Figure 2

Scenarios of recombination and pseudogene formation in Paratyphi A and Typhi. (a) True distribution of pseudogenes in the Paratyphi A AKU_12601 and Typhi CT18 genomes (gene order based on gene co-ordinates in Typhi CT18). (b-c) Distribution of pseudogenes resulting from data simulated under two scenarios, under both of which 40 pseudogenes are inherited from the most recent common ancestor of Paratyphi A and Typhi, and extensive accumulation of pseudogenes occurs before or after recombination of 25% of genes. For ease of simulation, the recombination shown is uni-directional, but bi-directional exchange would result in similar patterns. (b) Scenario 1: 150 additional pseudogenes accumulate in each serovar, followed by recombination. (c) Scenario 2: only 20 additional pseudogenes arise before recombination, after which a further 150 pseudogenes accumulate in each serovar.