Evolvability articles within Nature Communications

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  • Article
    | Open Access

    Genotype networks are sets of genotypes connected by small mutational changes that share the same phenotype. Here the authors combine construction of over 20 synthetic gene regulatory networks with mathematical modeling to exemplify how gene regulatory networks provide robustness in face of mutations while enabling transitions to innovative phenotypes.

    • Javier Santos-Moreno
    • , Eve Tasiudi
    •  & Yolanda Schaerli

  • Article
    | Open Access

    Both ecological opportunity and phenotypic modularity have been suggested to facilitate adaptive radiations. Feiner et al. show that Anolis lizards evolved a new modularity structure in their island adaptive radiation, but that this modularity did not produce the same extreme diversification when Anolis returned to the mainland.

    • Nathalie Feiner
    • , Illiam S. C. Jackson
    •  & Tobias Uller

  • Article
    | Open Access

    Autocatalytic networks may have started evolution during the origin of life. Here, the authors establish a landscape of thousands of RNA networks by barcoded sequencing and microfluidics, and derive relationships between topology and Darwinian properties such as variation and differential reproduction.

    • Sandeep Ameta
    • , Simon Arsène
    •  & Philippe Nghe

  • Article
    | Open Access

    Genome-wide studies of de novo genes have tended to focus on genomic open reading frames (ORFs). Here, Blevins et al. use deep transcriptomics and synteny information to identify de novo transcripts in the yeast Saccharomyces cerevisiae, many of which are expressed from the alternative DNA strand.

    • William R. Blevins
    • , Jorge Ruiz-Orera
    •  & M. Mar Albà

  • 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

    Cellular signalling networks provide information to the cell, but the trade-off between accuracy of information transfer and energetic cost of doing so has not been assessed. Here, the authors investigate a MAPK signalling cascade in budding yeast and find that information is maximised per unit energetic cost.

    • Alexander Anders
    • , Bhaswar Ghosh
    •  & Victor Sourjik

  • 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

    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

    Quantifying the effects of noise in gene expression is difficult since noise and mean expression are coupled. Here the authors determine fitness landscapes in mean-noise expression space to uncouple these two parameters and show that changes in noise and mean expression are similarly detrimental to fitness.

    • Jörn M. Schmiedel
    • , Lucas B. Carey
    •  & Ben Lehner

  • Article
    | Open Access

    In asexual populations selection at different genomic loci can interfere with each other. Here, using a biophysical model of molecular evolution the authors show that interference results in long-term degradation of molecular function, an effect that strongly depends on genome size.

    • Torsten Held
    • , Daniel Klemmer
    •  & Michael Lässig

  • Article
    | Open Access

    The mechanisms that accommodate variable external dependencies in evolution are not clear. Here, the authors show that switches between external and internal metabolic controls of carotenoid-producing networks in birds are linked to shifts in evolutionary rates, with internalization of control resulting in bursts of evolutionary diversification.

    • Alexander V. Badyaev
    • , Alexander B. Posner
    •  & Dawn M. Higginson

  • Article
    | Open Access

    The pathogen Pseudomonas aeruginosa undergoes complex trait adaptation within cystic fibrosis patients. Here, Bartell, Sommer, and colleagues use statistical modeling of longitudinal isolates to characterize the joint genetic and phenotypic evolutionary trajectories of P. aeruginosa within hosts.

    • Jennifer A. Bartell
    • , Lea M. Sommer
    •  & Helle Krogh Johansen

  • Article
    | Open Access

    The catalytic efficiency of many enzymes is lower than the theoretical maximum. Here, the authors combine genome-scale metabolic modeling with population genetics models to simulate enzyme evolution, and find that strong epistasis limits turnover numbers due to diminishing returns of fitness gains.

    • David Heckmann
    • , Daniel C. Zielinski
    •  & Bernhard O. Palsson

  • 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

    Eukaryotic cells rely on the ubiquitin-proteasome system for selective degradation of proteins, a process vital to organismal fitness. Here the authors show that the number of repeats in the polyubiquitin gene is evolutionarily unstable within and between yeast species, and that this variability may tune the cell’s capacity to respond to sudden environmental perturbations.

    • Rita Gemayel
    • , Yudi Yang
    •  & Kevin J. Verstrepen

  • Article
    | Open Access

    Limited specificity of transcription factor-DNA interactions leads to crosstalk in gene regulation. Here the authors consider global crosstalk in regulatory networks of growing size and complexity, and show that it imposes constraints on gene regulation and on the evolution of regulatory networks.

    • Tamar Friedlander
    • , Roshan Prizak
    •  & Gašper Tkačik

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