Population genetics articles within Nature Communications

Featured

  • Article
    | Open Access

    Birch pitch is thought to have been used in prehistoric times as hafting material or antiseptic and tooth imprints suggest that it was chewed. Here, the authors report a 5,700 year-old piece of chewed birch pitch from Denmark from which they successfully recovered a complete ancient human genome and oral microbiome DNA.

    • Theis Z. T. Jensen
    • , Jonas Niemann
    •  & Hannes Schroeder

  • Article
    | Open Access

    Relapse, reinfection and recrudescence can all cause recurrent infection after treatment of Plasmodium vivax malaria in endemic areas, but are difficult to distinguish. Here the authors show that they can be differentiated probabilistically and thereby demonstrate the high efficacy of primaquine treatment in preventing relapse.

    • Aimee R. Taylor
    • , James A. Watson
    •  & Nicholas J. White

  • Article
    | Open Access

    Structural variants may be omitted in sequence analysis despite their importance in genome variation and phenotypic impact. Here the authors present GraphTyper2, which uses pangenome graphs to genotype structural variants using short-reads and can be applied in large-scale sequencing studies.

    • Hannes P. Eggertsson
    • , Snaedis Kristmundsdottir
    •  & Pall Melsted

  • Article
    | Open Access

    Exceptional alpine plant diversity exists in the Hengduan Mountains. Here, through genome assembly and population genomics studies, the authors find notable intraspecific divergence among Cushion willow populations isolated by the sky island-like habitats and consider it contributes to speciation and biodiversity.

    • Jia-hui Chen
    • , Yuan Huang
    •  & Hang Sun

  • Article
    | Open Access

    Cucurbits fruits have diverse shapes and sizes, but their genomes evolution and genetic basis of diversity are unclear. Here, the authors show that the wax gourd genome has the most ancestral karyotype among cucurbits and identify candidate genes which contribute to large fruit size by comparative and population genomics analyses.

    • Dasen Xie
    • , Yuanchao Xu
    •  & Zhonghua Zhang

  • Article
    | Open Access

    The ‘parliament of genes’ hypothesis suggests that selfish genetic elements will be counteracted by suppressors that maintain equal transmission of the rest of the genome. Here, the authors find support for this hypothesis using mathematical models to explore a range of different scenarios.

    • Thomas W. Scott
    •  & Stuart A. West

  • Article
    | Open Access

    Various approaches are being used for polygenic prediction including Bayesian multiple regression methods that require access to individual-level genotype data. Here, the authors extend BayesR to utilise GWAS summary statistics (SBayesR) and show that it outperforms other summary statistic-based methods.

    • Luke R. Lloyd-Jones
    • , Jian Zeng
    •  & Peter M. Visscher

  • Article
    | Open Access

    Rare genetic disorders (RGDs) often exhibit significant clinical variability among affected individuals. Here, Oetjens et al. systematically study the contribution of common genetic variation to variable expressivity of RGDs and find it is frequently influenced by polygenic factors identified in genome-wide association studies of relevant traits.

    • M. T. Oetjens
    • , M. A. Kelly
    •  & D. H. Ledbetter

  • Article
    | Open Access

    Based on single worm whole genome sequencing, the authors here characterise the global evolution of the gastrointestinal parasite Haemonchus contortus and identify genes that play a role in drug resistance as well as climate-driven adaptations involving an epigenetic regulator.

    • G. Sallé
    • , S. R. Doyle
    •  & J. A. Cotton

  • Article
    | Open Access

    Date palm is an important fruit crop in the Middle East and North Africa. Here, the authors report an improved genome assembly of this species and perform GWAS mapping of sex determining region and 21 fruit traits using high density SNP data generated from re-sequencing of the mapping population.

    • Khaled M. Hazzouri
    • , Muriel Gros-Balthazard
    •  & Michael D. Purugganan

  • Article
    | Open Access

    Retrotransposition events have been linked to some human disorders. Here, Gardner et al. systematically search for mobile genetic elements (ME) in trio whole exome-sequencing datasets and ascertain 9 de novo MEs and further estimate genome-wide germline ME burden and constraint.

    • Eugene J. Gardner
    • , Elena Prigmore
    •  & Matthew E. Hurles

  • Article
    | Open Access

    Thousands of genetic loci are known to associate with human height, but these are mainly based on studies in European ancestry populations. Here, Akiyama et al. construct a genotype reference panel for the Japanese population followed by GWAS and report 573 height associated variants in 191,787 Japanese.

    • Masato Akiyama
    • , Kazuyoshi Ishigaki
    •  & Yoichiro Kamatani

  • Article
    | Open Access

    The majority of published GWAS was performed in European ancestry populations. Here, Kuchenbaecker et al., test to which extent lipid loci are shared and find that the major lipid loci are mostly transferrable between Europeans and Asians while there are notable exceptions for African populations.

    • Karoline Kuchenbaecker
    • , Nikita Telkar
    •  & Dieter Wolke

  • Article
    | Open Access

    Ecological speciation can proceed rapidly, but the origin of genetic variation facilitating it has remained elusive. Here, the authors show that secondary contact and introgression between deeply diverged lineages of stickleback fish facilitated rapid ecological speciation into lake and stream ecotypes in Lake Constance.

    • David A. Marques
    • , Kay Lucek
    •  & Ole Seehausen

  • Article
    | Open Access

    Low frequency coding single-nucleotide variants (SNVs) are predicted to disproportionately affect protein function. Here, the authors evaluate 2,009 missense SNVs across 2,185 protein-protein interactions using yeast two-hybrid and protein complementation assays and find that disruptive SNVs often occur in disease-associated genes.

    • Robert Fragoza
    • , Jishnu Das
    •  & Haiyuan Yu

  • Article
    | Open Access

    While many pleiotropic genetic loci have been identified, how they contribute to phenotypes across traits and diseases is unclear. Here, the authors propose decomposition of genetic associations (DeGAs), which uses singular value decomposition, to characterize the underlying latent structure of genetic associations of 2,138 phenotypes.

    • Yosuke Tanigawa
    • , Jiehan Li
    •  & Manuel A. Rivas

  • Article
    | Open Access

    Mating between first or second-degree relatives is prohibited in most countries, yet it occurs and is under-studied. Here, Yengo et al. use large runs of homozygosity from the UK Biobank resource to provide DNA-based quantification of extreme inbreeding and its consequence for health and other complex traits.

    • Loic Yengo
    • , Naomi R. Wray
    •  & Peter M. Visscher

  • Article
    | Open Access

    Here, Llewellyn and colleagues present evidence of meiotic sex in Trypanosoma cruzi, the causative agent of Chagas disease. These findings have implications for the epidemiology of the disease in endemic regions and challenge existing ideas that the parasites are strictly clonal.

    • Philipp Schwabl
    • , Hideo Imamura
    •  & Martin S. Llewellyn

  • Article
    | Open Access

    During meiotic recombination, genetic information is transferred or exchanged between parental chromosome copies. Using a large hybrid mouse pedigree, the authors generated high-resolution maps of these transfer/exchange events and discovered new properties governing their processing and resolution.

    • Ran Li
    • , Emmanuelle Bitoun
    •  & Simon R. Myers

  • Article
    | Open Access

    Remains of several hundred humans are scattered around Roopkund Lake, situated over 5,000 meters above sea level in the Himalayan Mountains. Here the authors analyze genome-wide data from 38 skeletons and find 3 clusters with different ancestries and dates, showing the people were desposited in multiple catastrophic events.

    • Éadaoin Harney
    • , Ayushi Nayak
    •  & Niraj Rai

  • Article
    | Open Access

    The genome of influenza is often incomplete in infected cells, but the implications for infection remain unclear. Here, Jacobs et al. show that an average of 3.6 particles is necessary for productive infection and that coinfection supports efficient complementation within a host but not upon transmission to a new host.

    • Nathan T. Jacobs
    • , Nina O. Onuoha
    •  & Anice C. Lowen

  • Article
    | Open Access

    Theory suggests that neutral genetic diversity is determined by census population size, but this is not observed empirically. Here, the authors show that in butterflies, neutral genetic diversity correlates with both body size and chromosome number, suggesting that linked selection is also an important factor.

    • Alexander Mackintosh
    • , Dominik R. Laetsch
    •  & Konrad Lohse

  • Article
    | Open Access

    Genetic adaptation and physiological acclimation can potentially buffer species against climate change. Here, the authors perform a long-term warming experiment of Antarctic encrusting communities and show that focal animal species failed to acclimate and lacked genetic variation in tolerance to warming.

    • Melody S. Clark
    • , Leyre Villota Nieva
    •  & Lloyd S. Peck

  • Article
    | Open Access

    Various host factors may impact within-host pathogen evolution. Here, the authors develop a Bayesian approach for identifying host-pathogen interactions using large data sets of pathogen diversity, and apply it to investigate HLA-induced selection in the HIV-1 genome.

    • Duncan S. Palmer
    • , Isaac Turner
    •  & Gil McVean

  • Article
    | Open Access

    The Atlantic salmon has suffered widespread population declines over the last century. Here, Lehnert et al. reconstruct changes in effective population size of 172 populations based on genomic linkage information revealing mostly temperature-associated population declines with over 60% of populations in decline since 1975.

    • S. J. Lehnert
    • , T. Kess
    •  & I. R. Bradbury

  • Article
    | Open Access

    Understanding genomic variation in Plasmodium falciparum parasites and inferring migration patterns can guide malaria elimination strategies. Using genome-wide data for 1722 parasites collected from 54 districts, the authors use identity-by-descent approaches to estimate regional parasite migration and spread of artemisinin drug resistance.

    • Amol C. Shetty
    • , Christopher G. Jacob
    •  & Marie A. Onyamboko

  • Article
    | Open Access

    In asexual populations selection at different genomic loci can interfere with each other. Here, using a biophysical model of molecular evolution the authors show that interference results in long-term degradation of molecular function, an effect that strongly depends on genome size.

    • Torsten Held
    • , Daniel Klemmer
    •  & Michael Lässig

  • Article
    | Open Access

    The pygmy hog (Porcula salvania), now highly endangered and restricted in a small region at the southern foothills of the Himalaya, is the only suid species in mainland Eurasia that outlived the expansion of wild boar (Sus scrofa). Here, the authors analyze genomes of pygmy hog and related suid species, and identify signals of introgression among these species.

    • Langqing Liu
    • , Mirte Bosse
    •  & Ole Madsen

  • Article
    | Open Access

    The corneal endothelium is crucial for proper vision. Here, Ivarsdottir et al. perform genome-wide association studies for various corneal endothelial cell measurements and find that an intergenic variant near ANAPC1 explains 24% of the variance of endothelial cell density and associates with corneal hysteresis.

    • Erna V. Ivarsdottir
    • , Stefania Benonisdottir
    •  & Kari Stefansson

  • Article
    | Open Access

    Central Anatolia harbored some of the earliest farming societies outside the Fertile Crescent of the Near East. Here, the authors report and analyze genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers, and suggest high genetic continuity between the hunter-gatherers and early farmers of Anatolia.

    • Michal Feldman
    • , Eva Fernández-Domínguez
    •  & Johannes Krause

  • Article
    | Open Access

    While the role of effective population size (Ne) in explaining variation in genetic diversity has received much attention, the role of spontaneous mutation rate is largely ignored. Here, Xu et al. show that giant duckweed has a high Ne yet low genetic diversity, likely due to its low mutation rate.

    • Shuqing Xu
    • , Jessica Stapley
    •  & Meret Huber

  • Article
    | Open Access

    Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses.

    • Zhenchang Liang
    • , Shengchang Duan
    •  & Yang Dong

  • Article
    | Open Access

    Estimates of the burden of malaria often don't take wider, indirect effects on overall health into consideration. Here, Uyoga et al. estimate the indirect impact of malaria on children’s health in a case-control study, using the sickle cell trait as a proxy indicator for an effective intervention.

    • Sophie Uyoga
    • , Alex W. Macharia
    •  & Thomas N. Williams

  • Article
    | Open Access

    The burden of asthma varies between ancestries, but GWAS have so far focused on mainly European ancestry populations. Here, Daya et al. perform GWAS for asthma in 14,654 individuals of African ancestry and, besides confirming previously known loci, identify two potentially African ancestry-specific loci.

    • Michelle Daya
    • , Nicholas Rafaels
    •  & Maria Yazdanbakhsh

  • Article
    | Open Access

    Negative selection removes deleterious genetic variation, and can influence genetic architectures and evolution of complex traits. Here, the authors analyze data from 25 UK Biobank diseases and complex traits, and quantify frequency-dependent genetic architectures which suggests actions of negative selection.

    • Armin P. Schoech
    • , Daniel M. Jordan
    •  & Alkes L. Price

  • Article
    | Open Access

    The Caucasus mountain range has impacted on the culture and genetics of the wider region. Here, the authors generate genome-wide SNP data for 45 Eneolithic and Bronze Age individuals across the Caucasus, and find distinct genetic clusters between mountain and steppe zones as well as occasional gene-flow.

    • Chuan-Chao Wang
    • , Sabine Reinhold
    •  & Wolfgang Haak

Browse broader subjects

Browse narrower subjects

Browse Population genetics across other nature.com journals