Turning a hobby into a job: How duplicated genes find new functions

@article{Conant2008TurningAH,
  title={Turning a hobby into a job: How duplicated genes find new functions},
  author={Gavin C. Conant and Kenneth H. Wolfe},
  journal={Nature Reviews Genetics},
  year={2008},
  volume={9},
  pages={938-950}
}
Gene duplication provides raw material for functional innovation. Recent advances have shed light on two fundamental questions regarding gene duplication: which genes tend to undergo duplication? And how does natural selection subsequently act on them? Genomic data suggest that different gene classes tend to be retained after single-gene and whole-genome duplications. We also know that functional differences between duplicate genes can originate in several different ways, including mutations… 
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References

SHOWING 1-10 OF 127 REFERENCES
Natural history and evolutionary principles of gene duplication in fungi
TLDR
This work develops a procedure that resolves the evolutionary history of all genes in a large group of species and applies it to seventeen fungal genomes to create a genome-wide catalogue of gene trees that determine precise orthology and paralogy relations across these species.
Gene duplication and the origin of novel proteins.
  • A. Hughes
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 2005
TLDR
The report in this issue of PNAS by Tocchini-Valentini and colleagues on tRNA endonucleases of Archaea is particularly welcome as a concrete example of how new protein functions can arise.
Rapid Subfunctionalization Accompanied by Prolonged and Substantial Neofunctionalization in Duplicate Gene Evolution
TLDR
It is shown that neither NF nor SF alone adequately explains the genome-wide patterns of yeast protein interaction and human gene expression for duplicate genes, suggesting a new model termed subneofunctionalization (SNF), and demonstrate that enormous numbers of new functions have originated via gene duplication.
The evolutionary fate and consequences of duplicate genes.
TLDR
Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.
Preferential Duplication of Conserved Proteins in Eukaryotic Genomes
TLDR
It is demonstrated that genes that have generated duplicates in the C. elegans and S. cerevisiae genomes were 25%–50% more constrained prior to duplication than the genes that failed to leave duplicates.
Preservation of duplicate genes by complementary, degenerative mutations.
TLDR
Focusing on the regulatory complexity of eukaryotic genes, it is shown how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions.
Conserved Functions of Yeast Genes Support the Duplication, Degeneration and Complementation Model for Gene Duplication
TLDR
Surprisingly, the results show that duplicated genes are maintained because each copy carries out a subset of the conserved functions that were already present in the preduplication gene.
Conserved Functions of Yeast Genes Support the Duplication, Degeneration and Complementation Model for Gene Duplication
TLDR
Surprisingly, the results show that duplicated genes are maintained because each copy carries out a subset of the conserved functions that were already present in the preduplication gene.
Gene duplication and the adaptive evolution of a classic genetic switch
TLDR
It is suggested that duplication of the ancestral bifunctional gene allowed for the resolution of an adaptive conflict between the transcriptional regulation of the two gene functions and became one of the most tightly regulated genes in the genome.
The evolution of functionally novel proteins after gene duplication
  • A. Hughes
  • Biology, Medicine
    Proceedings of the Royal Society of London. Series B: Biological Sciences
  • 1994
TLDR
A model for the development of new protein is proposed under which a period of gene sharing ordinarily precedes the evolution of functionally distinct proteins.
...
1
2
3
4
5
...