Population genetics articles within Nature

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  • 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

  • Letter |

    Genome sequencing analyses from 765 specimens of Anopheles gambiae and Anopheles coluzzii from 15 locations across Africa characterize patterns of gene flow and variations in population size, and provide a resource for studying the evolution of natural malaria vector populations.

    • Alistair Miles
    • , Nicholas J. Harding
    •  & Dominic P. Kwiatkowski

  • Letter |

    Analyses of digital corpora of annotated texts reveal the influence of stochastic drift versus selection in grammatical shifts in English and provide a general method for quantitatively testing theories of language change.

    • Mitchell G. Newberry
    • , Christopher A. Ahern
    •  & Joshua B. Plotkin

  • Letter |

    New genome-wide data for ancient, Bronze Age individuals, including Minoans, Mycenaeans, and southwestern Anatolians, show that Minoans and Mycenaeans were genetically very similar yet distinct, supporting the idea of continuity but not isolation in the history of populations of the Aegean.

    • Iosif Lazaridis
    • , Alissa Mittnik
    •  & George Stamatoyannopoulos

  • Letter |

    By sequencing the exomes of 10,503 individuals living in Pakistan, the authors identify rare predicted loss-of-function mutations that are estimated to knock out genes and correlate these mutations with a broad range of phenotypes, providing a framework for a human knockout project.

    • Danish Saleheen
    • , Pradeep Natarajan
    •  & Sekar Kathiresan

  • Article |

    Analysis of Aboriginal Australian mitochondrial genomes shows geographic patterns and deep splits across the major haplogroups that indicate a single, rapid migration along the coasts around 49–45 ka, followed by longstanding persistence in discrete geographic areas.

    • Ray Tobler
    • , Adam Rohrlach
    •  & Alan Cooper

  • Article |

    Natural isolates of Caenorhabditis elegans nematodes differ in their sensitivity to the anti-exploratory pheromone icas#9, yielding two distinct foraging strategies that possess different survival advantages depending on environmental conditions such as food distribution.

    • Joshua S. Greene
    • , Maximillian Brown
    •  & Cornelia I. Bargmann

  • 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

  • Article |

    Whole-genome sequence data for 108 individuals representing 28 language groups across Australia and five language groups for Papua New Guinea suggests that Aboriginal Australians and Papuans diverged from Eurasian populations approximately 60–100 thousand years ago, following a single out-of-Africa dispersal and subsequent admixture with archaic populations.

    • Anna-Sapfo Malaspinas
    • , Michael C. Westaway
    •  & Eske Willerslev

  • Article |

    Analysis of DNA from ancient individuals of the Near East documents the extreme substructure among the populations which transitioned to farming, a structure that was maintained throughout the transition from hunter–gatherer to farmer but that broke down over the next five thousand years.

    • Iosif Lazaridis
    • , Dani Nadel
    •  & David Reich

  • 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

  • Article |

    WebSchizophrenia is associated with genetic variation at the major histocompatibility complex locus; this study reveals that alleles at this locus associate with schizophrenia in proportion to their tendency to generate greater expression of complement component 4 (C4A) genes and that C4 promotes the elimination of synpases.

    • Aswin Sekar
    • , Allison R. Bialas
    •  & Steven A. McCarroll

  • Article |

    The first genome-wide scan for selection using ancient DNA, based on data from 230 West Eurasians dating between to 6500 and 300 bc and including new data from 163 individuals among which are 26 Neolithic Anatolians, provides a direct view of selection on loci associated with diet, pigmentation and immunity.

    • Iain Mathieson
    • , Iosif Lazaridis
    •  & David Reich

  • Article
    | Open Access

    Results for the final phase of the 1000 Genomes Project are presented including whole-genome sequencing, targeted exome sequencing, and genotyping on high-density SNP arrays for 2,504 individuals across 26 populations, providing a global reference data set to support biomedical genetics.

    • Adam Auton
    • , Gonçalo R. Abecasis
    •  & Gonçalo R. Abecasis

  • Letter |

    Previous genetic studies have suggested that the Americas were peopled by a single founding population of Eurasian origin, but a genome-wide study of 30 Native American groups shows that Amazonian Native Americans also have a second source of ancestry that is deeply related to indigenous Australians, New Guineans and Andaman Islanders.

    • Pontus Skoglund
    • , Swapan Mallick
    •  & David Reich

  • Letter
    | Open Access

    Kennewick Man, a 8,500-year-old male human skeleton discovered in Washington state, USA, has been the subject of scientific and legal controversy; here a DNA analysis shows that Kennewick Man is closer to modern Native Americans than to any other extant population worldwide.

    • Morten Rasmussen
    • , Martin Sikora
    •  & Eske Willerslev

  • Article |

    An analysis of 101 ancient human genomes from the Bronze Age (3000–1000 bc) reveals large-scale population migrations in Eurasia consistent with the spread of Indo-European languages; individuals frequently had light skin pigmentation but were not lactose tolerant.

    • Morten E. Allentoft
    • , Martin Sikora
    •  & Eske Willerslev

  • Article |

    Extensive genetic analysis of over 2,000 individuals from different locations in Britain reveals striking fine-scale patterns of population structure; comparisons with similar genetic data from the European continent reveal the legacy of earlier population migrations and information about the ancestry of current populations in specific geographic regions.

    • Stephen Leslie
    • , Bruce Winney
    •  & Walter Bodmer

  • Letter |

    Quantifying activity of cis-regulatory sequences controlling gene expression shows that selection on expression noise has a greater impact on sequence variation than selection on mean expression level.

    • Brian P. H. Metzger
    • , David C. Yuan
    •  & Patricia J. Wittkopp

  • Letter |

    A genome-wide analysis of 69 ancient Europeans reveals the history of population migrations around the time that Indo-European languages arose in Europe, when there was a large migration into Europe from the Eurasian steppe in the east (providing a genetic ancestry still present in Europeans today); these findings support a ‘steppe origin’ hypothesis for how some Indo-European languages arose.

    • Wolfgang Haak
    • , Iosif Lazaridis
    •  & David Reich

  • Article
    | Open Access

    The African Genome Variation Project contains the whole-genome sequences of 320 individuals and dense genotypes on 1,481 individuals from sub-Saharan Africa; it enables the design and interpretation of genomic studies, with implications for finding disease loci and clues to human origins.

    • Deepti Gurdasani
    • , Tommy Carstensen
    •  & Manjinder S. Sandhu

  • Article |

    The monarch butterfly, well known for its spectacular annual migration across North America, is shown by genome sequencing of monarchs from around the world to have been ancestrally migratory and to have dispersed out of North America to occupy its current broad distribution; the authors also discovered signatures of selection associated with migration within loci implicated in flight muscle function, leading to greater flight efficiency.

    • Shuai Zhan
    • , Wei Zhang
    •  & Marcus R. Kronforst

  • Letter |

    Admixture with other hominin species helped humans to adapt to high-altitude environments; the EPAS1 gene in Tibetan individuals has an unusual haplotype structure that probably resulted from introgression of DNA from Denisovan or Denisovan-related individuals into humans, and this haplotype is only found in Denisovans and Tibetans, and at low frequency among Han Chinese.

    • Emilia Huerta-Sánchez
    • , Xin Jin
    •  & Rasmus Nielsen

  • Letter |

    The phenomenon of sex-limited mimicry is phylogenetically widespread in the swallowtail butterfly genus Papilio — now, a single gene, doublesex, is shown to control supergene mimicry, a finding that is in contrast to the long-held view that supergenes are likely to be controlled by a tightly linked cluster of loci.

    • K. Kunte
    • , W. Zhang
    •  & M. R. Kronforst

  • Letter |

    A risk haplotype for type 2 diabetes is identified with four amino acid substitutions in SLC16A11, which is present at ∼50% frequency in Native American samples and ∼10% in east Asian samples, but is rare in European and African samples; SLC16A11 may alter hepatic lipid metabolism, causing an increase in triacylglycerol levels.

    • Amy L. Williams
    • , Suzanne B. R. Jacobs
    •  & Teresa Tusié-Luna

  • Letter |

    Draft genomes of two south-central Siberian individuals dating to 24,000 and 17,000 years ago show that they are genetically closely related to modern-day western Eurasians and Native Americans but not to east Asians; the results have implications for our understanding of the origins of Native Americans.

    • Maanasa Raghavan
    • , Pontus Skoglund
    •  & Eske Willerslev

  • Article |

    Sequencing and deep analysis of mRNA and miRNA from lymphoblastoid cell lines of 462 individuals from the 1000 Genomes Project reveal widespread genetic variation affecting the regulation of most genes, with transcript structure and expression level variation being equally common but genetically largely independent, and the analyses point to putative causal variants for dozens of disease-associated loci.

    • Tuuli Lappalainen
    • , Michael Sammeth
    •  & Emmanouil T. Dermitzakis

  • Brief Communications Arising |

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

  • Article
    | Open Access

    This report from the 1000 Genomes Project describes the genomes of 1,092 individuals from 14 human populations, providing a resource for common and low-frequency variant analysis in individuals from diverse populations; hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites, can be found in each individual.

    • Gil A. McVean
    • , David M. Altshuler (Co-Chair)
    •  & Gil A. McVean

  • Editorial |

    Collaboration between geneticists and economists has the potential to bear fruit.

  • Letter |

    A meta-analysis of genome-wide association studies of phenotypic variation for height and body mass index in human populations using 170,000 samples shows that one single nucleotide polymorphism at the FTO locus, which is associated with obesity, is also associated with phenotypic variation.

    • Jian Yang
    • , Ruth J. F. Loos
    •  & Peter M. Visscher

  • Article
    | Open Access

    An extensive map of human DNase I hypersensitive sites, markers of regulatory DNA, in 125 diverse cell and tissue types is described; integration of this information with other ENCODE-generated data sets identifies new relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns.

    • Robert E. Thurman
    • , Eric Rynes
    •  & John A. Stamatoyannopoulos

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