Figure 7

Unitary pseudogene relativity. Given the phylogeny of human, chimpanzee, and mouse, a human unitary pseudogenes can arise from a gene loss that occurred in different lineages, including: (a) the human lineage after the human-chimp divergence; (b) the human-ancestral lineage after the human-mouse divergence but before the human-chimp divergence; and under different circumstances, such as (c) loss of a subfunctionalized gene in the human lineage after a duplication event before the human-chimp divergence. Because the absence of a functional gene in a species is only identifiable through the comparison with another species that has the functional ortholog, the human unitary pseudogene can be identified in (a) by comparing the human gene set to either the chimp or the mouse set as both of them have the human ortholog. In (b, c), however, the human unitary pseudogene can only be identified by comparing the human gene set to one of either the mouse or chimp gene set, as the other one does not have the human ortholog given the evolutionary history of the gene under consideration.