Molecular evolution articles within Nature

Featured

  • Article |

    An analysis of staged hagfish embryos shows that the hagfish adenohypophysis is ectodermal in origin, revealing it to be a developmental quirk unique to hagfishes that was hitherto misleading; from this and other observations a ‘pan-cyclostome’ developmental pattern is derived, indicating that it was primitive for all vertebrates.

    • Yasuhiro Oisi
    • , Kinya G. Ota
    •  & Shigeru Kuratani

  • Article |

    The structure of the bacteriophage transposase MuA bound to DNA sequences that mimic both the transposon ends and the target DNA ends is solved; the picture of this synaptic complex illustrates the intricacy of Mu transposition, and exposes the architectural diversity among DDE recombinases in complex with substrate DNAs.

    • Sherwin P. Montaño
    • , Ying Z. Pigli
    •  & Phoebe A. Rice

  • News & Views |

    A quantitative analysis shows that epistasis — the fact that genetic background determines whether a mutation is beneficial, deleterious or inconsequential — is the main factor regulating evolution at the level of proteins. See Letter p.535

    • Günter P. Wagner

  • Article |

    In models of early life it has been suggested that life and evolution would be more easily achieved if RNA molecules could interact, rather than function independently; here an in vitro system is designed with several RNA fragments that can assemble into a ribozyme, showing that cooperative networks formed by these fragments outcompete self-catalytic RNA fragments.

    • Nilesh Vaidya
    • , Michael L. Manapat
    •  & Niles Lehman

  • Letter |

    A comparison of more than 1,000 orthologues of diverse proteins shows that the rate of amino-acid substitution in recent evolution is an order of magnitude lower than that expected in the absence of epistasis, indicating that epistasis is pervasive throughout protein evolution.

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

  • Letter |

    A high-throughput mutagenesis study in a PDZ domain shows that biochemical function and adaptation primarily originate from a collectively evolving amino acid network within the structure termed a protein sector.

    • Richard N. McLaughlin Jr
    • , Frank J. Poelwijk
    •  & Rama Ranganathan

  • Letter |

    This phylogenomic study shows that core muscle proteins were already present in unicellular organisms before the origin of multicellular animals, and supports a convergent evolutionary model for striated muscles in which new proteins are added to ancient contractile apparatus during independent evolution of bilaterians and some non-bilaterians, resulting in very similar ultrastructures.

    • Patrick R. H. Steinmetz
    • , Johanna E. M. Kraus
    •  & Ulrich Technau

  • News & Views |

    A genetic study of brain cancers in mice and humans reveals distinct mutations in primary tumours and their metastases, suggesting that the two disease 'compartments' may require different treatments.

    • Steven C. Clifford

  • News & Views |

    Although some genetic mutations have clear effects, others have been considered neutral and inconsequential. Such cryptic mutations can nonetheless facilitate adaptation to new environments. See Letter p.92

    • Jeremy A. Draghi
    •  & Joshua B. Plotkin

  • Letter |

    Pyrrolysine is the twenty-second naturally occurring amino acid, and it is required for the formation of methane from methylamines. Pyrrolysine is the last remaining natural amino acid with a poorly characterized biosynthetic pathway. Here it is shown that the radical SAM protein PylB converts lysine to 3-methylornithine, which then undergoes a PylC-catalysed condensation with another lysine to generate a product that is oxidized by PylD to generate pyrrolysine.

    • Marsha A. Gaston
    • , Liwen Zhang
    •  & Joseph A. Krzycki

  • Letter |

    How new phenotypes can be introduced during evolution without losses of fitness remains largely unexplained at the molecular level. By comparing the molecular details of a well known process — mating type determination — across a large diversity of yeast species, the network rewiring event of the intercalation of a new level of gene transcription control into an ancient regulatory circuit is shown, which allowed for the creation of a new phenotype — taking food availability into account when deciding to mate.

    • Lauren N. Booth
    • , Brian B. Tuch
    •  & Alexander D. Johnson

  • Letter |

    Here, whole-genome sequencing has been used to analyse primary pancreatic tumours and one or more metastases from the same patients. The findings show that tumours are composed of several geographically distinct subclones, and allow maps to be produced showing how metastatic cancer clones evolve within the primary tumour. Moreover, a quantitative analysis of the timing of the genetic evolution of pancreatic cancer has been performed.

    • Shinichi Yachida
    • , Siân Jones
    •  & Christine A. Iacobuzio-Donahue

  • Letter |

    The European corn borer consists of two sex pheromone races, leading to strong reproductive isolation which could represent a first step in speciation. Female sex pheromone production and male behavioural response are under the control of different genes, but the identity of these genes is unknown. These authors show that allelic variation in a gene essential for pheromone biosynthesis accounts for the phenotypic variation in female pheromone production, leading to race-specific signals.

    • Jean-Marc Lassance
    • , Astrid T. Groot
    •  & Christer Löfstedt

  • Letter |

    The need to maintain the structural and functional integrity of an evolving protein limits the range of acceptable amino-acid substitutions — but to what extent does this constrain how far homologous protein sequences can diverge? Here, sequence divergence data are used to explore the limits of protein evolution, and to conclude that ancient proteins are continuing to diverge from one another, indicating that the protein sequence universe is slowly expanding.

    • Inna S. Povolotskaya
    •  & Fyodor A. Kondrashov

  • Letter |

    The ability of plants to 'green' in the dark is attributed to the activity of the dark-operative protochlorophyllide oxidoreductase (DPOR). This enzyme catalyses the stereospecific reduction of the C17≡C18 double bond of protochlorophyllide to form chlorophyllide a, the direct precursor of chlorophyll a. The X-ray crystal structure of the catalytic component of DPOR has now been solved. A chemical mechanism is proposed by which the reduction of the double bond may occur.

    • Norifumi Muraki
    • , Jiro Nomata
    •  & Yuichi Fujita

  • Article |

    Here, the generation and evolution of the complex spotted wing pattern of Drosophila guttifera are investigated. The findings show that wing spots are induced by the Wingless morphogen, and that the elaborate spot pattern evolved from simpler schemes by co-option of Wingless expression at new sites. This type of process is likely to occur in other animals, too.

    • Thomas Werner
    • , Shigeyuki Koshikawa
    •  & Sean B. Carroll

  • Letter |

    The Red Queen hypothesis predicts that coevolution should increase the rate of evolution at the molecular level. Here, genome sequencing in an experimental phage–bacteria system is used to show that this is true, but the effect is concentrated on specific loci, and also that coevolution drives greater diversification of phage populations.

    • Steve Paterson
    • , Tom Vogwill
    •  & Michael A. Brockhurst

  • Letter |

    Evolution from one fitness peak to another must involve either transitions through intermediates of low fitness or skirting round the fitness valley through compensatory mutations elsewhere. Here, the base pairs in mitochondrial tRNA stems is used as a model to show that deep fitness valleys can be traversed. Transitions between AU and GC pairs have occurred during mammalian evolution without help from genetic drift or mutations elsewhere.

    • Margarita V. Meer
    • , Alexey S. Kondrashov
    •  & Fyodor A. Kondrashov

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