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Molecular Methods for Evolutionary Genetics pp 377–396Cite as

Experimental Approaches to Evaluate the Contributions of Candidate Protein-Coding Mutations to Phenotypic Evolution

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 772))

Abstract

Identifying mechanisms of molecular adaptation can provide important insights into the process of phenotypic evolution, but it can be exceedingly difficult to quantify the phenotypic effects of specific mutational changes. To verify the adaptive significance of genetically based changes in protein function, it is necessary to document functional differences between the products of derived and wild-type alleles and to demonstrate that such differences impinge on higher-level physiological processes (and ultimately, fitness). In the case of metabolic enzymes, this requires documenting in vivo differences in reaction rate that give rise to differences in flux through the pathway in which the enzymes function. These measured differences in pathway flux should then give rise to differences in cellular or systemic physiology that affect fitness-related variation in whole-organism performance. Efforts to establish these causal connections between genotype, phenotype, and fitness require experiments that carefully control for environmental variation and background genetic variation. Here, we discuss experimental approaches to evaluate the contributions of amino-acid mutations to adaptive phenotypic change. We discuss conceptual and methodological issues associated with in vitro and in vivo studies of protein function, and the evolutionary insights that can be gleaned from such studies. We also discuss the importance of isolating the effects of individual mutations to distinguish between positively selected substitutions that directly contribute to improvements in protein function versus positively selected, compensatory substitutions that mitigate negative pleiotropic effects of antecedent changes.

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Acknowledgments

We thank Z. Cheviron, W. Eanes, V. Orgogozo, and M. Rockman for helpful comments, and we thank R. Weber for providing Fig. 3. The authors acknowledge grants from the National Science Foundation grants (DEB-0614342 and IOS-0949931 to JFS; IOS-0516973 to AJZ) and the National Institutes of Health (R01 HL087216 and HL087216-S1 to JFS).

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  1. School of Biological Sciences, University of Nebraska, Lincoln, NE, USA

    Jay F. Storz & Anthony J. Zera

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  1. Jay F. Storz
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  2. Anthony J. Zera
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Correspondence to Jay F. Storz .

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Editors and Affiliations

  1. CNRS UMR7592, Université Paris VII, rue Hélène Brion 15, Paris, 75013, France

    Virginie Orgogozo

  2. Dept. Biology, New York University, Washington Square E. 100, New York, 10003-6688, New York, USA

    Matthew V. Rockman

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Storz, J.F., Zera, A.J. (2012). Experimental Approaches to Evaluate the Contributions of Candidate Protein-Coding Mutations to Phenotypic Evolution. In: Orgogozo, V., Rockman, M. (eds) Molecular Methods for Evolutionary Genetics. Methods in Molecular Biology, vol 772. Humana Press. https://doi.org/10.1007/978-1-61779-228-1_22

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