Accelerated evolution after gene duplication: a time-dependent process affecting just one copy

Gene duplication is widely regarded as a major mechanism modeling genome evolution and function. However, the mechanisms that drive the evolution of the two, initially redundant, gene copies are still ill defined. Many gene duplicates experience evolutionary rate acceleration, but the relative contr...

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Bibliographic Details
Published in:Molecular biology and evolution 2013-08, Vol.30 (8), p.1830-1842
Main Authors: Pegueroles, Cinta, Laurie, Steve, Albà, M Mar
Format: Article
Language:English
Subjects:
Animals
Chromosomal Position Effects
Drift
Evolution
Evolution, Molecular
Gene Duplication
Gene expression
Genes
Genes, Duplicate
Genomes
INDEL Mutation
Maximum likelihood method
Mice
Organ Specificity - genetics
Rats
Rodents
Selection, Genetic
Tissues
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Summary:Gene duplication is widely regarded as a major mechanism modeling genome evolution and function. However, the mechanisms that drive the evolution of the two, initially redundant, gene copies are still ill defined. Many gene duplicates experience evolutionary rate acceleration, but the relative contribution of positive selection and random drift to the retention and subsequent evolution of gene duplicates, and for how long the molecular clock may be distorted by these processes, remains unclear. Focusing on rodent genes that duplicated before and after the mouse and rat split, we find significantly increased sequence divergence after duplication in only one of the copies, which in nearly all cases corresponds to the novel daughter copy, independent of the mechanism of duplication. We observe that the evolutionary rate of the accelerated copy, measured as the ratio of nonsynonymous to synonymous substitutions, is on average 5-fold higher in the period spanning 4-12 My after the duplication than it was before the duplication. This increase can be explained, at least in part, by the action of positive selection according to the results of the maximum likelihood-based branch-site test. Subsequently, the rate decelerates until purifying selection completely returns to preduplication levels. Reversion to the original rates has already been accomplished 40.5 My after the duplication event, corresponding to a genetic distance of about 0.28 synonymous substitutions per site. Differences in tissue gene expression patterns parallel those of substitution rates, reinforcing the role of neofunctionalization in explaining the evolution of young gene duplicates.
ISSN:0737-4038
1537-1719
DOI:10.1093/molbev/mst083