Sequence similarity between the B6 and MSM and JF1 genomes. (A) Sliding window analysis of the discordance across chromosome 8 between the B6 and MSM or JF1 sequences. The reference B6 sequence was used for comparison with 500-kb windows and 100-kb sliding intervals. The horizontal blue line indicates a 99.85% sequence similarity level. Fine-scale phylogenetic discordance of chromosome 8 is shown below (PP indicates posterior probability). (B) Phylogenetic tree of the MDR sequences of wild-derived inbred strains. A neighbor-joining tree was generated for 67 concatenated MDR regions using MEGA4 software (Tamura et al. 2007). The 67 MDR regions show a single topology for B6/MSM, supported by a high posterior probability by BCA. The numbers adjacent to the branches indicate bootstrap values greater than 50 (1000 replicates). Subspecies names and the locations at which ancestors of the strains were collected are shown in parentheses. For more details, see Supplemental Table S1.
