How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution

Author:

Boffi Nicholas M1ORCID,Guo Yipei2,Rycroft Chris H34,Amir Ariel56ORCID

Affiliation:

1. Courant Institute of Mathematical Sciences, New York University

2. Janelia Research Campus

3. Department of Mathematics, University of Wisconsin–Madison

4. Mathematics Group, Lawrence Berkeley National Laboratory

5. Weizmann Institute of Science

6. John A. Paulson School of Engineering and Applied Sciences, Harvard University

Abstract

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population’s mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of a simulated evolving population subject to a standard serial dilution protocol. Through extensive numerical experimentation, we find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that increasing the level of clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but leaves the rate of growth invariant when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape. The simulation package for this work may be found at https://github.com/nmboffi/spin_glass_evodyn.

Funder

National Science Foundation

U.S. Department of Energy

Publisher

eLife Sciences Publications, Ltd

Reference74 articles.

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