Population genetics

  • Article
    | Open Access

    Whole-genome sequencing of 3,171 cultivated and 195 wild chickpea accessions is used to construct a chickpea pan-genome, providing insight into chickpea evolution and enabling breeding strategies that could improve crop productivity.

    • Rajeev K. Varshney
    • , Manish Roorkiwal
    •  & Xin Liu
  • Article
    | Open Access

    Whole-exome sequencing analysis of 454,787 individuals in the UK Biobank is used to examine the association of protein-coding variants with nearly 4,000 health-related traits, identifying 564 distinct genes with significant trait associations.

    • Joshua D. Backman
    • , Alexander H. Li
    •  & Manuel A. R. Ferreira
  • Article |

    Laser-capture microdissection and mini-bulk exome sequencing are combined to analyse somatic mutations in morphologically normal tissues from nine organs from five donors, revealing variation in mutation burdens, mutational signatures and clonal expansions.

    • Ruoyan Li
    • , Lin Di
    •  & Chen Wu
  • Article |

    The authors report the mutational landscape of 29 cell types from microdissected biopsies from 19 organs and explore the mechanisms underlying mutation rates in normal tissues.

    • Luiza Moore
    • , Alex Cagan
    •  & Raheleh Rahbari
  • Article |

    Genomic analyses of human populations in the Pacific provide insights into the peopling history of the region and reveal episodes of biological adaptation relating to the immune system and lipid metabolism through introgression from archaic hominins and polygenic adaptation.

    • Jeremy Choin
    • , Javier Mendoza-Revilla
    •  & Lluis Quintana-Murci
  • 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 |

    Genome-wide data from 166 East Asian individuals dating to between 6000 bc and ad 1000 and from 46 present-day groups provide insights into the histories of mixture and migration of human populations in East Asia.

    • Chuan-Chao Wang
    • , Hui-Yuan Yeh
    •  & David Reich
  • Article |

    Siberian mammoth genomes from the Early and Middle Pleistocene subepochs reveal adaptive changes and a key hybridization event, highlighting the value of deep-time palaeogenomics for studies of speciation and long-term evolutionary trends.

    • Tom van der Valk
    • , Patrícia Pečnerová
    •  & Love Dalén
  • Article
    | Open Access

    The goals, resources and design of the NHLBI Trans-Omics for Precision Medicine (TOPMed) programme are described, and analyses of rare variants detected in the first 53,831 samples provide insights into mutational processes and recent human evolutionary history.

    • Daniel Taliun
    • , Daniel N. Harris
    •  & Gonçalo R. Abecasis
  • Article
    | Open Access

    The genome of the biofuel crop switchgrass (Panicum virgatum) reveals climate–gene–biomass associations that underlie adaptation in nature and will facilitate improvements of the yield of this crop for bioenergy production.

    • John T. Lovell
    • , Alice H. MacQueen
    •  & Jeremy Schmutz
  • Article |

    Ancient DNA reveals genetic differences between stone-tool users and people associated with ceramic technology in the Caribbean and provides substantially lower estimates of population sizes in the region before European contact.

    • Daniel M. Fernandes
    • , Kendra A. Sirak
    •  & David Reich
  • Article
    | Open Access

    Chromosome-scale sequence assemblies of 20 diverse varieties of barley are used to construct a first-generation pan-genome, revealing previously hidden genetic variation that can be used by studies aimed at crop improvement

    • Murukarthick Jayakodi
    • , Sudharsan Padmarasu
    •  & Nils Stein
  • Article |

    Whole-genome sequencing analyses of African populations provide insights into continental migration, gene flow and the response to human disease, highlighting the importance of including diverse populations in genomic analyses to understand human ancestry and improve health.

    • Ananyo Choudhury
    • , Shaun Aron
    •  & Neil A. Hanchard
  • Article |

    Ancient DNA analyses reveal that Viking Age migrations from Scandinavia resulted in differential influxes of ancestry to different parts of Europe, and the increased presence of non-local ancestry within Scandinavia.

    • Ashot Margaryan
    • , Daniel J. Lawson
    •  & Eske Willerslev
  • Article |

    The building blocks of the nanostructures observed on Drosophila corneas are determined, and then used to create artificial nanostructures with anti-reflective and anti-adhesive properties.

    • Mikhail Kryuchkov
    • , Oleksii Bilousov
    •  & Vladimir L. Katanaev
  • Article |

    Genome-wide analysis of tandem DNA repeats in the genomes of individuals with autism spectrum disorder and control participants reveals a strong contribution of tandem repeat expansions to the genetic aetiology and phenotypic complexity of autism spectrum disorder.

    • Brett Trost
    • , Worrawat Engchuan
    •  & Ryan K. C. Yuen
  • Article |

    Genomic analyses of DNA from modern individuals show that, about 800 years ago, pre-European contact occurred between Polynesian individuals and Native American individuals from near present-day Colombia, while remote Pacific islands were still being settled.

    • Alexander G. Ioannidis
    • , Javier Blanco-Portillo
    •  & Andrés Moreno-Estrada
  • Article |

    Resequencing analyses of three species of wild sunflower identify large non-recombining haplotype blocks that correlate with ecologically relevant traits, soil and climate characteristics, and that differentiate species ecotypes.

    • Marco Todesco
    • , Gregory L. Owens
    •  & Loren H. Rieseberg
  • Article |

    Skeletal remains from the Neolithic passage tomb at Newgrange (Ireland) represent the adult son of a first-degree incestuous union, suggesting that a politico-religious elite may have controlled the construction of Irish sites of this type.

    • Lara M. Cassidy
    • , Ros Ó Maoldúin
    •  & Daniel G. Bradley
  • Article |

    Thousands of sperm genomes have been analysed with a new method called Sperm-seq, revealing interconnected meiotic variation at the single-cell and person-to-person levels, and suggesting chromosome compaction as a way to explain the relationships between diverse recombination phenotypes.

    • Avery Davis Bell
    • , Curtis J. Mello
    •  & Steven A. McCarroll
  • Article
    | Open Access

    A catalogue of predicted loss-of-function variants in 125,748 whole-exome and 15,708 whole-genome sequencing datasets from the Genome Aggregation Database (gnomAD) reveals the spectrum of mutational constraints that affect these human protein-coding genes.

    • Konrad J. Karczewski
    • , Laurent C. Francioli
    •  & Daniel G. MacArthur
  • Article
    | Open Access

    Using whole-genome sequencing data from 1,739 individuals, the GenomeAsia 100K Project catalogues genetic variation, population structure and disease associations to facilitate genetic studies in Asian populations and increase representation in genetics studies worldwide.

    • Jeffrey D. Wall
    • , Eric W. Stawiski
    •  & Andrew S. Peterson
  • Letter |

    Genetic analyses of ancestrally diverse populations show evidence of heterogeneity across ancestries and provide insights into clinical implications, highlighting the importance of including ancestrally diverse populations to maximize genetic discovery and reduce health disparities.

    • Genevieve L. Wojcik
    • , Mariaelisa Graff
    •  & Christopher S. Carlson
  • Article |

    Analyses of 34 ancient genomes from northeastern Siberia, dating to between 31,000 and 600 years ago, reveal at least three major migration events in the late Pleistocene population history of the region.

    • Martin Sikora
    • , Vladimir V. Pitulko
    •  & Eske Willerslev
  • Article
    | Open Access

    An improved, fully re-annotated Aedes aegypti genome assembly (AaegL5) provides insights into the sex-determining M locus, chemosensory systems that help mosquitoes to hunt humans and loci involved in insecticide resistance and will help to generate intervention strategies to fight this deadly disease vector.

    • Benjamin J. Matthews
    • , Olga Dudchenko
    •  & Leslie B. Vosshall
  • Article
    | Open Access

    Deep phenotype and genome-wide genetic data from 500,000 individuals from the UK Biobank, describing population structure and relatedness in the cohort, and imputation to increase the number of testable variants to 96 million.

    • Clare Bycroft
    • , Colin Freeman
    •  & Jonathan Marchini
  • Article |

    Sequences of 137 ancient and 502 modern human genomes illuminate the population history of the Eurasian steppes after the Bronze Age and document the replacement of Indo-European speakers of West Eurasian ancestry by Turkic-speaking groups of East Asian ancestry.

    • Peter de Barros Damgaard
    • , Nina Marchi
    •  & Eske Willerslev
  • Brief Communications Arising |

    • Cameron K. Ghalambor
    • , Kim L. Hoke
    •  & Kimberly A. Hughes
  • Article |

    Genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe between 12000 and 500 bc reveals that the region acted as a genetic crossroads before and after the arrival of farming.

    • Iain Mathieson
    • , Songül Alpaslan-Roodenberg
    •  & David Reich
  • Article |

    Genome-wide data from 400 individuals indicate that the initial spread of the Beaker archaeological complex between Iberia and central Europe was propelled by cultural diffusion, but that its spread into Britain involved a large-scale migration that permanently replaced about ninety per cent of the ancestry in the previously resident population.

    • Iñigo Olalde
    • , Selina Brace
    •  & David Reich