Molecular evolution articles within Nature

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  • Article
    | Open Access

    Patagia—the mammalian gliding membrane—repeatedly originated through a process of convergent genomic evolution, whereby the regulation of Emx2 was altered by distinct cis-regulatory elements in independently evolved species.

    • Jorge A. Moreno
    • , Olga Dudchenko
    •  & Ricardo Mallarino

  • Article
    | Open Access

    Citrate synthase from the cyanobacterium Synechococcus elongatus is shown to self-assemble into Sierpiński triangles, a finding that opens up the possibility that other naturally occurring molecular-scale fractals exist.

    • Franziska L. Sendker
    • , Yat Kei Lo
    •  & Georg K. A. Hochberg

  • Article
    | Open Access

    A comparison of two complete sets of human centromeres reveals that the centromeres show at least a 4.1-fold increase in single-nucleotide variation compared with their unique flanks, and up to 3-fold variation in size, resulting from an accelerated mutation rate.

    • Glennis A. Logsdon
    • , Allison N. Rozanski
    •  & Evan E. Eichler

  • Article
    | Open Access

    In Caenorhabditis tropicalis, selective expression of genetic alleles from one parent but not the other can arise from maternally inherited small transcripts acting via the PIWI-interacting RNA host defence pathway.

    • Pinelopi Pliota
    • , Hana Marvanova
    •  & Alejandro Burga

  • Article
    | Open Access

    A chromosome-scale genome assembly for the hagfish Eptatretus atami, combined with a series of phylogenetic analyses, sheds light on ancient polyploidization events that had a key role in the early evolution of vertebrates.

    • Ferdinand Marlétaz
    • , Nataliya Timoshevskaya
    •  & Daniel S. Rokhsar

  • Article
    | Open Access

    Analysis of naturally hybridizing swordtail fish species reveals a mitonuclear genetic incompatibility among three genes that encode components of mitochondrial respiratory complex I, providing insights into the emergence of hybrid incompatibilities and reproductive barriers.

    • Benjamin M. Moran
    • , Cheyenne Y. Payne
    •  & Molly Schumer

  • Article
    | Open Access

    Analyses of imputed ancient genomes and of samples from the UK Biobank indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.

    • Evan K. Irving-Pease
    • , Alba Refoyo-Martínez
    •  & Eske Willerslev

  • Article |

    Recent resurgences of highly pathogenic avian influenza H5 viruses have different origins and virus ecologies as their epicentres shift and viruses evolve, with changes indicating increased adaptation among domestic birds.

    • Ruopeng Xie
    • , Kimberly M. Edwards
    •  & Vijaykrishna Dhanasekaran

  • Article
    | Open Access

    The extent to which the AlphaFold database has structurally illuminated proteins that are challenging to annotate for function or putative biological role using standard homology-based approaches at high predicted accuracy is investigated.

    • Janani Durairaj
    • , Andrew M. Waterhouse
    •  & Joana Pereira

  • Article
    | Open Access

    An engineered minimal cell evolves to escape the negative consequences of genome streamlining.

    • R. Z. Moger-Reischer
    • , J. I. Glass
    •  & J. T. Lennon

  • Article |

    Analysis of sedimentary rocks from the mid-Proterozoic interval reveals traces of protosteroids, suggesting the widespread presence of stem-group eukaryotes that predated and co-existed with the crown-group ancestors of modern eukaryotes.

    • Jochen J. Brocks
    • , Benjamin J. Nettersheim
    •  & Janet M. Hope

  • Article
    | Open Access

    Deeply conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of the comb jellies (ctenophores)—placing ctenophores as the sister group to all other animals.

    • Darrin T. Schultz
    • , Steven H. D. Haddock
    •  & Daniel S. Rokhsar

  • Article |

    Complementary single-cell and single-nucleus transcriptomic analyses of Zea mays, Sorghum bicolor and Setaria viridis root cells provide insights into the evolution of cell types and gene modules that control key traits in these important crop species.

    • Bruno Guillotin
    • , Ramin Rahni
    •  & Kenneth D. Birnbaum

  • Article |

    Cryo-electron microscopy analyses reveal adaptations that facilitate the octopus chemotactile receptor’s evolutionary transition from an ancestral role in neurotransmission to detecting greasy environmental agonists for ‘taste by touch’ sensory behaviour.

    • Corey A. H. Allard
    • , Guipeun Kang
    •  & Nicholas W. Bellono

  • Article |

    Octopus and squid use cephalopod-specific chemotactile receptors to sense their respective marine environments, but structural adaptations in these receptors support the sensation of specific molecules suited to distinct physiological roles.

    • Guipeun Kang
    • , Corey A. H. Allard
    •  & Ryan E. Hibbs

  • Article |

    Combining genome-wide CRISPR screens with massively parallel analyses of human and random DNA sequences reveal a unified mechanism for the surveillance and evolution of translation products from annotated noncoding DNA.

    • Jordan S. Kesner
    • , Ziheng Chen
    •  & Xuebing Wu

  • Article
    | Open Access

    Cryo-electron microscopy analysis of the Deinococcus radiodurans ISDra2 TnpB in complex with its cognate ωRNA and target DNA provides insights into the mechanism of TnpB function and the evolution of CRISPR–Cas12 effectors.

    • Ryoya Nakagawa
    • , Hisato Hirano
    •  & Osamu Nureki

  • Article
    | Open Access

    Evolutionary analyses of single-nucleus transcriptome data for testes from 11 species are reported, illuminating the molecular evolution of spermatogenesis and associated forces, and providing a resource for investigating the testis across mammals.

    • Florent Murat
    • , Noe Mbengue
    •  & Henrik Kaessmann

  • Article |

    Provora is an ancient supergroup of microbial predators that are genetically, morphologically and behaviourally distinct from other eukaryotes, and comprise two divergent clades of predators—Nebulidia and Nibbleridia—that differ fundamentally in ultrastructure, behaviour and gene content.

    • Denis V. Tikhonenkov
    • , Kirill V. Mikhailov
    •  & Patrick J. Keeling

  • Article
    | Open Access

    Detailed ancestral gene content reconstruction shows that the large phenotypic differences between Metazoa and Fungi are the outcome of sharply contrasting trajectories of genomic changes that predated the origin of both groups.

    • Eduard Ocaña-Pallarès
    • , Tom A. Williams
    •  & Iñaki Ruiz-Trillo

  • Article |

    A bacterial antiviral defence system generates a cyclic tri-adenylate that binds to a TIR–SAVED effector, inducing formation of a superhelical structure with adjacent TIR domains organizing into an active site, allowing NAD+ degradation.

    • Gaëlle Hogrel
    • , Abbie Guild
    •  & Malcolm F. White

  • Article |

    Untreated, postconsumer-PET from 51 different thermoformed products can all be almost completely degraded by FAST-PETase in 1 week and PET can be resynthesized from the recovered monomers, demonstrating recycling at the industrial scale.

    • Hongyuan Lu
    • , Daniel J. Diaz
    •  & Hal S. Alper

  • Article |

    A framework for studying and engineering gene regulatory DNA sequences, based on deep neural sequence-to-expression models trained on large-scale libraries of random DNA, provides insight into the evolution, evolvability and fitness landscapes of regulatory DNA.

    • Eeshit Dhaval Vaishnav
    • , Carl G. de Boer
    •  & Aviv Regev

  • Article
    | Open Access

    Data on de novo mutations in Arabidopsis thaliana reveal that mutations do not occur randomly; instead, epigenome-associated mutation bias reduces the occurrence of deleterious mutations.

    • J. Grey Monroe
    • , Thanvi Srikant
    •  & Detlef Weigel

  • Article
    | Open Access

    An examination of motor cortex in humans, marmosets and mice reveals a generally conserved cellular makeup that is likely to extend to many mammalian species, but also differences in gene expression, DNA methylation and chromatin state that lead to species-dependent specializations.

    • Trygve E. Bakken
    • , Nikolas L. Jorstad
    •  & Ed S. Lein

  • Article |

    Structural, functional and localization studies reveal that Geobacter sulfurreducens pili cannot behave as microbial nanowires, instead functioning in a similar way to secretion pseudopili to export cytochrome nanowires that are essential for extracellular electron transfer.

    • Yangqi Gu
    • , Vishok Srikanth
    •  & Nikhil S. Malvankar

  • Article |

    The 501Y.V2 variant of SARS-CoV-2 in South Africa became dominant over other variants within weeks of its emergence, suggesting that this variant is linked to increased transmissibility or immune escape.

    • Houriiyah Tegally
    • , Eduan Wilkinson
    •  & Tulio de Oliveira

  • Article |

    Accumulation of hydrophobic residues at the interface between monomers may favour the maintenance of multimeric protein states during evolution, even if multimerization confers no functional advantage.

    • Georg K. A. Hochberg
    • , Yang Liu
    •  & Joseph W. Thornton

  • Article |

    An analysis using ribosome-profiling and matched RNA-sequencing data for three organs across five mammalian species and a bird enables the comparison of translatomes and transcriptomes, revealing patterns of co-evolution of these two expression layers.

    • Zhong-Yi Wang
    • , Evgeny Leushkin
    •  & Henrik Kaessmann

  • Article |

    Experimental analysis of reconstructed ancestral globins reveals that haemoglobin’s complex tetrameric structure and oxygen-binding functions evolved by simple genetic and biophysical mechanisms.

    • Arvind S. Pillai
    • , Shane A. Chandler
    •  & Joseph W. Thornton

  • Article
    | Open Access

    Whole-genome sequencing data for 2,778 cancer samples from 2,658 unique donors across 38 cancer types is used to reconstruct the evolutionary history of cancer, revealing that driver mutations can precede diagnosis by several years to decades.

    • Moritz Gerstung
    • , Clemency Jolly
    •  & Christian von Mering

  • 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

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