Evolution articles within Nature Communications

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  • 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

  • Article
    | Open Access

    Reconstructing language dispersal patterns is important for understanding cultural spread and demic diffusion. Here, the authors use a computational approach based on velocity field estimation to infer the dispersal patterns of Indo-European, Sino-Tibetan, Bantu, and Arawak language families.

    • Sizhe Yang
    • , Xiaoru Sun
    •  & Menghan Zhang

  • Article
    | Open Access

    Little is known about the genetic basis of many natural behaviours and how they contribute to speciation. Here the authors address this by identifying genes linked to migration of a songbird, investigating how these gene are regulated, and connecting them to potential barriers between species.

    • Matthew I. M. Louder
    • , Hannah Justen
    •  & Kira E. Delmore

  • Article
    | Open Access

    Centrioles have a conserved structure and function but have diversified in sperm. Here the authors provide insight into the molecular mechanisms and adaptive evolution underlying this diversification.

    • Sushil Khanal
    • , Ankit Jaiswal
    •  & Tomer Avidor-Reiss

  • Article
    | Open Access

    Here, the authors perform statistical analyses to demonstrate that epistasis is highly pervasive in adaptive evolutionary trajectories of enzymes. Using epistatic data, they expose higher-order rewiring of intramolecular amino acid networks.

    • Karol Buda
    • , Charlotte M. Miton
    •  & Nobuhiko Tokuriki

  • Article
    | Open Access

    Hyoscyamine and scopolamine (HS) are two tropane alkaloids with medicinal significance produced by distantly related lineages in the Solanaceae family. Here, the authors assemble the genome of three HS-producing and one non-HS-producing species within Solanaceae, and reveal the evolution of the biosynthetic pathway.

    • Jiao Yang
    • , Ying Wu
    •  & Jianquan Liu

  • Article
    | Open Access

    Heeren et al study the evolutionary genomics of leishmaniasis in Peru and Bolivia to show that parasite hybridization increases the prevalence, diversity and spread of viruses that have been previously associated with disease severity and treatment failure.

    • Senne Heeren
    • , Ilse Maes
    •  & Frederik Van den Broeck

  • Article
    | Open Access

    Cyprinids fish species contain multiple subgenomes as a result of past duplications. Here, Xu et al. report new genomes of 21 cyprinid fish and conclude that observed subgenome dominance patterns are likely due to both maternal dominance and transposable element densities in each polyploid.

    • Min-Rui-Xuan Xu
    • , Zhen-Yang Liao
    •  & Hua-Hao Zhang

  • Article
    | Open Access

    Little is known about how malaria parasites adapt the speed of their development to their mosquito vectors. Using an evolutionary modelling framework, this study predicts that the metabolic status of mosquitoes shapes the parasites’ life-history strategies and transmission dynamics.

    • Paola Carrillo-Bustamante
    • , Giulia Costa
    •  & Elena A. Levashina

  • Article
    | Open Access

    Slowly evolving cnidarians are useful models to study genome architecture. This study shows that sea anemones have a high degree of chromosomal macrosynteny, but poor microsynteny conservation. This is correlated with a small genome size and short distances of cis-regulatory elements to genes.

    • Bob Zimmermann
    • , Juan D. Montenegro
    •  & Ulrich Technau

  • Article
    | Open Access

    Control of sound production by fast vocal muscle is critical to vocal communication. Here the authors show that zebra finches need daily singing exercise to build and maintain peak vocal muscle performance. Lack of exercise alters vocal muscle physiology and reduces attractiveness to females.

    • Iris Adam
    • , Katharina Riebel
    •  & Coen P. H. Elemans

  • Comment
    | Open Access

    Will protein structure search tools like AlphaFold replace protein sequence search with BLAST? We discuss the promises, using structure search for remote homology detection, and why protein BLAST, as the leading sequence search tool, should strive to incorporate structural information

    • Ali Al-Fatlawi
    • , Martin Menzel
    •  & Michael Schroeder

  • Article
    | Open Access

    The butterfly Parnassius glacialis experienced vast environmental transition when it dispersed out of the Qinghai-Tibet plateau. Here, the authors find that P. glacialis has an unusually large genome with rapid accumulation of transposable elements possibly facilitating its evolutionary adaptation.

    • Youjie Zhao
    • , Chengyong Su
    •  & Jiasheng Hao

  • Article
    | Open Access

    The mechanisms generating montane biodiversity remain incompletely understood. Here, the authors study the passerine avifauna of Indo-Pacific island mountains, finding that Eurasian-origin species colonized directly from other mountains, while Australo-Papuan-origin species made upslope range shifts from the lowlands.

    • Andrew Hart Reeve
    • , Jonathan David Kennedy
    •  & Knud Andreas Jønsson

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