Fig. 1

Emergence of homology classes distinguished by chronology of duplication and speciation events. a: An ancient duplication creates seq1’ as a daughter copy of seq1 in the ancestor’s genome. Then as the ancestor diverges into two offspring, A and B, seq1 and seq1’ are inherited by both the offspring’s genomes. b: seq2 of the ancestor’s genome is inherited by both the offspring’s genomes A and B, then in the genome of B, a recent duplication creates Bseq2’ as a daughter copy of Bseq2. c: similar to subfigure (b), only recent duplications in both genome A and genome B create Aseq3’ and Bseq3’ as daughter copies of Aseq3 and Bseq3 respectively. d-f: exhibit exactly the same evolutionary histories as subfigures (a)-(c) in gene trees. Dashed rectangles indicate genomes of different species. Solid edges (inherited branches) indicate evolutionary paths along which “inheritance between successive generations” applies. Dashed edges (derived branches) indicate creation of new duplicates. In this context, the evolutionary path connecting a pair of primary orthologs must consist of inherited branches only. Primary orthologs are conjectured to conserve their ancestral genomic positions, and to undergo constrained evolution. This figure can be compared with the figures in the Ensembl documentation page for “homology types” [8], and Fig. 1 in [9], whose “divergent edges” correspond to our “derived branches.”