Figure 3

Evolution of a FUE is reticulate on the micro scale but tree-like on the macro scale. The cartoon schematically depicts the evolution of 4 FUEs shown by different colors. The divergence history of each FUE was simulated under the model of random homologous recombination, with the probability of recombination exponentially decreasing with sequence divergence. At each simulation step, the two daughter FUEs diverge by a constant amount (clock-like divergence) and either undergo homologous recombination (which brings the difference between the two back to zero) or not, preserving the existing state of divergence. After a number of short periods of divergence and recombination, the FUEs stochastically diverge far enough for recombination to become extremely unlikely after which point they continue diverging without recombination. At a macro scale this appears as a simple bifurcation in the tree-graph.