Figure 1.

Simulation of four-taxon sequence evolution with a single (a) reciprocal or (b) non-reciprocal recombination event. The simulation of sequence substitution was divided into three phases: a pre-recombination phase representing the evolutionary history prior to recombination; a recombination phase in which the recombination event occurs; and a post-recombination phase representing subsequent evolution after the recombination event. The recombination event was either (a) reciprocal or (b) non-reciprocal in nature: in both cases recombination was performed between a predefined pair of breakpoints r₁ and r₂. The lineages of length θ₁ and θ₂ represent the pre- and post-speciation lineage respectively, at the pre-recombination phase. In a reciprocal recombination event, the segments of sequences 2 and 3 between the recombination breakpoints were exchanged. As a consequence, the canonical relationships between sequences were preserved in the non-recombined region, with sequence pairs (1,2) and (3,4) most-similar to one another, while in the recombined region sequence pairs (1,3) and (2,4) were most-similar. In a non-reciprocal recombination event, the region of sequence 3 between breakpoints r₁ and r₂ was replaced by the homologous region from sequence 1, while sequences 2 and 4 did not donate or receive any genetic material. The recombined regions of sequences 1 and 3 were identical immediately after a non-reciprocal event. During the post-recombination phase, subsequent substitutions were simulated no each sequence independently at λ substitutions per site.