Experimental evolution articles within Nature Communications

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  • 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

  • Article
    | Open Access

    Mycelial fusion can favour fungal strains that exploit each other, but the mechanism is not well understood. Here, Grum-Grzhimaylo et al. show that different cheater lineages share similar deficiencies in initiating fusion that nevertheless enable them to preferentially obtain the benefits of fusion initiated by wild-type mycelia.

    • Alexey A. Grum-Grzhimaylo
    • , Eric Bastiaans
    •  & Duur K. Aanen

  • Article
    | Open Access

    Mutualists benefit their partners by providing resources that would be difficult to obtain independently. Here, the authors show in a bacterial community and with mathematical modeling how a mutualist can promote coexistence between competitors by providing them with different limiting resources.

    • Sarah P. Hammarlund
    • , Tomáš Gedeon
    •  & William R. Harcombe

  • Article
    | Open Access

    The PAM specificity of SpCas9 can be altered with positive selection during directed evolution. Here the authors use simultaneous positive and negative selection to improve activity on NAG PAMs while reducing activity on NGG PAMs.

    • Gregory W. Goldberg
    • , Jeffrey M. Spencer
    •  & Marcus B. Noyes

  • Article
    | Open Access

    Understanding evolutionary constraints in antibiotic resistance is crucial for prediction and control. Here, the authors use high-throughput laboratory evolution of Escherichia coli alongside machine learning to identify trade-off relationships associated with drug resistance.

    • Tomoya Maeda
    • , Junichiro Iwasawa
    •  & Chikara Furusawa

  • Article
    | Open Access

    Some bacterial lineages appear to be pre-disposed to evolving antibiotic resistance. Here, the authors show that differential expression of an efflux pump causes widespread variation in evolvability across Staphylococcus aureus isolates, and chemical inhibition of the pump prevents resistance evolution.

    • Andrei Papkou
    • , Jessica Hedge
    •  & R. Craig MacLean

  • Article
    | Open Access

    The antibiotic resistance crisis calls for new ways of restricting the ability of bacteria to evolve resistance. Here, Lukačišinová et al. perform highly controlled evolution experiments in E. coli strains to identify genetic perturbations that strongly limit the evolution of antibiotic resistance through epistasis.

    • Marta Lukačišinová
    • , Booshini Fernando
    •  & Tobias Bollenbach

  • Article
    | Open Access

    Acquired resistance to cancer therapies reflects the ability of cancers to adapt to therapy-imposed selective pressures. Here, the authors elucidate the dynamics of developing resistance to ALK inhibitors in an ALK+ lung cancer cell line showing that resistance originates from drug-specific tolerant cancer cells and it develops as a gradual adaptation.

    • Robert Vander Velde
    • , Nara Yoon
    •  & Andriy Marusyk

  • Article
    | Open Access

    Many industrial organisms are the result of recent or ancient allopolypoidy events. Here the authors iteratively combine the genomes of six yeast species to generate a viable hybrid.

    • David Peris
    • , William G. Alexander
    •  & Chris Todd Hittinger

  • Article
    | Open Access

    Beta-lactam antibiotics and beta-lactamase inhibitors compete for the same binding site on beta-lactamases; thus, mutations that increase beta-lactamase activity likely increase also susceptibility to the inhibitor. Here, Russ et al. identify rare mutations in the ampC beta-lactamase gene that escape this adaptive tradeoff specifically for certain drug combinations.

    • Dor Russ
    • , Fabian Glaser
    •  & Roy Kishony

  • Article
    | Open Access

    The authors study the interactions between chromosomal mutations and horizontally acquired genes in the evolution of antibiotic resistance in experimental evolution assays. They identify constraints that may allow better prediction and control of antibiotic resistance evolution.

    • Andreas Porse
    • , Leonie J. Jahn
    •  & Morten O. A. Sommer

  • Article
    | Open Access

    A species’ ability to adapt to a new environment may be influenced by both intrinsic factors and extrinsic factors. Here, Scheuerl et al. show that bacterial adaptation to low pH depends on not only its genome size and initial level of adaptation, but also the diversity of the community.

    • Thomas Scheuerl
    • , Meirion Hopkins
    •  & Thomas Bell

  • Article
    | Open Access

    Few studies empirically pinpoint how balanced polymorphisms are maintained. “Mérot et al”. identify an inversion polymorphism that is maintained in seaweed fly populations because of antagonistic pleiotropy that mediates a classic life history tradeoff between larval survival and adult reproduction.

    • Claire Mérot
    • , Violaine Llaurens
    •  & Maren Wellenreuther

  • Article
    | Open Access

    Aneuploidy (abnormal chromosome number) can enable rapid adaptation to stress conditions, but it also entails fitness costs from gene imbalance. Here, the authors experimentally evolve yeast while forcing maintenance of aneuploidy to identify the mechanisms that promote tolerance of aneuploidy.

    • Alaattin Kaya
    • , Marco Mariotti
    •  & Vadim N. Gladyshev

  • Article
    | Open Access

    Newly acquired plasmids are frequently lost due to fitness costs. Here, Zhang et al. show that the evolution of satellite plasmids with gene deletions can reduce fitness costs by driving down the copy number of full plasmids and thus favor maintenance of the full plasmid and its novel accessory genes.

    • Xue Zhang
    • , Daniel E. Deatherage
    •  & Jeffrey E. Barrick

  • Article
    | Open Access

    Antimicrobial peptides (AMPs) are emerging as drug candidates, but the risk of pathogen resistance is not well understood. Here, the authors investigate AMP resistance evolution in E. coli, finding physicochemical features that make AMPs less prone to resistance and no cross- or horizontally-acquired resistance.

    • Réka Spohn
    • , Lejla Daruka
    •  & Csaba Pál

  • Article
    | Open Access

    Predator-prey coevolution is expected to hasten evolutionary rates, but this is difficult to test in long-lived species. Here, the authors report consequences of experimental coevolution between bacterial predators and prey, including accelerated molecular evolution and parallel genomic and phenotypic adaptation.

    • Ramith R. Nair
    • , Marie Vasse
    •  & Gregory J. Velicer

  • Article
    | Open Access

    Hybridization across species can lead to offspring with reduced fertility. Here, the authors experimentally evolve yeast and show that whole-genome duplication during asexual reproduction can restore fertility in hybrids over a relatively short evolutionary timespan.

    • Guillaume Charron
    • , Souhir Marsit
    •  & Christian R. Landry

  • Article
    | Open Access

    The role of gene expression noise in the evolution of drug resistance in mammalian cells is unclear. Here, by uncoupling noise from mean expression of a drug resistance gene in CHO cells the authors show that noisy expression aids adaptation to high drug levels, but delays it at low drug levels.

    • Kevin S. Farquhar
    • , Daniel A. Charlebois
    •  & Gábor Balázsi

  • Article
    | Open Access

    It is expected that plasmids are costly and therefore that selection is required to maintain them within bacterial populations. Here, Wein et al. show that plasmid stability can emerge even in the absence of positive selection and that loss may be determined by transcription-replication conflict.

    • Tanita Wein
    • , Nils F. Hülter
    •  & Tal Dagan

  • Article
    | Open Access

    Sexual selection has the potential to either increase or decrease absolute fitness. Here, Cally et al. perform a meta-analysis of 65 experimental evolution studies and find that sexual selection on males tends to increase fitness, especially in females evolving under stressful conditions.

    • Justin G. Cally
    • , Devi Stuart-Fox
    •  & Luke Holman

  • Article
    | Open Access

    Females are choosy about their mates, which should erode genetic diversity but in practice does not. Here, selection and genomic resequencing of Drosophila supports the hypothesis that this paradox can be explained by sexually selected traits reflecting genetic variation in condition.

    • Robert J. Dugand
    • , Joseph L. Tomkins
    •  & W. Jason Kennington

  • Article
    | Open Access

    The evolution of resistance to an antibiotic can render bacteria more susceptible, or more resistant, to a second antibiotic. Here, Nichol et al. provide evidence that the final outcome can be fairly stochastic and depends on the shape of the evolutionary fitness landscape.

    • Daniel Nichol
    • , Joseph Rutter
    •  & Jacob G. Scott

  • Article
    | Open Access

    Transient aneuploidy enables cells to survive sudden environmental changes before longterm cellular adaptations are established. Here, the authors show that yeast cells respond to the acute loss of Ulp2 SUMO protease by rapid induction of aneuploidy, and reveal predictable long-term adaptation mechanisms that restore euploidy.

    • Hong-Yeoul Ryu
    • , Francesc López-Giráldez
    •  & Mark Hochstrasser

  • Article
    | Open Access

    Although men have lower survival across ages, women have poorer health than men as they age. Here, Archer et al. suggest that this pattern is explained by intralocus sexual conflict and provide supporting evidence from a mathematical model and experiments with Drosophila.

    • C. Ruth Archer
    • , Mario Recker
    •  & David J. Hosken

  • Article
    | Open Access

    Organisms could respond to essential resource limitation by increasing metabolic efficiency or resource acquisition ability. Here, the authors experimentally evolve green algae under different resource limitations and show convergent evolution of core metabolism rather than resource specialization.

    • Manu Tamminen
    • , Alexander Betz
    •  & Anita Narwani

  • Article
    | Open Access

    Some daughter cells inherit the maternal old pole during bacterial division, but does this correspond to aging? Here, Proenca et al. show that constant patterns of aging and rejuvenation connect distinct growth equilibria within bacterial clonal populations, providing evidence for deterministic age structures.

    • Audrey M. Proenca
    • , Camilla Ulla Rang
    •  & Lin Chao

  • Article
    | Open Access

    Higher-order interactions occur when one species mediates the interaction between two others. Here, the authors model microbial growth and competition to show that higher-order interactions can arise from tradeoffs in growth traits, leading to neutral coexistence and other complex dynamics.

    • Michael Manhart
    •  & Eugene I. Shakhnovich

  • Article
    | Open Access

    It is unclear if experimental evolution is a good model for natural processes. Here, Clerissi et al. find parallels between the evolution of symbiosis in rhizobia after horizontal transfer of a plasmid over 10 million years ago and experimentally evolved symbionts.

    • Camille Clerissi
    • , Marie Touchon
    •  & Eduardo P. C. Rocha

  • Article
    | Open Access

    SCRaMbLE has been used to rearrange synthetic chromosomes that have been introduced into host yeast. Here the authors produce semi-synthetic heterozygous diploid strains for rapid selection of phenotypes and map the rearrangements underlying selected phenotypes such as thermoresistance and caffeine resistance.

    • Michael J. Shen
    • , Yi Wu
    •  & Jef D. Boeke

  • Article
    | Open Access

    A better mechanistic understanding of how marine diatoms adapt to global warming is pertinent to project changes in global ocean primary production. Here, Schaum et al. show substantial phenotypic and genomic changes in Thalassiosira pseudonana during a 300-generation selection experiment in stable and fluctuating environments.

    • C.-Elisa Schaum
    • , A. Buckling
    •  & G. Yvon-Durocher

  • Article
    | Open Access

    Pathogens exert strong selection on hosts and thus may promote parallel evolution. Here, the authors find that hosts experimentally coevolving with a virus have parallel changes in population size, phenotype, and genomic regions, but accelerated divergence in genome sequence likely due to population size fluctuation.

    • Jens Frickel
    • , Philine G. D. Feulner
    •  & Lutz Becks

  • Article
    | Open Access

    Mating-type switching enables self-compatible reproduction in fungi, but switching ability is variable even within species. Here, the authors find de novo evolution of switching genotypes in experimentally evolved fission yeast populations and show a trade-off between mating success and growth.

    • Bart P. S. Nieuwenhuis
    • , Sergio Tusso
    •  & Simone Immler

  • Article
    | Open Access

    Mutational antibiotic resistance can emerge under either high or low antibiotic levels. Here, the authors show several small-effect resistance mutations are combined to confer high-level resistance in Salmonella enterica exposed to sub-MIC levels of streptomycin.

    • Erik Wistrand-Yuen
    • , Michael Knopp
    •  & Dan I. Andersson

  • Article
    | Open Access

    Bacterial promoters initiate gene transcription and have distinct sequence features. Here, the authors show that random sequences that contain no information are just on the verge of functioning as promoters in Escherichia coli.

    • Avihu H. Yona
    • , Eric J. Alm
    •  & Jeff Gore

  • Article
    | Open Access

    Dinoflagellates are known to use dinoflagellate-viral-nucleoproteins (DVNPs) in place of histones, yet this evolutionary transition is not well understood. Here, Irwin et al. use yeast expressing DVNP to show that DVNP displaces histones and that histone reduction allows cells to cope with DVNP.

    • Nicholas A. T. Irwin
    • , Benjamin J. E. Martin
    •  & LeAnn J. Howe

  • Article
    | Open Access

    Engineering synthetic methylotrophy remains challenging. Here, the authors engineer a methanol-essential E. coli by an in silico-guided multiple knockout approach and show a laboratory evolved strain can incorporate up to 24% methanol into core metabolites during growth.

    • Fabian Meyer
    • , Philipp Keller
    •  & Julia A. Vorholt

  • Article
    | Open Access

    Phenotypic plasticity has been suggested to facilitate survival in new environments and subsequent adaptation. Here, the authors reanalyze transcriptomic data from experimental evolution studies in combination with computational metabolic network analysis and show that genetic adaptation tends to reverse plastic changes in order to recover fitness.

    • Wei-Chin Ho
    •  & Jianzhi Zhang

  • Article
    | Open Access

    The ‘pace of life’ depends on both metabolic rate and life history traits; however, whether these evolve similarly in response to the environment is not clear. Here, Auer et al. show parallel evolution of metabolic rate and a suite of life history traits in response to predator environment in Trinidadian guppies.

    • Sonya K. Auer
    • , Cynthia A. Dick
    •  & David N. Reznick

  • Article
    | Open Access

    Sexual recombination and mutation rate may play different roles in adaptive evolution depending on the fitness landscape. Here, Peabody et al. examine how the two factors affect the rate of adaptation of an E. coli strain capable of sexual recombination, under different conditions during experimental evolution.

    • George L. Peabody V
    • , Hao Li
    •  & Katy C. Kao

  • Article
    | Open Access

    Evolution of resistance is a common cause of cancer treatment failure and tumor progression. Here, the authors present a method for integrating evolutionary principles based on adaptive therapy into abiraterone therapy for metastatic castrate-resistant prostate cancer and show the positive results of an interim analysis of a trial cohort.

    • Jingsong Zhang
    • , Jessica J. Cunningham
    •  & Robert A. Gatenby

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