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Correlated Evolution of Synonymous and Nonsynonymous Sites in Drosophila

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Abstract

Recent work has shown that Drosophila melanogaster genes with fast-evolving nonsynonymous sites have lower codon usage bias. This pattern has been attributed to interference between positive selection at nonsynonymous sites and weak selection on codon usage. Here we have looked for this correlation in a much larger and less biased dataset, comprising 630 gene pairs from D. melanogaster and D. yakuba. We confirmed that there is a negative correlation between the rate of nonsynonymous substitutions (dN) and codon bias in D. melanogaster. We then tested the interference hypothesis and other alternative explanations, including one involving gene expression. We found that dN indeed correlates with the level of gene expression. Given that gene expression is a strong determinant of codon bias, the relationship between dN and codon bias might be a by-product of gene expression. However, our tests show that none of the hypotheses we consider seem to explain the data fully.

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Acknowledgments

We thank Andrea Betancourt for kindly providing her dataset to us. We are grateful to Hiroshi Akashi, Daven Presgraves, and two anonymous referees for valuable comments on our manuscript. Experimental work was supported by a Deutsche Forschungsgemeinschaft (DFG) grant to D.T. and T.D. (Ta99-17). G.M. is a European Union Marie Curie postdoctoral fellow.

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Authors and Affiliations

  1. Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, EH9 3JT, Scotland, UK

    Gabriel Marais & Brian Charlesworth

  2. Institut für Genetik der Universität zu Köln, Weyertal 121, 50931, Köln, Germany

    Tomislav Domazet-Lošo & Diethard Tautz

  3. Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, HR-10002, Zagreb, Croatia

    Tomislav Domazet-Lošo

Authors
  1. Gabriel Marais
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  2. Tomislav Domazet-Lošo
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  3. Diethard Tautz
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  4. Brian Charlesworth
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Correspondence to Tomislav Domazet-Lošo.

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Reviewing Editor: Dr. John Huelsenbeck

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Marais, G., Domazet-Lošo, T., Tautz, D. et al. Correlated Evolution of Synonymous and Nonsynonymous Sites in Drosophila. J Mol Evol 59, 771–779 (2004). https://doi.org/10.1007/s00239-004-2671-2

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  • DOI: https://doi.org/10.1007/s00239-004-2671-2

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