BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Fig 4
The multispecies coalescent (MSC) model with three species and a single gene tree.
A separate coalescent process applies to each of the five branches in the tree; the branches for the extant species A (red), B (green) and C (blue), the ancestral branch of A and B (yellow), and the root branch (grey). Several individuals have been sampled per species. In this example the ancestral lineage of individual b4 does not coalesce in species B or ancestral species 4. In ancestral species 5, it coalesces with the ancestral lineage of species C. This leads to incomplete lineage sorting and enables gene tree discordance—in this example b4 is a sister taxon to individuals from species C, rather than to individuals from its own species, or sister species A. If b4 was the representative individual for its species, then this gene would exhibit gene tree discordance. Other individuals which show concordance at this locus are expected to show discordance at other unlinked loci when populations are large or speciation times are recent.