Examples of recombination events that create an outgroup clade.

Each panel shows an example of a local genealogical tree (solid lines) for the currently sampled yeast populations (green), with samples from the wine/European (W/E), North American (N.A.), sake (S), West African (W.A.), and Malaysian (M) populations. In each panel, a dot indicates a recombination event. The dashed line indicates the recombinant lineage, which determines a new local tree on the other side of the breakpoint in which the three Malaysian strains are now at the outgroup position. In the absence of gene flow from an unsampled donor, two possible causes are A, the recombination occurred in a lineage ancestral to the Malaysian samples; and B, the recombination occurred in a lineage not ancestral to the Malaysian samples. C, Gene flow into the Malaysian population from an unsampled source (orange) will manifest as an inference of the former type of recombination.