Article

Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster

  • Nature Ecology & Evolution 1, Article number: 0025 (2017)
  • doi:10.1038/s41559-016-0025
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Abstract

Identifying the genetic basis for adaptive differences between species requires explicit tests of historical hypotheses concerning the effects of past changes in gene sequence on molecular function, organismal phenotype and fitness. We address this challenge by combining ancestral protein reconstruction with biochemical experiments and physiological analysis of transgenic animals that carry ancestral genes. We tested a widely held hypothesis of molecular adaptation—that changes in the alcohol dehydrogenase protein (ADH) along the lineage leading to Drosophilamelanogaster increased the catalytic activity of the enzyme and thereby contributed to the ethanol tolerance and adaptation of the species to its ethanol-rich ecological niche. Our experiments strongly refute the predictions of the adaptive ADH hypothesis and caution against accepting intuitively appealing accounts of historical molecular adaptation that are based on correlative evidence. The experimental strategy we employed can be used to decisively test other adaptive hypotheses and the claims they entail about past biological causality.

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Acknowledgements

We thank L. Picton, K. O’Brien, K. Gordon and members of the C. Meiklejohn and K. Montooth laboratories for technical assistance. We thank D. Matute for providing polymorphism data for D.yakuba. We thank M. Kreitman, members of the J. Thornton laboratory and D. Anderson for comments and suggestions that enriched the project. The project was supported by a National Science Foundation (NSF) grant (DEB-1501877; J.W.T./M.A.S.), an NSF graduate research fellowship (M.A.S.), National Institutes of Health (NIH) grant (R01-GM104397; J.W.T.), NSF CAREER Award (1505247; K.L.M.) and an NIH training grant (T32-GM007197; M.A.S.). D.W.L. was supported by a Howard Hughes Medical Institute postdoctoral fellowship from the Life Sciences Research Foundation and an investigatorship to S. B. Carroll from the Howard Hughes Medical Institute.

Author information

Affiliations

  1. Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA

    • Mohammad A. Siddiq
    •  & Joseph W. Thornton
  2. Laboratory of Cell & Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA

    • David W. Loehlin
  3. Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA

    • David W. Loehlin
  4. School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA

    • Kristi L. Montooth
  5. Department of Human Genetics, University of Chicago, Chicago, Illinois, USA

    • Joseph W. Thornton

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Contributions

M.A.S. and J.W.T. conceived the project. All authors participated in the experimental design. M.A.S. performed the phylogenetic and population genetic analyses. D.W.L. constructed the transgenic animals. M.A.S., D.W.L. and K.L.M. performed the functional experiments. All authors participated in data analysis and interpretation. M.A.S. and J.W.T. wrote the paper with contributions from D.W.L. and K.L.M.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Joseph W. Thornton.

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