1 Phylogenetic relationship between fog (A), pcl (B) and mav (C) haplotypes of the D.  melanogaster subgroup.

Fig. S2 Frequency distribution of the different mitochondrial groups per collection.

Table S1 Collection details and samples sizes used for each analysis.

Table S2 List of primers used for amplification and sequencing for mitochondrial and nuclear genes, and microsatellites.

Table S3 Expected heterozygosity based on random discarded datasets.

Table S4Fst between collections.

Table S5 Sample identification labels and haplotypes.

Table S6 Parameter estimates of the IM model.

Table S7 Percentage of Wolbachia infected and uninfected individuals for a given fly collection.

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