Phylogenetic tree of mitochondria based on 291 genome-wide SNPs. ML tree (mid-point rooted) based on SNP-data from 45 samples of historic and contemporary samples that were either infected with wMel (blue) or wMelCS (red) and uninfected specimens are shown in white. The 24 historic samples that were included in this analysis are highlighted in green. Roman numbers indicate clusters that correspond to subgroups of D. melanogaster-specific Wolbachia strains as previously defined by Richardson et al. (2012). Blue numbers indicate bootstrap values > 75% from 100 rounds of bootstrapping.