Fig. 1.

Simulations of bacterial recombinations. The diagram shows the underlying simulation method, and here the case of P = 2 populations is considered: blue and red. Populations were simulated under a clonal model of evolution for a given set of parameters (see Methods section). Three types of recombinations were then simulated using the clonal alignment. Ancestral recombinations (case 1) occurred before the most recent common ancestor of both populations, and thus were present in all isolates of the recipient lineage. Intermediate recombinations (case 2) occurred sometime between the time when populations emerged and present time (t = 0), and thus were typically present in multiple isolates. Recent recombinations (case 3) occurred in the last few generations, and thus were typically present in few isolates. To clarify, our method identifies events of type 1 as ancestral recombinations, whereas all other recombinations, affecting less than any whole lineage (cases 2 and 3), are inferred as multiple recent recombinations present in multiple individual strains.