Abstract
The loss of functional redundancy is the key process in the evolution of duplicated genes. Here we systematically assess the extent of functional redundancy among a large set of duplicated genes in Saccharomyces cerevisiae. We quantify growth rate in rich medium for a large number of S. cerevisiae strains that carry single and double deletions of duplicated and singleton genes. We demonstrate that duplicated genes can maintain substantial redundancy for extensive periods of time following duplication (∼100 million years). We find high levels of redundancy among genes duplicated both via the whole genome duplication and via smaller scale duplications. Further, we see no evidence that two duplicated genes together contribute to fitness in rich medium substantially beyond that of their ancestral progenitor gene. We argue that duplicate genes do not often evolve to behave like singleton genes even after very long periods of time.
Highlights
Gene duplication is the primary source of new genes [1] and provides essential raw material for the evolution of functional novelty
We demonstrate that the fitness effects of double deletions of duplicate genes are indistinguishable from our best estimate of the fitness effects of deletions of their ancestral singleton genes
Our results suggest that subfunctionalization does not generally proceed to completion, even after very long periods of time, and that neofunctionalization is either rare or of little consequence, at least under some growth conditions
Summary
Gene duplication is the primary source of new genes [1] and provides essential raw material for the evolution of functional novelty. Deletions of individual duplicate genes tend to have less severe impacts on growth rate than deletions of individual singleton genes in S. cerevisiae [5] This result has been interpreted as evidence that duplicate genes have higher levels of functional redundancy than singletons. Further supporting this possibility is the observation that deletions of a number of pairs of duplicated genes are synthetically lethal [6,7] whereas synthetic lethality is extremely rare for double deletions of unrelated singleton genes [8]. This demonstrates that at least some pairs of duplicate genes are redundant for an essential function
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