Evolutionary genetics articles within Nature

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  • Article |

    The adrenal gland of the oldfield mouse (Peromyscus polionotus) has a recently evolved cell type that promotes monogamous-typical parenting behaviour and is not present in closely related species.

    • Natalie Niepoth
    • , Jennifer R. Merritt
    •  & Andres Bendesky

  • Article
    | Open Access

    Genomic studies of Heliconius butterflies provide evidence that Heliconius elevatus is a hybrid species, and that its speciation was driven by introgression of traits from Heliconius melpomene into the other parent, an ancestor of Heliconius pardalinus.

    • Neil Rosser
    • , Fernando Seixas
    •  & Kanchon K. Dasmahapatra

  • Article
    | Open Access

    A comparison of two complete sets of human centromeres reveals that the centromeres show at least a 4.1-fold increase in single-nucleotide variation compared with their unique flanks, and up to 3-fold variation in size, resulting from an accelerated mutation rate.

    • Glennis A. Logsdon
    • , Allison N. Rozanski
    •  & Evan E. Eichler

  • Article
    | Open Access

    An insertion of an Alu element into an intron of the TBXT gene is identified as a genetic mechanism of tail-loss evolution in humans and apes, with implications for human health today.

    • Bo Xia
    • , Weimin Zhang
    •  & Itai Yanai

  • Article |

    The Chinese Liver Cancer Atlas project depicts a panoramic genomic landscape of hepatocellular carcinoma, covering candidate coding and non-coding drivers, mutational signatures, extrachromosomal circular DNA, subclonal catastrophic events and detailed evolutionary history.

    • Lei Chen
    • , Chong Zhang
    •  & Hongyang Wang

  • Article
    | Open Access

    Reconstruction of four Treponema pallidum genomes associated with human remains from around 2,000 years ago suggests that T. pallidum existed in the Americas and diverged to its modern subspecies before the fifteenth century European contact with the Americas.

    • Kerttu Majander
    • , Marta Pla-Díaz
    •  & Verena J. Schuenemann

  • Article
    | Open Access

    A chromosome-scale genome assembly for the hagfish Eptatretus atami, combined with a series of phylogenetic analyses, sheds light on ancient polyploidization events that had a key role in the early evolution of vertebrates.

    • Ferdinand Marlétaz
    • , Nataliya Timoshevskaya
    •  & Daniel S. Rokhsar

  • Article
    | Open Access

    Analysis of naturally hybridizing swordtail fish species reveals a mitonuclear genetic incompatibility among three genes that encode components of mitochondrial respiratory complex I, providing insights into the emergence of hybrid incompatibilities and reproductive barriers.

    • Benjamin M. Moran
    • , Cheyenne Y. Payne
    •  & Molly Schumer

  • 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

    A single-cell multiomics analysis of over 200,000 cells of the primary motor cortex of human, macaque, marmoset and mouse shows that divergence of transcription factor expression corresponds to species-specific epigenome landscapes, and conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome.

    • Nathan R. Zemke
    • , Ethan J. Armand
    •  & Bing Ren

  • 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 |

    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

    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

    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

    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

    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

    By using phylogenetic analyses of multiple microdissected samples from both cancer and non-cancer lesions, unique evolutionary histories of breast cancers harbouring a common driver alteration are shown, providing new insight into how breast cancer evolves.

    • Tomomi Nishimura
    • , Nobuyuki Kakiuchi
    •  & Seishi Ogawa

  • 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 |

    A study reports the development of an algorithm, BISCUT, that detects genomic loci under selective pressure by relying on the distribution of breakpoints across chromosome arms, and uses it to explore how aneuploidies affect tumorigenesis.

    • Juliann Shih
    • , Shahab Sarmashghi
    •  & Rameen Beroukhim

  • 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

    Deeply conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of the comb jellies (ctenophores)—placing ctenophores as the sister group to all other animals.

    • Darrin T. Schultz
    • , Steven H. D. Haddock
    •  & Daniel S. Rokhsar

  • 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

    A phylogeny-guided genome-resolved metagenomic analysis of DNA viruses in the ocean reveals atypical plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota.

    • Morgan Gaïa
    • , Lingjie Meng
    •  & Tom O. Delmont

  • Article
    | Open Access

    A longitudinal evolutionary analysis of 126 lung cancer patients with metastatic disease reveals the timing of metastatic divergence, modes of dissemination and the genomic events subject to selection during the metastatic transition.

    • Maise Al Bakir
    • , Ariana Huebner
    •  & Charles Swanton

  • 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
    | 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
    | Open Access

    Evolutionary analyses of single-nucleus transcriptome data for testes from 11 species are reported, illuminating the molecular evolution of spermatogenesis and associated forces, and providing a resource for investigating the testis across mammals.

    • Florent Murat
    • , Noe Mbengue
    •  & Henrik Kaessmann

  • Article
    | Open Access

    Intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer, with most genetic intratumour variation having no detected phenotypic consequence and transcriptional plasticity being widespread within a tumour.

    • Jacob Househam
    • , Timon Heide
    •  & Trevor A. Graham

  • Article |

    Klunk and colleagues identify signatures of natural selection imposed by Yersinia pestis and demonstrate their effect on genetic diversity and susceptibility to certain diseases in the present day.

    • Jennifer Klunk
    • , Tauras P. Vilgalys
    •  & Luis B. Barreiro

  • 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

    High-quality diploid assemblies of potato genomes from 24 wild and 20 cultivated potatoes provide insights into the complex evolution and diversity of potatoes, and could have applications in the breeding of hybrid potatoes.

    • Dié Tang
    • , Yuxin Jia
    •  & Sanwen Huang

  • Article
    | Open Access

    A strong association has been found between three regions of the Plasmodium falciparum genome and sickle haemoglobin in children with severe malaria, suggesting parasites have adapted to overcome natural host immunity.

    • Gavin Band
    • , Ellen M. Leffler
    •  & Dominic P. Kwiatkowski

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