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Experimental evolution in an era of molecular manipulation

Nature Reviews Genetics (2025)Cite this article

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Abstract

Laboratory evolution experiments in microbial and viral populations have provided great insight into the dynamics and predictability of evolution. The rise of high-throughput sequencing technologies over the past two decades has driven a massive expansion in the scale and power of these experiments. However, until recently our abilities to connect genetic with phenotypic changes and analyse the molecular basis of adaptation have remained limited. Rapid technical advances to measure and manipulate both genotypes and phenotypes are now providing opportunities to investigate the genetic basis of phenotypic evolution and the forces that drive evolutionary dynamics. Here we review how these methodological advances are being used to predict and manipulate the course of laboratory evolution, analyse eco-evolutionary interactions, and how they are beginning to bridge the gap between laboratory and natural evolution.

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Fig. 1: Barcoding, lineage tracking and high-throughput phenotyping methods.
Fig. 2: Construction and manipulation of genotypes.
Fig. 3: Examples of repeatability and predictability in evolution.
Fig. 4: Evolution of frequency-dependent interactions.

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Authors and Affiliations

  1. Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, MA, USA

    Joao A. Ascensao & Michael M. Desai

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  1. Joao A. Ascensao
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Glossary

Background fitness

The overall fitness of a genetic background upon which additional mutations occur; it serves as a baseline for evaluating the fitness effects of new mutations.

Clonal interference

The competition between multiple beneficial mutations that arise in competing lineages within large asexual populations, ultimately slowing fixation rates. This phenomenon can substantially alter evolutionary trajectories by hindering the fixation of moderately beneficial alleles in favour of strongly beneficial ones.

Clonal microbial population

A population derived from a single progenitor cell, where all individuals initially have identical genotypes.

Cross-feeding

An ecological interaction where the metabolic by-products of one organism serve as resources for another organism.

Deep mutational scanning

A high-throughput technique that systematically quantifies the effects of single (and sometimes multiple) amino acid substitutions in a protein. This approach enables researchers to map protein fitness landscapes at high resolution and predict evolutionary trajectories.

Diminishing returns

A pattern of epistasis where beneficial mutations yield progressively smaller fitness gains when introduced into more fit genetic backgrounds. This phenomenon has been widely observed across experimental evolution systems and helps explain convergent fitness trajectories despite genetic divergence.

Directional selection

A form of natural selection that consistently favours traits at one extreme of the phenotypic distribution, driving evolutionary change in a specific direction.

Distribution of fitness effects

The statistical distribution describing the probability that a new mutation has a given fitness consequence. This fundamental property shapes evolutionary dynamics and can change depending on environmental conditions and genetic background.

dN/dS ratios

The ratio of non-synonymous substitutions per non-synonymous site (dN) to synonymous substitutions per synonymous site (dS), providing a measure of selection pressure on protein-coding genes. Values below one typically indicate purifying selection, whereas values above one suggest positive selection.

Effective population sizes

A measure of the strength of genetic drift in a population, often used to summarize genetic diversity in neutrally evolving populations. It is often smaller than the census population size owing to various factors including reproductive variance and population bottlenecks.

Epistasis

The phenomenon where the phenotypic effect of a mutation depends on the presence or absence of other genetic variants. Epistatic interactions can substantially shape evolutionary trajectories by making certain mutational pathways more accessible than others.

Fitness landscapes

A conceptual framework representing the relationship between genotype and fitness, where height on the landscape corresponds to fitness. Valleys represent low-fitness genotypes, peaks represent high-fitness genotypes and the topography influences evolutionary trajectories.

Fixation

The process by which a genetic variant increases in frequency until it is present in all individuals in a population, replacing all alternative variants (at that genetic locus).

Global epistasis

A pattern where the fitness effect of a mutation correlates primarily with the overall fitness of the genetic background, rather than with specific mutations in that background. This pattern enables the projection of complex epistatic interactions onto a simpler low-dimensional space.

Historical contingency

The dependency of future evolutionary trajectories on prior evolutionary history. This concept emphasizes how chance events and the specific sequence of mutations can substantially influence subsequent evolutionary possibilities.

Idiosyncratic interactions

Specific epistatic interactions between particular mutations that cannot be predicted from general patterns. These interactions form the underlying basis from which broader patterns (such as global epistasis) emerge.

Negative frequency-dependent selection

A form of selection where the fitness of a phenotype decreases as its frequency in the population increases. This selective pattern can maintain genetic diversity and lead to stable polymorphisms in evolving populations.

Niche partitioning

The process by which competing species or subpopulations use different resources or adopt different ecological strategies, reducing direct competition and enabling coexistence.

Purifying selection

A form of natural selection that removes deleterious mutations from a population, maintaining functional genetic sequences.

Resource partitioning

An ecological process where different lineages evolve to specialize on distinct components of available resources, reducing competition and enabling stable coexistence.

Selective sweeps

The process by which beneficial mutations increase in frequency and eventually reach fixation in a population, often eliminating genetic variation at linked sites.

Spatial niche construction

The process by which organisms modify their physical environment, creating or altering spatial niches that can be exploited by themselves or other organisms.

Standing genetic variation

The genetic diversity present within a population prior to a selective event, as opposed to variation arising from new mutations. This existing variation can provide an immediate substrate for adaptation to new environments.

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Ascensao, J.A., Desai, M.M. Experimental evolution in an era of molecular manipulation. Nat Rev Genet (2025). https://doi.org/10.1038/s41576-025-00867-6

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