Population genetics articles within Nature Reviews Genetics

Featured

  • Comment |

    A recent patent granted for methods for diagnosing autism spectrum disorder (ASD) raises several ethical concerns beyond the fundamental question of whether genomic sequences are patentable, as it suggests that genetic testing can provide a diagnosis of ASD even before behavioural symptoms present.

    • Kristien Hens
    • , Ilse Noens
    •  & Jean Steyaert

  • Review Article |

    Runs of homozygosity (ROH) are genomic regions of homozygosity where the identical maternal and paternal haplotypes are descended from a shared common ancestor, and they are well known to occur as a result of inbreeding. This article discusses strategies for detecting ROH, their underappreciated prevalence across diverse outbred populations and implications for complex traits and human disease.

    • Francisco C. Ceballos
    • , Peter K. Joshi
    •  & James F. Wilson

  • Editorial |

    Two articles in this issue of Nature Reviews Genetics discuss our maturing understanding of gene essentiality in cells and humans

  • Review Article |

    Genetic architecture describes the characteristics of genetic variation that are responsible for phenotypic variability. This Review discusses the types of genetic architecture that have been observed, how they can be measured and how genetic architecture informs the scientific and clinical goals of human genetics.

    • Nicholas J. Timpson
    • , Celia M. T. Greenwood
    •  & J. Brent Richards

  • Science and Society |

    Including diverse populations in genomic studies has the potential to improve the use of genomic data in the clinic. Here, members of the National Human Genome Research Institute review the benefits of increasing diversity, the challenges to overcome and key recommendations for how to achieve this goal.

    • Lucia A. Hindorff
    • , Vence L. Bonham
    •  & Eric D. Green

  • Analysis |

    Characterizing the essentiality of human genes provides insights into gene function and genome evolution and facilitates the clinical interpretation of genetic variants. This article analyses essentiality metrics based on the statistical intolerance to loss-of-function mutations in human population sequencing studies and discusses commonalities and distinctions relative to data sets from knockout mice and functional genomics screens in human cell culture. Implications for disease genetics and extrapolation to non-coding regions are also discussed.

    • István Bartha
    • , Julia di Iulio
    •  & Amalio Telenti

  • Review Article |

    Sexual conflict is thought to increase population genetic diversity though balancing selection, which has important evolutionary implications. This Review discusses how population genomic approaches are contributing to a deeper understanding of sexual conflict and how it is resolved.

    • Judith E. Mank

  • Analysis |

    Recent large-scale genome-wide association studies have identified numerous variants that are associated with obesity-relevant traits such as body mass index or body fat percentage. Here, the authors explore to what extent this genomic evidence matches the evidence from functional and mechanistic studies.

    • Sujoy Ghosh
    •  & Claude Bouchard

  • Review Article |

    Despite being a single species, dogs represent nearly 400 breeds with substantial genetic, morphological and behavioural diversity. In this Review, Ostranderet al. discuss how genomics studies of dogs have enhanced our understanding of dog and human population history, the desired and unintended consequences of trait-based selective breeding, and potentially human-applicable insights into cancer, ageing, behaviour and neurological diseases.

    • Elaine A. Ostrander
    • , Robert K. Wayne
    •  & Brian W. Davis

  • Review Article |

    Ancient genomes can inform our understanding of the history of human adaptation through the direct tracking of changes in genetic variant frequency across different geographical locations and time periods. The authors review recent ancient DNA analyses of human, archaic hominin, pathogen, and domesticated animal and plant genomes, as well as the insights gained regarding past human evolution and behaviour.

    • Stephanie Marciniak
    •  & George H. Perry

  • Review Article |

    For clinical cases of Mendelian disease that lack a genetic diagnosis, genome and exome sequencing are increasingly used for seeking the genetic cause. This Review discusses the strategies and computational tools for prioritizing the many genetic variants identified in each genome into those that are most likely to be causal for disease. The authors discuss how diverse types of biochemical, evolutionary, pedigree and clinical-phenotype information are used, and they highlight common pitfalls to be aware of for responsible variant prioritization.

    • Karen Eilbeck
    • , Aaron Quinlan
    •  & Mark Yandell

  • Review Article |

    The last 25 years has seen a revolution in sequencing, with more than 100 vertebrate genome sequences now available. In this Review, Meadows and Lindblad-Toh discuss how the genomics of non-human organisms can provide insights into vertebrate biology and conservation, and how they can contribute to the understanding of human health and disease.

    • Jennifer R. S. Meadows
    •  & Kerstin Lindblad-Toh

  • Review Article |

    Genetic variation of the human Y chromosome plays a key part in studies of human evolution, population history, genealogy, forensics and male medical genetics. This Review outlines how next-generation sequencing has contributed to recent progress in these fields.

    • Mark A. Jobling
    •  & Chris Tyler-Smith

  • Review Article |

    To characterize the genetic underpinnings of speciation, genome scans can identify genomic regions that differ between divergent populations of wild organisms. In this Review, Wolf and Ellegren describe the methodological details of these approaches and how genomic islands of differentiation should be interpreted cautiously in the search for 'speciation genes'. They also discuss methodological best practice that takes into consideration genomic differentiation occurring through speciation-independent evolutionary processes.

    • Jochen B. W. Wolf
    •  & Hans Ellegren

  • Opinion |

    Mutation is the source of genetic diversity on which natural selection acts, therefore understanding the rates of mutations is crucial for understanding evolutionary trajectories. In this Opinion article, the authors discuss how emerging experimental mutation-rate data from genome-wide sequencing studies, combined with population-genetic theory, can provide unifying explanations for the diversity in mutation rates between species and across genomic locations.

    • Michael Lynch
    • , Matthew S. Ackerman
    •  & Patricia L. Foster

  • Review Article |

    Marine vertebrates are key contributors to global biodiversity and human food supply. In this Review, the authors discuss how comparative genomics studies in marine vertebrates have provided insight into major evolutionary transitions between the land and sea, as well as intra-species adaptation to diverse types of aquatic environments. They also highlight applications in species management and conservation.

    • Joanna L. Kelley
    • , Anthony P. Brown
    •  & Andrew D. Foote

  • Review Article |

    The degree of genetic diversity differs greatly among species and across genomic loci within genomes. The wide ranges in genetic diversity have important implications, including for evolution, conservation and management of wild and domesticated species. In this Review, the authors discuss how genome-scale sequencing strategies are providing insight into the varied determinants of genetic variation both among species and across genomic regions.

    • Hans Ellegren
    •  & Nicolas Galtier

  • Review Article |

    The authors review recent studies into the heritable basis of population epigenomic variation and discuss important challenges when interpreting results from these genetic studies in different species to highlight the state of knowledge regarding how genetic variation can influence differences in chromatin states between individuals.

    • Aaron Taudt
    • , Maria Colomé-Tatché
    •  & Frank Johannes

  • Review Article |

    Gene loss is emerging as a pervasive source of genetic variation. The authors review the mechanisms by which gene loss has influenced evolution of different species and discuss insights from comparative population genomics studies of gene loss. Further, they highlight future directions for the study of gene losses and their relevance in evolutionary biology and biomedicine.

    • Ricard Albalat
    •  & Cristian Cañestro

  • Review Article |

    RNA-guided endonucleases have the potential to revolutionize the engineering of synthetic gene drives, which may be particularly useful for the control of vector-borne diseases. Here, the authors review different types of engineered gene drives and their potential applications, as well as considerations regarding the safety and regulation of gene drives for the manipulation of wild populations.

    • Jackson Champer
    • , Anna Buchman
    •  & Omar S. Akbari

  • Review Article |

    The rapid accumulation and increasing quality of human DNA sequence-variation data brought about by advances in genome-scale sequencing present opportunities to investigate human evolution. The authors discuss the statistical methods and models that can be used to gain insight into the evolution of human populations from analyses of large-scale genomic data sets, as well as the challenges associated with these approaches.

    • Joshua G. Schraiber
    •  & Joshua M. Akey

  • Review Article |

    Combining experimental evolution with next-generation sequencing, the evolve and resequence (E&R) approach is a powerful method for dissecting the genomic changes underlying the adaptation of populations of laboratory organisms or molecules. This Review describes the E&R results from diverse systems and discusses the extent to which various features, including population genetics, experimental setups and reproduction modes, account for the distinct observed outcomes.

    • Anthony Long
    • , Gianni Liti
    •  & Olivier Tenaillon

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