Evolution articles within Nature Communications

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  • Article
    | Open Access

    The evolutionary origin of the domestic dog is uncertain. Here, the authors sequence the whole genomes of 9 extinct Japanese wolves and 11 modern Japanese dogs, applying a phylogenetic analysis to show that dogs may have originated in East Asia from a common ancestor with the Japanese wolf.

    • Jun Gojobori
    • , Nami Arakawa
    •  & Yohey Terai

  • Article
    | Open Access

    Dipterocarp trees are iconic but severely threatened species in Asian rainforests. This study assembles high-quality genomes of seven dipterocarp species to reveal the molecular basis of key adaptations and identifies a recent sharp population decline coinciding with local human activity.

    • Rong Wang
    • , Chao-Nan Liu
    •  & Xiao-Yong Chen

  • Article
    | Open Access

    The evolutionary trajectory of avian sex chromosomes may be more intricate than previously understood. In this study, sequencing and analysis of the neo-sex chromosomes and genome of the Crested Ibis suggests a multidirectional evolution of sex chromosomes in core waterbirds.

    • Lulu Xu
    • , Yandong Ren
    •  & Gang Li

  • Article
    | Open Access

    Selection is expected to act differently on aposematic and cryptic species. Analysis of wing images revealed that camouflaged moths exhibit higher wing pattern variability than aposematic moths, supporting the theory that camouflaged species display more variability, consistent with anti-predator strategy.

    • Ossi Nokelainen
    • , Sanni A. Silvasti
    •  & Johanna Mappes

  • Article
    | Open Access

    Polyploidization-rediploidization process plays an important role in plant adaptive evolution. Here, the authors assemble the genomes of mangrove species Sonneratia alba and its inland relative Lagerstroemia speciosa, and reveal genomic evidence for rediploidization and adaptive evolution after the whole-genome triplication.

    • Xiao Feng
    • , Qipian Chen
    •  & Ziwen He

  • Article
    | Open Access

    Genome-wide evidence to support that wild rice can contribute to weedy rice evolution by hybridization and adaptive introgression is very limited. Here, the authors sequence the weedy rice genomes and show reproductively compatible wild rice can contribute to weedy rice evolution.

    • Lin-Feng Li
    • , Tonapha Pusadee
    •  & Kenneth M. Olsen

  • Article
    | Open Access

    Cytochrome c maturation (CCM) is the process of covalent attachment of a heme group to the conserved cysteines to form the holocytochrome. Here, the authors report that the non-adaptive convergent evolution at the pathway level leads to mosaic distribution of CCM systems I and III among Archaeplastida species.

    • Huang Li
    • , Soujanya Akella
    •  & Jeffrey P. Mower

  • Article
    | Open Access

    Retinoic acid signaling is involved in patterning the embryonic antero-posterior axis, and also regulates hindbrain segmentation in jawed vertebrates. Here they show that retinoic acid signaling plays important roles in hindbrain segmentation in a jawless vertebrate, the lamprey, thus indicating this feature of hindbrain development is conserved in all vertebrates.

    • Alice M. H. Bedois
    • , Hugo J. Parker
    •  & Robb Krumlauf

  • Article
    | Open Access

    Phage-plasmids are mobile genetic elements that transfer horizontally between bacterial cells as viruses, and vertically within bacterial lineages as plasmids. Here, Pfeifer & Rocha show that phage-plasmids can mediate gene transfer across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.

    • Eugen Pfeifer
    •  & Eduardo P. C. Rocha

  • 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

    Criteria for evaluating joint articulation in vertebrates are lacking. Here, the authors propose an approach for combining measurements of 3D articular overlap, symmetry, and congruence into a single metric, and apply this to examine the walking stride of Deinonychus antirrhopus.

    • Armita R. Manafzadeh
    • , Stephen M. Gatesy
    •  & Bhart-Anjan S. Bhullar

  • Article
    | Open Access

    Chemoreception - the ability to smell and taste - relies on diverse receptor genes. Examining 1,527 vertebrate genomes, this study explores the dynamic evolution, lineage-specific expansions and losses of chemoreceptor genes as well as ecological and morphological factors associated with these.

    • Maxime Policarpo
    • , Maude W. Baldwin
    •  & Walter Salzburger

  • Article
    | Open Access

    Bats have been suggested to be resistant to cancer due to mechanisms related to their evolved longevity, but the associated molecular drivers are still understudied. Here, the authors examine cancer resistance mechanisms across seven bat species using in vitro and in vivo models, and identify HIF1A, COPS5, and RPS3 as related genes.

    • Rong Hua
    • , Yuan-Shuo Ma
    •  & Zhen Liu

  • Article
    | Open Access

    Escherichia coli ST131 is a globally dominant multidrug resistant clone associated with high rates of recurring urinary tract infections. In this genomic epidemiology study, the authors describe the evolution, population structure, and antimicrobial resistance in 142 E. coli ST131 samples from Wales, UK.

    • Rhys T. White
    • , Matthew J. Bull
    •  & Scott A. Beatson

  • Article
    | Open Access

    Here the authors show that genetic changes between species often alter gene expression in a cell type-specific manner. Most of this variability is driven by locally functioning cis-acting variation, and this contributes to the speed at which cell types accumulate expression changes.

    • Jasper Panten
    • , Tobias Heinen
    •  & Duncan T. Odom

  • Article
    | Open Access

    Heterostylous plants have floral morphs bearing female and male sex organs at reciprocal heights. Here the authors show that, across angiosperms, heterostyly is associated with tubed flowers pollinated by long-tongued insects, supporting the Darwinian hypothesis about precise pollen transfer between heterostylous morphs.

    • Violeta Simón-Porcar
    • , Marcial Escudero
    •  & Juan Arroyo

  • Article
    | Open Access

    Lithic cutting-edge productivity is a way of quantifying prehistoric human technological evolution. Here, the authors examine the Middle-to-Upper Paleolithic transition across eight assemblages in the eastern Mediterranean, finding the transition to be later than expected and associated with bladelet technology development.

    • Seiji Kadowaki
    • , Joe Yuichiro Wakano
    •  & Sate Massadeh

  • Article
    | Open Access

    The origins of alpine plant diversity are unclear. Here, the authors provide a time-calibrated molecular phylogenetic tree for Saxifraga, a diverse alpine plant clade, and show that upslope biome shifts into the alpine zone occurred more often than dispersal between alpine regions.

    • Tom Carruthers
    • , Michelangelo S. Moerland
    •  & Wolf L. Eiserhardt

  • Article
    | Open Access

    Rickettsiales encompass diverse host-associated bacteria, including pathogens, parasites, and mutualists. This study shows that obligate associations with their hosts likely evolved multiple times independently, thus providing an alternative, generalisable view, on evolution of intracellularity.

    • Michele Castelli
    • , Tiago Nardi
    •  & Davide Sassera

  • Article
    | Open Access

    Chemosensory tissues are remarkably variable between species but the cause of this diversity is unclear. Here, the authors conduct transcriptomic analyses of chemosensory tissues from diverse Drosophila species, revealing evidence of stabilizing selection and recent species- and sex-specific changes.

    • Gwénaëlle Bontonou
    • , Bastien Saint-Leandre
    •  & J. Roman Arguello

  • Article
    | Open Access

    Telomeres protect the extremities of linear chromosomes and are involved in ageing, senescence and genome stability. Here, the authors have identified peculiar and specific telomeric DNA repeats in the genomes of devastating plant-parasitic nematodes, opening new perspectives for their control.

    • Ana Paula Zotta Mota
    • , Georgios D. Koutsovoulos
    •  & Etienne G. J. Danchin

  • Article
    | Open Access

    Using a dataset that included 341,846 species in 391 angiosperm floras worldwide, this study finds that the global phylogenetic structure of angiosperms shows clear and meaningful relationships with environmental factors and that current climatic variables have the highest predictive power for phylogenetic metrics reflecting recent evolutionary relationships.

    • Hong Qian
    • , Shenhua Qian
    •  & Michael Kessler

  • Article
    | Open Access

    CRISPR-based gene drives have the potential to spread within populations and are considered as promising vector control tools. Here the authors show an anti-drive mosquito strain that prevents the spread and collapse of a population suppression gene drive in laboratory Anopheles mosquito large cage trials in complex ecological and behavioral conditions.

    • Rocco D’Amato
    • , Chrysanthi Taxiarchi
    •  & Ruth Müller

  • Article
    | Open Access

    Plant cell-surface receptors perceive both self- and nonself-molecules to regulate biological processes. Here the authors show that a subclass of phytohormone and immune receptors share a common origin, which have diverged to perceive distinct ligands and activate differential downstream responses.

    • Bruno Pok Man Ngou
    • , Michele Wyler
    •  & Ken Shirasu

  • Article
    | Open Access

    It is unclear whether naturally evolved de novo proteins have stable, folded structures. Here, systematic identification and structural modeling of de novo genes, this study reveals that a small subset of these proteins may have well-folded structures, and were likely born with these structures.

    • Balázs Bálint
    • , Zsolt Merényi
    •  & László G. Nagy

  • 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

    It is unclear whether naturally evolved de novo proteins have stable, folded structures. Here, through systematic identification and structural modeling of de novo genes, this study reveals that a small subset of these proteins may have well-folded structures, and were likely born with these structures.

    • Junhui Peng
    •  & Li Zhao

  • Article
    | Open Access

    Varroa and Tropilaelaps mites threaten honeybee health. This study finds that mites alter feeding habits depends on their own, and hosts’, life history stage. Mites feed on the host hemolymph when parasitizing pupae during their reproductive stage but consume fat body during their dispersal stage.

    • Bin Han
    • , Jiangli Wu
    •  & Shufa Xu

  • Article
    | Open Access

    Bacterial viruses (phages) are generally recognised as rapidly evolving biological entities. Here, Rozwalak et al. analyse DNA sequence datasets generated from ancient palaeofaeces and identify 298 phage genomes from the last 5300 years, including a 1300-year-old phage genome nearly identical to a present-day virus that infects human gut bacteria.

    • Piotr Rozwalak
    • , Jakub Barylski
    •  & Andrzej Zielezinski

  • Article
    | Open Access

    Interactions with angiosperms are thought to have had a significant impact on insect diversification. Here, the authors use a Bayesian process-based approach to find that angiosperm radiation played a dual role that changed through time, mitigating insect extinction in the Cretaceous and promoting insect origination in the Cenozoic.

    • David Peris
    •  & Fabien L. Condamine

  • Article
    | Open Access

    Chronic SARS-CoV-2 infections have been hypothesised to be sources of new variants. Here, the authors use large-scale genome sequencing data to identify mutations predictive of chronic infections, which may therefore be relevant in future variants.

    • Sheri Harari
    • , Danielle Miller
    •  & Adi Stern

  • Article
    | Open Access

    Live poultry markets in rural areas can be hotspots for transmission of pathogens, but the effects of markets on selection of viral virulence are not known. This study demonstrates through mathematical modelling that high turnover rate and persistence of viral particles can select for highly virulent pathogens in markets.

    • Justin K. Sheen
    • , Fidisoa Rasambainarivo
    •  & C. Jessica E. Metcalf

  • Article
    | Open Access

    Frogs are an ancient and ecologically diverse group of amphibians that include important model systems. This paper reports genome sequences of multiple frog species, revealing remarkable stability of frog chromosomes and centromeres, along with highly recombinogenic extended subtelomeres.

    • Jessen V. Bredeson
    • , Austin B. Mudd
    •  & Daniel S. Rokhsar

  • Article
    | Open Access

    A key assumption of ageing research is that old males are less fertile. A meta-analysis of ejaculate traits challenges this, by showing senescence is not consistently observed across 157 species of animals, but is specific to only certain taxa and ejaculate traits. The study also highlights methodological factors that might modulate the evidence for reproductive senescence.

    • Krish Sanghvi
    • , Regina Vega-Trejo
    •  & Irem Sepil

  • Article
    | Open Access

    What a microbial strain is and how many strains make up a natural bacterial population remain elusive concepts. Here, Viver et al. analyse Salinibacter ruber isolates and metagenomes from two solar salterns, revealing gaps within the species sequence space that they use to define and quantify sub-species categories, such as genomovars and strains, that co-exist in a saltern pond.

    • Tomeu Viver
    • , Roth E. Conrad
    •  & Ramon Rossello-Mora

  • Article
    | Open Access

    The archaeal ancestor of eukaryotes belonged to the phylum Asgardarchaeota, or Asgard archaea. Here, the authors use ancestral sequence reconstruction and experimentally determine the optimal GDP-binding temperature of a translation elongation factor from ancient and extant Asgard archaea, to infer optimal growth temperatures for eukaryotes’ ancestors.

    • Zhongyi Lu
    • , Runyue Xia
    •  & Meng Li

  • Article
    | Open Access

    DNA sequencing methods for characterizing microbial communities are well developed for bacteria, archaea and fungi, but less so for eukaryotic parasites and commensals. Here, the authors present an optimized and validated metabarcoding protocol for host-associated eukaryotic communities.

    • Leah A. Owens
    • , Sagan Friant
    •  & Tony L. Goldberg

  • Article
    | Open Access

    The evolution of cicadas is unclear due to a lack of understanding of transitional features. Here, the authors assess adult and nymph mid-Cretaceous cicadas, to elucidate their morphological evolution and identify evidence of the origins of cicada sound-generation and subterranean lifestyle.

    • Hui Jiang
    • , Jacek Szwedo
    •  & Bo Wang

  • Article
    | Open Access

    Sponges, being early-diverging metazoans and the only animals to develop extensive skeletons of silica, have potential to inform about the evolutionary steps of metazoan traits, including biomineralization. Here, the authors characterize two proteins associated with the hexactinellid sponge silica.

    • Katsuhiko Shimizu
    • , Michika Nishi
    •  & Manuel Maldonado

  • Article
    | Open Access

    Here, Rühlemann et al. analyze the gut microbiome of wild-living African great apes (Gorillas, Bonobos, Chimpanzees) in comparison to that of humans, identifying host specific patterns and shared evolutionary conserved traits disrupted in humans.

    • M. C. Rühlemann
    • , C. Bang
    •  & A. Franke

  • Article
    | Open Access

    Although intraspecific dominance hierarchies are common, large scale interspecific dominance hierarchies are unknown. Using data from hundreds of avian species, the authors find that species that are more familiar with each other engage in less aggression and the aggression is resolved more directly.

    • Gavin M. Leighton
    • , Jonathan P. Drury
    •  & Eliot T. Miller

  • Article
    | Open Access

    The origin of the genus Homo is debated. Here, the authors investigate the morphology of the H. habilis enamel-dentine junction using a sample of 911 hominin and extant ape teeth, finding that H. habilis has more in common with Australopithecus than later members of the genus Homo.

    • Thomas W. Davies
    • , Philipp Gunz
    •  & Matthew M. Skinner

  • Article
    | Open Access

    Much is still unknown of the evolution of animal metabolic enzymes. This study describes a new enzyme family bridging the production of polyketides and membrane lipids. This expands the known biochemical repertoire of animals for making ecologically and biomedically important natural products.

    • Zhenjian Lin
    • , Feng Li
    •  & Eric W. Schmidt

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