Evolution articles within Nature Communications

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  • Article
    | Open Access

    In nature, soil, pollinators, and herbivores are the main drivers of plant adaptation and diversification. This study reveals that the interaction between soil and biotic pollination causes divergent evolution where pollinators play a key role, leading to strong divergence among plants in different soils.

    • Thomas Dorey
    •  & Florian P. Schiestl

  • Article
    | Open Access

    The naked mole-rat exhibits extreme longevity, resistance to hypoxia and absence of cardiovascular disease. Here, Faulkes et al. identify mechanisms behind these traits by comparing cardiac metabolomes and transcriptomes of naked more-rats to other African mole-rat genera and evolutionary divergent mammals.

    • Chris G. Faulkes
    • , Thomas R. Eykyn
    •  & Dunja Aksentijevic

  • Article
    | Open Access

    Hanley et al show that transmission of dengue and Zika virus from Old and New World monkeys is shaped by an immunologically-mediated trade-off between magnitude and duration of replication. Patterns of Zika transmission suggests high risk of spillback into neotropical monkeys.

    • Kathryn A. Hanley
    • , Hélène Cecilia
    •  & Shannan L. Rossi

  • Article
    | Open Access

    Correspondence between genome and organismal complexity over macroevolutionary time is poorly understood. Here the authors show that multicellular eukaryotes increasingly simplify their genomes and suggest that the concept of functional outsourcing, via ecological interactions, could explain this paradoxical complexity decoupling.

    • Mirjana Domazet-Lošo
    • , Tin Široki
    •  & Tomislav Domazet-Lošo

  • Article
    | Open Access

    Pseudomonas putida is becoming a host of choice for the valorization of lignocellulosic substrates. Here, the authors provide insight into the adaptation of this bacterium to the non-native substrate D-xylose, enabled by metabolic engineering and adaptive laboratory evolution.

    • Pavel Dvořák
    • , Barbora Burýšková
    •  & Martin Benešík

  • Article
    | Open Access

    The timing and chronology of the movement of Homo sapiens after migration out of Africa remains unclear. Here, the authors combine a genetic approach with a palaeoecological model to estimate that the Persian Plateau could have been a hub for migration out of Africa, suggesting the environment may have been suitable for population maintenance.

    • Leonardo Vallini
    • , Carlo Zampieri
    •  & Luca Pagani

  • Article
    | Open Access

    In this work, authors combine computational models with single-cell and population-level data showing the variability in plasmid copy number within bacterial populations leads to phenotypic diversity. They reveal how multicopy plasmids contribute to bacterial transient antibiotic resistance.

    • J. Carlos R. Hernandez-Beltran
    • , Jerónimo Rodríguez-Beltrán
    •  & Rafael Peña-Miller

  • Article
    | Open Access

    Seasonal influenza vaccine effectiveness depends on including virus strains in the vaccine that closely match those circulating in the upcoming season. In this study, the authors develop a computational model of influenza virus evolution to predict future circulating strains and therefore support vaccine strain selection.

    • Jingzhi Lou
    • , Weiwen Liang
    •  & Maggie Haitian Wang

  • Article
    | Open Access

    Subgenome dominance is widely observed in allopolyploid species, but the molecular mechanisms remain unclear. Here, the authors generate genome-wide map of accessible chromatin regions (ACRs) in allo-octoploid cultivated strawberry and reveal that dynamics of the ACRs play an important role in its subgenome dominance.

    • Chao Fang
    • , Ning Jiang
    •  & Jiming Jiang

  • Article
    | Open Access

    Diels-Alderases (DAs), enzymes catalyzing [4 + 2] cycloaddition reactions, are of high interest, but insights into their evolution are lacking. Here, the authors investigate the evolutionary origins of the intermolecular DAs in the biosynthesis of Moraceae plant-derived Diels-Alder-type secondary metabolites, suggesting they evolved from an ancestor functioning as a flavin adenine dinucleotide-dependent oxidocyclase.

    • Qi Ding
    • , Nianxin Guo
    •  & Xiaoguang Lei

  • Article
    | Open Access

    Recent phylogenetic analyses have identified orphan clades, including Xenacoelomorphs, that can offer insights into bilaterian evolution. Here they generate a cell type atlas of Xenoturbella bockithat highlights cellular diversity in the nervous system and other tissues, reinforcing the idea of parallel evolution of cell types across animals.

    • Helen E. Robertson
    • , Arnau Sebé-Pedrós
    •  & Heather Marlow

  • Article
    | Open Access

    Hair is the main skin appendage of mammals. Here, the authors show that claws of clawed frogs and hair contain homologous keratins and depend on the same transcription factor, Hoxc13, suggesting a common evolutionary origin of these skin appendages.

    • Marjolein Carron
    • , Attila Placido Sachslehner
    •  & Leopold Eckhart

  • Article
    | Open Access

    There is limited data on immune factors contributing to SARS-CoV-2 viral clearance in people living with HIV. Here, the authors show that re-emergence of the neutralizing antibody response may be key to clearing persistent SARS-CoV-2 infection in ART-mediated recovery from immunosuppression in advanced HIV disease.

    • Farina Karim
    • , Catherine Riou
    •  & Alex Sigal

  • 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

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