Evolutionary biology

  • Article
    | Open Access

    Genome-wide data for the three oldest known modern human remains in Europe, dated to around 45,000 years ago, shed light on early human migrations in Europe and suggest that mixing with Neanderthals was more common than is often assumed.

    • Mateja Hajdinjak
    • , Fabrizio Mafessoni
    •  & Svante Pääbo
  • Article
    | Open Access

    A chromosome-quality genome of the lungfish Neoceratodus fosteri sheds light on the development of obligate air-breathing and the gain of limb-like gene expression in lobed fins, providing insights into the water-to-land transition in vertebrate evolution.

    • Axel Meyer
    • , Siegfried Schloissnig
    •  & Manfred Schartl
  • Article |

    Single-nucleus RNA-sequencing analyses of brain from humans, macaques, marmosets, mice and ferrets reveal diverse ways that interneuron populations have changed during evolution.

    • Fenna M. Krienen
    • , Melissa Goldman
    •  & Steven A. McCarroll
  • Article
    | Open Access

    Reference-quality genomes for six bat species shed light on the phylogenetic position of Chiroptera, and provide insight into the genetic underpinnings of the unique adaptations of this clade.

    • David Jebb
    • , Zixia Huang
    •  & Emma C. Teeling
  • Article |

    A method termed ac4C-seq is introduced for the transcriptome-wide mapping of the RNA modification N4-acetylcytidine, revealing widespread temperature-dependent acetylation that facilitates thermoadaptation in hyperthermophilic archaea.

    • Aldema Sas-Chen
    • , Justin M. Thomas
    •  & Schraga Schwartz
  • Article |

    Analyses of the proteomes of dental enamel from Homo antecessor and Homo erectus demonstrate that the Early Pleistocene H. antecessor is a close sister lineage of later Homo sapiens, Neanderthal and Denisovan populations in Eurasia.

    • Frido Welker
    • , Jazmín Ramos-Madrigal
    •  & Enrico Cappellini
  • Article |

    Phenotypic selection analysis is used to estimate the type and strength of selection that acts on more than 15,000 transcripts in rice (Oryza sativa), which provides insight into the adaptive evolutionary role of selection on gene expression.

    • Simon C. Groen
    • , Irina Ćalić
    •  & Michael D. Purugganan
  • Article |

    The leg-enriched sensory appendage protein, SAP2, confers pyrethroid resistance to Anopheles gambiae, through high-affinity binding of pyrethroid insecticides; an observed selective sweep in field mosquitoes mirrors the increasing resistance reported in Africa.

    • Victoria A. Ingham
    • , Amalia Anthousi
    •  & Hilary Ranson
  • Article |

    In patients with ulcerative colitis, chronic inflammation can lead to remodelling of the colorectal epithelium through positive selection of clones with mutations in genes related to IL-17 signalling, which, however, might be negatively selected during colitis-associated carcinogenesis.

    • Nobuyuki Kakiuchi
    • , Kenichi Yoshida
    •  & Seishi Ogawa
  • Letter |

    Species of the eukaryotic phylum Rhodelphidia are non-photosynthetic, flagellate predators with gene-rich genomes, in contrast to their closely related sister lineage—the red algae—which are immotile, typically photoautotrophic and have relatively small intron-poor genomes and reduced metabolism.

    • Ryan M. R. Gawryluk
    • , Denis V. Tikhonenkov
    •  & Patrick J. Keeling
  • Letter |

    Comparison of transcriptomes, cell fates and behaviour of three primary cell types from the sponge Amphimedon queenslandica with choanoflagellates and other unicellular holozoans suggests that the first animal cells transitioned between multiple states.

    • Shunsuke Sogabe
    • , William L. Hatleberg
    •  & Bernard M. Degnan
  • Article |

    In physiologically normal epithelia, age-related expansion of clones that carry mutations in NOTCH1 and other driver genes is accelerated by risk factors for developing oesophageal squamous cell carcinoma, such as alcohol consumption or smoking.

    • Akira Yokoyama
    • , Nobuyuki Kakiuchi
    •  & Seishi Ogawa
  • Letter |

    Genetic similarity among late Neanderthals is predicted well by their geographical location, and although some of these Neanderthals were contemporaneous with early modern humans, their genomes show no evidence of recent gene flow from modern humans.

    • Mateja Hajdinjak
    • , Qiaomei Fu
    •  & Janet Kelso
  • Letter |

    Analysis of ancient DNA from four individuals who lived in Vanuatu and Tonga between 2,300 and 3,100 years ago suggests that the Papuan ancestry seen in present-day occupants of this region was introduced at a later date.

    • Pontus Skoglund
    • , Cosimo Posth
    •  & David Reich
  • Letter |

    Whole-genome sequencing of individuals from 125 populations provides insight into patterns of genetic diversity, natural selection and human demographic history during the peopling of Eurasia and finds evidence for genetic vestiges of an early expansion of modern humans out of Africa in Papuans.

    • Luca Pagani
    • , Daniel John Lawson
    •  & Mait Metspalu
  • Letter |

    The zebrafish cloche gene is required for the formation of most endothelial and haematopoietic cells, however, it has been difficult to isolate; this study reveals that cloche encodes a PAS-domain-containing bHLH transcription factor, and a mammalian orthologue can partially rescue cloche mutants, indicating a possible conserved role in mammals.

    • Sven Reischauer
    • , Oliver A. Stone
    •  & Didier Y. R. Stainier
  • Article |

    Analysis of ancient genomic data of 51 humans from Eurasia dating from 45,000 to 7,000 years ago provides insight into the population history of pre-Neolithic Europe and support for recurring migration and population turnover in Europe during this period.

    • Qiaomei Fu
    • , Cosimo Posth
    •  & David Reich
  • Letter |

    Nuclear DNA sequences from Middle Pleistocene Sima de los Huesos hominins show they were more closely related to Neanderthals than to Denisovans, and indicate a population divergence between Neanderthals and Denisovans that predates 430,000 years ago.

    • Matthias Meyer
    • , Juan-Luis Arsuaga
    •  & Svante Pääbo
  • Article |

    It is known that there was gene flow from Neanderthals to modern humans around 50,000 years ago; now, analysis of a Neanderthal genome from the Altai Mountains in Siberia reveals evidence of gene flow 100,000 years ago in the other direction—from early modern humans to Neanderthals.

    • Martin Kuhlwilm
    • , Ilan Gronau
    •  & Sergi Castellano
  • Article |

    PRDM9 is a DNA-binding protein that controls the position of double-strand breaks in meiosis, and the gene that encodes it is responsible for hybrid infertility between closely related mouse species; this hybrid infertility is eliminated by introducing the zinc-finger domain sequence from the human version of the PRDM9 gene, a change which alters both the position of double-strand breaks and the symmetry of PRDM9 binding and suggests that PRDM9 may have a more general but transient role in the early stages of speciation.

    • Benjamin Davies
    • , Edouard Hatton
    •  & Peter Donnelly
  • Letter |

    In vitro evolution experiments on haploid, diploid, and tetraploid yeast strains show that adaptation is faster in tetraploids, providing direct quantitative evidence that in some environments polyploidy can accelerate evolutionary adaptation.

    • Anna M. Selmecki
    • , Yosef E. Maruvka
    •  & David Pellman
  • 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
  • Article
    | Open Access

    Genomes and transcriptomes of five distinct lineages of African cichlids, a textbook example of adaptive radiation, have been sequenced and analysed to reveal that many types of molecular changes contributed to rapid evolution, and that standing variation accumulated during periods of relaxed selection may have primed subsequent diversification.

    • David Brawand
    • , Catherine E. Wagner
    •  & Federica Di Palma
  • Letter
    | Open Access

    A map of genome-wide binding locations of 165 human, 93 worm and 52 fly transcription-regulatory factors (almost 50% presented for the first time) from diverse cell types, developmental stages, or conditions reveals that gene-regulatory properties previously observed for individual factors may be general principles of metazoan regulation that are well preserved.

    • Alan P. Boyle
    • , Carlos L. Araya
    •  & Michael Snyder
  • Letter |

    The formation of a new species can occur by an asexual mechanism by transfer of entire nuclear genomes between plant cells as shown by the creation of a new allopolyploid plant from parental herbaceous and woody plant species, this mechanism is a potential new tool for crop improvement.

    • Ignacia Fuentes
    • , Sandra Stegemann
    •  & Ralph Bock
  • Article |

    The molecular basis for mating-type determination in the ciliate Paramecium has been elucidated, revealing a novel function for a class of small RNAs — these scnRNAs are typically involved in reprogramming the Paramecium genome during sexual reproduction by recognizing and excising transposable elements, but they are now found to be co-opted to switch off expression of the newly identified mating-type gene mtA by excising its promoter, and to mediate epigenetic inheritance of mating types across sexual generations.

    • Deepankar Pratap Singh
    • , Baptiste Saudemont
    •  & Eric Meyer
  • Letter |

    A full mitochondrial genome from a 400,000-year-old Middle Pleistocene hominin from Spain unexpectedly reveals a close relationship to Denisovans, a sister group to the Neanderthals, raising interesting questions about the origins of Neanderthals and Denisovans.

    • Matthias Meyer
    • , Qiaomei Fu
    •  & Svante Pääbo
  • Letter |

    Induced pluripotent stem-cell characterization reveals phenotypical differences between humans and non-human primates (NHPs): gene expression analysis shows differences in the regulation of long interspersed element-1 (L1) transposons, and in the expression of L1-restricting genes APOBEC3B and PIWIL2, correlating with higher L1 mobility in NHPs; this indicates that L1 mobility differences may have differentially shaped the human and NHP genomes.

    • Maria C. N. Marchetto
    • , Iñigo Narvaiza
    •  & Fred H. Gage
  • Letter |

    Wild Soay sheep rams with large horns have more offspring, yet there is considerable genetic variation at RXFP2, a locus strongly implicated in horn size (with different alleles conferring either large or small horns); this study finds that although the larger horn allele leads to more offspring, the smaller horn allele leads to increased survival, meaning heterozygous rams (which develop medium-sized horns) have high reproductive success and survival, providing a rare example of heterozygote advantage.

    • Susan E. Johnston
    • , Jacob Gratten
    •  & Jon Slate
  • Letter
    | Open Access

    The genome of the asexual rotifer Adineta vaga lacks homologous chromosomes; instead, its allelic regions are rearranged and sometimes found on the same chromosome in a palindromic fashion, a structure reminiscent of the primate Y chromosome and of other mitotic lineages such as cancer cells.

    • Jean-François Flot
    • , Boris Hespeels
    •  & Karine Van Doninck
  • Letter
    | Open Access

    High-coverage sequencing of 79 (wild and captive) individuals representing all six non-human great ape species has identified over 88 million single nucleotide polymorphisms providing insight into ape genetic variation and evolutionary history and enabling comparison with human genetic diversity.

    • Javier Prado-Martinez
    • , Peter H. Sudmant
    •  & Tomas Marques-Bonet
  • Letter |

    Populations experiencing environmental change can often only avoid extinction through evolutionary change; in a system in which Escherichia coli has to evolve resistance to an antibiotic, the authors show that gradual environmental change allows mutational pathways that rapid change precludes, and can therefore make the difference between extinction and survival.

    • Haley A. Lindsey
    • , Jenna Gallie
    •  & Benjamin Kerr
  • Letter
    | Open Access

    The Gossypium genus is used to investigate emergent consequences of polyploidy in cotton species; comparative genomic analyses reveal a complex evolutionary history including interactions among subgenomes that result in genetic novelty in elite cottons and provide insight into the evolution of spinnable fibres.

    • Andrew H. Paterson
    • , Jonathan F. Wendel
    •  & Jeremy Schmutz
  • Letter |

    Resequencing of genes from individuals of European and African American ancestry indicates that approximately 73% of all protein-coding SNVs and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000–10,000 years, and that European Americans carry an excess of deleterious variants in essential and Mendelian disease genes compared to African Americans.

    • Wenqing Fu
    • , Timothy D. O’Connor
    •  & Joshua M. Akey