Figure 3.

Generative process for the DLCoal model. (A) Given a species tree S with known topology and divergence times, a top-down dup-loss process generates a locus tree T^L, which contains duplication nodes (star), and each daughter duplicate is indicated by a daughter edge δ^L (dark red). From the locus tree, the bottom-up multilocus coalescent (MLC) process generates a gene tree T^G. Mappings between the trees represented by R^G and R^L indicate how one tree “fits inside” the other. This diagram depicts the same gene family as Figure 2A. (B) The multispecies coalescent and dup-loss model are special cases of DLCoal. When there are no duplications or losses (i.e., locus tree and species tree congruence), the model simplifies to the multispecies coalescent. (C) When ILS is assumed not to occur (i.e., gene tree and locus tree congruence), the model simplifies to the birth–death model for duplication and loss.