Evolution articles within Nature Communications

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  • Article
    | Open Access

    The narrative that larger males are the norm in mammals has predominated for over a century. An analysis of body mass dimorphism across mammals, sampling families by their species richness, indicates that males are not larger than females in most mammals and that monomorphism is almost as prevalent.

    • Kaia J. Tombak
    • , Severine B. S. W. Hex
    •  & Daniel I. Rubenstein

  • Article
    | Open Access

    The relative importance of the various mechanisms that can drive microbial speciation is poorly understood. Here, Stanojković et al. explore the diversification of the soil cyanobacterium Microcoleus, showing that this genus represents a global speciation continuum of at least 12 lineages, with lineage divergence driven by selection, geographical distance, and the environment.

    • Aleksandar Stanojković
    • , Svatopluk Skoupý
    •  & Petr Dvořák

  • Article
    | Open Access

    Bet hedging is an evolutionary strategy facilitating survival in randomly fluctuating environments. Here, the authors report bet hedging in the unicellular microalga Haematococcus pluvialis, undergoing reversible diversification into mobile and non-mobile cells.

    • Si Tang
    • , Yaqing Liu
    •  & Zhonghua Cai

  • Article
    | Open Access

    Amaryllidaceae alkaloids, such as the Alzheimer’s medication galantamine, are currently extracted from low-yielding daffodils. Here, authors pair biosensor-assisted screening with machine learning-guided protein design to rapidly engineer an improved Amaryllidaceae enzyme in a microbial host.

    • Simon d’Oelsnitz
    • , Daniel J. Diaz
    •  & Andrew D. Ellington

  • Article
    | Open Access

    DNA methylation plays a major role in establishing cell identity, but the dynamics of DNA methylation patterns are highly variable across species. Here, the authors discover extensive DNA methylation reprogramming during embryonic development of the sea lamprey, a jawless fish with a distinctive, highly disordered methylome.

    • Allegra Angeloni
    • , Skye Fissette
    •  & Ozren Bogdanovic

  • Article
    | Open Access

    Extinction threatens to erode the Tree of Life. Here, the authors calculate extinction risk for jawed vertebrates, predicting a loss of 86–150 billion years (11–19%) of evolutionary history through the next 50–500 years and indicating that cartilaginous fish, ray-finned fish, and turtles are most at risk from a phylogenetic perspective.

    • Rikki Gumbs
    • , Oenone Scott
    •  & James Rosindell

  • Article
    | Open Access

    Pathogenic germline variants associated with childhood cancer risk could be subject to evolutionary constraints. Here, the authors analyse publicly available germline data in large cohorts and observe that paediatric cancer predisposition syndrome genes are highly constrained in the general population.

    • Ulrik Kristoffer Stoltze
    • , Jon Foss-Skiftesvik
    •  & Kjeld Schmiegelow

  • 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

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