Population genetics articles within Nature Communications

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  • Article
    | Open Access

    There are challenges with transferring genetic risk scores from ancestry in which they were generated to another. Here, the authors investigate the use of multi-ancestry versus single-ancestry training sets to construct polygenic scores and find that the optimal strategy varies across traits.

    • Brieuc Lehmann
    • , Maxine Mackintosh
    •  & Chris Holmes

  • Article
    | Open Access

    A major part of the human Y chromosome consists of palindromes with multiple copies of genes primarily expressed in testis. Here, the authors investigate copy number variation in these palindromes based on whole genome sequence data from 11,527 Icelandic men.

    • Elise A. Lucotte
    • , Valdís Björt Guðmundsdóttir
    •  & Kari Stefansson

  • Article
    | Open Access

    Sequencing malaria parasites from low density infections in small amounts of dried blood is important for large-scale genomic surveillance. Here, the authors develop and validate a highly multiplexed droplet digital PCR-based amplicon deep sequencing assay and apply it to data from Zanzibar, Tanzania.

    • Aurel Holzschuh
    • , Anita Lerch
    •  & Cristian Koepfli

  • Article
    | Open Access

    For most ancient genomes, low sequencing depth restricts genotyping, limiting their study. Here, the authors test imputation performance of ancient human genomes by estimating error rates and potential bias introduced in downstream analyses.

    • Bárbara Sousa da Mota
    • , Simone Rubinacci
    •  & Olivier Delaneau

  • Comment
    | Open Access

    Whole genome sequencing has enabled new insights into the genetic architecture of complex traits, especially through access to low-frequency and rare variation. This Comment highlights the key contributions from this technology and discusses considerations for its use and future perspectives.

    • Ozvan Bocher
    • , Cristen J. Willer
    •  & Eleftheria Zeggini

  • Article
    | Open Access

    Current methods for detecting insertions from short read sequencing data generally have low sensitivity. Here, the authors develop a new tool that runs quickly and detects significantly more true positive insertions compared to any combination of existing methods.

    • Ramesh Rajaby
    • , Dong-Xu Liu
    •  & Wing-Kin Sung

  • Article
    | Open Access

    Epidemiological models are commonly fit to case and pathogen sequence data to estimate parameters and to reconstruct disease dynamics. Here, the authors present an inference approach based on sequence data that is well suited for model fitting early on during the expansion of a viral lineage.

    • Yeongseon Park
    • , Michael A. Martin
    •  & Katia Koelle

  • Article
    | Open Access

    Repeated evolution provides valuable insight into adaptation. In this study, the authors found that repeated evolution of cave-adapted phenotypes of a fish (Astyanax mexicanus) was driven by selection on standing genetic variation and novel mutations and genes repeatedly under selection are longer compared to the rest of the genome.

    • Rachel L. Moran
    • , Emilie J. Richards
    •  & Suzanne E. McGaugh

  • Article
    | Open Access

    Short tandem repeat studies in humans have often focused on European populations. Here, the authors report a comprehensive map of 366,013 polymorphic short tandem repeats in Chinese individuals and their mutational patterns, functional properties, gene regulatory effects and population characteristics.

    • Yirong Shi
    • , Yiwei Niu
    •  & Shunmin He

  • Article
    | Open Access

    Ambrosia artemisiifolia is an invasive weed and primary cause of pollen-induced hayfever. Here, the authors report its chromosome-level phased genome assembly, examine genome-wide variation among modern and historic accessions, and identify large haploblocks underling rapid adaptation.

    • Paul Battlay
    • , Jonathan Wilson
    •  & Kathryn A. Hodgins

  • Article
    | Open Access

    A variant of MHC class I is protective against severe malaria disease and enriched in affected African populations. Here, Wroblewski et al., characterise the consequences of malaria infection in wild bonobo populations showing that the presence of malaria drives a similar evolution in immune genes.

    • Emily E. Wroblewski
    • , Lisbeth A. Guethlein
    •  & Peter Parham

  • Article
    | Open Access

    Here, the authors describe the geographies, hosts, substrates, and phylogenetic relationships for 1,794 Saccharomyces strains. They provide insight into the genetic and phenotypic diversity in the genus, not seen through prior work focused on the model species Saccharomyces cerevisiae.

    • David Peris
    • , Emily J. Ubbelohde
    •  & Chris Todd Hittinger

  • Article
    | Open Access

    Here, using Citrobacter rodentium colonization of mice as a model, the authors characterize the impact of pathogen dose on the number of bacteria that initiate infection in the mouse gut, providing a framework for quantifying the host bottlenecks that eliminate pathogens to protect from infection.

    • Ian W. Campbell
    • , Karthik Hullahalli
    •  & Matthew K. Waldor

  • Article
    | Open Access

    Rearrangements in the genome are important for local adaptation and speciation but are often difficult to identify reliably. Here the authors show that rearrangements underlie large chromosome regions that separate differentially migratory willow warblers.

    • Max Lundberg
    • , Alexander Mackintosh
    •  & Staffan Bensch

  • Article
    | Open Access

    Our understanding of the genetic contribution to human adiposity is incomplete, as few studies measure adiposity directly. Here, the authors impute whole-body imaging adiposity phenotypes in large biobanks, enhancing their power to discover genes driving human adiposity, and further investigate one such gene using a mouse model.

    • Katherine A. Kentistou
    • , Jian’an Luan
    •  & Nicholas M. Morton

  • Article
    | Open Access

    Little is known about the causes of sex differences in disease prevalence and treatment outcomes. Here, the authors study the interaction between drug metabolism enzymes and transporters genes and sex in complex human traits to uncover sex differences in the genetic regulation of gene expression, serum biomarkers, and metabolism of drugs.

    • Yingbo Huang
    • , Yuting Shan
    •  & R. Stephanie Huang

  • Article
    | Open Access

    Elevated body mass index is heritable and associated with many health conditions that impact morbidity and mortality. Here, the authors identify greater than 900 genetic loci for body mass index (BMI) and find over 300 diagnoses associated with increasing BMI.

    • Jie Huang
    • , Jennifer E. Huffman
    •  & Christopher J. O’Donnell

  • Article
    | Open Access

    How highly inbred populations generate novel genetic variations upon which natural selection can act is unclear. Here, the authors reveal the effect of transposable elements on the genome-wide heterozygosity landscape across a natural inbreeding gradient of Arabidopsis lyrata and reducing the probability of inbreeding depression.

    • Hanne De Kort
    • , Sylvain Legrand
    •  & James Buckley

  • Article
    | Open Access

    Helicobacter pylori is a major human pathogen whose population structure is similar to that of its host. Here, the authors show that H. pylori has repeatedly spread out of Africa recently, replacing deleterious variants that accumulated during the original out of Africa migrations more than 50,000 years ago.

    • Harry A. Thorpe
    • , Elise Tourrette
    •  & Daniel Falush

  • Article
    | Open Access

    Factors defining wheat stem rust pathogen (Pgt) virulence remain poorly characterized. Comparative population genomics based on Pgt haplotypes suggest that structural variation and admixture through somatic hybridization and sexual recombination play an important role in broadening Pgt virulence.

    • Yuanwen Guo
    • , Bliss Betzen
    •  & Eduard Akhunov

  • Article
    | Open Access

    Endogenous retroviruses (ERV) are inherited remains of retroviruses that have colonized host genomes during evolution. Here the authors observe considerable species-specific ERV variation among Darwin’s finches, reflecting historic retrovirus-host interactions.

    • Jason Hill
    • , Mette Lillie
    •  & Patric Jern

  • Article
    | Open Access

    This study uses a compilation of 58 population genetic studies of 47 phylogenetically divergent marine sedentary species over the Mediterranean basin to assess how genetic differentiation is predicted by different dispersal models. Multi-generation dispersal models reveal implicit links among siblings from a common ancestor (coalescent connectivity) that could improve spatial conservation planning.

    • Térence Legrand
    • , Anne Chenuil
    •  & Vincent Rossi

  • Article
    | Open Access

    This study found that millennial periods of higher rainfall combined with rising sea level enhanced sediment accumulation in Amazonian rivers valleys. This fuelled synchronous expansion of vegetation adapted to seasonally flooded substrates and its specialized bird populations, showing how global climate changes can affect specific Amazonian species.

    • A. O. Sawakuchi
    • , E. D. Schultz
    •  & C. C. Ribas

  • Article
    | Open Access

    Observational studies have found overlap between Alzheimer’s disease and other diseases and phenotypes, although the causal relationships are unclear. Here, the authors perform an age-stratified phenome-wide association study of Alzheimer’s disease (AD) genetic liability and follow-up Mendelian randomization analyses to examine whether these phenotypes have a causal effect on AD.

    • Roxanna Korologou-Linden
    • , Laxmi Bhatta
    •  & Neil M. Davies

  • Article
    | Open Access

    Here, the authors study adaptation to altitude in 518 whole genomes from two species of tropical butterflies. They find repeated genetic differentiation within species, little molecular parallelism between these species, and introgression from closely related species, concluding that standing genetic variation promotes parallel local adaptation.

    • Gabriela Montejo-Kovacevich
    • , Joana I. Meier
    •  & Chris D. Jiggins

  • Article
    | Open Access

    The fungus Blumeria graminis f. sp. tritici causes wheat powdery mildew disease. Here, Sotiropoulos et al. analyze a global sample of 172 mildew genomes, providing evidence that humans drove global spread of the pathogen throughout history and that mildew rapidly evolved through hybridization with local fungal strains.

    • Alexandros G. Sotiropoulos
    • , Epifanía Arango-Isaza
    •  & Thomas Wicker

  • Article
    | Open Access

    Previous work has investigated selection in the coding genome, but it is not as well characterized in the non-coding genome. By analyzing rare variants in 70k genome sequences from gnomAD, the authors detect very strong purifying selection ("ultraselection”) across the human genome, finding it in some microRNAs and coding sequences but generally rare in regulatory sequences.

    • Noah Dukler
    • , Mehreen R. Mughal
    •  & Adam Siepel

  • Article
    | Open Access

    The inherited basis of body fat distribution is not fully understood. Here, the authors use genetic data and MRI-derived measures of local adiposity to highlight fat depot-specific genetic architecture with implications for cardiometabolic health.

    • Saaket Agrawal
    • , Minxian Wang
    •  & Amit V. Khera

  • Article
    | Open Access

    The impact of germline variants on somatic alterations in cancer remains to be explored in large-scale datasets. Here, the authors study the association of rare germline variants with somatic mutational processes in more than 15,000 tumors, and reveal that damaging variants in newly-identifed genes are prevalent in the population.

    • Mischan Vali-Pour
    • , Solip Park
    •  & Fran Supek

  • Article
    | Open Access

    Not just differential gene expression but also differential gene regulation in immune cells account for individual differences in the immune response. Authors show here by single-cell RNA-sequencing of peripheral blood mononuclear cells from a large cohort of genetically diverse individuals that gene expression and regulatory changes in these cells depend on the context of and interactions between cell types, genetics, type of pathogen and time after exposure.

    • Roy Oelen
    • , Dylan H. de Vries
    •  & Monique G. P. van der Wijst

  • Article
    | Open Access

    Biobanks of genetic data have been primarily in European populations, which gives us an incomplete understanding of complex traits across populations. Here, the authors initiate the Westlake BioBank for Chinese (WBBC) pilot project with 4,535 whole genome sequences and 5,841 high-density genotypes from China, characterizing large-scale genomic variation in Chinese populations.

    • Pei-Kuan Cong
    • , Wei-Yang Bai
    •  & Hou-Feng Zheng

  • Comment
    | Open Access

    Tissue-based functional genomics resources including molecular quantitative trait loci datasets lack diversity in ancestry and tissue types and thus are inadequate for comprehensively investigating gene regulation. Global efforts to increase the tissue diversity will help achieve more equitable medical care.

    • Erping Long
    • , Montserrat García-Closas
    •  & Jiyeon Choi

  • Article
    | Open Access

    Empirical evidence on the process of founding new populations for assisted colonisations is limited. This work examined two wild populations of green turtles in the Cayman Islands following a reintroduction program started 50 years ago. They show both populations are highly related to the captive population and that philopatry may reinforce the success of new populations.

    • Anna Barbanti
    • , Janice M. Blumenthal
    •  & Carlos Carreras

  • Article
    | Open Access

    The genetic prehistory of central America has not been well explored. Here, the authors find evidence from ancient DNA from twenty individuals who lived in Belize 9,600 to 3,700 years ago of a migration from the south that coincided with the first evidence for forest clearing and the spread of maize horticulture.

    • Douglas J. Kennett
    • , Mark Lipson
    •  & David Reich

  • Article
    | Open Access

    Tracking low frequency intra-host variants has helped understanding within-host viral population dynamics and transmission. Precise tracking, however, depends partially on the error rate of the sequencing platforms used. Here, Liu et al. present Variabel, a method to rescue low frequency intra-host variants from Oxford Nanopore Technologies (ONT) platforms and validate their approach on Ebola virus, norovirus, and SARS-CoV-2 datasets.

    • Yunxi Liu
    • , Joshua Kearney
    •  & Todd J. Treangen

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