Figure 1

Pseudogenization, Duplication, Loss, Sequence evolution & Rates (PDLRS). Evolution of a gene and pseudogene lineages inside a species tree edge is modelled by a birth-death process. A gene/pseudogene lineage may come across a duplication event, or a speciation event. A gene lineage (represented by black lineages) may convert into a pseudogene lineage (represented by brown lineages). Every time a gene/pseudogene lineage passes through a speciation event, it splits into two independent gene lineages. A gene lineage may also be lost. After pruning all lost lineages, the final gene tree is obtained. A relaxed molecular clock is employed to obtain branch lengths. Finally, a standard sequence evolution model generates sequences over the gene tree with branch lengths. Green and brown colors represents gene and pseudogene sequence evolution, respectively.