Mutation bias interacts with composition bias to influence adaptive evolution.

Alejandro V Cano,Joshua L Payne,Predrag Radivojac

doi:10.1371/journal.pcbi.1008296

Alejandro V Cano, Joshua L Payne + Show 1 more

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https://doi.org/10.1371/journal.pcbi.1008296

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Abstract

Mutation is a biased stochastic process, with some types of mutations occurring more frequently than others. Previous work has used synthetic genotype-phenotype landscapes to study how such mutation bias affects adaptive evolution. Here, we consider 746 empirical genotype-phenotype landscapes, each of which describes the binding affinity of target DNA sequences to a transcription factor, to study the influence of mutation bias on adaptive evolution of increased binding affinity. By using empirical genotype-phenotype landscapes, we need to make only few assumptions about landscape topography and about the DNA sequences that each landscape contains. The latter is particularly important because the set of sequences that a landscape contains determines the types of mutations that can occur along a mutational path to an adaptive peak. That is, landscapes can exhibit a composition bias-a statistical enrichment of a particular type of mutation relative to a null expectation, throughout an entire landscape or along particular mutational paths-that is independent of any bias in the mutation process. Our results reveal the way in which composition bias interacts with biases in the mutation process under different population genetic conditions, and how such interaction impacts fundamental properties of adaptive evolution, such as its predictability, as well as the evolution of genetic diversity and mutational robustness.

Highlights

Mutation exhibits many forms of bias, both in genomic location and toward particular DNA sequence changes [1]
Mutation bias can be an orienting factor in adaptive evolution, influencing the mutational trajectories populations follow toward higher-fitness genotypes
We found that mutation bias could either enhance or diminish landscape navigability, relative to an unbiased mutation supply, depending upon whether the bias in mutation supply aligned with the composition bias of the accessible mutational paths in the landscape

Summary

Introduction

Mutation exhibits many forms of bias, both in genomic location and toward particular DNA sequence changes [1]. The topography of a genotype-phenotype landscape influences a wide range of evolutionary phenomena [19,20,21], including the evolution of genetic diversity, mutational robustness, and evolvability, as well as the predictability of the evolutionary process itself [19]. It influences landscape navigability—the ability of an evolving population to reach the global adaptive peak via DNA mutation and natural selection [22]. Smooth, singlepeaked landscapes are highly navigable, whereas rugged landscapes are not, because evolving populations can become trapped on local peaks [23], which frustrates further adaptive change [19, 21, 24]

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