Duplications, losses, and deep coalescence. In A–C, evolutionary events are depicted using the unified model (left), the gene tree evolving “inside” the locus tree (middle), and the LCT (right). (A) Gene duplication was discussed in Figure 1. Evolution within a single species tree branch is shown. (B) Similar to duplication, a gene loss starts in one chromosome and drifts until it fixates or goes extinct. Evolution within a single species tree branch is shown. (C) Deep coalescence occurs when two lineages fail to coalesce before either can coalesce with a third lineage. This results in extra lineages at the top of a locus tree branch (top). Within a single species tree branch, multiple lineages can exist at the top of a locus tree branch created by a speciation (middle) or at the top of a locus tree branch created by a duplication (bottom). (D) Events are counted in the LCT of Figure 1D.
