Evolution of specificity and diversity
Evolution of specificity and diversity
The divergence of proteins following gene duplication has long been recognized as an important process in the evolution of both new and specific protein functions. For functional divergence to occur, the duplicated gene has to survive duplication and avoid becoming a pseudogene (gene death). The mechanism by which a gene duplicates survive is still under some debate, but it is thought that maintenance of duplicate pairs can be accomplished by the evolution of novel functions, splitting ancestral functions between duplicate pairs called paralogs, or some combination of both neo- and subfunctionalization. Although no consensus has been reached as to which process plays a more dominant role in the generation and maintenance of duplicates at the genomic or protein level, the distinction is somewhat irrelevant for the bioinformatic prediction of individual specificity-determining sites; that is, those sites that are important for differences in gene function between paralogs. Instead, the evolutionary history and changing selective constraints for individual residues is important for the interpretation of results. This chapter examines the types of substitution that occur at these sites and the phylogenetic signals that they leave.
Keywords: proteins, gene duplication, functional change, paralogs, specificity-determining sites, evolutionary change
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