(a) Simplified diagram of homology subtypes (showing orthologs and paralogs, but not xenologs); adapted from . Speciation events produce the species A, B and C. The genes A1, B1, B2, C1, C2, and C3 have descended from the ancestral gene following evolutionary events of speciation and gene duplication. (b,c) Evolutionary descent of an ancestral gene to paralogs and orthologs following gene duplication in species 0, and then speciation to yield species 1 and 2. Diagram (b) shows the resulting relationship between paralogs and orthologs as illustrated by Koonin in his comment . Diagram (c) is my version of Koonin's diagram using a Fitch diagram for visualization. Note that the two evolutionary events depicted are a subset of the four shown in (a) (gene duplication 1 and speciation 2), and that the use of capital letters for genes and numbers for species is the opposite of that used in (a).
Jensen Genome Biology 2001 2:interactions1002.1-interactions1002.3 doi:10.1186/gb-2001-2-8-interactions1002