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Evolution

Genomic pacemakers or ticking clocks?

Nature Reviews Genetics volume 14, page 81 (2013)Cite this article

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Under the molecular clock model, the rate of evolution of a particular gene remains constant, and therefore this could explain why relative rates of evolution between genes also remain constant. However, the data do not fit a strict molecular clock model, and a 'relaxed' molecular clock model is now more widely used. The alternative, more general UPM model proposes that the rate of evolution of a gene may vary arbitrarily, but changes in gene-specific rates are correlated. That is, evolutionary rates of all genes in a genome in a particular lineage increase or decrease together.

To test the models, the authors used phylogenetic trees for 2,294 orthologous gene families, including data from 41 archaeal genomes and 59 bacterial genomes. Under the constraints of the molecular clock model or the UPM model, they fitted these gene trees to 'supertrees', which reflect the dominant trend in the evolution of these species. They then assessed how good the fit is between the gene trees and the supertree under each of the models and found that the fit for the UPM model was significantly better. The authors concluded that the UPM is sufficient to explain the correlations in evolutionary rates across genes in a genome. This work on bacteria and archaea also fits previous observations of lineage-specific changes in evolutionary rate in mammals.

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References

ORIGINAL RESEARCH PAPER

  1. Snir, S., Wolf, Y. I. & Koonin, E. V. Universal pacemaker of genome evolution. PLoS Comput. Biol. 8, e1002785 (2012)

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FURTHER READING

  1. Yang, Z. & Rannala, B. Molecular phylogenetics: principles and practice. Nature Rev. Genet. 13, 303–314 (2012)

    Article  CAS  Google Scholar 

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Authors
  1. Mary Muers
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Muers, M. Genomic pacemakers or ticking clocks?. Nat Rev Genet 14, 81 (2013). https://doi.org/10.1038/nrg3410

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