Gene families: the taxonomy of protein paralogs and chimeras

Abstract

Ancient duplications and rearrangements of protein-coding segments have resulted in complex gene family relationships. Duplications can be tandem or dispersed and can involve entire coding regions or modules that correspond to folded protein domains. As a result, gene products may acquire new specificities, altered recognition properties, or modified functions. Extreme proliferation of some families within an organism, perhaps at the expense of other families, may correspond to functional innovations during evo-lution. The underlying processes are still at work, and the large fraction of human and other genomes consisting of transposable elements may be a manifestation of the evolutionary benefits of genomic flexibility. Linnaeus introduced a universal classifica-tion system of living things that was able to organize the enormous complexity of bio-logical relationships. A universal gene clas-sification system presents a similar chal-lenge but with added complexity. If a singl