Evolution articles within Nature Communications

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  • Article
    | Open Access

    Crocodilians are ambush predators that possess haemoglobin with an allosteric switch between R (high oxygen affinity) and T (low oxygen affinity) forms strongly controlled by bicarbonate ions, a unique evolutionary feature that helps the animal to stay underwater for extended periods of time.

    • Katsuya Takahashi
    • , Yongchan Lee
    •  & Jeremy R. H. Tame

  • Article
    | Open Access

    Marine life depends on zooplankton like krill, but it’s uncertain how these species will respond to a warming ocean. This study of genome variation in the Northern krill uncovered many gene variants that could be crucial for environmental adaptation and support stock assessment under climate change.

    • Per Unneberg
    • , Mårten Larsson
    •  & Andreas Wallberg

  • Article
    | Open Access

    Bacteria possess many types of antiviral immune systems, some of which are present also in eukaryotes. Here, Leão et al. explore the diversity and distribution of antiviral defense systems in archaea and their evolutionary relationships with bacterial and eukaryotic immune systems, supporting that Asgard archaea played important roles in the origin of eukaryotic innate immunity.

    • Pedro Leão
    • , Mary E. Little
    •  & Brett J. Baker

  • Article
    | Open Access

    The roles of Asgard archaea in soil ecosystems are unclear. In this study, the authors report complete genomes and metatranscriptomic data of Asgard archaea that indicate a role in production and consumption of carbon compounds known to serve as substrates for methane production in wetland soils.

    • Luis E. Valentin-Alvarado
    • , Kathryn E. Appler
    •  & Jillian F. Banfield

  • Article
    | Open Access

    Formaldehyde-preserved museum specimens have produced genetic data. Here, the authors generate chromatin profiles from museum specimens 117 years old and experimentally demonstrate chromatin profile presence in formalin-fixed mouse and yeast models.

    • Erin E. Hahn
    • , Jiri Stiller
    •  & Clare E. Holleley

  • Article
    | Open Access

    Pollinator-driven evolution of floral traits is thought to be a major driver of angiosperm speciation and diversification. Here, the authors assemble the chromosome-scale genome of the sexually deceptive orchid Ophrys sphegodes and reveal insights into sexual deception and pollinator adaptation.

    • Alessia Russo
    • , Mattia Alessandrini
    •  & Philipp M. Schlüter

  • Article
    | Open Access

    Engineered DNA will slow the growth of a host cell if it redirects limiting resources or otherwise interferes with homeostasis. Here the authors measure how 301 BioBrick plasmids affected Escherichia coli growth and found that 19.6% were burdensome, primarily because they depleted the limited gene expression resources of host cells.

    • Noor Radde
    • , Genevieve A. Mortensen
    •  & Jeffrey E. Barrick

  • Article
    | Open Access

    New protein coding genes can emerge de novo overlapping existing protein genes but in the opposite orientation. Here, the authors investigate the possibility of such events using mathematical modelling and data analysis, and find that emergence of a protein coding region is generally most likely in one frame of overlap (frame 1).

    • Bharat Ravi Iyengar
    • , Anna Grandchamp
    •  & Erich Bornberg-Bauer

  • Article
    | Open Access

    The evolution of sperm length remains an elusive topic. This study applies the Pareto multi-task evolution framework to investigate sperm length variation in relation to body mass across tetrapods and find that sperm length evolution is mainly driven by sperm competition and clutch size.

    • Loren Koçillari
    • , Silvia Cattelan
    •  & Andrea Pilastro

  • Article
    | Open Access

    Gut microbiota are hypothesized to shape the ecology and evolution of animal life but robust estimates of natural selection acting on gut microbiome variation is lacking. This study provides evidence that variation in the gut microbiome is associated with survival in a population of feral horses.

    • Mason. R. Stothart
    • , Philip. D. McLoughlin
    •  & Jocelyn. Poissant

  • Article
    | Open Access

    Brucella melitensis is a zoonotic bacterial pathogen of livestock that can infect humans and causes brucellosis. Here, the authors sequence an ancient specimen of B. melitensis and show that the species emerged in the Neolithic period, around the time of development of animal management practices.

    • Louis L’Hôte
    • , Ian Light
    •  & Kevin G. Daly

  • Article
    | Open Access

    Fungi and bacteria fight coevolutionary wars using antimicrobial compounds that animal cells cannot usually produce. This study finds that bdelloid rotifers attacked by a fungal pathogen express genes acquired horizontally from bacteria, including some resembling antibiotic synthesis clusters.

    • Reuben W. Nowell
    • , Fernando Rodriguez
    •  & Christopher G. Wilson

  • Article
    | Open Access

    The role of altered replication timing (ART) during malignant transformation requires further exploration. Here, analysis of replication-timing sequencing and whole genome sequencing reveals a significant association of ART with the genomic and transcriptomic landscape during cancer evolution in lung and breast tumours.

    • Michelle Dietzen
    • , Haoran Zhai
    •  & Nnennaya Kanu

  • Comment
    | Open Access

    Yeast is a widely used cell factory for the conversion of sugar into fuels, chemicals and pharmaceuticals. Establishing yeast as being autotrophic can enable it to grow solely on CO2 and light, and hereby yeast can be used as a wider platform for transition to a sustainable society.

    • Jens Nielsen

  • Article
    | Open Access

    Transforming model heterotrophs into autotrophs is usually accomplished by engineering one carbon assimilation pathway and/or employing laboratory evolution. Here, the authors report the engineering of cyanobacterial endosymbionts in yeasts to achieve photosynthetic growth, carbon assimilation and natural products production.

    • Yang-le Gao
    • , Jason E. Cournoyer
    •  & Angad P. Mehta

  • Article
    | Open Access

    For sexually reproducing organisms, experimental models to study the evolution of primary sex-determining loci are scarce. This study shows male-determining loci on  proto-Y chromosomes of the housefly, containing the same gene, can genomically diverge into regions of various complexity.

    • Xuan Li
    • , Sander Visser
    •  & Leo W. Beukeboom

  • Article
    | Open Access

    Bats are remarkably tolerant to viral infections and their unique immune system, characterized by high level of tissue protection and dampened inflammatory responses, contributes to their longevity. Here authors show that the diversity of the bat antibody repertoire changes according to the body temperature and metabolic activity of the animals and higher activity directs their specificity towards eliminating damaged epithelial and endothelial cells.

    • Nia Toshkova
    • , Violeta Zhelyzkova
    •  & Jordan D. Dimitrov

  • Article
    | Open Access

    The deletion and duplication of genes can be major facilitators of evolution. Here, the role of such variation was investigated in over a thousand genomes characterizing the global spread of a major fungal pathogen of wheat. The study suggests that gene loss likely facilitated the pathogen’s colonization of new continents by modulating climate tolerance and metabolic capabilities.

    • Sabina Moser Tralamazza
    • , Emile Gluck-Thaler
    •  & Daniel Croll

  • Article
    | Open Access

    Systematic studies are needed to form a general understanding of the genomic basis of adaptation. In this work, authors perform laboratory evolution of 3360 yeast populations in 252 environments of varying levels of stress to uncover the genomic principles of environmental adaptation.

    • Piaopiao Chen
    •  & Jianzhi Zhang

  • Article
    | Open Access

    Pacific Biosciences (PacBio) High Fidelity (HiFi) long-read sequencing usually requires a relatively high amount of DNA input ( > 1 µg). Here the authors develop LILAP, a Low-Input (100 ng), Low-cost, and Amplification-free library-generation method for PacBio sequencing, enabling the generation of two high-quality individual fly genomes.

    • Hangxing Jia
    • , Shengjun Tan
    •  & Yong E. Zhang

  • Article
    | Open Access

    The impact of ocean warming on fish size structure is debated. Here, the authors test mass scaling of metabolism and swimming performance of fish across different water temperatures and regions, suggesting that resource-acquisition explains size reduction due to ocean warming.

    • Jacob L. Johansen
    • , Matthew D. Mitchell
    •  & John A. Burt

  • Article
    | Open Access

    Eukaryotic Argonaute proteins participate in RNA-guided RNA silencing pathways and are divided into AGO and PIWI clades, with functional and mechanistic differences. Here, the authors show that a deep-branching PIWI protein from Asgard archaea (the closest prokaryotic relatives of eukaryotes) displays hybrid features and may reflect an ancestral molecular architecture that preceded the divergence of eukaryotic AGOs and PIWIs.

    • Carolien Bastiaanssen
    • , Pilar Bobadilla Ugarte
    •  & Fabai Wu

  • Article
    | Open Access

    Global trends in biodiversity are subject to regionally heterogeneous diversification processes. Here, the authors examine Late Cretaceous ammonoids, modelling the impact of sampling bias and potential biotic and abiotic drivers on our understanding of their biodiversity trends towards the Cretaceous-Paleogene boundary.

    • Joseph T. Flannery-Sutherland
    • , Cameron D. Crossan
    •  & James D. Witts

  • Article
    | Open Access

    Folliculogenesis and ovulation are regulated by separate hormones (FSH and LH), though the release of both has been thought to be regulated by the same upstream hormone, GnRH. Here they show that in fish, FSH release is regulated by a distinct hormone, FSH-RH, thereby revisiting our current understanding of gonadotropin release.

    • Shun Kenny Uehara
    • , Yuji Nishiike
    •  & Shinji Kanda

  • Article
    | Open Access

    Zika and Dengue virus non-structural protein 5 can antagonise STAT2 modulating the host response and this interaction is involved in determining tropism. Here the authors show mammals independently evolved resistance to flavivirus NS5 multiple times, involving complex genetic changes in STAT2 which balance viral defence whilst maintaining STAT2’s critical functions.

    • Ethan C. Veit
    • , Madihah S. Salim
    •  & Matthew J. Evans

  • Article
    | Open Access

    Some mite species infect only one mammal host, while other typically more dangerous species, infect multiple hosts. This study developed a model using parasite, host, climate, and habitat data to predict potential host range expansions in single-host mites and the probability of single-host parasites to become multi-hosts.

    • Pavel B. Klimov
    •  & Qixin He

  • Article
    | Open Access

    Cochlearia is an evolutionarily dynamic genus with different base chromosome numbers and ploidal levels. Here, the authors construct a graph-based pangenome for Cochlearia and reveal that whole-genome duplication associated with greater diversity of genomic structural variation and their possible function in adaptation.

    • Tuomas Hämälä
    • , Christopher Moore
    •  & Levi Yant

  • Article
    | Open Access

    Bacterial resistance to beta-lactam antibiotics is on the rise, but laboratory evolution studies do not always recapitulate clinical resistance levels. Here, the authors select Escherichia coli mutants with varying degrees of beta-lactam resistance, showing that combinations of distinct genetic mutations, accessible at large population sizes, can drive high-level resistance independently of beta-lactamases.

    • Rotem Gross
    • , Idan Yelin
    •  & Roy Kishony

  • Article
    | Open Access

    Evolutionary multiplayer games in structured populations illustrate a variety of phenomena in natural and social systems. This research provides a mathematical framework to analyze multiplayer games with an arbitrary number of strategies on regular graphs.

    • Chaoqian Wang
    • , Matjaž Perc
    •  & Attila Szolnoki

  • Article
    | Open Access

    Conodonts, early vertebrates, are thought to have evolved complex tooth tissue as an adaptation for feeding. Here, the authors use Electron Backscatter Diffraction to show increasing dental crystallographic order through conodont evolution, in parallel with dietary adaptations.

    • Bryan Shirley
    • , Isabella Leonhard
    •  & Emilia Jarochowska

  • Article
    | Open Access

    Little is known about the interaction of different ecological factors in shaping adaptive evolution in natural habitats. This study found that plants evolved local adaption to different soils, but only when they interacted with aphid- herbivores and bumblebee-pollinators.

    • Thomas Dorey
    • , Léa Frachon
    •  & Florian P. Schiestl

  • Article
    | Open Access

    The role of ecological trade-offs in delineating species distribution is often unclear. This study finds that the rapid expansion of A. thaliana in Europe is explained by dispersal ability, but relict genetic variants for competitive ability and stress resistance are maintained at the range margins.

    • Cristina C. Bastias
    • , Aurélien Estarague
    •  & François Vasseur

  • Article
    | Open Access

    Nature is full of ultraviolet coloration, invisible to the human eye. This study shows that “hidden” UV coloration in snakes is widespread and may have evolved in response to predators and habitat rather than for reproductive functions.

    • Hayley L. Crowell
    • , John David Curlis
    •  & Alison R. Davis Rabosky

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