Figure 3

Pseudogene formation in the evolutionary histories of Paratyphi A and Typhi. Phylogenetic tree based on multiple alignments of all nonrecombined genes as defined in [15], rooted using S. bongori and E. coli as outgroups. Scale bar is nucleotide divergence. The timing of the recombination between Paratyphi A and Typhi is an approximation inferred from published divergence data [15]. Group (i) pseudogenes were inactivated prior to the divergence of Paratyphi A and Typhi, some are also inactivated in Typhimurium and Paratyphi B; following their divergence Paratyphi A and Typhi likely accumulated few additional pseudogenes; during the recombination of 23% of their genomes (direction of transfer unknown) 18 pseudogene sequences were shared between Paratyphi A and Typhi, including five non-ancestral pseudogenes (group ii); many pseudogenes were formed during a period of accelerated pseudogene accumulation in both serovars, including most group (iii) pseudogenes; pseudogenes continue to accumulate in individual sub-lineages after the most recent common ancestor of each serovar (group iv).