Competition and fixation of cohorts of adaptive mutations under Fisher geometrical model.

Jorge A Moura De Sousa,Isabel Gordo,Paulo R.A Campos,João Alpedrinha

doi:10.7717/peerj.2256

Jorge A Moura De Sousa, Isabel Gordo + Show 2 more

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https://doi.org/10.7717/peerj.2256

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Abstract

One of the simplest models of adaptation to a new environment is Fisher’s Geometric Model (FGM), in which populations move on a multidimensional landscape defined by the traits under selection. The predictions of this model have been found to be consistent with current observations of patterns of fitness increase in experimentally evolved populations. Recent studies investigated the dynamics of allele frequency change along adaptation of microbes to simple laboratory conditions and unveiled a dramatic pattern of competition between cohorts of mutations, i.e., multiple mutations simultaneously segregating and ultimately reaching fixation. Here, using simulations, we study the dynamics of phenotypic and genetic change as asexual populations under clonal interference climb a Fisherian landscape, and ask about the conditions under which FGM can display the simultaneous increase and fixation of multiple mutations—mutation cohorts—along the adaptive walk. We find that FGM under clonal interference, and with varying levels of pleiotropy, can reproduce the experimentally observed competition between different cohorts of mutations, some of which have a high probability of fixation along the adaptive walk. Overall, our results show that the surprising dynamics of mutation cohorts recently observed during experimental adaptation of microbial populations can be expected under one of the oldest and simplest theoretical models of adaptation—FGM.

Highlights

Understanding the mechanisms and dynamics underneath the adaptive process is still a great challenge in evolutionary biology
By tracking each individual mutation during the adaptive walk as the populations approach the optimum, we find that the simplest version of Fisher’s Geometric Model (FGM) can generate the complex mutation cohort dynamics observed in microbial adaptation experiments, under specific evolutionary parameters within a biological realistic range
We note that FGM does not consider social and ecological interactions that are likely to be important in explaining genetic diversity in natural populations (Cordero & Polz, 2014), nor does it consider frequency dependent selection, which has been shown to occur in laboratory evolving microbial populations adapting to simple ecological conditions (Maharjan et al, 2012; Herron & Doebeli, 2013)

Summary

Introduction

Understanding the mechanisms and dynamics underneath the adaptive process is still a great challenge in evolutionary biology. The input of new mutations can be so high that new mutants emerge in backgrounds already carrying other mutations, leading to the formation and competition between mutation cohorts Such competition results in longer times for mutations to reach fixation and complex dynamics, as different mutations aggregate in separate groups. Synchronous increase or decrease in frequency of these mutations, competition between distinct cohorts and the simultaneous fixation of the mutations that form the cohorts is a pervasive observation during this laboratory microbial adaptations (Sniegowski, Gerrish & Lenski, 1997; Tenaillon et al, 2001; Barrick et al, 2009; Wielgoss et al, 2013; Lee & Marx, 2013; Lang et al, 2013; Maddamsetti, Lenski & Barrick, 2015)

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