Gene duplication and the origin of novel proteins.

Evolutionary biologists agree that gene duplication has played an important role in the history of life on Earth, providing a supply of novel genes that make it possible for organisms to adapt to new environments (1). The existence of diverse multigene families, particularly in eukaryotes, provides evidence that numerous events of gene duplication followed by functional diversification have shaped genomes as we know them. But it is less certain how this panoply of new functions actually arises, leaving room for ingenious speculation but not much rigor. Cases where we can reconstruct with any confidence the evolutionary steps involved in the functional diversification are relatively few. Thus the report in this issue of PNAS by Tocchini-Valentini and colleagues (2) on tRNA endonucleases of Archaea is particularly welcome as a concrete example of how new protein functions can arise. The first hypothesis regarding the origin of new gene function was that of Ohno (3), who assumed that, after duplication, one gene copy would be entirely redundant and thus freed from all constraint. This redundant copy would become a nonfunctional pseudogene in most cases. But occasionally, Ohno postulated, such a gene would reemerge from nonfunctionality with a new function acquired as a result of chance mutations. There are a number of reasons for doubting this hypothesis. First, as the late Marianne Hughes and I (4) showed in the case of the tetraploid frog Xenopus laevis , duplicate genes are not in general freed from all functional constraint. Rather, purifying selection acts to eliminate deleterious nonsynonymous (amino acid-altering) mutations even in apparently redundant gene copies. Furthermore, there are a number of multigene families where there is evidence that positive Darwinian selection has acted to promote amino acid changes in functionally important regions of proteins (5). In these families, new function clearly has not arisen …