Getting higher on rugged landscapes: Inversion mutations open access to fitter adaptive peaks in NK fitness landscapes.
PLoS Comput Biol 2022;
18:e1010647. [PMID:
36315581 PMCID:
PMC9648849 DOI:
10.1371/journal.pcbi.1010647]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 11/10/2022] [Accepted: 10/09/2022] [Indexed: 11/12/2022] Open
Abstract
Molecular evolution is often conceptualised as adaptive walks on rugged fitness landscapes, driven by mutations and constrained by incremental fitness selection. It is well known that epistasis shapes the ruggedness of the landscape’s surface, outlining their topography (with high-fitness peaks separated by valleys of lower fitness genotypes). However, within the strong selection weak mutation (SSWM) limit, once an adaptive walk reaches a local peak, natural selection restricts passage through downstream paths and hampers any possibility of reaching higher fitness values. Here, in addition to the widely used point mutations, we introduce a minimal model of sequence inversions to simulate adaptive walks. We use the well known NK model to instantiate rugged landscapes. We show that adaptive walks can reach higher fitness values through inversion mutations, which, compared to point mutations, allows the evolutionary process to escape local fitness peaks. To elucidate the effects of this chromosomal rearrangement, we use a graph-theoretical representation of accessible mutants and show how new evolutionary paths are uncovered. The present model suggests a simple mechanistic rationale to analyse escapes from local fitness peaks in molecular evolution driven by (intragenic) structural inversions and reveals some consequences of the limits of point mutations for simulations of molecular evolution.
Ninety years ago, Wright translated Darwin’s core idea of survival of the fittest into rugged landscapes—a highly influential metaphor—with peaks representing high values of fitness separated by valleys of lower fitness. In this picture, once a population has reached a local peak, the adaptive dynamics may stall as further adaptation requires crossing a valley. At the DNA level, adaptation is often modelled as a space of genotypes that is explored through point mutations. Therefore, once a local peak is reached, any genotype fitter than that of the peak will be away from the neighbourhood of genotypes accessible through point mutations. Here we present a simple computational model for inversion mutations, one of the most frequent structural variations, and show that adaptive processes in rugged landscapes can escape from local peaks through intragenic inversion mutations. This new escape mechanism reveals the innovative role of inversions at the DNA level and provides a step towards more realistic models of adaptive dynamics, beyond the dominance of point mutations in theories of molecular evolution.
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