Probability density function of Wallace values for simulated populations. Multilocus sequence types of a pneumococcal population were generated with an adapted infinite allele model . It includes an additional locus for CSP type and a new parameter IPR that, given a recombination event, defines the probability that the two recombining strains have different pherotypes. The prevalence of each pherotype in the population was fixed during the simulation at 70% for CSP-1 and 30% for CSP-2. (A) From 1,000 simulations, the probability density functions of Wallace values for Clonal Complex predicting pherotype were computed for three scenarios: (1) pherotype is a barrier to recombination (IPR = 0.1, red line), (2) pherotype has no impact in gene exchange (equivalent to IPR = 0.42, black dashed line) and (3) inter-pherotype recombination is favored (IPR = 0.9, green dotted line). The vertical blue line indicates the observed Wallace value in the studied sample. (B) To identify the value of the IPR parameter that is in best agreement with the data, the probability density at the observed Wallace values was computed for simulated populations with varying inter-pherotype recombination probabilities (IPR from 0.1 to 0.9), both for Wallace indexes of sequence type (blue line) and of clonal complex (red line) predicting pherotype.