Evolution articles within Nature Communications

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  • Article
    | Open Access

    The 2023 monkeypox outbreak was caused by a subclade IIb monkeypox virus (MPXV). Here, using advanced sequencing techniques, the authors identify variations on low-complexity regions of the MPXV genome and describe their potential as evolutionary drivers.

    • Sara Monzón
    • , Sarai Varona
    •  & Gustavo Palacios

  • Article
    | Open Access

    Reynolds and colleagues examine a biochemically-mediated epistatic interaction between metabolic enzymes involved in folate metabolism and show that biochemical coupling shapes the range of enzyme activities sufficient to rescue cell growth.

    • Thuy N. Nguyen
    • , Christine Ingle
    •  & Kimberly A. Reynolds

  • Article
    | Open Access

    Trait correlations impact evolvability as selection on one trait can influence others. Here, the authors examine trait correlation in two proteins, a fluorescent protein & an antibiotic resistance enzyme, observing rapid evolution of trait correlations through changes in the biophysical properties of these proteins.

    • Pouria Dasmeh
    • , Jia Zheng
    •  & Andreas Wagner

  • Article
    | Open Access

    Grasses share a whole-genome duplication called rho, but the adaptive implications are unclear. Here, the authors conduct phylogenomic and phylotranscriptomic analyses of 363 grasses, identifying additional whole-genome duplications and finding that duplicates are implicated in environmental adaptations or morphogenesis.

    • Taikui Zhang
    • , Weichen Huang
    •  & Hong Ma

  • Article
    | Open Access

    SARS-CoV-2 constantly evolves but the roles of resulting mutations are not always clear. In this study, the authors report that ORF8 knockout confers a fitness advantage to SARS-CoV-2 using genomic surveillance data, highlighting how different types of adaptations across the SARS-CoV-2 genome can drive variant fitness.

    • Cassia Wagner
    • , Kathryn E. Kistler
    •  & Trevor Bedford

  • Article
    | Open Access

    The cellular atlas of Pristina leidyi reveals cell type diversity in adult annelids by single cell transcriptomics, discovering several novel cell types and suggesting a pluripotent stem cell signature associated with adult cell type differentiation

    • Patricia Álvarez-Campos
    • , Helena García-Castro
    •  & Jordi Solana

  • Article
    | Open Access

    Hepatocellular carcinomas (HCC) present spatial intratumour heterogeneity (sITH). Here, the authors perform a genomic and phylogenetic analysis of spatially-sampled HCC tumour sections, observe block-shaped sITH, and find ongoing natural selection where ancestral and derived clones spatially compete in the same tumor.

    • Xiaodong Liu
    • , Ke Zhang
    •  & Weiwei Zhai

  • Article
    | Open Access

    Naked mole-rats are long-lived rodents with remarkable resistance to cancer. Here authors show that their T-cell compartment is different from that of mice in that they have a large population of circulating cytotoxic γδ T cells harboring a dominant clonotype, and the clonotypic diversity of their conventional cytotoxic αβ T cells is more modest than that of mice.

    • Tzuhua D. Lin
    • , Nimrod D. Rubinstein
    •  & Rochelle Buffenstein

  • Article
    | Open Access

    Endogenous retroviruses (ERVs) are remnants of ancient viruses embedded in animal DNA. This study found that the solitary long terminal repeats of ERVs in birds, particularly Passeriformes, have evolved to influence gene expression, potentially contributing to adaptive diversification of species.

    • Guangji Chen
    • , Dan Yu
    •  & Shaohong Feng

  • Article
    | Open Access

    Collective cooperation is found across many social and biological systems. Here, the authors find that infrequent hub updates promote the emergence of collective cooperation and develop an algorithm that optimises collective cooperation with update rates.

    • Yao Meng
    • , Sean P. Cornelius
    •  & Aming Li

  • Article
    | Open Access

    This study on respiratory syncytial virus (RSV) reveals global genomic gaps. Using INFORM-RSV data, it uncovers selection’s impact on RSVA and RSVB diversity. Analysing full genomes, it highlights non-neutral epidemic processes. The research emphasises air travel’s influence on global spread, underscoring the need for comprehensive RSV genomic surveillance.

    • Annefleur C. Langedijk
    • , Bram Vrancken
    •  & Shabir A. Madhi

  • Article
    | Open Access

    Hawaiian endemic mints represent the second largest plant radiation in the archipelago. Here, the authors present a reference genome and numerous resequenced individuals to uncover evidence for polyploidy, geographic speciation and localized hybridization underlying diversification in this lineage

    • Crystal M. Tomlin
    • , Sitaram Rajaraman
    •  & Charlotte Lindqvist

  • Article
    | Open Access

    Modern sugarcane cultivars have complicated genome due to interspecific crosses and multiple backcrossing. Here, the authors report the haplotype-resolved, chromosome-level genome assembly of a modern hybrid sugarcane cultivar and reveal the expansion of genes related to sugar accumulation and smut resistance.

    • Yixue Bao
    • , Qing Zhang
    •  & Muqing Zhang

  • Article
    | Open Access

    Bergmann’s Rule predicts larger body sizes in colder climates. Here, the authors examine extinct and extant dinosaurs (birds) and mammaliaforms, finding no evidence of body size variation with latitude in any group, but a small variation with temperature in extant birds.

    • Lauren N. Wilson
    • , Jacob D. Gardner
    •  & Chris L. Organ

  • Article
    | Open Access

    Hepatitis B virus is an ancient human pathogen that dates back more than 10,000 years. Here, the authors investigate the evolutionary history of the virus in Eastern Eurasia by sequencing 34 genomes dating from approximately 400–5,000 years ago and comparing them with other contemporary sequences.

    • Bing Sun
    • , Aida Andrades Valtueña
    •  & Yinqiu Cui

  • Article
    | Open Access

    Pliobates cataloniae is a small-bodied Miocene catarrhine primate with unclear systematic status. Here, the authors present additional dental remains from this species, conducting cladistic analyses that indicate it is a pliopithecoid convergent with apes in elbow and wrist morphology.

    • Florian Bouchet
    • , Clément Zanolli
    •  & David M. Alba

  • Article
    | Open Access

    The effect of temperature fluctuations on the evolution of new phenotypes is largely unknown. Using experimental evolution of fluorescent protein in E. coli, this study shows that a cooling environment can accelerate, and a warming environment decelerate, the evolution of a new protein phenotype.

    • Jia Zheng
    • , Ning Guo
    •  & Andreas Wagner

  • Article
    | Open Access

    The natural hallucinogen psilocybin — produced by so-called magic mushrooms — holds promise for the treatment of depression and other mental health conditions. Here, the authors provide a structural and biochemical analysis of the Psilocybe methyl transferase PsiM that provides mechanistic insight into the last step of psilocybin biosynthesis.

    • Jesse Hudspeth
    • , Kai Rogge
    •  & Sebastiaan Werten

  • 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

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