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Testing the neutral theory of molecular evolution with genomic data fromDrosophila

Naturevolume 415, pages1024–1026 (2002)Cite this article

Abstract

Although positive selection has been detected in many genes, its overall contribution to protein evolution is debatable1. If the bulk of molecular evolution is neutral, then the ratio of amino-acid (A) to synonymous (S) polymorphism should, on average, equal that of divergence2. A comparison of theA/S ratio of polymorphism inDrosophila melanogaster with that of divergence fromDrosophila simulans shows that theA/S ratio of divergence is twice as high—a difference that is often attributed to positive selection. But an increase in selective constraint owing to an increase in effective population size could also explain this observation, and, if so, all genes should be affected similarly. Here we show that the difference between polymorphism and divergence is limited to only a fraction of the genes, which are also evolving more rapidly, and this implies that positive selection is responsible. A higherA/S ratio of divergence than of polymorphism is also observed in other species, which suggests a rate of adaptive evolution that is far higher than permitted by the neutral theory of molecular evolution.

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Figure 1: The distribution of the excess of amino-acid divergence contributed by each gene.

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Acknowledgements

This work was supported by grants from the NIH and NSF to C.-I.W. and a Genetics Training Grant and a Department of Education PhD fellowship to J.C.F.

Author information

Author notes

  1. Chung-I Wu

    Present address: Department of Ecology and Evolution, University of Chicago, Chicago, 60637, Illinois, USA

  2. Justin C. Fay

    Present address: Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, 94720

  3. Gerald J. Wyckoff

    Present address: Department of Human Genetics, University of Chicago, Chicago, Illinois, 60637, USA

Authors and Affiliations

  1. Committee on Genetics, University of Chicago, Chicago, 60637, Illinois, USA

    Justin C. Fay, Gerald J. Wyckoff & Chung-I Wu

Authors
  1. Justin C. Fay
  2. Gerald J. Wyckoff
  3. Chung-I Wu

Corresponding author

Correspondence toJustin C. Fay.

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Competing interests

The authors declare no competing financial interests.

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Fay, J., Wyckoff, G. & Wu, CI. Testing the neutral theory of molecular evolution with genomic data fromDrosophila.Nature415, 1024–1026 (2002). https://doi.org/10.1038/4151024a

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