Population genetics articles within Nature Reviews Genetics

Featured

  • Comment |

    In this Comment, Lamkin and Gymrek discuss recent results that suggest that the systematic incorporation of tandem repeats into complex trait analyses will yield a rich source of causal variants and new biological insights.

    • Michael Lamkin
    •  & Melissa Gymrek

  • Review Article |

    In this Review, Mackay and Anholt discuss how epistasis and pleiotropy contribute to the genetic architecture of quantitative traits and outline factors that might explain observed differences in their prevalence between model organisms and humans.

    • Trudy F. C. Mackay
    •  & Robert R. H. Anholt

  • Review Article |

    In this Review, the authors compare the characteristics and detection methods of germline and somatic variants. Furthermore, they outline how the interplay between the two types of genetic variation can affect human health.

    • Zhi Yu
    • , Tim H. H. Coorens
    •  & Pradeep Natarajan

  • Journal Club |

    Reflecting on the importance of short tandem repeats (STRs) in population genetics, Ning Xie highlights a 2023 publication that characterized genome-wide STR variation in global human genomes to expand our understanding of STR genetic diversity within and across populations.

    • Ning Xie

  • Research Highlight |

    A publication in Nature reports the data release of around 245,000 clinical-grade whole-genome sequences as part of the NIH’s All of Us Research Programme. Several companion papers highlight the value of better capturing global genomic diversity.

    • Linda Koch

  • Journal Club |

    In this Journal Club, Yoav Ram recalls how he reconciled results from his own research with the reduction principle through the help of a paper published in PNAS by Altenberg et al.

    • Yoav Ram

  • Review Article |

    In this Review, Sayers et al. summarize findings from recent large-scale genetic epidemiology studies on the genetic underpinnings of chronic respiratory diseases. Furthermore, they outline how insights gained from such studies can improve treatment approaches.

    • Ian Sayers
    • , Catherine John
    •  & Ian P. Hall

  • Review Article |

    This Review describes tools and approaches for characterizing short tandem repeats in the human genome from whole-genome sequencing data. Furthermore, the authors discuss how these recent developments have helped to better understand the effect of short tandem repeats on human health and disease.

    • Hope A. Tanudisastro
    • , Ira W. Deveson
    •  & Daniel G. MacArthur

  • Research Highlight |

    Four papers in Nature describe how ancient European migration patterns have shaped the modern human genome.

    • Michael Attwaters

  • Perspective |

    In this Perspective, Carolyn Hogg discusses the utility of genomic data to conservation and the importance of adopting a translational mindset to ensure that genomics is used to its full potential to protect Earths’ declining biodiversity.

    • Carolyn J. Hogg

  • Review Article |

    Species and communities can respond to global climate change by genetically adapting to new environmental conditions, by shifting their range or through phenotypic plasticity. This Review summarizes approaches that apply and integrate omics tools to experimentally investigate, monitor and predict these species responses.

    • Louis Bernatchez
    • , Anne-Laure Ferchaud
    •  & Amanda Xuereb

  • Journal Club |

    Luis Barreiro highlights a 2007 paper by Tishkoff et al. that identified genetic variants associated with lactose persistence in East African populations, representing one of the first examples of convergent evolution in humans.

    • Luis B. Barreiro

  • Review Article |

    Ancient DNA studies over the past decade have yielded a plethora of insights into the Denisovan archaic hominin group. The authors review our understanding of Denisovan population history and their interactions with other human groups, insights from studies of Denisovan ancestry in modern humans, what we know about the Denisovan phenotype and their impact on our own evolutionary history.

    • Stéphane Peyrégne
    • , Viviane Slon
    •  & Janet Kelso

  • Review Article |

    Applying deep learning to large-scale genomic data of species or populations is providing new opportunities to understand the evolutionary forces that drive genetic diversity. This Review introduces common deep learning architectures and provides comprehensive guidelines to implement deep learning models for population genetic inference. The authors also discuss current opportunities and challenges for deep learning in population genetics.

    • Xin Huang
    • , Aigerim Rymbekova
    •  & Martin Kuhlwilm

  • Review Article |

    This Review summarizes the genetic and non-genetic factors that impact the transferability of polygenic risk scores (PRSs) across populations, highlighting the technical challenges of existing PRS construction methods for diverse ancestries and the emerging resources for more widespread use of PRSs.

    • Linda Kachuri
    • , Nilanjan Chatterjee
    •  & Tian Ge

  • Research Highlight |

    In five new studies, the Human Pangenome Reference Consortium reports the generation and initial characterization of a draft human pangenome.

    • Michael Attwaters

  • Review Article |

    This Review discusses the range of methods used for assessing the growth and fitness of SARS-CoV-2 variants, from classic population genetics to phylogenetics and epidemiological data, and describes future perspectives for surveillance of SARS-CoV-2.

    • Erik Volz

  • Journal Club |

    Tanja Woyke highlights a 2014 study by Kashtan et al., who applied single-cell genomics to populations of the marine cyanobacterium Prochlorococcus, revealing hundreds of subpopulations with distinct genomic backbones of this wild uncultured microorganism.

    • Tanja Woyke

  • Review Article |

    In this Review, the authors describe the emerging field of single-cell genetics, which lies at the intersection of single-cell genomics and human genetics. They review the first single-cell expression quantitative trait loci studies, which combine single-cell information with genotype data at the population scale and thereby link genetic variation to the cellular processes underpinning key aspects of human biology and disease.

    • Anna S. E. Cuomo
    • , Aparna Nathan
    •  & Joseph E. Powell

  • Journal Club |

    Sophie von der Heyden highlights a paper by Barber et al. that examined variations in the genetic structuring of populations of the mantis shrimp Haptosquilla pulchella, furthering our understanding of the evolutionary dynamics of marine species.

    • Sophie von der Heyden

  • Review Article |

    Variant calling is the process of identifying genetic variants, which is important for characterizing population genetic diversity and for identifying disease-associated variants in clinical sequencing projects. In this Review, the authors discuss the state-of-the-art in variant calling, focusing on challenging types of genetic variants, advances in both sequencing technologies and computational pipelines, and benchmarking strategies to assess the robustness of variant-calling strategies.

    • Nathan D. Olson
    • , Justin Wagner
    •  & Justin M. Zook

  • Journal Club |

    In this Journal Club article, María Ávila-Arcos discusses a paper on a medically relevant genetic variant that was found exclusively in Indigenous populations from the Americas. She describes how this work served as inspiration for the inclusion of more diverse populations in the 1000 Genomes Project.

    • María C. Ávila-Arcos

  • Research Highlight |

    A new study in Cell has characterized genome-wide dosage sensitivity for 54 human disorders, providing insight into the causal genes and disease mechanisms associated with rare copy-number variants.

    • Dorothy Clyde

  • Research Highlight |

    Two new papers in Nature report copy-number-based classification systems across cancer types that provide routes for personalized therapy.

    • Darren J. Burgess

  • Review Article |

    In this article, Niemi, Daly and Ganna discuss how large-scale genomics studies are providing a rapidly maturing understanding of the influence of host genetics on coronavirus disease 2019 (COVID-19) susceptibility and severity. They also describe the implications for identifying causal mechanisms of pathology and potential therapeutic opportunities.

    • Mari E. K. Niemi
    • , Mark J. Daly
    •  & Andrea Ganna

  • Viewpoint |

    In this Viewpoint, we asked six experts to give their opinions on the utility of polygenic scores, their strengths and limitations, and the remaining barriers that need to be overcome for their equitable use.

    • Iftikhar J. Kullo
    • , Cathryn M. Lewis
    •  & Nilanjan Chatterjee

  • In Brief |

    Using whole-genome sequencing and haplotype tracking, Viluma et al. show that the small, highly inbred Scandinavian wolf population has lost substantial genetic diversity over a 30-year period. Their findings have important implications for the management and conservation of endangered species.

    • Dorothy Clyde

  • Review Article |

    The reduction in individual and mean population fitness induced by novel deleterious genetic variation is known as the genetic load. Bertorelle et al. review the definition of the genetic load and its components as well as the impact of whole-genome sequencing on the theoretical and applied study of the genetic load.

    • Giorgio Bertorelle
    • , Francesca Raffini
    •  & Cock van Oosterhout

  • In Brief |

    A study in eLife identifies 71 nuclear loci associated with mitochondrial DNA copy number (mtDNA-CN) and reveals a putative causal role for mtDNA-CN in dementia.

    • Dorothy Clyde

  • Journal Club |

    In this Journal Club article, Fowzan Alkuraya describes how a paper outlining the mathematical foundations of homozygosity mapping provided a route to disease gene identification that still benefits his patients in clinical practice today.

    • Fowzan S. Alkuraya

  • Review Article |

    In this Review, Loos and Yeo summarize our current understanding of the genetic underpinnings of monogenic and polygenic obesity. They highlight the commonalities revealed by recent studies and discuss the implications for treatment and prediction of obesity risk.

    • Ruth J. F. Loos
    •  & Giles S. H. Yeo

  • Review Article |

    Regular physical activity reduces the risk of chronic disease and mortality, but the mechanisms underpinning this protective effect are poorly understood. Here, Kim et al. review candidate genes and pathways implicated in human performance by genetic, genomic and multi-omic studies.

    • Daniel Seung Kim
    • , Matthew T. Wheeler
    •  & Euan A. Ashley

  • Review Article |

    Leigh and colleagues describe the potential of the emerging field of macrogenetics to improve conservation and biodiversity management. Challenges preventing the field from reaching its full promise are highlighted and possible solutions and a framework for future macrogenetic studies are proposed.

    • Deborah M. Leigh
    • , Charles B. van Rees
    •  & Ivan Paz-Vinas

  • Review Article |

    In this Review, Ethan Bier discusses how several impactful technical advancements, particularly involving CRISPR-based methods, are providing a diverse toolkit of gene-drive systems for the control of populations such as insect vectors of disease.

    • Ethan Bier

  • In Brief |

    A recent study has analysed publicly available long-read sequencing data to characterize human-specific variable number tandem repeats at high resolution.

    • Linda Koch

  • Research Highlight |

    Capturing rare protein-coding variation by whole-exome sequencing in large and diverse population samples can help identify large-effect associations and drug targets, suggest two recent publications.

    • Linda Koch

  • In Brief |

    A study in the American Journal of Human Genetics shows that using the GRCh37 versus GRCh38 version of the human reference genome makes a meaningful difference to the calling of human genetic variants, with implications for research-based and clinical-based human sequencing studies.

    • Darren Burgess

  • Review Article |

    McLaren and Fellay review our current understanding of the effects of human genetic variation on HIV infection and disease progression and how this knowledge is contributing to preventative and therapeutic approaches.

    • Paul J. McLaren
    •  & Jacques Fellay

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