Figure 10

Overview of data simulation.

Step 1: The simulation starts with a single ancestor and generates 16 sequences, which serve as ancestors for each group (variation between groups). Step 2: Within each group we generate 16 descendants (variation within groups), then add LGT events between these groups. Step 3: Finally we simulate variation post-LGT, which may include deletion. From each initial ancestor the simulation generates 256 sequences. Symbols: DNA sequences which are ancestors of the sequence groups. Phylogenetic tree used to generate populations of each group. DNA sequences that constitute groups. LGTs events are added between them. LGT between two sequences. Phylogenetic tree on which the evolutionary process post-LGT is simulated. This process tends to obscure the LGT events. Branch length determines the ‘age’ of the LGT events. Regions of the sequences may be deleted at this step. DNA sequences generated by the simulation.