Evolution articles within Nature Communications

Featured

  • Article
    | Open Access

    The role of DNA methylation in insects is poorly understood. Here, the authors knock out the DNA methyltransferase DNMT1 in an ant and find no obvious effects on development, rather showing that this enzyme seems to play a crucial role during early oogenesis.

    • Iryna Ivasyk
    • , Leonora Olivos-Cisneros
    •  & Daniel J. C. Kronauer

  • Article
    | Open Access

    Developmental plasticity allows organisms to match traits to their environment, however, there are few known molecular mechanisms underlying such plasticity. Here, the authors show that feeding morphs in adult Pristionchus nematodes are set during a critical window in juveniles and identify H4K5/12ac as the environmental information carrier.

    • Michael S. Werner
    • , Tobias Loschko
    •  & Ralf J. Sommer

  • Article
    | Open Access

    Indirect reciprocity describes how cooperation arises in a community when its members value their reputation. Here, the authors show that nuanced assessments of observations can mitigate disagreements and errors when the opinions of community members are not synchronized.

    • Laura Schmid
    • , Farbod Ekbatani
    •  & Krishnendu Chatterjee

  • Article
    | Open Access

    Phage-plasmids are bacterial extrachromosomal elements that act both as plasmids and as viruses. Here, Shan et al. show that segregational drift and loss-of-function mutations play key roles in the infection dynamics of a cosmopolitan phage-plasmid, allowing it to create continuous productive infections in marine bacteria.

    • Xiaoyu Shan
    • , Rachel E. Szabo
    •  & Otto X. Cordero

  • Article
    | Open Access

    Geographical hotspots with high frequency of multi-drug resistant tuberculosis (MDR-TB) have been observed in several locations, such as the country of Georgia. Here, the authors analyse genomic sequences from tuberculosis bacteria isolated from Georgia to show that the transmission fitness of MDR-TB strains is heterogeneous, and highly drug-resistant and transmissible isolates contribute to the emergence and maintenance of MDR-TB hotspots.

    • Chloé Loiseau
    • , Etthel M. Windels
    •  & Sebastien Gagneux

  • Article
    | Open Access

    Bacteria of the genus Streptomyces have complex life cycles involving cellular differentiation and multicellular structures that have never been observed in archaea. Here, the authors show that several halophilic archaea display a life cycle resembling that of Streptomyces bacteria, undergoing cellular differentiation into mycelia and spores.

    • Shu-Kun Tang
    • , Xiao-Yang Zhi
    •  & Ping Xu

  • Article
    | Open Access

    G protein-coupled receptors are a major class of drug targets. Here, the authors develop a method whereby their biophysical and functional properties can be altered through directed evolution in mammalian cells, leading to variants exhibiting features such as high stability and expression, or increased allosteric coupling.

    • Christoph Klenk
    • , Maria Scrivens
    •  & Andreas Plückthun

  • Article
    | Open Access

    Different muscle cell types account for specific abilities in animals, yet how their diversification arose remains unclear. Here, the authors show that gene duplications of bHLH transcription factors and effector genes contributed to the diversification of muscle cell types in the sea anemone Nematostella.

    • Alison G. Cole
    • , Stefan M. Jahnel
    •  & Ulrich Technau

  • Article
    | Open Access

    Escherichia albertii is an emerging gastrointestinal pathogen that causes disease in humans and animals, notably birds. In this genomic epidemiology study, the authors investigate characteristics of isolates sampled from humans and birds in Great Britain and find that they tend to cluster separately.

    • Rebecca J. Bengtsson
    • , Kate S. Baker
    •  & Becki Lawson

  • Article
    | Open Access

    Ambrosia artemisiifolia is an invasive weed and primary cause of pollen-induced hayfever. Here, the authors report its chromosome-level phased genome assembly, examine genome-wide variation among modern and historic accessions, and identify large haploblocks underling rapid adaptation.

    • Paul Battlay
    • , Jonathan Wilson
    •  & Kathryn A. Hodgins

  • 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

    Pan-genomes provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Here, the authors report a new rice pan-genome including 73 Asian rice and two wild relatives (Oryza rufipogon and O. punctata), and reveal the prevalence and scale of large inversions across the pan-genome.

    • Yong Zhou
    • , Zhichao Yu
    •  & Rod A. Wing

  • 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

    Tropane alkaloids (TAs) are synthesized by some species in Solanaceae. Here, the authors assemble the genomes of two representative TAs producing species, show that gene loss shapes uneven distribution of TAs in Solanaceae, and identify a cytochrome P450 gene catalyzing N-demethylation of hyoscyamine to generate norhyoscyamine.

    • Fangyuan Zhang
    • , Fei Qiu
    •  & Zhihua Liao

  • Article
    | Open Access

    How has the genome duplication impacted the diversification of sexual characteristics in the teleost lineage? This study shows that androgen receptor ohnologs in medaka appear to have diverged in their roles for regulating morphological and behavioural sexual characteristics after loss from an ancestral role in spermatogenesis.

    • Yukiko Ogino
    • , Satoshi Ansai
    •  & Taisen Iguchi

  • Article
    | Open Access

    Maternally inherited symbionts that kill male insect hosts are well known in bacteria, but are also beginning to be recognised in viruses. In this study, the authors identify a gene from a symbiotic virus genome that is responsible for the male-killing phenotype of this virus in the fly Drosophila biauraria.

    • Daisuke Kageyama
    • , Toshiyuki Harumoto
    •  & Masayoshi Watada

  • Article
    | Open Access

    It can be challenging to identify extinct organisms with morphology alone. Here, the authors use non-destructive Fourier Transform Infrared Spectroscopy to determine the molecular fingerprints of eukaryotes and prokaryotes from the 407 Ma Rhynie chert fossil assemblage of Aberdeenshire, Scotland.

    • C. C. Loron
    • , E. Rodriguez Dzul
    •  & S. McMahon

  • Article
    | Open Access

    Hymenoptera is an incredibly diverse order, with numerous behavioral and morphological innovations. Here, the authors compile a time-calibrated Hymenoptera phylogeny and find that secondary transitions to phytophagy, plant feeding, are associated with significant increases in diversification rate in this group.

    • Bonnie B. Blaimer
    • , Bernardo F. Santos
    •  & Matthew L. Buffington

  • Article
    | Open Access

    The evolution and systematics of Madagascar’s extinct elephant birds remains unclear. Here, the authors recover genetic, stable isotope, morphological, and geographic data from fossil eggshell to describe variation among clades, identifying cryptic diversity and potential drivers of speciation.

    • Alicia Grealy
    • , Gifford H. Miller
    •  & Michael Bunce

  • Article
    | Open Access

    Little is known about genetic heterogeneity within deep sea cold seep microbial populations. From examining 39 abundant microbial species identified in sediment layers below the sea floor and across six cold seep sites, this study reports that their evolutionary trajectories are depth-dependent and differ across phylogenetic clades.

    • Xiyang Dong
    • , Yongyi Peng
    •  & Casey R. J. Hubert

  • Article
    | Open Access

    Bergmann’s and Allen’s rules are speculated to describe alternative strategies of thermal adaptation. Here, Frӧhlich et al. explore global variation across avian species to show that the way in which relative length of beaks and tarsi co-vary with ambient temperature depends on body mass and vice versa.

    • Arkadiusz Frӧhlich
    • , Dorota Kotowska
    •  & Matthew R. E. Symonds

  • Article
    | Open Access

    Cellular plasticity is a core biological process; however, observing diversity in non-genetic inheritance and the resulting phenotypic outputs, is challenging. Here the authors develop a non-genetically based tracing technology which can be used to reveal lineage-linked transcriptome plasticity.

    • Yelyzaveta Shlyakhtina
    • , Bianca Bloechl
    •  & Maximiliano M. Portal

  • Article
    | Open Access

    The interplay of migration and adaptation was key in shaping species’ responses to Quaternary climate change. Illustrating this, Luqman et al. show that adaptive responses in a plant species emerged from climate-induced range shifts due to heterogenous sieving of adaptive alleles across space and time.

    • Hirzi Luqman
    • , Daniel Wegmann
    •  & Alex Widmer

  • Article
    | Open Access

    A key hypothesis for the evolution of division of labour in social insects is that a shared set of genes – a genetic toolkit - regulates reproductive castes across species. Here, the authors analyze brain transcriptomes from nine species of social wasps to identify the factors that shape this toolkit.

    • Christopher Douglas Robert Wyatt
    • , Michael Andrew Bentley
    •  & Seirian Sumner

  • 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

    A variant of MHC class I is protective against severe malaria disease and enriched in affected African populations. Here, Wroblewski et al., characterise the consequences of malaria infection in wild bonobo populations showing that the presence of malaria drives a similar evolution in immune genes.

    • Emily E. Wroblewski
    • , Lisbeth A. Guethlein
    •  & Peter Parham

  • Article
    | Open Access

    The opportunity for sexual selection is a key evolutionary parameter but we know little about its temporal dynamics. Using data from multiple animal species the authors show that this metric varies rapidly through time and that simulations should be used to avoid substantial misinterpretation.

    • Rômulo Carleial
    • , Tommaso Pizzari
    •  & Grant C. McDonald

  • Article
    | Open Access

    Understanding how new cell types arise is essential for understanding the evolution of animal diversity. This study shows that a single gene, NvSox2, acts as a simple switch controlling the development of two alternative types of stinging cells in the sea anemone Nematostella vectensis.

    • Leslie S. Babonis
    • , Camille Enjolras
    •  & Mark Q. Martindale

  • 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

    Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, the authors provide evidence that eukaryotic and Asgard thymidylate synthases (required for DNA synthesis) may have a bacterial origin, and additional lateral transfer of bacterial genes may have shaped the metabolism of Asgard archaea.

    • Jonathan Filée
    • , Hubert F. Becker
    •  & Hannu Myllykallio

  • Article
    | Open Access

    Pachytene Piwi-interacting RNAs (piRNAs) expressed in mammalian germ lines are abundant, but their evolution and function are not fully understood. Here, the authors find that pachytene piRNA loci are hotspots of structural variation, which underlies rapid piRNA birth, divergence, and loss.

    • Yu H. Sun
    • , Hongxiao Cui
    •  & Xin Zhiguo Li

  • 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

    This study finds that high-latitude fish clades with the fastest speciation rates also exhibit elevated rates of depth evolution, creating a prevailing latitudinal gradient of deep-sea invasions concentrated in poleward regions. These results advance our understanding of how niche lability and climate shape global patterns of species distributions.

    • Sarah T. Friedman
    •  & Martha M. Muñoz

  • 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

    Living snakes replace their teeth without external resorption. Here, the authors use histology to show that odontoclasts resorb dentine internally and investigate this mechanism in fossil snakes.

    • A. R. H. LeBlanc
    • , A. Palci
    •  & M. W. Caldwell

  • Article
    | Open Access

    Here, the authors describe the geographies, hosts, substrates, and phylogenetic relationships for 1,794 Saccharomyces strains. They provide insight into the genetic and phenotypic diversity in the genus, not seen through prior work focused on the model species Saccharomyces cerevisiae.

    • David Peris
    • , Emily J. Ubbelohde
    •  & Chris Todd Hittinger

  • 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

    The phylogenetic relationship among genera within the walnut family Juglandaceae remains unclear. Here, the authors assemble the genomes of Rhoiptelea chiliantha and Engelhardia roxburghiana, resolve the topology of this family, and propose a hybrid origin of the family from progenitors nested within or sister to Myricaceae.

    • Ya-Mei Ding
    • , Xiao-Xu Pang
    •  & Wei-Ning Bai

  • 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

    To elucidate the relationship between sociality and longevity, the authors perform phylogenetic and transcriptomic comparative analysis of mammals. They find that group-living species lived longer than solitary species and identify 31 genes, hormones, and immunity-related pathways involved in this connection.

    • Pingfen Zhu
    • , Weiqiang Liu
    •  & Xuming Zhou

Browse broader subjects

Browse narrower subjects

Browse Evolution across other nature.com journals