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Identifying Targets of Selection in Laboratory Evolution Experiments

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Abstract

Adaptive evolution navigates a balance between chance and determinism. The stochastic processes of mutation and drift generate phenotypic variation; however, once mutations reach an appreciable frequency in the population, their fate is governed by the deterministic action of selection, enriching for favorable genotypes and purging the less-favorable ones. The net result is that replicate populations will traverse similar—but not identical—pathways to higher fitness. This parallelism in evolutionary outcomes can be leveraged to identify the genes and pathways under selection. However, distinguishing between beneficial and neutral mutations is challenging because many beneficial mutations will be lost due to drift and clonal interference, and many neutral (and even deleterious) mutations will fix by hitchhiking. Here, we review the best practices that our laboratory uses to identify genetic targets of selection from next-generation sequencing data of evolved yeast populations. The general principles for identifying the mutations driving adaptation will apply more broadly.

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Acknowledgements

We thank Dimitra Aggeli for comments on the manuscript. This study was supported by the National Institutes of Health: R01GM127420.

Funding

The National Institute of General Medical Sciences, R01GM127420, Gregory Lang.

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Authors and Affiliations

  1. Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA

    Artemiza A. Martínez & Gregory I. Lang

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  1. Artemiza A. Martínez
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  2. Gregory I. Lang
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Correspondence to Gregory I. Lang.

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Martínez, A.A., Lang, G.I. Identifying Targets of Selection in Laboratory Evolution Experiments. J Mol Evol 91, 345–355 (2023). https://doi.org/10.1007/s00239-023-10096-2

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