Molecular evolution articles within Nature Communications

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  • Article
    | Open Access

    White-tailed deer are an important reservoir of SARS-CoV-2 in the USA and continued monitoring of the virus in deer populations is needed. In this genomic epidemiology study from Ohio, the authors show that the virus has been introduced multiple times to deer from humans, and that it has evolved faster in deer.

    • Dillon S. McBride
    • , Sofya K. Garushyants
    •  & Andrew S. Bowman

  • Article
    | Open Access

    Ongoing retroviral invasion into vertebrates has been rarely documented. Here the authors have identified 412 endogenous retroviruses that are invading the genomes of over a hundred vertebrate species. This may be relevant to conservation of threatened species, zoonoses in the wild, and emerging infectious diseases in humans.

    • Jianhua Wang
    •  & Guan-Zhu Han

  • Article
    | Open Access

    3-finger toxins are unique to the venoms of caenophidian snakes. This study traces the evolution of these toxins in snakes, highlighting a key shift from membrane-bound to secretory proteins. This transformation, involving the loss of a membrane-anchoring domain and changes in gene expression, paved the way for their venomous function.

    • Ivan Koludarov
    • , Tobias Senoner
    •  & Burkhard Rost

  • Article
    | Open Access

    The SARS-CoV-2 virus has been documented to transmit between humans and animals, providing opportunities for viral reservoirs. Here, the authors show SARS-CoV-2 lineages in free-ranging white-tailed deer across the United States, long after the lineages had declined in human populations.

    • Aijing Feng
    • , Sarah Bevins
    •  & Xiu-Feng Wan

  • Article
    | Open Access

    Diverse bacteria exhibit phenotypically plastic multicellular clustering. Here the authors show that a single mutation can genetically assimilate ancestrally inducible multicellularity by modulating plasticity at multiple levels of organization to make E. coli grow constitutively as macroscopic multicellular clusters.

    • Yashraj Chavhan
    • , Sutirth Dey
    •  & Peter A. Lind

  • Article
    | Open Access

    Highly pathogenic avian influenza A(H5N1) viruses of clade 2.3.4.4b underwent an explosive geographic expansion in 2021 among wild birds and domestic poultry. Here, Kandeil et al. show that the Western movement of this clade was followed by reassortment with viruses circulating in wild birds in North America which resulted in different genotypes exhibiting a wide range of disease severity in mammal models (mice, ferrets, chicken) ranging from asymptomatic disease to severe neurological pathology.

    • Ahmed Kandeil
    • , Christopher Patton
    •  & Richard J. Webby

  • Article
    | Open Access

    RNA viruses are defined by linear RNA genomes encoding an RNA-dependent RNA polymerase, while viroid-like elements consist of small, single-stranded, circular RNA genomes that, in some cases, encode self-cleaving catalytic RNAs. Here, the authors identify over 20,000 candidate viroid-like elements, and show that infectious agents of fungi display hybrid features of viroid-like RNAs and RNA viruses.

    • Marco Forgia
    • , Beatriz Navarro
    •  & Marcos de la Peña

  • Article
    | Open Access

    Repeated evolution provides valuable insight into adaptation. In this study, the authors found that repeated evolution of cave-adapted phenotypes of a fish (Astyanax mexicanus) was driven by selection on standing genetic variation and novel mutations and genes repeatedly under selection are longer compared to the rest of the genome.

    • Rachel L. Moran
    • , Emilie J. Richards
    •  & Suzanne E. McGaugh

  • Article
    | Open Access

    Disentangling how evolutionary history and environmental adaptation shape metabolic phenotypes is an open problem, especially for microbes whose phenotypes cannot be determined directly and are inferred from genomic information. Here, Ramon & Stelling propose sensitivity correlations to quantify similarity of predicted metabolic network responses to perturbations, and link genotype and environment to phenotype for 245 bacterial species.

    • Charlotte Ramon
    •  & Jörg Stelling

  • Article
    | Open Access

    The molecular mechanisms that ensure faithful transcription of genetic information are still unclear. Chung et al. identify various genes, alleles and processes that affect the fidelity of transcription multiple organisms, suggesting evolutionary conservation of fidelity factors, and compare the error rate of transcription among these species.

    • Claire Chung
    • , Bert M. Verheijen
    •  & Marc Vermulst

  • Article
    | Open Access

    Detoxification enzymes are crucial for the survival of animals in new environments. Here, the authors study the molecular mechanism behind the catalytic diversification of a major family of tetrapod detoxification enzymes—the FMOs—during evolution.

    • Gautier Bailleul
    • , Guang Yang
    •  & Maria Laura Mascotti

  • Article
    | Open Access

    The genetic basis of spider major ampullate (Ma) gland silk production remains unknown. Hu et al. unveil a molecular atlas of this gland for the golden orb-weaving spider combining genome assembly and multiomics, revealing the single-cell spatial architecture of silk production in the Ma gland.

    • Wenbo Hu
    • , Anqiang Jia
    •  & Yi Wang

  • Article
    | Open Access

    Characterizing genomic elements under accelerated evolution is crucial for understanding the genomic basis of human evolution and disease. Here, Zhang et al. introduce GroupAcc, a collection of two pooling-based phylogenetic methods with enhanced sensitivity to examine accelerated evolution in transcription factor binding sites.

    • Xinru Zhang
    • , Bohao Fang
    •  & Yi-Fei Huang

  • Article
    | Open Access

    Custom proteases find applications as therapeutics, in research and in biotechnological applications. Here, the authors establish a protease selection system based on bacterial alpha-2-macroglobulin protease inhibitors and evolve staphylococcal proteases for increased activity and altered specificity.

    • Philipp Knyphausen
    • , Mariana Rangel Pereira
    •  & Florian Hollfelder

  • Article
    | Open Access

    Bacteria can exchange DNA through extracellular appendages (‘mating pili’) in a process known as conjugation. Here, Beltran et al. determine atomic structures by cryo-electron microscopy of a bacterial conjugative pilus and two archaeal pili, showing that the archaeal pili are homologous to bacterial mating pili.

    • Leticia C. Beltran
    • , Virginija Cvirkaite-Krupovic
    •  & Mart Krupovic

  • Article
    | Open Access

    Many eukaryotic and archaeal tRNAs carry a modified adenosine (t6A) that is synthesized by the KEOPS complex, which is composed of four subunits. A fifth subunit (Gon7) is found only in fungi and metazoa. Here the authors show that archaea also possess a fifth subunit, which is structurally and functionally similar to eukaryotic Gon7.

    • Marie-Claire Daugeron
    • , Sophia Missoury
    •  & Tamara Basta

  • Article
    | Open Access

    In this work the authors investigate the structure-sequence dependance. The ability to design and characterize proteins at interfaces between three common folds suggests that fold switching is an intrinsic feature of protein folding language and likely important in the evolution of protein structure and function.

    • Biao Ruan
    • , Yanan He
    •  & Philip N. Bryan

  • Article
    | Open Access

    Venom is a complex trait with unresolved underlying toxin expression dynamics. Here, the authors compare expression across sea anemone species, revealing variation in dominant toxin diploid copy number across populations which generates distinct haplotypes.

    • Edward G. Smith
    • , Joachim M. Surm
    •  & Yehu Moran

  • Article
    | Open Access

    Here, the authors report accelerated intrahost evolution of SARS-CoV-2 in an immunocompromised patient with non-Hodgkin’s lymphoma with 318 days long COVID-19, and show that changes in the viral genome resulted in escape from T cellular immune response.

    • Oksana V. Stanevich
    • , Evgeniia I. Alekseeva
    •  & Georgii A. Bazykin

  • Article
    | Open Access

    Design of recombinases with new target sites is usually achieved through cycles of directed molecular evolution. Here the authors report Recombinase Generator, RecGen, an algorithm for generation of designer-recombinases; they perform experimental validation to show that this can predict recombinase sequences.

    • Lukas Theo Schmitt
    • , Maciej Paszkowski-Rogacz
    •  & Frank Buchholz

  • Article
    | Open Access

    Seahorses may have required adaptations to avoid immunological rejection of allogenic embryos by males. The authors show that a single substitution in tlx1 is associated with loss of the spleen in seahorses, and that across the clade, degree of male pregnancy is negatively correlated with immune gene repertoire complexity.

    • Yali Liu
    • , Meng Qu
    •  & Qiang Lin

  • Article
    | Open Access

    Ribosomal RNA genes are abundant in eukaryotic genomes and code for the universal and essential RNA components of the ribosome. This study uncovers high sequence diversity of the genes within a single species and discusses the contribution of selection in the evolution of ribosomal RNA.

    • Daniel Sultanov
    •  & Andreas Hochwagen

  • Article
    | Open Access

    Sociality has evolved repeatedly in arthropods. Tong et al. compare the genomes of 22 spider species with a range of social complexity and eight independent origins of sociality, and identify specific genetic changes associated with the evolution of sociality in spiders.

    • Chao Tong
    • , Leticia Avilés
    •  & Timothy A. Linksvayer

  • Article
    | Open Access

    Translation of 100 to 300 micropeptides from small ORFs within lncRNA was detected by Ribosomal Profiling in Drosophila embryos. These translated small ORFs showed natural selection conserving micropeptide sequence and function.

    • Pedro Patraquim
    • , Emile G. Magny
    •  & Juan Pablo Couso

  • Article
    | Open Access

    Endogenous retroviruses (ERV) are inherited remains of retroviruses that have colonized host genomes during evolution. Here the authors observe considerable species-specific ERV variation among Darwin’s finches, reflecting historic retrovirus-host interactions.

    • Jason Hill
    • , Mette Lillie
    •  & Patric Jern

  • Article
    | Open Access

    Influenza A virus (IAV) nonstructural protein 1 (NS1) is a multifunctional virulence factor that interacts with several host factors such as phosphatidylinositol-3-kinase (PI3K). NS1 binds specifically to the p85β regulatory subunit of PI3K and subsequently activates PI3K signaling. Here, Kim et al. show that functionally near-neutral, strain-specific NS1 mutations lead to variations in binding kinetics to p85β exhibit long-range epistatic interactions. Applying NMR they provide evidence that the structural dynamics of the NS1 hydrophobic core have evolved over time and contributed to epistasis.

    • Iktae Kim
    • , Alyssa Dubrow
    •  & Jae-Hyun Cho

  • Article
    | Open Access

    Barley β-d-glucan glucohydrolase is a glycoside hydrolase family 3 (GH3) enzyme critical for growth and development. Here the authors carryout mutagenesis, structural analyses and multi-scale molecular dynamics to examine the binding and conformational behaviour of several β-d-glucosides during the substrate-product assisted catalysis that operates in GH3 hydrolases.

    • Sukanya Luang
    • , Xavier Fernández-Luengo
    •  & Maria Hrmova

  • Article
    | Open Access

    By constructing an evolutionary trajectory of the cyclostome-gnathostome Pou5 gene family and comparing the structural and phenotypic protein variations, the authors uncover the origin of functional characteristics for the pluripotency factor Oct4.

    • Woranop Sukparangsi
    • , Elena Morganti
    •  & Joshua M. Brickman

  • Article
    | Open Access

    Here, the authors characterize a case of SARS-CoV-2 superinfection with Alpha and Epsilon variants, in which, via full genome sequencing analyses, they identify recombinant haplotypes in the spike, nucleocapsid, and ORF 8 coding regions, suggesting recombination could play a role in SARS-CoV-2 genetic diversity.

    • Joel O. Wertheim
    • , Jade C. Wang
    •  & Scott Hughes

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