Evolution articles within Nature Communications

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  • Article
    | Open Access

    Microbes adapting to broad and specialized ranges of environments (generalists and specialists) have distinct ecological roles and properties. Via meta-analysis of community sequencing datasets, Sriswasdi et al. show that generalists have higher speciation rates and persistence advantage over specialists.

    • Sira Sriswasdi
    • , Ching-chia Yang
    •  & Wataru Iwasaki

  • Article
    | Open Access

    Few studies have explored the effect of a changing environment on artificial chemical evolution. Here, the authors develop an evolutionary platform that alters the physical environment of droplet protocells, showing that a population of simple chemical species can adapt to its surroundings, in analogy to natural evolution.

    • Juan Manuel Parrilla-Gutierrez
    • , Soichiro Tsuda
    •  & Leroy Cronin

  • Article
    | Open Access

    Genetic rescue can be valuable for the conservation of small populations threatened by low genetic diversity, but it carries the perceived risk of outbreeding depression. Here, Weeks et al. report increased hybrid fitness in a rescued population of the mountain pygmy possum, which likely contributed to population growth following genetic rescue.

    • Andrew R. Weeks
    • , Dean Heinze
    •  & Ian Mansergh

  • Article
    | Open Access

    Genetic accommodation is a potential mechanism for the phenotypic divergence of species. Here, Kulkarni et al. compare endocrine responses of three spadefoot toad species to pond drying and suggest how evolution of mechanisms of developmental plasticity may account for trait variation among species.

    • Saurabh S. Kulkarni
    • , Robert J. Denver
    •  & Daniel R. Buchholz

  • Article
    | Open Access

    Genetic drift can reduce fitness in small populations by counteracting selection against deleterious mutations. Here, LaBar and Adami demonstrate through a mathematical model and simulations that small populations tend to evolve to drift-robust fitness peaks, which have a low likelihood of slightly-deleterious mutations.

    • Thomas LaBar
    •  & Christoph Adami

  • Article
    | Open Access

    Proteases are promising therapeutics to treat diseases such as hemophilia which are due to endogenous protease deficiency. Here the authors use phage-assisted continuous evolution to evolve a variant TEV protease with altered target peptide sequence specificities.

    • Michael S. Packer
    • , Holly A. Rees
    •  & David R. Liu

  • Article
    | Open Access

    The pattern of body size evolution in hominids can provide insight into historical human ecology. Here, Grabowski and Jungers use comparative phylogenetic analysis to reconstruct the likely size of the ancestor of humans and chimpanzees and the evolutionary history of selection on body size in primates.

    • Mark Grabowski
    •  & William L. Jungers

  • Article
    | Open Access

    Asexual reproduction is thought to be an evolutionary dead end in eukaryotes because deleterious mutations will not be purged effectively. Here, Brandt and colleagues show that anciently asexual oribatid mites in fact have reduced accumulation of deleterious mutations compared to their sexual relatives.

    • Alexander Brandt
    • , Ina Schaefer
    •  & Jens Bast

  • Article
    | Open Access

    Mass extinctions are thought to produce ‘disaster faunas’, communities dominated by a small number of widespread species. Here, Button et al. develop a phylogenetic network approach to test this hypothesis and find that mass extinctions did increase faunal cosmopolitanism across Pangaea during the late Palaeozoic and early Mesozoic.

    • David J. Button
    • , Graeme T. Lloyd
    •  & Richard J. Butler

  • Article
    | Open Access

    Horizontal gene transfer (HGT) is an important mechanism for genome evolution and adaptation in bacteria. Here, Oliveira and colleagues find HGT hotspots comprising  ~ 1% of the chromosomal regions in 80 bacterial species.

    • Pedro H. Oliveira
    • , Marie Touchon
    •  & Eduardo P. C. Rocha

  • Article
    | Open Access

    While X-chromosome gene content tends to be conserved, Y-chromosome evolution is dynamic and difficult to reconstruct. Here, Mahajan and Bachtrog use a subtraction pipeline to identify Y-linked genes in 22 Diptera species, revealing patterns of Y-chromosome gene-content evolution.

    • Shivani Mahajan
    •  & Doris Bachtrog

  • Article
    | Open Access

    The structure and dynamics of microbial communities reflect trade-offs in the ability to use different resources. Here, Josephides and Swain incorporate metabolic trade-offs into an eco-evolutionary model to predict networks of mutational paths and the evolutionary outcomes for microbial communities.

    • Christos Josephides
    •  & Peter S. Swain

  • Article
    | Open Access

    Punishment by peers can enforce social norms, such as contributing to a public good. Here, Abbink and colleagues show that individuals will enforce norms even when contributions reduce the net benefit of the group, resulting in the maintenance of wasteful contributions.

    • Klaus Abbink
    • , Lata Gangadharan
    •  & John Thrasher

  • Article
    | Open Access

    Lab strains of Pseudomonas are model systems for the evolution of cooperation over public goods (iron-scavenging siderophores). Here, Butaitė et al. add ecological and evolutionary insight into this system by showing that cheating and resistance to cheating both shape competition for iron in natural Pseudomonas communities.

    • Elena Butaitė
    • , Michael Baumgartner
    •  & Rolf Kümmerli

  • Article
    | Open Access

    Non-human animals are known to exhibit behaviours suggestive of empathy, but the development and maintenance of these traits is unexplored. Here, Webb and colleagues quantify individual consolation tendencies over 10 years across two chimpanzee groups and show evidence of consistent ‘empathetic personalities’.

    • Christine E. Webb
    • , Teresa Romero
    •  & Frans B. M. de Waal

  • Article
    | Open Access

    Nematodes use a characteristic set of movements, called nictation, to hitchhike on more mobile animals. Here, Lee et al. identify a genetic locus in the nematode Caenorhabditis elegans that underlies nictation and contributes to successful hitchhiking, but at expense of reduced offspring production.

    • Daehan Lee
    • , Heeseung Yang
    •  & Junho Lee

  • Article
    | Open Access

    Behavioral manipulation of host by pathogens has been observed in vertebrates, invertebrates, and plants. Here the authors show that in Drosophila, infection with pathogenic bacteria leads to increased pheromone release, which attracts healthy flies. This process benefits the pathogen since it enhances bacterial dispersal, but is detrimental to the host.

    • Ian W. Keesey
    • , Sarah Koerte
    •  & Bill S. Hansson

  • Article
    | Open Access

    The three-spined stickleback is a model species for the study of adaptive divergence. Here, Raeymaekers et al. compare how the three-spined stickleback and its relative the nine-spined stickleback vary at the phenotypic and genomic levels in response to the same spatial and environmental drivers.

    • Joost A. M. Raeymaekers
    • , Anurag Chaturvedi
    •  & Filip A. M. Volckaert

  • Article
    | Open Access

    Early molecules of life likely served both as templates and catalysts, raising the question of how functionally distinct genomes and enzymes arose. Here, the authors show that conflict between evolution at the molecular and cellular levels can drive functional differentiation of the two strands of self-replicating molecules and lead to copy number differences between the two.

    • Nobuto Takeuchi
    • , Paulien Hogeweg
    •  & Kunihiko Kaneko

  • Article
    | Open Access

    Gene networks evolve by transcription factor (TF) duplication and divergence of their binding site specificities, but little is known about the global constraints at play. Here, the authors study the coevolution of TFs and binding sites using a biophysical-evolutionary approach, and show that the emerging complex fitness landscapes strongly influence regulatory evolution with a role for crosstalk.

    • Tamar Friedlander
    • , Roshan Prizak
    •  & Gašper Tkačik

  • Article
    | Open Access

    The fossil record of flowers is limited, necessitating other approaches to understanding floral evolution. Here, Sauquet and colleagues reconstruct the characteristics and diversification of ancient angiosperm flowers by combining models of flower evolution with an extensive database of extant floral traits.

    • Hervé Sauquet
    • , Maria von Balthazar
    •  & Jürg Schönenberger

  • Article
    | Open Access

    The transcription factor Nkx2.5 is essential for heart development. Here, the authors identify a previously unknown expression domain for Nkx2.5 in the emu wing and explore its role in diminished wing bud development in the flightless emu, compared with three other birds that have functional wings.

    • Peter G. Farlie
    • , Nadia M. Davidson
    •  & Craig A. Smith

  • Article
    | Open Access

    Arms races between phage and bacteria are well known from lab experiments, but insight from field systems is limited. Here, the authors show changes in the resistance and CRISPR loci of bacteria and the infectivity, host range and genome size of phage over multiple years in an aquaculture environment.

    • Elina Laanto
    • , Ville Hoikkala
    •  & Lotta-Riina Sundberg

  • Article
    | Open Access

    The emergence of novel catalytic functions in ancient proteins likely played a role in the evolution of modern enzymes. Here, the authors use protein sequences from Precambrian beta-lactamases and demonstrate that a single hydrophobic-to-ionizable amino acid mutation can lead to substantial Kemp eliminase activity.

    • Valeria A. Risso
    • , Sergio Martinez-Rodriguez
    •  & Jose M. Sanchez-Ruiz

  • Article
    | Open Access

    The European continent is thought to have played a major role in the origins of modern dogs. Here, analysing two ancient dog genomes from Germany, the authors find significant genetic continuity throughout the Neolithic period and time dog domestication to ∼20,000–40,000 years ago.

    • Laura R. Botigué
    • , Shiya Song
    •  & Krishna R. Veeramah

  • Article
    | Open Access

    Evolution can occur rapidly enough to influence population growth, though this possibility tends to be discounted for human populations. Here, the authors analyse genealogical records and show that evolution of women’s age at first reproduction contributed significantly to the growth of the île aux Coudres population.

    • Fanie Pelletier
    • , Gabriel Pigeon
    •  & Emmanuel Milot

  • Article
    | Open Access

    Hosts vary in how dependent they are on their beneficial symbionts. Here, Fisher and colleagues analyse the results of symbiont-removal experiments from 106 symbioses in a phylogenetic context and show that host dependence is associated with symbiont transmission mode, function, and genome size.

    • Roberta M. Fisher
    • , Lee M. Henry
    •  & Stuart A. West

  • Article
    | Open Access

    Ancient DNA keeps expanding our understanding of complex genetic relationships between Pleistocene hominins. Here, Posth and colleagues analyse the mitochondrial genome of an archaic human that diverged from other Neanderthals ∼270,000 years ago, providing the minimum age for an African introgression into Neanderthals.

    • Cosimo Posth
    • , Christoph Wißing
    •  & Johannes Krause

  • Article
    | Open Access

    Classification of the extinct South American native ungulates (SANUs) has posed a challenge given the absence of close, surviving relatives. Here, Westburyet al. sequence the mitochondrial genome of the extinct SANU Macrauchenia patachonicaand reconstruct the evolutionary history of the lineage.

    • Michael Westbury
    • , Sina Baleka
    •  & Michael Hofreiter

  • Article
    | Open Access

    Diversification may be driven by diversity, a concept Calcagnoet al. explore using models of intra- and inter-specific ecological interactions. A threshold number of species is sometimes required before adaptive radiations can occur; a phenomenon they term diversity-dependent adaptive radiation.

    • Vincent Calcagno
    • , Philippe Jarne
    •  & Patrice David

  • Article
    | Open Access

    It is unclear whether strategies involving antibiotic cycling can efficiently control the emergence of antibiotic-resistant bacteria. Here, Yoshidaet al. show that the evolution of multi-drug-resistant bacteria in vitrocan be manipulated by administering pairs of antibiotics and switching between them.

    • Mari Yoshida
    • , Sabrina Galiñanes Reyes
    •  & Leroy Cronin

  • Article
    | Open Access

    Some antibiotic resistance genes found in pathogenic bacteria might derive from antibiotic-producing actinobacteria. Here, Jianget al. provide bioinformatic and experimental evidence supporting this hypothesis, and propose a specific mechanism for the transfer of these genes between bacterial phyla.

    • Xinglin Jiang
    • , Mostafa M. Hashim Ellabaan
    •  & Sang Yup Lee

  • Article
    | Open Access

    Systematically understanding the sequence determinants to substrate specificity for enzymes has implications in areas from evolutionary biology to biocatalysis. Here, Whitehead and colleagues generate and analyse near-comprehensive single-mutation fitness landscapes for an amidase with three different substrates.

    • Emily E. Wrenbeck
    • , Laura R. Azouz
    •  & Timothy A. Whitehead

  • Article
    | Open Access

    Although all known RNA polymerases have multiple subunits, unrelated single-subunit polymerases have also been described. Here, the authors describe a single-subunit RNA polymerase from the SPβ prophage ofBacillus subtilis, which shares homology to multi-subunit enzymes.

    • David Forrest
    • , Katherine James
    •  & Nikolay Zenkin

  • Article
    | Open Access

    Multicellularity can arise by cells aggregating or remaining connected after cell division. Here, Driscoll and Travisano show that both mechanisms operate in experimentally evolved strains of the yeastKluyveromyces lactis, with transient aggregation facilitating the coexistence of unicellular and multicellular genotypes.

    • William W Driscoll
    •  & Michael Travisano

  • Article
    | Open Access

    The range of odours that an insect can detect depends on its olfactory receptors. Here, the authors functionally characterize the olfactory receptor repertoire of the mothSpodoptera littoralis using the Drosophilaempty neuron system and reconstruct the evolution of these receptors in the Lepidoptera.

    • Arthur de Fouchier
    • , William B. Walker III
    •  & Emmanuelle Jacquin-Joly

  • Article
    | Open Access

    Water is a fundamental resource, but its role in hominin evolution is not well explored. Here, the authors use a combination of groundwater, climate and agent-based models to show that groundwater availability may be critical to past patterns of taxonomic diversity in hominin development in East Africa.

    • M. O. Cuthbert
    • , T. Gleeson
    •  & G. M. Ashley

  • Article
    | Open Access

    De-domestication is the process by which cultivated plants adopt characteristics similar to that of their wild predecessors. Here Qiuet al. re-sequence de-domesticated weedy rice and matched cultivated varieties and identify genetic variants indicative of convergent evolution across multiple de-domestication events.

    • Jie Qiu
    • , Yongjun Zhou
    •  & Yongliang Lu

  • Article
    | Open Access

    Species richness increases with area sampled, potentially confounding biodiversity patterns from the fossil record. Here, the authors standardize spatial sampling to control for this bias and show that terrestrial vertebrate diversification was bounded during the Mesozoic but that equilibria were reset following the K/Pg extinction.

    • Roger A. Close
    • , Roger B.J. Benson
    •  & Richard J. Butler

  • Article
    | Open Access

    Detection ofde novo, low frequency mutations is important for characterising heterogeneous cell populations, such as those found in cancer cell populations. Here the authors present o2n-seq, an ultrasensitive method with highly efficient data usage for detection of rare mutations.

    • Kaile Wang
    • , Shujuan Lai
    •  & Jue Ruan

  • Article
    | Open Access

    Mistranslation results in amino acid changes in proteins known as phenotypic mutations and these occur at a much higher rate than DNA mutations. Here, the authors show that mistranslation can increase the response to directional selection by exacerbating the fitness effects of deleterious DNA mutations.

    • Sinisa Bratulic
    • , Macarena Toll-Riera
    •  & Andreas Wagner

  • Article
    | Open Access

    In animals with complex life cycles, selection on one life phase may constrain adaptation in another phase. Here the authors find that, during the adaptive radiation of mantellid frogs, the evolution of tadpole and adult morphologies has been uncoupled through phase-specific gene expression.

    • Katharina C. Wollenberg Valero
    • , Joan Garcia-Porta
    •  & Miguel Vences

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