Population genetics articles within Nature

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  • Article
    | Open Access

    Analysis of ancient DNA from 424 individuals in the Avar period, from the sixth to the ninth century AD, reveals population movement from the steppe and the prolonged existence of a steppe nomadic descent system centred around patrilineality and female exogamy in central Europe.

    • Guido Alberto Gnecchi-Ruscone
    • , Zsófia Rácz
    •  & Zuzana Hofmanová

  • Article
    | Open Access

    A study describes the release of clinical-grade whole-genome sequence data for 245,388 diverse participants by the All of Us Research Program and characterizes the properties of the dataset.

    • Alexander G. Bick
    • , Ginger A. Metcalf
    •  & Joshua C. Denny

  • Article
    | Open Access

    Through archaeological excavation, morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains, a study reports the presence of Homo sapiens in Germany north of the Alps more than 45,000 years ago.

    • Dorothea Mylopotamitaki
    • , Marcel Weiss
    •  & Jean-Jacques Hublin

  • Article |

    Analysis of data from the Born in Guangzhou Cohort Study comprising mainly of trios and mother–infant pairs reveals novel East Asian-specific genetic associations with maternal bile acid, gestational weight gain and infant cord blood traits.

    • Shujia Huang
    • , Siyang Liu
    •  & Xiu Qiu

  • Article
    | Open Access

    Integrated data, including 100 human genomes from the Mesolithic, Neolithic and Early Bronze Age periods show that two major population turnovers occurred over just 1,000 years in Neolithic Denmark, resulting in dramatic changes in the genes, diet and physical appearance of the local people, as well as the landscape in which they lived.

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

  • Article
    | Open Access

    An analysis involving the shotgun sequencing of more than 300 ancient genomes from Eurasia reveals a deep east–west genetic divide from the Black Sea to the Baltic, and provides insight into the distinct effects of the Neolithic transition on either side of this boundary.

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

  • 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
    | Open Access

    Analysis of the genomes of 159 individuals from four Indigenous communities in Australia shows a high level of genetic variation and demonstrates the need for greater representation of Indigenous Australians in reference panels and clinical databases.

    • Matthew Silcocks
    • , Ashley Farlow
    •  & Stephen Leslie

  • Article
    | Open Access

    Population-scale whole-genome sequencing across four remote Indigenous Australian communities reveals a large fraction of structural variants that are unique to these populations, emphasizing the genetic distinctiveness of and diversity among Indigenous Australians.

    • Andre L. M. Reis
    • , Melissa Rapadas
    •  & Ira W. Deveson

  • Article |

    A genomic constraint map for the human genome constructed using data from 76,156 human genomes from the Genome Aggregation Database shows that non-coding constrained regions are enriched for regulatory elements and variants associated with complex diseases and traits.

    • Siwei Chen
    • , Laurent C. Francioli
    •  & Konrad J. Karczewski

  • Article
    | Open Access

    We gathered genetic data for 1,763 individuals from 147 populations across 14 African countries, and 12 Late Iron Age individuals, to trace the expansion of Bantu-speaking peoples over the past 6,000 years.

    • Cesar A. Fortes-Lima
    • , Concetta Burgarella
    •  & Carina M. Schlebusch

  • Article
    | Open Access

    Whole-genome alignment of 239 primate species reveals noncoding regulatory elements that are under selective constraint in primates but not in other placental mammals, that are enriched for variants that affect human gene expression and complex traits in diseases.

    • Lukas F. K. Kuderna
    • , Jacob C. Ulirsch
    •  & Kyle Kai-How Farh

  • Article
    | Open Access

    Genotype and exome sequencing of 150,000 participants and whole-genome sequencing of 9,950 selected individuals recruited into the Mexico City Prospective Study constitute a valuable, publicly available resource of non-European sequencing data.

    • Andrey Ziyatdinov
    • , Jason Torres
    •  & Roberto Tapia-Conyer

  • Article
    | Open Access

    Comparisons of phenotypic and genetic association with protein levels from Icelandic and UK Biobank cohorts show that using multiple analysis platforms and stratifying populations by ancestry improves the detection of associations and allows the refinement of their location within the genome.

    • Grimur Hjorleifsson Eldjarn
    • , Egil Ferkingstad
    •  & Kari Stefansson

  • Article
    | Open Access

    The Pharma Proteomics Project generates the largest open-access plasma proteomics dataset to date, offering insights into trans protein quantitative trait loci across multiple biological domains, and highlighting genetic influences on ligand–receptor interactions and pathway perturbations across a diverse collection of cytokines and complement networks.

    • Benjamin B. Sun
    • , Joshua Chiou
    •  & Christopher D. Whelan

  • Review Article |

    This Review provides a perspective on the development of non-cancer therapies based on human genetics studies and suggests measures that can be taken to streamline the pipeline from initial genetic discovery to approved therapy.

    • Katerina Trajanoska
    • , Claude Bhérer
    •  & Vincent Mooser

  • Article |

    We present the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference.

    • Arang Rhie
    • , Sergey Nurk
    •  & Adam M. Phillippy

  • Article
    | Open Access

    Population differences in immune responses to SARS-CoV-2 can be explained by environmental exposures, but also by local adaptation acting through genetic variants acquired after admixture with archaic hominin forms.

    • Yann Aquino
    • , Aurélie Bisiaux
    •  & Lluis Quintana-Murci

  • Article
    | Open Access

    The burial community at Gurgy ‘les Noisats’ (France) was genetically connected by two main pedigrees, spanning seven generations, that were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups.

    • Maïté Rivollat
    • , Adam Benjamin Rohrlach
    •  & Wolfgang Haak

  • Article
    | Open Access

    A study reports data from the first phase of the Chinese Pangenome Consortium including 116 de novo assemblies from 58 core samples representing 36 minority Chinese ethnic groups.

    • Yang Gao
    • , Xiaofei Yang
    •  & Shuhua Xu

  • Article
    | Open Access

    Genome sequencing of nine individuals shows ancestry shifts in the Neolithization of northwestern Africa that probably mirrored a heterogeneous economic and cultural landscape in a more multifaceted process than observed in other regions.

    • Luciana G. Simões
    • , Torsten Günther
    •  & Mattias Jakobsson

  • Article
    | Open Access

    An analysis of 780 breast cancer genomes shows that focal amplifications are frequently preceded by dicentric chromosome formation from inter-chromosomal translocations associated with oestrogen receptor binding, which leads to chromosome bridge formation and breakage, initiating the amplification process.

    • Jake June-Koo Lee
    • , Youngsook Lucy Jung
    •  & Peter J. Park

  • Article |

    An analysis of models of human populations in Africa, using some newly sequenced genomes, finds that human origins in the continent can best be described by a weakly structured stem model.

    • Aaron P. Ragsdale
    • , Timothy D. Weaver
    •  & Simon Gravel

  • Article
    | Open Access

    A study comparing the pattern of single-nucleotide variation between unique and duplicated regions of the human genome shows that mutation rate and interlocus gene conversion are elevated in duplicated regions.

    • Mitchell R. Vollger
    • , Philip C. Dishuck
    •  & Evan E. Eichler

  • Article
    | Open Access

    Comparisons within the human pangenome establish that homologous regions on short arms of heterologous human acrocentric chromosomes actively recombine, leading to the high rate of Robertsonian translocation breakpoints in these regions.

    • Andrea Guarracino
    • , Silvia Buonaiuto
    •  & Erik Garrison

  • Article
    | Open Access

    Analysis of ancient human DNA from the Swahili coast reveals that predominantly African female ancestors and Asian male ancestors formed families after around ad 1000 and lived in elite communities in coastal stone towns.

    • Esther S. Brielle
    • , Jeffrey Fleisher
    •  & Chapurukha M. Kusimba

  • Article |

    A machine learning approach is used to analyse multi-omics (proteomics, metabolomics and transcriptomics) data, producing genetic scores for more than 17,000 biomolecular traits in human blood, and identifying possible associations with disease.

    • Yu Xu
    • , Scott C. Ritchie
    •  & Michael Inouye

  • Article
    | Open Access

    Combined analysis of new genomic data from 116 ancient hunter-gatherer individuals together with previously published data provides insights into the genetic structure and demographic shifts of west Eurasian forager populations over a period of 30,000 years.

    • Cosimo Posth
    • , He Yu
    •  & Johannes Krause

  • Article |

     An analysis of rare coding variants across 22 common traits and diseases indicates that these variants will contribute substantially to biological insights but modestly to population risk stratification.

    • Daniel J. Weiner
    • , Ajay Nadig
    •  & Luke J. O’Connor

  • Article
    | Open Access

    Genome-wide association studies of individuals from an isolated population (data from the Finnish biobank study FinnGen) and consequent meta-analyses facilitate the identification of previously unknown coding variant associations for both rare and common diseases.

    • Mitja I. Kurki
    • , Juha Karjalainen
    •  & Aarno Palotie

  • Article
    | Open Access

    Genetic data for 13 Neanderthals from 2 Middle Palaeolithic sites in the Altai Mountains of southern Siberia presented provide insights into the social organization of an isolated Neanderthal community at the easternmost extent of their known range.

    • Laurits Skov
    • , Stéphane Peyrégne
    •  & Benjamin M. Peter

  • Article
    | Open Access

    Archaeogenetic study of ancient DNA from medieval northwestern Europeans reveals substantial increase of continental northern European ancestry in Britain, suggesting mass migration across the North Sea during the Early Middle Ages.

    • Joscha Gretzinger
    • , Duncan Sayer
    •  & Stephan Schiffels

  • Article
    | Open Access

    To measure selection on variants, whole-genome sequencing of approximately 150,000 individuals from the UK Biobank is used to rank sequence variants by their level of depletion.

    • Bjarni V. Halldorsson
    • , Hannes P. Eggertsson
    •  & Kari Stefansson

  • Article
    | Open Access

    DNA analysis of 6 individuals from eastern and south-central Africa spanning the past approximately 18,000 years, and of 28 previously published ancient individuals, provides genetic evidence supporting hypotheses of increasing regionalization at the end of the Pleistocene.

    • Mark Lipson
    • , Elizabeth A. Sawchuk
    •  & Mary E. Prendergast

  • Article
    | Open Access

    A meta-analysis combining whole-exome sequencing data from UK Biobank participants and imputed genotypes from FinnGen participants enables identification of genetic associations with human disease in the rare and low-frequency allelic spectrum

    • Benjamin B. Sun
    • , Mitja I. Kurki
    •  & Heiko Runz

  • 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 |

    Genome-wide ancient DNA data from individuals from the Middle Bronze Age to Iron Age documents large-scale movement of people from the European continent between 1300 and 800 bc that was probably responsible for spreading early Celtic languages to Britain.

    • Nick Patterson
    • , Michael Isakov
    •  & David Reich

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