Molecular evolution articles within Nature

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  • Article
    | Open Access

    The genome of the tropical blue-petal water lily Nymphaea colorata and the transcriptomes from 19 other Nymphaeales species provide insights into the early evolution of angiosperms.

    • Liangsheng Zhang
    • , Fei Chen
    •  & Haibao Tang

  • Article |

    Analysis of multiple structures of the Helicoverpa zea DNA transposase Transib, determined by X-ray crystallography and cryo-electron microscopy, reveals the detailed pathway of the transposition reaction and sheds light on the evolution of the RAG recombinase.

    • Chang Liu
    • , Yang Yang
    •  & David G. Schatz

  • Article
    | Open Access

    The One Thousand Plant Transcriptomes Initiative provides a robust phylogenomic framework for examining green plant evolution that comprises the transcriptomes and genomes of diverse species of green plants.

    • James H. Leebens-Mack
    • , Michael S. Barker
    •  & Gane Ka-Shu Wong

  • Article |

    The transcriptomes of seven major organs across developmental stages from several mammalian species are used for comparative analyses of gene expression and evolution across organ development.

    • Margarida Cardoso-Moreira
    • , Jean Halbert
    •  & Henrik Kaessmann

  • Article |

    The presence of blubber and distribution of melanophores in a countershading pattern in an Early Jurassic ichthyosaur demonstrate that the evolutionary convergence of these reptiles with extant marine amniotes extends to the cellular and molecular levels.

    • Johan Lindgren
    • , Peter Sjövall
    •  & Mary H. Schweitzer

  • Letter |

    By engineering entropy-tuning changes into distal sites of a bacterial adenylate kinase, an allosteric tuning mechanism based on protein dynamics is revealed.

    • Harry G. Saavedra
    • , James O. Wrabl
    •  & Vincent J. Hilser

  • Article |

    Around 200 new vertebrate-specific viruses are discovered, and every vertebrate-specific viral family known to infect mammals and birds is also present in amphibians, reptiles or fish, suggesting that evolution of vertebrate viruses mirrors that of vertebrate hosts.

    • Mang Shi
    • , Xian-Dan Lin
    •  & Yong-Zhen Zhang

  • Letter |

    Phytotransferrin, a functional analogue of transferrin, has an obligate requirement for carbonate to bind iron, which suggests that acidification-driven declines in the concentration of seawater carbonate ions may negatively affect diatom iron acquisition.

    • Jeffrey B. McQuaid
    • , Adam B. Kustka
    •  & Andrew E. Allen

  • Letter |

    An immune fitness model for tumours under checkpoint blockade immunotherapy is proposed, through which the authors show that the presentation and recognition properties of dominant neoantigens distributed over tumour subclones are predictive of response in melanoma and lung cancer cohorts.

    • Marta Łuksza
    • , Nadeem Riaz
    •  & Benjamin D. Greenbaum

  • Article |

    Using data from sixty thousand generations of the E. coli long-term evolution experiment, the authors shed new light on the processes that govern molecular evolution.

    • Benjamin H. Good
    • , Michael J. McDonald
    •  & Michael M. Desai

  • Letter |

    Combining ancestral protein reconstruction with deep mutational scanning to characterize alternative histories in the sequence space around an ancient transcription factor reveals hundreds of alternative protein sequences that use diverse biochemical mechanisms to perform the derived function at least as well as the historical outcome.

    • Tyler N. Starr
    • , Lora K. Picton
    •  & Joseph W. Thornton

  • Letter
    | Open Access

    The genome of the Southern Ocean phytoplankton Fragilariopsis cylindrus differs markedly from the genomes of its more temperate relatives, with divergent alleles being differentially expressed in environmentally specific conditions such as freezing and darkness.

    • Thomas Mock
    • , Robert P. Otillar
    •  & Igor V. Grigoriev

  • Letter |

    Drosophila sechellia, a species closely related to the model species Drosophila melanogaster, bypasses a premature stop codon in neuronal cells to express a functional olfactory receptor protein from an assumed pseudogene template.

    • Lucia L. Prieto-Godino
    • , Raphael Rytz
    •  & Richard Benton

  • Article
    | Open Access

    The two homoeologous subgenomes in the allotetraploid frog Xenopus laevis evolved asymmetrically; one often retained the ancestral state, whereas the other experienced gene loss, deletion, rearrangement and reduced gene expression.

    • Adam M. Session
    • , Yoshinobu Uno
    •  & Daniel S. Rokhsar

  • Letter |

    The observations that introns are acquired in bursts and that exons are often nucleosome-sized can be explained by the generation of introns from DNA transposons, which insert between nucleosomes.

    • Jason T. Huff
    • , Daniel Zilberman
    •  & Scott W. Roy

  • Letter |

    A nanopore DNA sequencer is used for real-time genomic surveillance of the Ebola virus epidemic in the field in Guinea; the authors demonstrate that it is possible to pack a genomic surveillance laboratory in a suitcase and transport it to the field for on-site virus sequencing, generating results within 24 hours of sample collection.

    • Joshua Quick
    • , Nicholas J. Loman
    •  & Miles W. Carroll

  • Letter |

    Bacterial cells evolved an immune system known as CRISPR–Cas to protect themselves from viral infection, triggering viruses to evolve anti-CRISPR proteins; here, three anti-CRISPR proteins are characterized, with each one interfering with the host CRISPR system at a different point.

    • Joseph Bondy-Denomy
    • , Bianca Garcia
    •  & Alan R. Davidson

  • Article |

    Eukaryotes acquired their prokaryotic genes in two episodes of evolutionary influx corresponding to the origin of mitochondria and plastids, respectively, followed by extensive differential gene loss, uncovering a massive imprint of endosymbiosis in the nuclear genomes of complex cells.

    • Chuan Ku
    • , Shijulal Nelson-Sathi
    •  & William F. Martin

  • Letter |

    Epistatic interactions, whereby a mutation's effect is contingent on another mutation, have been shown to constrain evolution within single proteins, and how such interactions arise in gene regulatory networks has remained unclear; here the appearance of pheromone-response regulator binding sites in the regulatory DNA of the a-specific genes of Saccharomyces cerevisiae are shown to have required specific changes in a second pathway during the evolution from its common ancestor with Candida albicans.

    • Trevor R. Sorrells
    • , Lauren N. Booth
    •  & Alexander D. Johnson

  • Article |

    The emRiboSeq sequencing method is used to track polymerase activity genome-wide in vivo; despite Okazaki fragment processing, DNA synthesized by error-prone polymerase-α (Pol-α) is retained in vivo and comprises ∼1.5% of the genome, establishing Pol-α as an important source of genomic variability and providing a mechanism for site-specific variation in nucleotide substitution rates.

    • Martin A. M. Reijns
    • , Harriet Kemp
    •  & Martin S. Taylor

  • Article |

    Essential enzymes in genetically modified organisms are computationally redesigned to functionally depend on non-standard amino acids, thereby achieving biocontainment with unprecedented resistance to escape by evolution or by supplementation with environmental metabolites.

    • Daniel J. Mandell
    • , Marc J. Lajoie
    •  & George M. Church

  • Letter |

    Construction of a series of genomically recoded organisms whose growth is restricted by the expression of essential genes dependent on exogenously supplied synthetic amino acids introduces novel orthogonal barriers between these engineered organisms and the environment, thereby creating safer genetically modified organisms.

    • Alexis J. Rovner
    • , Adrian D. Haimovich
    •  & Farren J. Isaacs

  • Letter |

    A comparison of protein-coding genes from 134 archaeal genomes with their homologues in 1,847 bacterial genomes reveals that, during evolution, genes are transferred more often from bacteria to archaea than vice versa, and that gene influxes from bacteria can bring about the origin of major archaeal groups.

    • Shijulal Nelson-Sathi
    • , Filipa L. Sousa
    •  & William F. Martin

  • Letter |

    The authors show that two primate-specific genes encoding KRAB domain containing zinc finger proteins, ZNF91 and ZNF93, have evolved during the last 25 million years to repress retrotransposon families that emerged during this time period; according to the new data KZNF gene expansion limits the activity of newly emerged retrotransposons, which subsequently mutate to evade repression.

    • Frank M. J. Jacobs
    • , David Greenberg
    •  & David Haussler

  • Letter |

    Crystal structures of human and prokaryotic ribosomal oxygenases reported here, with and without their ribosomal protein substrates, support their assignments as hydroxylases, and provide insights into the evolution of the JmjC-domain-containing hydroxylases and demethylases.

    • Rasheduzzaman Chowdhury
    • , Rok Sekirnik
    •  & Christopher J. Schofield

  • Article |

    Using high-throughput genome and transcriptome sequencing, Y chromosome evolution across 15 representative mammals is explored, with results providing evidence for three independent sex chromosome originations in mammals and birds.

    • Diego Cortez
    • , Ray Marin
    •  & Henrik Kaessmann

  • Article |

    A computational approach for predicting the future evolution of the human influenza virus, based on population-genetic data of previous strains, is presented; this model holds promise for improving vaccine strain selection for seasonal influenza.

    • Marta Łuksza
    •  & Michael Lässig

  • Article
    | Open Access

    Whole-genome analysis of the elephant shark, a cartilaginous fish, shows that it is the slowest evolving of all known vertebrates, lacks critical bone formation genes and has an unusual adaptive immune system.

    • Byrappa Venkatesh
    • , Alison P. Lee
    •  & Wesley C. Warren

  • Letter |

    In the predominantly diploid yeast Saccharomyces cerevisiae, regulatory control of mating is separate from meiosis; here the related hemiascomycete yeast Candida lusitaniae is shown to have coordinated regulatory control of mating and meiosis, favouring the formation of haploids.

    • Racquel Kim Sherwood
    • , Christine M. Scaduto
    •  & Richard J. Bennett

  • Article |

    The spliceosome is shown to catalyse splicing through the RNA and not the protein components of the spliceosome; pre-messenger RNA splicing requires U6 snRNA acting by a mechanism similar to that used by group II self-splicing introns.

    • Sebastian M. Fica
    • , Nicole Tuttle
    •  & Joseph A. Piccirilli

  • Letter |

    A computational analysis of the ability of a metabolic reaction network to synthesize all biomass from a single source of carbon and energy shows that when such networks are required to be viable on one particular carbon source, they are typically also viable on multiple other carbon sources that were not targets of selection.

    • Aditya Barve
    •  & Andreas Wagner

  • Brief Communications Arising |

    • Michael S. Breen
    • , Carsten Kemena
    •  & Fyodor A. Kondrashov

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