Experimental evolution articles within Nature Communications

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  • Article
    | Open Access

    The effect of temperature fluctuations on the evolution of new phenotypes is largely unknown. Using experimental evolution of fluorescent protein in E. coli, this study shows that a cooling environment can accelerate, and a warming environment decelerate, the evolution of a new protein phenotype.

    • Jia Zheng
    • , Ning Guo
    •  & Andreas Wagner

  • Article
    | Open Access

    In nature, soil, pollinators, and herbivores are the main drivers of plant adaptation and diversification. This study reveals that the interaction between soil and biotic pollination causes divergent evolution where pollinators play a key role, leading to strong divergence among plants in different soils.

    • Thomas Dorey
    •  & Florian P. Schiestl

  • Article
    | Open Access

    Pseudomonas putida is becoming a host of choice for the valorization of lignocellulosic substrates. Here, the authors provide insight into the adaptation of this bacterium to the non-native substrate D-xylose, enabled by metabolic engineering and adaptive laboratory evolution.

    • Pavel Dvořák
    • , Barbora Burýšková
    •  & Martin Benešík

  • Article
    | Open Access

    In this work, authors combine computational models with single-cell and population-level data showing the variability in plasmid copy number within bacterial populations leads to phenotypic diversity. They reveal how multicopy plasmids contribute to bacterial transient antibiotic resistance.

    • J. Carlos R. Hernandez-Beltran
    • , Jerónimo Rodríguez-Beltrán
    •  & Rafael Peña-Miller

  • Article
    | Open Access

    Mobile genetic elements can promote the duplication of antibiotic resistance genes which may in turn accelerate the evolution of resistance to new drugs. Here, the authors show that duplicated antibiotic resistance genes are enriched in bacterial isolates from environments associated with rampant antibiotic use.

    • Rohan Maddamsetti
    • , Yi Yao
    •  & Lingchong You

  • Article
    | Open Access

    Niche theory is often invoked to explain biodiversity, but it does not explain how species evolve to exploit unique niches. Using a combination of experimental and computational approaches, this study shows that resource competition can deform fitness landscapes, opening new pathways that promote ecological speciation.

    • Michael B. Doud
    • , Animesh Gupta
    •  & Justin R. Meyer

  • Article
    | Open Access

    How much the environment influences inherited adaptive traits is debated and challenging to demonstrate in mammals. Here the authors performed a multigeneration study that failed to morphologically replicate enhanced wound healing response following ancestral liver injury in rats. However, heritable transcriptional effects suggest transmission at the molecular level, albeit of unclear functional relevance.

    • Johanna Beil
    • , Juliane Perner
    •  & Rémi Terranova

  • Article
    | Open Access

    Previous, a long-term evolution experiment in E.coli resulted in spontaneous emergence of ecotypes that coexisted for more than 14,000 generations. Here, the authors show that the emergence and persistence of this phenomenon results from two interacting trade-offs, rooted in biochemical constraints.

    • Avik Mukherjee
    • , Jade Ealy
    •  & Markus Basan

  • Article
    | Open Access

    Diverse bacteria exhibit phenotypically plastic multicellular clustering. Here the authors show that a single mutation can genetically assimilate ancestrally inducible multicellularity by modulating plasticity at multiple levels of organization to make E. coli grow constitutively as macroscopic multicellular clusters.

    • Yashraj Chavhan
    • , Sutirth Dey
    •  & Peter A. Lind

  • Article
    | Open Access

    Phage-plasmids are bacterial extrachromosomal elements that act both as plasmids and as viruses. Here, Shan et al. show that segregational drift and loss-of-function mutations play key roles in the infection dynamics of a cosmopolitan phage-plasmid, allowing it to create continuous productive infections in marine bacteria.

    • Xiaoyu Shan
    • , Rachel E. Szabo
    •  & Otto X. Cordero

  • Article
    | Open Access

    G protein-coupled receptors are a major class of drug targets. Here, the authors develop a method whereby their biophysical and functional properties can be altered through directed evolution in mammalian cells, leading to variants exhibiting features such as high stability and expression, or increased allosteric coupling.

    • Christoph Klenk
    • , Maria Scrivens
    •  & Andreas Plückthun

  • Article
    | Open Access

    Fitness landscapes largely shape the dynamics of evolution, but it is unclear how they shift upon ecological diversification. By engineering genome-wide knockout libraries of a nascent bacterial community, Ascensao et al. show how ecological and epistatic patterns combine to shape adaptive landscapes.

    • Joao A. Ascensao
    • , Kelly M. Wetmore
    •  & Oskar Hallatschek

  • Article
    | Open Access

    Bacteria and their viruses coexist and coevolve in nature, but maintaining them together in the lab is challenging. Here, a spatially structured environment allowed prolonged coevolution, with bacteria and phage diversifying into multiple ecotypes, uncovering gene mechanisms affecting phage-bacteria interactions.

    • Einat Shaer Tamar
    •  & Roy Kishony

  • Article
    | Open Access

    Antibiotic and anti-cancer therapy are challenged by mutation-mediated treatment resistance despite many mutations being maladaptive. Here, the authors introduce a system that shows how the probability of the long-term persistence of drug-resistant mutant lineages can be increased in dense microbial populations by acquiring multiple mutations.

    • Serhii Aif
    • , Nico Appold
    •  & Jona Kayser

  • Article
    | Open Access

    This study shows that sea anemones acclimated to high temperatures exhibit increased resistance to thermal stress and that this improved fitness can be transferred by microbiome transplantation. These results indicate that plasticity mediated by the microbiota might be an important factor facilitating thermal adaptations in animals.

    • Laura Baldassarre
    • , Hua Ying
    •  & Sebastian Fraune

  • Article
    | Open Access

    In Streptomyces coelicolor, a subpopulation of cells can arise that produce metabolically costly antibiotics and a division of labor that maximizes colony fitness. This study uses experimental evolution to understand the reproductive and genomic fate of these mutant cells, showing that the arising altruistic cells are analogous to the reproductively sterile castes of social insects.

    • Zheren Zhang
    • , Shraddha Shitut
    •  & Daniel E. Rozen

  • Article
    | Open Access

    The endosymbiotic theory posits that chloroplasts in eukaryotes arise from bacterial endosymbionts. Here, the authors engineer the yeast/cyanobacteria chimeras and show that the engineered cyanobacteria perform chloroplast-like functions to support the growth of yeast cells under photosynthetic conditions.

    • Jason E. Cournoyer
    • , Sarah D. Altman
    •  & Angad P. Mehta

  • Article
    | Open Access

    ‘A supergene that underlies variation in male mating phenotypes has consequences for female reproduction. Here, the authors use evolutionary models to show that the rarest variant of this supergene is maintained by disproportionally high male reproductive success.’

    • Lina M. Giraldo-Deck
    • , Jasmine L. Loveland
    •  & Clemens Küpper

  • Article
    | Open Access

    Rapid adaptation will facilitate species resilience under global climate change, but its effects on plasticity are less commonly investigated. This study shows that 20 generations of experimental adaptation in a marine copepod drives a rapid loss of plasticity that carries costs and might have impacts on future resilience to environmental change.

    • Reid S. Brennan
    • , James A. deMayo
    •  & Melissa H. Pespeni

  • Article
    | Open Access

    Antibiotic persisters are phenotypic variants within an isogenic bacterial population that are transiently tolerant to antibiotic treatment. Here, the authors provide evidence that cytoplasmic acidification, amplified by a compromised respiratory complex I, can act as a signaling hub for perturbed metabolic homeostasis in antibiotic persisters.

    • Bram Van den Bergh
    • , Hannah Schramke
    •  & Matthias Heinemann

  • Article
    | Open Access

    Cooperative mutualisms are widespread in many ecosystems but how they affect the ability of organisms to adapt to changing conditions was unclear. This study experimentally demonstrates that members of obligate cooperative mutualisms are less able to adapt evolutionarily to external selection pressures and are more likely to return to metabolic autonomy than their free-living counterparts.

    • Benedikt Pauli
    • , Leonardo Oña
    •  & Christian Kost

  • Article
    | Open Access

    Mutational hotspots can determine evolutionary outcomes and make evolution repeatable. Experiments in bacteria reveal that a powerfully deterministic genetic hotspot can be built and broken by a handful of silent mutations, highlighting an underappreciated role for silent genetic variation in determining adaptive outcomes.

    • James S. Horton
    • , Louise M. Flanagan
    •  & Tiffany B. Taylor

  • Article
    | Open Access

    Microbial evolution often involves transient phenotypes and sequential development of multiple mutations of unclear relevance. Here, the authors show that the evolution of non-growing E. coli cells can be driven by alterations in pyrimidine nucleoside levels associated with colony ageing and/or due to mutations in metabolic or regulatory genes.

    • Ida Lauritsen
    • , Pernille Ott Frendorf
    •  & Morten H. H. Nørholm

  • Article
    | Open Access

    While a correlation between epigenetic modifications and mutation rates has been observed, experimental evidence of causality is limited. Here the authors measure the mutation rate in fungal mutants lacking histone modifications and confirm experimentally a causal effect of epigenetic modifications on mutation rates.

    • Michael Habig
    • , Cecile Lorrain
    •  & Eva H. Stukenbrock

  • Article
    | Open Access

    Analyses of both natural and experimental evolution suggest that adaptation depends on the evolutionary past and adaptive potential decreases over time. Here, by tracking yeast adaptation with DNA barcoding, the authors show that such evolutionary phenomena can be observed even after a single adaptive step.

    • Dimitra Aggeli
    • , Yuping Li
    •  & Gavin Sherlock

  • Perspective
    | Open Access

    The microbiome is becoming recognized as a key determinant of host phenotype. Here, Henry et al. present a framework for building our understanding of how the microbiome also influences host evolution, review empirical examples and research approaches, and highlight emerging questions.

    • Lucas P. Henry
    • , Marjolein Bruijning
    •  & Julien F. Ayroles

  • Article
    | Open Access

    Multicellularity is a major evolutionary transition that remains poorly characterized at the ecological and genetic level. Exposing unicellular green algae to a rotifer predator showed that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.

    • Joana P. Bernardes
    • , Uwe John
    •  & Lutz Becks

  • Article
    | Open Access

    Beneficial plant-microbe interactions are common in nature, but direct evidence for the evolution of mutualism is scarce. Here, Li et al. experimentally evolve a rhizospheric bacterium and find that it can evolve into a mutualist on a relatively short timescale.

    • Erqin Li
    • , Ronnie de Jonge
    •  & Alexandre Jousset

  • Article
    | Open Access

    Natural and sexual selection can be in opposition favouring different trait sizes, but disentangling these processes empirically is difficult. Here Okada et al. show that predation on males shifts the balance of selection in experimentally evolving beetle populations, disfavoring a sexually-selected male trait but increasing female fitness.

    • Kensuke Okada
    • , Masako Katsuki
    •  & David J. Hosken

  • Article
    | Open Access

    Long-term infection of cystic fibrosis patients with Pseudomonas aeruginosa is often accompanied by a reduction in bacterial growth rate. Here, La Rosa et al. use adaptive laboratory evolution to increase the growth rate of clinical isolates, and identify mechanisms and evolutionary trajectories that, in reverse direction, may help the pathogen to adapt to the patients’ airways.

    • Ruggero La Rosa
    • , Elio Rossi
    •  & Søren Molin

  • Article
    | Open Access

    The interaction between hybridisation and polyploidisation is thought to play an important role in eukaryote speciation. Here the authors sequence yeast crosses and show associations between hybridisation, genome instability, and genome duplication, suggesting these may have roles in the establishment of new hybrids.

    • S. Marsit
    • , M. Hénault
    •  & C. R. Landry

  • Article
    | Open Access

    The evolution of multicellular life is hypothesized to have been promoted by rising oxygen levels. Through experimental evolution and modeling, Bozdag et al. demonstrate that our planet’s first oxygenation would have strongly constrained, not promoted, the evolution of multicellular life.

    • G. Ozan Bozdag
    • , Eric Libby
    •  & William C. Ratcliff

  • Article
    | Open Access

    Trait-based approaches assume upper critical thermal limits (CTLs) are good predictors of climate change vulnerability. Here, the authors show that male fertility thermal limits, which are lower than CTLs, are better at predicting Drosophila extinction in the lab, suggesting species may be living close to their thermal limits.

    • Belinda van Heerwaarden
    •  & Carla M. Sgrò

  • Article
    | Open Access

    Anthropogenic changes, such as eutrophication from lake pollution, can lead to rapid evolution. Comparing Daphnia resurrected from generations adapted to historical pollution to contemporary, post-cleanup populations finds that Daphnia rapidly reversed their evolved resistance to harmful cyanobacteria.

    • Jana Isanta-Navarro
    • , Nelson G. Hairston Jr
    •  & Dominik Martin-Creuzburg

  • Article
    | Open Access

    The genomic details of adaptation to extreme environments remain challenging to characterize. Using new methods to analyze flies experimentally evolved to survive extreme O2 conditions, the authors find a surprising level of synchronicity in selective sweeps, de novo mutations and adaptive recombination events.

    • Arya Iranmehr
    • , Tsering Stobdan
    •  & Gabriel G. Haddad

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