Population genetics articles within Nature Communications

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  • Article
    | Open Access

    Upstream open reading frames (uORFs) have widespread regulatory functions in eukaryotes, their genomic distribution and evolution is understudied. Here, the authors characterise ~17 million putative uORFs across 478 eukaryotic species, showing how evolution has shaped uORF contents and distribution.

    • Hong Zhang
    • , Yirong Wang
    •  & Jian Lu

  • Article
    | Open Access

    Identifying structural variants (SVs) from whole genome sequence data has been a significant bioinformatic challenge. Here, the authors describe PopDel, which uses a joint SV detection approach to reliably and efficiently identify 500-10,000 bp deletions across large population cohorts.

    • Sebastian Niehus
    • , Hákon Jónsson
    •  & Birte Kehr

  • Article
    | Open Access

    Mendelian randomization is a popular method to detect causal relationships between traits, but can be confounded by instances of horizontal pleiotropy. Here, the authors present a Mendelian randomization workflow which includes causal discovery analysis and filtering of genetic instruments based on their conditional independencies.

    • David Amar
    • , Nasa Sinnott-Armstrong
    •  & Manuel A. Rivas

  • Article
    | Open Access

    The accumulation of recombination events in selfing species may lead to a rapid fixation of both beneficial and deleterious mutations. Here, the authors resequence 781 soybean accessions, show purging of deleterious mutation during domestication, and report genome-wide associations for seed protein and oil traits.

    • Myung-Shin Kim
    • , Roberto Lozano
    •  & Soon-Chun Jeong

  • Article
    | Open Access

    Gene flow is classically thought to impede local adaptation via parallel evolution. However, a genomic study on Hawaiian crickets from different island populations finds evidence of parallel adaptation to the same lethal parasitoid in spite of strong ongoing gene flow.

    • Xiao Zhang
    • , Jack G. Rayner
    •  & Nathan W. Bailey

  • Article
    | Open Access

    Ancient, asexual lineages are rare as a lack of recombination is usually an evolutionary dead end. Here, authors compare complete genomes of 11 individual bdelloid rotifers that suggest evidence of regular genetic exchange between individuals in a species that was previously thought to be asexual.

    • Olga A. Vakhrusheva
    • , Elena A. Mnatsakanova
    •  & Alexey S. Kondrashov

  • Article
    | Open Access

    Accurately measuring genetic relatedness by Identical-By-Descent (IBD) segments is challenging in biobank-level genome data. The authors present IBD method FastSMC, which when applied to the UK Biobank gives a detailed picture of genetic relatedness and evolutionary history in the UK over the past 2000 years.

    • Juba Nait Saada
    • , Georgios Kalantzis
    •  & Pier Francesco Palamara

  • Article
    | Open Access

    This study resolves a long-standing mystery of why t haplotypes, an example of selfish genes, have persisted at unexpectedly low frequencies in wild mouse populations. It shows that multiple mating by females, which is more common at higher mouse population densities, decreases the frequency of driving t haplotypes.

    • Andri Manser
    • , Barbara König
    •  & Anna K. Lindholm

  • Article
    | Open Access

    The human reference genome does not fully reflect human genetic diversity. Here, the authors analyse 338 human genome assemblies from diverse populations to identify missing sequences, define non-reference unique insertions and construct a Human Diversity Reference.

    • Karen H. Y. Wong
    • , Walfred Ma
    •  & Pui-Yan Kwok

  • Article
    | Open Access

    This study presents and validates a novel approach to reliably identify structural variations (SVs) in non-model genomes using whole genome sequencing, which was used to detect 15,483 SVs in 492 Atlantic salmon, shedding light on their roles in genome evolution and the genetic architecture of domestication.

    • Alicia C. Bertolotti
    • , Ryan M. Layer
    •  & Daniel J. Macqueen

  • Article
    | Open Access

    Principal component analysis is often used in studies of ancient DNA, but does not account for the age of the samples. Here, the authors present a factor analysis (FA) which corrects for this by including the effect of allele frequency drift over time.

    • Olivier François
    •  & Flora Jay

  • Article
    | Open Access

    Schizophrenia has been associated with increased risk of breast cancer, yet the risk of schizophrenia following breast cancer is unclear. Here, the authors show a bidirectional association between breast cancer and schizophrenia in Sweden and a shared genetic contribution to both diseases.

    • Donghao Lu
    • , Jie Song
    •  & Unnur A. Valdimarsdóttir

  • Article
    | Open Access

    Genetic variation in modern humans can reveal information about a population’s history and migration patterns. Here, the authors describe the ancestry and geospatial genetic structure of the Netherlands, and demonstrate the utility of haplotype-based covariates in genome-wide association studies.

    • Ross P. Byrne
    • , Wouter van Rheenen
    •  & Russell L. McLaughlin

  • Article
    | Open Access

    Pleistocene population dynamics can inform the consequences of current climate change. This phylogeography of 35 complete American mastodon mitochondrial genomes suggests distinct lineages in this species repeatedly expanded northwards and then went locally extinct in response to glacial cycles.

    • Emil Karpinski
    • , Dirk Hackenberger
    •  & Hendrik N. Poinar

  • Article
    | Open Access

    Structural genomic variation can fuel evolution. Here, authors present genome data from seven Corvus species and unearth structural variants that vary between incipient crow species in Europe, with implications for premating isolation involving plumage patterning.

    • Matthias H. Weissensteiner
    • , Ignas Bunikis
    •  & Jochen B. W. Wolf

  • Article
    | Open Access

    Evidence that somatic mutation rates in introns exceed those in exons challenges the molecular evolution tenet that mutation rate and sequence function are independent. Here, authors analyze germline de novo mutations and reveal no evidence for mutation rate differences between exons and introns.

    • Miguel Rodriguez-Galindo
    • , Sònia Casillas
    •  & Antonio Barbadilla

  • Article
    | Open Access

    Reduction of pollen grain number is widespread in selfing plants, but the determining gene is unknown. Here, the authors show that a ribosome-biogenesis factor encoding gene RDP1 is responsible for adaptive reduction of male gamete number in Arabidopsis thaliana.

    • Takashi Tsuchimatsu
    • , Hiroyuki Kakui
    •  & Kentaro K. Shimizu

  • Article
    | Open Access

    Multi-nucleotide variants (MNV) are genetic variants in close proximity of each other on the same haplotype whose functional impact is difficult to predict if they reside in the same codon. Here, Wang et al. use the gnomAD dataset to assemble a catalogue of MNVs and estimate their global mutation rate.

    • Qingbo Wang
    • , Emma Pierce-Hoffman
    •  & Daniel G. MacArthur

  • Article
    | Open Access

    Hybrid genomes provide a window into the speciation process over time. Here, Chaturvedi et al. use Lycaeides butterflies from hybrid zones of different ages to show that selection and recombination have repeatable effects on hybrid genome composition across timescales.

    • Samridhi Chaturvedi
    • , Lauren K. Lucas
    •  & Zachariah Gompert

  • Article
    | Open Access

    Sorting insects based on sex is error prone and frequently labour intensive. Here, the authors present a drug-inducible sex separation system based on sex-specific rescue from antibotic toxicity.

    • Nikolay P. Kandul
    • , Junru Liu
    •  & Omar S. Akbari

  • Article
    | Open Access

    Mutations in PTEN have been associated with various human disease, including autism spectrum disorder (ASD) and cancer. Here, the authors assess the function of 106 PTEN variants in yeast, invertebrate models and cell culture and report that PTEN variants generally decrease protein stability.

    • Kathryn L. Post
    • , Manuel Belmadani
    •  & Kurt Haas

  • Article
    | Open Access

    Empirical examples documenting the pace of adaptation across the whole genome in wild populations are scarce. Here the authors study wild stickleback populations from lake and stream habitats and show that there is a genome-wide signature of adaptation to stream habitats within just one generation.

    • Telma G. Laurentino
    • , Dario Moser
    •  & Daniel Berner

  • Article
    | Open Access

    European populations underwent strong genetic changes during the Neolithic. Here, Furtwängler et al. provide ancient nuclear and mitochondrial genomic data from the region of Switzerland during the end of the Neolithic and the Early Bronze Age that reveal a complex genetic turnover during the arrival of steppe ancestry.

    • Anja Furtwängler
    • , A. B. Rohrlach
    •  & Johannes Krause

  • Article
    | Open Access

    Polygenic scores are believed to hold future promise for trait prediction and personalized medicine, but are sensitive to demographic history. Here, Marnetto et al. develop partial polygenic scores supplemented with local ancestry deconvolution which improves prediction accuracy into recently admixed European populations.

    • Davide Marnetto
    • , Katri Pärna
    •  & Luca Pagani

  • Article
    | Open Access

    Population structure, even subtle differences within seemingly homogenous populations, can have an impact on the accuracy of polygenic prediction. Here, Sakaue et al. use dimensionality reduction methods to reveal fine-scale structure in the Biobank Japan cohort and explore the performance of polygenic risk scores.

    • Saori Sakaue
    • , Jun Hirata
    •  & Yukinori Okada

  • Article
    | Open Access

    In the Indo-Pacific, multiple Anguilla eel species overlap in their spawning. Here, the authors sequence three Anguilla genomes and with genome-wide data of four more congeners, investigate contemporary hybridization, historical introgression, and the maintenance of species boundaries despite substantial gene flow.

    • Julia M. I. Barth
    • , Chrysoula Gubili
    •  & Robert Schabetsberger

  • Article
    | Open Access

    CRISPR homing gene drives are highly invasive and can fail due to the rapid evolution of resistance. Here the authors present TARE drive, inspired by naturally occurring selfish genetic elements, which is less vulnerable to resistance and can potentially be confined to a target population.

    • Jackson Champer
    • , Esther Lee
    •  & Philipp W. Messer

  • Article
    | Open Access

    Ancient DNA analysis of early European farmers has found a high level of genetic affinity with present-day Sardinians. Here, the authors generate genome-wide capture data for 70 individuals from Sardinia spanning the Middle Neolithic to Medieval period to reveal relationships with mainland European populations shifting over time.

    • Joseph H. Marcus
    • , Cosimo Posth
    •  & John Novembre

  • Article
    | Open Access

    Although there is extensive theory predicting the effects of population bottlenecks on mutation load, there is little empirical evidence from recent bottlenecks. Here, Grossen et al. compare the consequences of population bottlenecks in six ibex species for genome-wide variation and mutation load.

    • Christine Grossen
    • , Frédéric Guillaume
    •  & Daniel Croll

  • Article
    | Open Access

    Dingoes evolved in isolation from both their domesticated and wild ancestors. Here, the authors investigate the genomic basis of the feralization of dingoes and trace their origin to domestic dogs that migrated to Australia approximately 8300 years ago.

    • Shao-jie Zhang
    • , Guo-Dong Wang
    •  & Ya-ping Zhang

  • Article
    | Open Access

    Few studies empirically pinpoint how balanced polymorphisms are maintained. “Mérot et al”. identify an inversion polymorphism that is maintained in seaweed fly populations because of antagonistic pleiotropy that mediates a classic life history tradeoff between larval survival and adult reproduction.

    • Claire Mérot
    • , Violaine Llaurens
    •  & Maren Wellenreuther

  • Article
    | Open Access

    Discovery of causal variants for monogenic disorders has been facilitated by whole exome and genome sequencing, but does not provide a diagnosis for all patients. Here, the authors propose a Full Spectrum of Intolerance to Loss-of-Function (FUSIL) categorization that integrates gene essentiality information to aid disease gene discovery.

    • Pilar Cacheiro
    • , Violeta Muñoz-Fuentes
    •  & Coleen Kane

  • Article
    | Open Access

    Population-based association analyses of rare genetic variants with complex traits are limited by the availability of data from sufficiently large cohorts. Here, Cirulli et al. report gene-based collapsing analysis of exomes from 49,960 participants of the UK Biobank and 21,866 participants of the Healthy Nevada Project over a total of 4377 traits.

    • Elizabeth T. Cirulli
    • , Simon White
    •  & Nicole L. Washington

  • Article
    | Open Access

    G-quadruplexes (G4s) are secondary structures that can form in both DNA and RNA from guanine-rich sequences which are enriched in untranslated regions (UTRs). Here, Lee et al. find that putative G4-forming sequences are evolutionarily constrained, enriched for RNA-binding protein interactions and enriched for disease genetic associations.

    • David S. M. Lee
    • , Louis R. Ghanem
    •  & Yoseph Barash

  • Article
    | Open Access

    Healthspan and healthy aging are areas of research with potential socioeconomic impact. Here, the authors present the Medical Genome Reference Bank (MGRB) which consist of over 4,000 individuals aged 70 years and older without a history of the major age-related diseases and report on results from whole-genome sequencing and association analyses.

    • Mark Pinese
    • , Paul Lacaze
    •  & David M. Thomas

  • Article
    | Open Access

    RNA-sequencing is mostly used to assess gene expression; however, it can also give information about genetic variants. Here, the authors present CaSpER, a statistical framework that utilises RNA-sequencing reads to identify and visualise CNV events by integrating transcriptome-wide expression and allelic shift profiles.

    • Akdes Serin Harmanci
    • , Arif O. Harmanci
    •  & Xiaobo Zhou

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