Histogram of the parsimony score Sp of the presence/absence of the variable regions of size greater than 500 bp, computed for the tree shown in Figure 1. For a given dispensable region, Sp represents the number of acquisition and loss events (Sp = Na + Nl, where Na and Nl are the number of acquisitions and losses, respectively) required for its pattern of presence/absence on the tree in Figure 1. The colors indicate the number of acquisitions Na, while the number of losses can be calculated as Nl = Sp -Na. For simplicity, all segments with Na > 1 have been collapsed in a single bar. Since an acquisition followed by a recombination event can always be explained by multiple acquisitions, events with Na > 1 are possible intra-species recombination events.
Donati et al. Genome Biology 2010 11:R107 doi:10.1186/gb-2010-11-10-r107