Population genetics articles within Nature Communications

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  • Article
    | Open Access

    Population structure can bias the results of genetic and epidemiological analysis. Here, Haworth et al. report that fine-scale structure is detectable in apparently homogeneous samples such as ALSPAC when measured very precisely, and remains detectable in UK Biobank despite conventional approaches to account for it.

    • Simon Haworth
    • , Ruth Mitchell
    •  & Nicholas J. Timpson

  • Article
    | Open Access

    Introgression of Neanderthals and Denisovans left genomic signals in anatomically modern human after Out-of-Africa event. Here, the authors identify a third archaic introgression common to all Asian and Oceanian human populations by applying an approximate Bayesian computation with a Deep Learning framework.

    • Mayukh Mondal
    • , Jaume Bertranpetit
    •  & Oscar Lao

  • Article
    | Open Access

    Stocking of hatchery produced fish is widely used to supplement wild fish populations. Here, the authors show that supplementary stocking can unintentionally favour introgressed individuals with domestic genotypes and compromise the fitness of a wild population of Atlantic salmon.

    • Ingerid J. Hagen
    • , Arne J. Jensen
    •  & Sten Karlsson

  • Article
    | Open Access

    Examples of overdominance are usually explained by deleterious effects in homozygotes. Here, Kellenberger et al. describe a case of overdominance in the floral color of the Alpine orchid Gymnadenia rhellicani apparently maintained by pollinator preferences without deleterious effects in homozygotes.

    • Roman T. Kellenberger
    • , Kelsey J. R. P. Byers
    •  & Philipp M. Schlüter

  • Article
    | Open Access

    The origin of Tibetan barley (qingke) has been a controversial issue for many years. Here, the authors conduct population genomics study to support that qingke is derived from eastern domesticated barley instead of Tibetan wild barley and suggest southern Tibetan Plateau as its introduction route.

    • Xingquan Zeng
    • , Yu Guo
    •  & Nyima Tashi

  • Article
    | Open Access

    Male pattern baldness (MPB) is a polygenic trait that affects the majority of European men. Here, Yap et al. estimate heritability, partitioned by autosomes and the X-chromosome, of MPB in the UK Biobank cohort, perform GWAS for MPB and find genetic correlation with other sex-specific traits.

    • Chloe X. Yap
    • , Julia Sidorenko
    •  & Peter M. Visscher

  • Article
    | Open Access

    Latin Americans trace their ancestry to the admixture of Native Americans, Europeans and Sub-Saharan Africans. Here, the authors develop a novel haplotype-based approach and analyse over 6,500 Latin Americans to infer the geographically-detailed genetic structure of this population.

    • Juan-Camilo Chacón-Duque
    • , Kaustubh Adhikari
    •  & Andrés Ruiz-Linares

  • Article
    | Open Access

    Candida auris is an emergent fungal pathogen that is resistant to multiple antifungals. Here, Muñoz et al. analyse genomic sequences for isolates from each of the four major C. auris clades and for three related species, and identify genetic features associated with virulence, antifungal resistance and mating.

    • José F. Muñoz
    • , Lalitha Gade
    •  & Christina A. Cuomo

  • Article
    | Open Access

    Northern tree populations may not benefit under climate change, with implications for assisted migration and range expansion. Here, Isaac-Renton et al. show that leading-edge lodgepole pine populations have fewer characteristics of drought-tolerance, so may not adapt to tolerate drier conditions.

    • Miriam Isaac-Renton
    • , David Montwé
    •  & Kerstin Treydte

  • Article
    | Open Access

    Populations from North-eastern Europe, in particular those speaking Uralic languages, carry additional ancestry in similarity with modern East Asian populations. Here, the authors analyse ancient genomic data from 11 individuals from Finland and Northwest Russia, and identify genomic signals of migrations from Siberia that began at least 3500 years ago.

    • Thiseas C. Lamnidis
    • , Kerttu Majander
    •  & Stephan Schiffels

  • Article
    | Open Access

    Rare genetic variants can contribute to complex traits but this contribution is not well understood. Here, the authors analyse deep whole genome sequencing data across 1457 individuals from an isolated Greek population and find association of rare variant burdens with cardiometabolic traits.

    • Arthur Gilly
    • , Daniel Suveges
    •  & Eleftheria Zeggini

  • Article
    | Open Access

    Mutations in genes encoding NAPDH oxidase subunits are known to be causative for the primary immunodeficiency chronic granulomatous disease (CGD). Here, the authors identify CYBC1 mutations in patients with CGD and show that CYBC1 is important for formation of the NADPH complex and respiratory burst.

    • Gudny A. Arnadottir
    • , Gudmundur L. Norddahl
    •  & Kari Stefansson

  • Article
    | Open Access

    The Longobards invaded and conquered much of Italy after the fall of the Western Roman Empire. Here, the authors sequence and analyze ancient genomic DNA from 63 samples from two cemeteries associated with the Longobards and identify kinship networks and two distinct genetic and cultural groups in each.

    • Carlos Eduardo G. Amorim
    • , Stefania Vai
    •  & Krishna R. Veeramah

  • Article
    | Open Access

    Japonica rice can grow further north than wild or indica rice and is more tolerant of cold climates. Here, the authors show that bZIP73 likely underwent selection in the early phase of rice domestication to facilitate cold tolerance in japonica by modulating ABA and ROS homeostasis.

    • Citao Liu
    • , Shujun Ou
    •  & Chengcai Chu

  • Article
    | Open Access

    Clustering methods such as STRUCTURE and ADMIXTURE are widely used in population genetic studies to investigate ancestry. Here, the authors provide a tutorial on how to interpret results of these analyses and a tool to test the goodness of fit of the model.

    • Daniel J. Lawson
    • , Lucy van Dorp
    •  & Daniel Falush

  • Article
    | Open Access

    Ducks, one of the most common domestic fowls, originated from mallards. Here, the authors perform whole-genome sequencing of mallards, indigenous-breed ducks, and Pekin ducks, as well as 1026 ducks from a population generated by wild × domestic crosses to identify selection signals and map variants associated with body size and plumage color.

    • Zhengkui Zhou
    • , Ming Li
    •  & Yu Jiang

  • Article
    | Open Access

    Dominance is difficult to measure in natural populations as it is confounded with fitness. Here, Huber et al. developed a new approach to co-estimate dominance and selection coefficients, and found that the observed relationship is best fit by a new model of dominance based on gene expression level.

    • Christian D. Huber
    • , Arun Durvasula
    •  & Kirk E. Lohmueller

  • Article
    | Open Access

    Since the 1980s, hypervirulent clonal-group CG23 serotype K1 Klebsiella pneumoniae has been recognised as a prominent cause of community-acquired liver abscess and other severe infections. Here, the authors investigate the genomic evolutionary history of CG23 and suggest a new reference strain for CG23.

    • Margaret M. C. Lam
    • , Kelly L. Wyres
    •  & Kathryn E. Holt

  • Article
    | Open Access

    An understanding of the domestication of the yeast Saccharomyces cerevisiae has important implications for studying its evolution and diversity. Here, the authors show that Far East Asia is likely the center of origin of the domesticated populations of the yeast based on genomic and phenotypic characterization of a large collection of isolates.

    • Shou-Fu Duan
    • , Pei-Jie Han
    •  & Feng-Yan Bai

  • Article
    | Open Access

    Circulating lipoprotein(a) is an important risk factor for cardiovascular disease and shows variability between different ethnic groups. Here, Zekavat et al. perform whole-genome sequencing in individuals of European and African ancestries and find ancestry-specific genetic determinants for lipoprotein(a) levels.

    • Seyedeh M. Zekavat
    • , Sanni Ruotsalainen
    •  & Sebastian Zoellner

  • Article
    | Open Access

    Plasmodium vivax incidence in Malaysia has declined markedly over the last decade, despite evidence of chloroquine resistance. Here, Auburn et al. compare population structure of P. vivax in Malaysia to regions with intermediate and high transmission and identify genetic regions under putative selection.

    • Sarah Auburn
    • , Ernest D. Benavente
    •  & Ric N. Price

  • Article
    | Open Access

    The speciation process tends to generate ‘genomic islands’ of increased divergence. Here, the authors use haplotype–resolved whole-genome sequences of European sea bass lineages to infer divergence history and show that linked selection generated genomic islands that resist introgression at secondary contact.

    • Maud Duranton
    • , François Allal
    •  & Pierre-Alexandre Gagnaire

  • Article
    | Open Access

    Sex-specific meiotic crossover (CO) landscapes have been identified in multiple species. Here, the authors show that male and female meioses in maize have similar CO landscapes, and differences between COs in the two sexes only exists in their location relative to transcription start sites and some chromatin marks.

    • Penny M. A. Kianian
    • , Minghui Wang
    •  & Wojciech P. Pawlowski

  • Article
    | Open Access

    The fungal pathogen Candida albicans can undergo a parasexual process that may contribute to genetic diversity, but its actual relevance is unclear. Here, Ropars et al. analyse the genomic sequences of 182 C. albicans isolates collected worldwide and find evidence of gene flow and thus parasexuality in nature.

    • Jeanne Ropars
    • , Corinne Maufrais
    •  & Christophe d’Enfert

  • Article
    | Open Access

    Pathogens exert strong selection on hosts and thus may promote parallel evolution. Here, the authors find that hosts experimentally coevolving with a virus have parallel changes in population size, phenotype, and genomic regions, but accelerated divergence in genome sequence likely due to population size fluctuation.

    • Jens Frickel
    • , Philine G. D. Feulner
    •  & Lutz Becks

  • Article
    | Open Access

    Mating-type switching enables self-compatible reproduction in fungi, but switching ability is variable even within species. Here, the authors find de novo evolution of switching genotypes in experimentally evolved fission yeast populations and show a trade-off between mating success and growth.

    • Bart P. S. Nieuwenhuis
    • , Sergio Tusso
    •  & Simone Immler

  • Article
    | Open Access

    Recent natural selection left signals in human genomes. Here, Okada et al. generate high-depth whole-genome sequence (WGS) data (25.9×) from 2,234 Japanese people of the BioBank Japan Project (BBJ), and identify signals of recent natural selection which overlap variants associated with human traits.

    • Yukinori Okada
    • , Yukihide Momozawa
    •  & Yoichiro Kamatani

  • Article
    | Open Access

    Host immune responses exert selective pressure on Plasmodium falciparum. Here, the authors show that allele-specific immunity impacts the antigenic diversity of individual malaria infections. This process partially explains the extreme amino acid diversity of many parasite antigens and suggests that vaccines should account for allele-specific immunity.

    • Angela M. Early
    • , Marc Lievens
    •  & Daniel E. Neafsey

  • Article
    | Open Access

    Individuals with different genotypes may respond differently to environmental variation. Here, Favé et al. find substantial impacts of different environment exposures on the transcriptome and clinical endophenotypes when controlling for genetic ancestry by analyzing data from ∼1000 individuals from a founder population in Quebec.

    • Marie-Julie Favé
    • , Fabien C. Lamaze
    •  & Philip Awadalla

  • Article
    | Open Access

    The sheep and goat were domesticated ~10,500 years ago in the same region of the Middle-East. Here, Alberto et al compare the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds and find common targets of selection related to domestication and improvement in sheep and goats.

    • Florian J. Alberto
    • , Frédéric Boyer
    •  & François Pompanon

  • Article
    | Open Access

    The population of Madagascar arose from admixture of Austronesian and Bantu genetic backgrounds. Analyzing local ancestry in genomes of 700 Malagasy, Pierron et al. identify signals of recent positive selection for African ancestry in a region on chromosome 1 with implications for physiology and disease risk.

    • Denis Pierron
    • , Margit Heiske
    •  & Thierry Letellier

  • Article
    | Open Access

    The declining performance of scale-up bioreactor cultures is commonly attributed to phenotypic and physical heterogeneities. Here, the authors reveal multiple recurring intra-pathway error modes that limit engineered E. coli mevalonic acid production over time- and industrial-scale fermentations.

    • Peter Rugbjerg
    • , Nils Myling-Petersen
    •  & Morten O. A. Sommer

  • Article
    | Open Access

    Selective sweeps are events in which beneficial mutations spread rapidly through a population. Here, Sugden et al. develop SWIF(r), a probabilistic classification framework for detecting and localizing selective sweeps, and apply it to genomic data from the ‡Khomani San.

    • Lauren Alpert Sugden
    • , Elizabeth G. Atkinson
    •  & Sohini Ramachandran

  • Article
    | Open Access

    Long-read sequencing technologies facilitate efficient and high quality genome assembly. Here Michael et al. achieve a fast reference assembly for Arabidopsis thaliana KBS-Mac-74 accession using the handheld Oxford Nanopore MinION sequencer and consumer computing hardware, and demonstrate its usefulness in resolving complex structural variation.

    • Todd P. Michael
    • , Florian Jupe
    •  & Joseph R. Ecker

  • Article
    | Open Access

    The population history of Europe is complex and its very north has not yet been comprehensively studied at a genetic level. Here, Mittnik et al. report genome-wide data from 38 ancient individuals from the Eastern Baltic, Russia and Scandinavia to analyse gene flow throughout the Mesolithic and Bronze Age.

    • Alissa Mittnik
    • , Chuan-Chao Wang
    •  & Johannes Krause

  • Article
    | Open Access

    African populations show a high level of genetic diversity and extensive regional admixture. Here, the authors sequence the whole genomes of 24 South African individuals of different ethnolinguistic origin and find substantive genomic divergence between two southeastern Bantu-speaking groups.

    • Ananyo Choudhury
    • , Michèle Ramsay
    •  & Michael S. Pepper

  • Article
    | Open Access

    Selection for recombination requires genetic diversity and negative linkage disequilibrium, which can be produced by coevolutionary arms races. Here the authors propose a qualitatively different scenario that can favour recombination in seasonal environments through the ‘genomic storage effect’.

    • Davorka Gulisija
    •  & Joshua B. Plotkin

  • Article
    | Open Access

    The evolution of new sex chromosomes potentially generates reproductive isolation. Here, Bracewell et al. combine crossing experiments with population and functional genomics to characterize neo-sex chromosome evolution and incipient speciation in the mountain pine beetle, Dendroctonus ponderosae.

    • Ryan R. Bracewell
    • , Barbara J. Bentz
    •  & Jeffrey M. Good

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