Experimental evolution of evolvability
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Abstract
Evolvability—the capacity to generate adaptive variation—is a trait that can itself evolve through natural selection. However, the idea that mutation can become biased toward adaptive outcomes remains controversial. In this work, we report the evolution of enhanced evolvability through localized hypermutation in experimental populations of bacteria. The evolved mechanism is analogous to the mutation-prone sequences of contingency loci observed in pathogenic bacteria. Central to this outcome was a lineage-level selection process, where success depended on the capacity to evolve between two phenotypic states. Subsequent evolution showed that the hypermutable locus is itself evolvable with respect to alterations in the frequency of environmental change. Lineages with localized hypermutability were more likely to acquire additional adaptive mutations, revealing an unanticipated benefit.
Article activity feed
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Experimental evidence for lineage-level evolution of evolvability, by Barnett M, Meister L and PB Rainey (2025) Experimental evolution of evolvability | Science www.science.org/doi/10.1126/... 🧪
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Study demonstrating how selection can incorporate evolutionary history into the genetic architecture of a single cell, giving rise to a hypermutable locus that appears to anticipate environmental change, thereby accelerating adaptive evolution. #Evolution 🧪🧬🌐 www.science.org/doi/10.1126/...
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Can natural selection shape the ability to evolve? New study shows bacteria evolving mutations that speed up adaptation—suggesting mutations are not purely random but can be biased toward adaptive outcomes www.science.org/doi/10.1126/...
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오늘도 박테리아를 괴롭히며 이상한 실험을 하는 생물학자들… Experimental evolution of evolvability | Science www.science.org/doi/10.1126/...
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25-019 www.science.org/doi/10.1126/...
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Can the capacity to evolve be selected by natural selection for greater ability to evolve? Experimental evolution of evolvability 🧪 www.science.org/doi/10.1126/... Provides an evolutionary mechanism for increasing the capacity for evolvability toward specific adaptive outcomes
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Paul Rainey @paulbrainey.bsky.social, professeur ESPCI (Laboratoire de Biophysique et évolution), publie dans @science.org : Experimental evolution of evolvability www.science.org/doi/10.1126/... Explications sur le site de l’ESPCI : www.espci.psl.eu/fr/actualite... 3/3
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How selection can incorporate evolutionary history into the genetic architecture of a single cell, giving rise to a hypermutable locus that appears to anticipate environmental change, thereby accelerating adaptive evolution. www.science.org/doi/10.1126/...
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A recent paper www.science.org/doi/10.1126/... described the evolution of evolvability in 46 mutational steps. The refining hand of selection - working lineages - was key, but @michael-barnett.bsky.social used just 8 lineages 🫠. Can selection above the level of the individual really be so potent?
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🔗 Publication in @science.org :https://www.science.org/doi/10.1126/science.adr2756 🔗Perspective : www.science.org/doi/10.1126/... 🔗 FR version : www.espci.psl.eu/fr/actualite...
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www.science.org/doi/10.1126/...
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Fantastic work from the lab of @maxplanck.de colleague Paul Rainey, demonstrating how a locus can evolve to become hypermutable. Mutation rates depend on evolutionary relevance of this evolved locus! www.science.org/doi/10.1126/...
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Experimental evolution of evolvability | Science www.science.org/doi/10.1126/...
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Nearly 20 years ago, theory predicted that evolution can evolve “mutation sensors” to improve evolvability. Michael Barnett et all et al. now show this in a beautiful experiment! ❤️ www.science.org/doi/10.1126/...
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Super intriguing paper from Rainey's Lab. It is possible to experimentally evolve *evolvabiliy*. But could we evolve bacteria also towards non-evolvability or non-evolution 🤔 www.science.org/doi/10.1126/...
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Experimental evolution of evolvability | Science www.science.org/doi/10.1126/...
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I wrote about their work last year, and the paper is now out in Science 2/ doi.org/10.1126/scie...
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"Can natural selection structure genetic and developmental systems to bias mutations toward adaptive outcomes?" 🦠💫 #microsky www.science.org/doi/10.1126/...
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Lovely paper. The bug we work on, Neisseria gonorrhoeae, has *hundreds* of genes that can phase-vary (stochastically switch on and off), to allow immune evasion and adaptation to different niches within and between hosts. 1/
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Experimental evolution of evolvability @science.org by Michael Barnett, Lena Meister, and paul Rainey at @mpi-evolbio.bsky.social www.science.org/doi/10.1126/...
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Experimental evolution of evolvability www.science.org/doi/10.1126/...
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Experimental evolution of evolvability | Science https://www.science.org/doi/abs/10.1126/science.adr2756?af=R
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Experimental evolution of evolvability | Science
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Capacity to generate adaptive variation can evolve by natural selection. However, the idea that mutation becomes biased toward specific adaptive outcomes is controversial. Here, using experimental bacterial p
I greatly enjoyed reading this preprint. The dissection of the origin of the de novo contingency locus was very cool.
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Central to our findings was a selective process where lineages better able to generate, by mutation, adaptive phenotypic variants, replaced those that were less proficient (Figure 1). In one metapopulation, a single lineage emerged with capacity to transition rapidly between phenotypic states via expansion and contraction of a short nucleotide repeat in a manner precisely analogous to that of contingency loci in pathogenic bacteria
Do you have any thoughts on why global mutator alleles underpinned evolvability in two populations, and a local mechanism in the other? Seems that increased mutation rates are a common by-product of experimental evolution (e.g. instances in the LTEE). There is a nice paper in yeast that has demonstrated that mutator alleles tend to be favoured in cases where local population size is high (which allows …
Central to our findings was a selective process where lineages better able to generate, by mutation, adaptive phenotypic variants, replaced those that were less proficient (Figure 1). In one metapopulation, a single lineage emerged with capacity to transition rapidly between phenotypic states via expansion and contraction of a short nucleotide repeat in a manner precisely analogous to that of contingency loci in pathogenic bacteria
Do you have any thoughts on why global mutator alleles underpinned evolvability in two populations, and a local mechanism in the other? Seems that increased mutation rates are a common by-product of experimental evolution (e.g. instances in the LTEE). There is a nice paper in yeast that has demonstrated that mutator alleles tend to be favoured in cases where local population size is high (which allows selection to more efficiently act on the beneficial variants they produce). Might be relevant here: Sign of selection on mutation rate modifiers depends on population size, Raynes et al.,2018
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As the number of repeats increased, the rate at which transitions occurred visibly increased (Figure 3E).
What a cool result. This reminds me of the observation in stickleback that the independent evolution of loss of pelvic hindfins tends to target the same locus because of the specific molecular characteristics of that stretch of sequence. This may be of relevance to this study: DNA fragility in the parallel evolution of pelvic reduction in stickleback fish, Xie et al. 2019.
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The selective regime employed was contrived, with selection on lineages being strictly enforced. Such stringent conditions are likely limited in nature. However, microbial pathogens faced with the challenge of persistence in face of the host immune response, will experience strong lineage-level selection, with repeated transitions through selective bottlenecks [38]. As we have shown here, precisely these conditions can promote the evolution of evolvability.
It seem to me that the key component of the experimental selection regime is that individual level and lineage level selection were allowed to act in separate consecutive timesteps, shielding lineage level selection from being swamped out by 'short-sighted' individual level selection. I wonder how likely this scenario is to play out in circumstances such as pathogen evolution where …
The selective regime employed was contrived, with selection on lineages being strictly enforced. Such stringent conditions are likely limited in nature. However, microbial pathogens faced with the challenge of persistence in face of the host immune response, will experience strong lineage-level selection, with repeated transitions through selective bottlenecks [38]. As we have shown here, precisely these conditions can promote the evolution of evolvability.
It seem to me that the key component of the experimental selection regime is that individual level and lineage level selection were allowed to act in separate consecutive timesteps, shielding lineage level selection from being swamped out by 'short-sighted' individual level selection. I wonder how likely this scenario is to play out in circumstances such as pathogen evolution where I would imagine that both levels of selection should still be acting concurrently. I agree however that the presence of contingency loci implies that some form of ecological conditions likely exist that allows for this to happen.
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Experimental evolution of evolvability https://www.biorxiv.org/content/10.1101/2024.05.01.592015v1
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Experimental evolution of evolvability https://www.biorxiv.org/content/10.1101/2024.05.01.592015v1
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