Outline of a phylogenomic methodology. In this method, information about the evolutionary relationships among genes is used to predict the functions of uncharacterized genes (see text for details). Two hypothetical scenarios are presented and the path of trying to infer the function of two uncharacterized genes in each case is traced. (A) A gene family has undergone a gene duplication that was accompanied by functional divergence. (B) Gene function has changed in one lineage. The true tree (which is assumed to be unknown) is shown at the bottom. The genes are referred to by numbers (which represent the species from which these genes come) and letters (which in A represent different genes within a species). The thin branches in the evolutionary trees correspond to the gene phylogeny and the thick gray branches in A (bottom) correspond to the phylogeny of the species in which the duplicate genes evolve in parallel (as paralogs). Different colors (and symbols) represent different gene functions; gray (with hatching) represents either unknown or unpredictable functions.
