Fig. 2
Local genealogical variation: a species phylogeny view. The illustration shows two different pairs of incongruent local genealogies evolving within a species phylogeny: one pair involving incomplete lineage sorting, and the other involving hybrid origin from two different parental populations. The species phylogeny involves three populations A, B, and H. Populations A and B diverged at time t 1. At time t 2, a hybridization event between the ancestral populations of A and B occurred, giving rise to a hybrid population H. a The genealogies of two different loci (green and blue) are shown. A lineage in H originated from the ancestral population of B with probability γ (blue locus) or the ancestral population of A with probability 1−γ (green locus). b The genealogies of two different loci (green and red) are shown. The H alleles at both loci originated from the ancestral population of A. For the green locus, the H lineage and A lineage coalesce between time t 2 and t 1. For the red locus, tracing backwards in time we find that no coalescence events occur until after time t 1, resulting in ancestral polymorphism and incomplete lineage sorting. Note that local genealogical variation can involve both topological differences (as shown here) and branch length differences