Figure 4.

Schematic model of genome inversions. The model shows an initial speciation event, followed by a series of inversions in the different lineages (A and B). Inversions occur between the asterisks (^*). Numbers on the chromosome refer to hypothetical genes 1-32. At time point 1, the genomes of the two species are still co-linear (as indicated in the scatterplot of A1 versus B1). Between time point 1 and time point 2, each species (A and B) undergoes a large inversion about the terminus (as indicated in the scatterplots of A1 versus A2 and B1 versus B2). This results in the between-species scatterplot looking as if there have been two nested inversions (A2 versus B2), similar to that seen for C. trachomatis versus C. pneumoniae (see Figure 2). Between time point 2 and time point 3 each species undergoes an additional inversion (as indicated in the scatterplots of B2 versus B3 and A2 versus A3). This results in the between-species scatterplots beginning to resemble an X-alignment, similar to that seen in M. tuberculosis versus M. leprae (see Figure 2).