Molecular evolution articles within Nature Communications

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  • Article
    | Open Access

    Here, Tan et al. find that the rapid spread of SARS-CoV-2 in mink and deer required minimal adaptation, has only caused moderate changes to the evolutionary trajectory of the virus, and has not led to viral mutations that greatly improve human transmission thus far.

    • Cedric C. S. Tan
    • , Su Datt Lam
    •  & François Balloux

  • Article
    | Open Access

    Non-pharmaceutical interventions for COVID-19 also reduced incidence of respiratory pathogens such as respiratory syncytial virus (RSV). Here, the authors report the resurgence of RSV in Australia following lifting of some of the restrictions and describe reduction in genetic diversity in circulating clades.

    • John-Sebastian Eden
    • , Chisha Sikazwe
    •  & Tyna Tran

  • Article
    | Open Access

    In this genomic epidemiology study from Ghana, the authors sequence ~1,000 SARS-CoV-2 whole genomes from March 2020 to September 2021. They describe changes in the predominant circulating lineages over time and infer how variants of concern were likely introduced into the country.

    • Collins M. Morang’a
    • , Joyce M. Ngoi
    •  & Gordon A. Awandare

  • Article
    | Open Access

    Cephalopods are an enigmatic animal group with complex and adaptive behaviors such as camouflage; however the genetic basis for these traits is not well understood. Here the authors reveal a set of cephalopod-restricted rearranged genomic loci, involving known neuronal regulators but also unexpected gene families, that confer topological organization and gene regulation.

    • Hannah Schmidbaur
    • , Akane Kawaguchi
    •  & Oleg Simakov

  • Article
    | Open Access

    It remains unclear how rapid antibiotic switching affects the evolution of antibiotic resistance in individual patients. Here, Chung et al. combine short- and long-read sequencing and resistance phenotyping of 420 serial isolates of Pseudomonas aeruginosa collected from the onset of respiratory infection, and show that rare resistance mutations can increase by nearly 40-fold over 5–12 days in response to antibiotic changes, while mutations conferring resistance to antibiotics not administered diminish and even go to extinction.

    • Hattie Chung
    • , Christina Merakou
    •  & Gregory P. Priebe

  • Article
    | Open Access

    Gene blaNDM, conferring resistance to carbapenem antibiotics, is globally distributed across Gram-negative bacteria on multiple plasmids. Here, Acman et al. study the dynamics underlying blaNDM dissemination across over 6000 bacterial genomes, and identify mobile genetic elements and specific mobilisation events likely involved in the gene’s global spread.

    • Mislav Acman
    • , Ruobing Wang
    •  & Francois Balloux

  • Article
    | Open Access

    Eukaryotic DNA can be methylated as 5-methylcytosine and N6-methyladenine, but whether other forms of DNA methylation occur has been controversial. Here the authors show that a bacterial DNA methyltransferase was acquired >60 Mya in bdelloid rotifers that catalyzes N4-methylcytosine addition and is involved in suppression of transposon proliferation.

    • Fernando Rodriguez
    • , Irina A. Yushenova
    •  & Irina R. Arkhipova

  • Article
    | Open Access

    Interferons are critical soluble components of the inflammatory process and are composed of three types with associated receptor complexes. Here the authors identify and characterise the type IV interferon, IFN-υ, and identify its associated receptors, denote functionality during in vivo infection and ascertain its genomic localisation.

    • Shan Nan Chen
    • , Zhen Gan
    •  & Pin Nie

  • Article
    | Open Access

    Methods to probe DNA methylation in the majority of non-human mammals are lacking. Here the authors developed a Mammalian Methylation Array that includes 36k well-conserved CpGs in mammals which will facilitate cross-species comparisons. They annotate the conserved CpGs in > 200 species. The array allows one to measure methylation in all mammalian species including unsequenced ones.

    • Adriana Arneson
    • , Amin Haghani
    •  & Steve Horvath

  • Article
    | Open Access

    Escherichia coli ST58 has recently emerged as a globally disseminated extra-intestinal pathogen. Here, Reid et al. present a pan-genomic analysis of a global collection of ST58 isolates from animal and human sources, showing that ColV plasmid acquisition likely contributed to the divergence of a major sub-lineage that has a broad host range but is more commonly found in poultry and swine.

    • Cameron J. Reid
    • , Max L. Cummins
    •  & Steven P. Djordjevic

  • Article
    | Open Access

    Many parasitic organisms contain molecular structures that are drastically smaller than analogous structures in non-parasitic organisms. Here the authors describe a cryo-EM structure of the ribosome from E. cuniculi that reveals that it compensated rRNA truncations by evolving the ability to use small molecules as ribosomal building blocks.

    • David Nicholson
    • , Marco Salamina
    •  & Sergey V. Melnikov

  • Article
    | Open Access

    Correction of disease-causing large genomic inversions remains challenging. Here, the authors developed a dual designer-recombinase system (RecF8) that efficiently corrects a 140 kb inversion frequently found in patients with severe Hemophilia A.

    • Felix Lansing
    • , Liliya Mukhametzyanova
    •  & Frank Buchholz

  • Article
    | Open Access

    Here the authors report single-nucleus RNA sequencing for several anatomical locations in 11 species, including cat, dog, hamster, lizard, goat, rabbit, duck, pigeon, pangolin, tiger, and deer, highlighting coexpression of SARS-CoV-2 entry factors ACE2 and TMPRSS2.

    • Dongsheng Chen
    • , Jian Sun
    •  & Xun Xu

  • Article
    | Open Access

    SARS-CoV-2 was detected in mink farms in the Netherlands in the first wave of the pandemic with evidence of human-to-mink and mink-to-human transmission. Here, the authors investigate this outbreak using phylodynamic analysis and show that personnel links and spatial proximity are predictors of transmission between farms.

    • Lu Lu
    • , Reina S. Sikkema
    •  & Marion P. G. Koopmans

  • Article
    | Open Access

    In this study, Delaune et al., isolate and characterise a SARS-CoV-2-related coronavirus from two bats sampled in Cambodia. Their findings suggest that the geographic distribution of SARS-CoV-2-related viruses is wider than previously reported.

    • Deborah Delaune
    • , Vibol Hul
    •  & Veasna Duong

  • Article
    | Open Access

    Staphylococcus epidermidis is a widespread early colonizer in the neonatal skin and a cause of hospital-acquired infections. Here, using whole-genome sequencing of 632 cultured S. epidermidis isolates derived from premature infants, the authors characterize the spatiotemporally strain-level genomic variability, finding patient-specific colonization signatures and a fast gain and loss of the antibiotic resistance gene mecA via the evolution of genotypically diverse structural variants.

    • Manoshi S. Datta
    • , Idan Yelin
    •  & Roy Kishony

  • Article
    | Open Access

    The Lake Malawi cichlid fishes are an example of extreme vertebrate radiation; however, there is very little sequence divergence among the species. Here the authors present a comparative genome-wide methylome study to suggest DNA methylation played a major role in the extensive phenotypic diversity amongst these fishes.

    • Grégoire Vernaz
    • , Milan Malinsky
    •  & Eric A. Miska

  • Article
    | Open Access

    Epistasis plays an important role in the evolution of novel protein functions because it determines the mutational path a protein takes. Here, the authors combine functional, structural and biophysical analyses to characterize epistasis in a computationally redesigned ligand-inducible allosteric transcription factor and found that epistasis creates distinct biophysical and biological functional landscapes.

    • Kyle K. Nishikawa
    • , Nicholas Hoppe
    •  & Srivatsan Raman

  • Article
    | Open Access

    Analyses of both natural and experimental evolution suggest that adaptation depends on the evolutionary past and adaptive potential decreases over time. Here, by tracking yeast adaptation with DNA barcoding, the authors show that such evolutionary phenomena can be observed even after a single adaptive step.

    • Dimitra Aggeli
    • , Yuping Li
    •  & Gavin Sherlock

  • Article
    | Open Access

    Unicellular fungi with free-living flagellated stages (zoospores) remain poorly known. Here, Galindo et al. sequence single-cell genomes for two atypical parasitic fungi with amoeboid zoospores, and re-evaluate the branching order of early-diverging fungi and the evolution of fungal multicellularity and flagellum-mediated motility.

    • Luis Javier Galindo
    • , Purificación López-García
    •  & David Moreira

  • Article
    | Open Access

    Early vertebrate genomes were shaped by multiple whole-genome duplication (WGD) events of debated timings. Here the authors’ reconstruction of ancestral genomes using the probabilistic macrosynteny model supports a WGD shared by all vertebrates and a gnathostome-specific WGD, and reveals evidence of a cyclostome-specific genome triplication.

    • Yoichiro Nakatani
    • , Prashant Shingate
    •  & Byrappa Venkatesh

  • Article
    | Open Access

    Pyrrolysine (Pyl) exists in nature as the 22nd proteinogenic amino acid, but studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, the authors developed an improved PANCE approach to evolve the pylBCD pathway for increased production of Pyl proteins in E. coli.

    • Joanne M. L. Ho
    • , Corwin A. Miller
    •  & Matthew R. Bennett

  • Article
    | Open Access

    Molecular phylogenies are traditionally based on sequence variation, but genome rearrangements also contain phylogenetic information. Here, Zhao et al. develop an approach to reconstruct phylogenies based on microsynteny and illustrate it with a reconstruction of the angiosperm phylogeny.

    • Tao Zhao
    • , Arthur Zwaenepoel
    •  & Yves Van de Peer

  • Article
    | Open Access

    Dating early bacterial evolution is challenging due to the limited bacterial fossil record. Here Wang and Luo use the close evolutionary relationship between Alphaproteobacteria and mitochondria to leverage the eukaryotic fossil record in dating Alphaproteobacteria origin and diversification.

    • Sishuo Wang
    •  & Haiwei Luo

  • Article
    | Open Access

    Natural selection may favor traits underlying aging-related diseases if they benefit the young. Wang et al. find that oxidative activation of CaMKII provides physiological benefits critical to the initial and continued success of vertebrates but at the cost of disease, frailty, and shortened lifespan.

    • Qinchuan Wang
    • , Erick O. Hernández-Ochoa
    •  & Mark E. Anderson

  • Article
    | Open Access

    Comparative epigenomics has revealed principles underlying the evolution of gene expression regulation, and the integration of epigenomic data is important for a deeper understanding of this evolution. Here the authors report the evolutionary dynamics of the epigenomic regulatory landscape in primates and their impact in recent human evolution.

    • Raquel García-Pérez
    • , Paula Esteller-Cucala
    •  & Tomàs Marquès-Bonet

  • Article
    | Open Access

    Here, the authors report a large-scale comparative analysis of <30,000 Diversity-Generating Retroelements (DGRs) across ~9000 metagenomes (representing diverse taxa and biomes), to identify patterns in terms of prevalence and activity. Combined with examination of longitudinal data on <100 metagenomes part of time series, they demonstrate that DGRs are broadly and consistently active, implying an important role in microbiota ecology and evolution.

    • Simon Roux
    • , Blair G. Paul
    •  & Emiley A. Eloe-Fadrosh

  • Article
    | Open Access

    The efficacy of the antibiotic trimethoprim, which inhibits bacterial dihydrofolate reductase (DHFR), is limited by the rapid emergence of resistant bacteria. Here, Manna et al. show that 4’-desmethyltrimethoprim inhibits DHFR and a common TMP-resistant variant, and impedes evolution of antibiotic resistance by selecting against the emergence of this variant.

    • Madhu Sudan Manna
    • , Yusuf Talha Tamer
    •  & Erdal Toprak

  • Article
    | Open Access

    Many obligate symbionts, including parasites, have reduced genomes. A comparison of leaf-cutter ant genomes reveals parallel gene losses, particularly in olfactory receptors, in socially parasitic species compared to their closely-related hosts, consistent with relaxed selection for cooperative colony life in the parasites.

    • Lukas Schrader
    • , Hailin Pan
    •  & Christian Rabeling

  • Article
    | Open Access

    The SARS-CoV-2 gene set remains unresolved, hindering dissection of COVID-19 biology. Comparing 44 Sarbecovirus genomes provides a high-confidence protein-coding gene set. The study characterizes protein-level and nucleotide-level evolutionary constraints, and prioritizes functional mutations from the ongoing COVID-19 pandemic.

    • Irwin Jungreis
    • , Rachel Sealfon
    •  & Manolis Kellis

  • Article
    | Open Access

    A fundamental principle of evolutionary theory is that the force of natural selection is weaker on traits expressed late in life relative to traits expressed early. Here, the authors find strong and consistent patterns of molecular evolution reflecting this principle in four species of animals, including humans.

    • Changde Cheng
    •  & Mark Kirkpatrick

  • Article
    | Open Access

    DNA methylation plays an important role in brain development and function. Here, the authors compare whole-genome methylation in neurons and oligodendrocytes in humans, chimpanzees and macaques to reconstruct evolution of DNA methylation at cell-type level, including in regions associated with schizophrenia heritability.

    • Hyeonsoo Jeong
    • , Isabel Mendizabal
    •  & Soojin V. Yi

  • Article
    | Open Access

    Likelihood optimization in phylogenetic tree reconstruction is computationally intensive, especially as the number of sequences and taxa included increase. Here, Azouri et al. show how an artificial intelligence approach can reduce computational time without losing accuracy of tree inference.

    • Dana Azouri
    • , Shiran Abadi
    •  & Tal Pupko

  • Article
    | Open Access

    Cryptophytes acquired plastids from red algae but replaced the light-harvesting phycobilisome with a unique cryptophyte antenna. Here via analysis of phycobilisome cryo-EM structures, Rathbone et al. propose that the α subunit of the cryptophyte antenna originated from phycobilisome linker proteins

    • Harry W. Rathbone
    • , Katharine A. Michie
    •  & Paul M. G. Curmi

  • Article
    | Open Access

    Previous work identified goddard as a putative de novo evolved gene in Drosophila melanogaster. Here, the authors characterize the structure and function of the Goddard protein in D. melanogaster, and they infer its ancestral and extant structures across the Drosophila genus.

    • Andreas Lange
    • , Prajal H. Patel
    •  & Erich Bornberg-Bauer

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