Fig. 8.

Example of non additivity among gene quartet distances. (A). The two Arabidopsis genes arose from a duplication within the plants, which can be inferred from a tree inferred using a multiple sequence alignment. (B) However, if we consider pairwise distances estimated from independent pairwise alignments, one Arabidopsis gene appears to be closer to the human sequence, while the other appears to be closer to the opossum gene. In the original OMA algorithm, this would result in these Arabidopsis genes being erroneously used as witnesses of non-orthology; in the new algorithm, the non additivity of these distances (in Point Accepted Mutation units, with estimator variance in parentheses) is detected and the Arabidospsis genes are not used. (UniProt IDs of sequence involved: Human → Q16874, Opossum → F7FI80, Arabidopsis a → Q93ZB2, Arabidopsis b → Q9LNJ4)