Molecular evolution articles within Nature Communications

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  • Article
    | Open Access

    Dengue is a major public health concern in the Americas, and the Caribbean can be a source for reintroduction and spread. Here, the authors use travel surveillance data and genomic epidemiology to reconstruct Dengue epidemic dynamics in the Caribbean from 2009-2022.

    • Emma Taylor-Salmon
    • , Verity Hill
    •  & Nathan D. Grubaugh

  • Article
    | Open Access

    Non-pharmaceutical interventions for COVID-19 also impacted the transmission of other viruses including respiratory syncytial virus (RSV). Here the authors describe the changing epidemiology, clinical severity, and genetic diversity of RSV in Chicago, Illinois, from July 2010 to April 2023.

    • Estefany Rios-Guzman
    • , Lacy M. Simons
    •  & Judd F. Hultquist

  • 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

    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

    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

    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

    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

    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

    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

    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

    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, 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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    Extinction of megafauna is a defining trend of the last 50,000 years. Here, the authors use genomic data to infer population histories of 139 extant megafauna, suggesting that their population decline is better explained by Homo sapiens expansion than by climate change.

    • Juraj Bergman
    • , Rasmus Ø. Pedersen
    •  & Jens-Christian Svenning

  • Article
    | Open Access

    Bdelloid rotifers can withstand a wide range of genotoxic stresses. Here the authors reveal that a DNA ligase of bacterial origin was acquired by horizontal gene transfer to confer high resistance to ionizing radiation in bdelloid rotifers and other organisms known for their extreme tolerance to stress.

    • Emilien Nicolas
    • , Paul Simion
    •  & Karine Van Doninck

  • Article
    | Open Access

    The timing of cellular evolution is poorly constrained. Here, the authors used improved molecular dating approaches to study the evolution of the ATP synthase in light of a dated tree of life thereby providing an absolute timescale for cellular evolution including eukaryotic origins.

    • Tara A. Mahendrarajah
    • , Edmund R. R. Moody
    •  & Anja Spang

  • Article
    | Open Access

    Non-ammonia oxidising Thaumarachaeota lineages are common in acidic soils, but their evolution is unclear. Here, the authors assemble 15 genomes from deeply rooted Thaumarachaeota in topsoils and subsoils, investigating evolutionary divergence in the family Gagatemarchaeaceae.

    • Paul O. Sheridan
    • , Yiyu Meng
    •  & Cécile Gubry-Rangin

  • Article
    | Open Access

    The Marine Alveolates (MALVs) include important parasites of other protists/animals. Here, using new data from MALV-I, the psammosids, and a new group called the eleftherids, the authors show MALVs, and therefore parasitism in early dinoflagellates, evolved from two distinct free-living ancestors.

    • Corey C. Holt
    • , Elisabeth Hehenberger
    •  & Patrick J. Keeling

  • Article
    | Open Access

    Mutations provide the genetic variability required for evolutionary change. Here, using pedigree-based whole genome sequencing, the authors determine that the Epaulette shark appears to have the lowest mutation rate identified in a vertebrate, providing a potential explanation for slow evolution in the shark lineage.

    • Ashley T. Sendell-Price
    • , Frank J. Tulenko
    •  & Manfred Schartl

  • Article
    | Open Access

    West Nile virus is an animal pathogen that has spread rapidly in Europe in recent years, causing several human deaths. This study investigates the spatial and temporal dynamics of the virus circulation between Africa (its place of origin) and Europe.

    • Giulia Mencattelli
    • , Marie Henriette Dior Ndione
    •  & Giovanni Savini

  • Comment
    | Open Access

    A recent study demonstrated the existence of mutations that facilitate access to efficient evolutionary solutions. Here I discuss the implications of this finding and the potential to open a new chapter in the study of evolvability.

    • C. Brandon Ogbunugafor

  • Article
    | Open Access

    Chronic infection with the bacterium Pseudomonas aeruginosa often leads to coexistence of heterogeneous bacterial populations carrying diverse mutations. Here, Zhao et al. use genetic and multi-omics functional analyses to shed light on the multistage evolution of bacterial populations in the lungs of chronically infected patients.

    • Kelei Zhao
    • , Xiting Yang
    •  & Xikun Zhou

  • Article
    | Open Access

    Genetic bases of grain shape differentiation between the two subspecies of Asian cultivated rice have not been fully elucidated. Here, the authors report GSE9, a de novo gene evolved from a non-coding region of wild rice through acquisition of start codon, contributes to the grain shape difference between the two subspecies.

    • Rujia Chen
    • , Ning Xiao
    •  & Zefeng Yang

  • Article
    | Open Access

    The diverse Heliconius butterflies have evolved key innovations, including pollen feeding, and are a quintessential example of adaptive radiation. Using comparative genomics, Cicconardi et al. identify targets of selection at coding and non-coding loci during major ecological transitions in Heliconius.

    • Francesco Cicconardi
    • , Edoardo Milanetti
    •  & Stephen H. Montgomery

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