Figure 1

The three submodels of DLRS are shown. (A) Evolution of a gene lineage inside a species tree edge is modeled by a birth-death process. A gene lineage may come across a duplication event (represented by a green vertex), or a speciation event (represented by a black vertex). Every time a gene lineage passes through a speciation event, it splits into two independent gene lineages. A gene lineage may also be lost (represented by a red cross). After pruning all lost lineages, the final gene tree is obtained. (B) A relaxed molecular clock is employed to achieve branch lengths. (C) Finally, a standard sequence evolution model generates sequences over the gene tree with branch lengths.