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| Open AccessA chickpea genetic variation map based on the sequencing of 3,366 genomes
Whole-genome sequencing of 3,171 cultivated and 195 wild chickpea accessions is used to construct a chickpea pan-genome, providing insight into chickpea evolution and enabling breeding strategies that could improve crop productivity.
- Rajeev K. Varshney
- , Manish Roorkiwal
- & Xin Liu
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Article
| Open AccessThe genomic origins of the Bronze Age Tarim Basin mummies
A genomic analysis of human remains from the Bronze Age provides insights into the origin of the Tarim Basin mummies from the Xinjiang region.
- Fan Zhang
- , Chao Ning
- & Yinqiu Cui
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Article
| Open AccessThe origins and spread of domestic horses from the Western Eurasian steppes
Analysis of 273 ancient horse genomes reveals that modern domestic horses originated in the Western Eurasian steppes, especially the lower Volga-Don region.
- Pablo Librado
- , Naveed Khan
- & Ludovic Orlando
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Article
| Open AccessExome sequencing and analysis of 454,787 UK Biobank participants
Whole-exome sequencing analysis of 454,787 individuals in the UK Biobank is used to examine the association of protein-coding variants with nearly 4,000 health-related traits, identifying 564 distinct genes with significant trait associations.
- Joshua D. Backman
- , Alexander H. Li
- & Manuel A. R. Ferreira
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Article |
Paths and timings of the peopling of Polynesia inferred from genomic networks
Analysis of genomic networks from 430 modern individuals across 21 Pacific island populations reveals the human settlement history of Polynesia.
- Alexander G. Ioannidis
- , Javier Blanco-Portillo
- & Andrés Moreno-Estrada
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Article
| Open AccessGenome of a middle Holocene hunter-gatherer from Wallacea
The palaeogenomic analysis of a pre-Neolithic skeleton associated with a Toalean burial context from Wallacea.
- Selina Carlhoff
- , Akin Duli
- & Adam Brumm
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Article |
A body map of somatic mutagenesis in morphologically normal human tissues
Laser-capture microdissection and mini-bulk exome sequencing are combined to analyse somatic mutations in morphologically normal tissues from nine organs from five donors, revealing variation in mutation burdens, mutational signatures and clonal expansions.
- Ruoyan Li
- , Lin Di
- & Chen Wu
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Article |
The mutational landscape of human somatic and germline cells
The authors report the mutational landscape of 29 cell types from microdissected biopsies from 19 organs and explore the mechanisms underlying mutation rates in normal tissues.
- Luiza Moore
- , Alex Cagan
- & Raheleh Rahbari
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Article
| Open AccessRare variant contribution to human disease in 281,104 UK Biobank exomes
The authors analyse rare protein-coding genetic variants for association with 18,780 traits in the UK Biobank cohort.
- Quanli Wang
- , Ryan S. Dhindsa
- & Slavé Petrovski
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Article
| Open AccessPleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave
Ancient mitochondrial DNA from sediments reveals the sequence of Denisovan, Neanderthal and faunal occupation of Denisova Cave, and evidence for the appearance of modern humans at least 45,000 years ago.
- Elena I. Zavala
- , Zenobia Jacobs
- & Matthias Meyer
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Review Article |
Peopling of the Americas as inferred from ancient genomics
A review of the ancient human genomic record sheds light on the peopling processes of the Americas.
- Eske Willerslev
- & David J. Meltzer
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Article |
Genomic insights into population history and biological adaptation in Oceania
Genomic analyses of human populations in the Pacific provide insights into the peopling history of the region and reveal episodes of biological adaptation relating to the immune system and lipid metabolism through introgression from archaic hominins and polygenic adaptation.
- Jeremy Choin
- , Javier Mendoza-Revilla
- & Lluis Quintana-Murci
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Article
| Open AccessInitial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry
Genome-wide data for the three oldest known modern human remains in Europe, dated to around 45,000 years ago, shed light on early human migrations in Europe and suggest that mixing with Neanderthals was more common than is often assumed.
- Mateja Hajdinjak
- , Fabrizio Mafessoni
- & Svante Pääbo
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Article |
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
Genetic and testing data from England show that the SARS-CoV-2 variant of concern B.1.1.7 has a transmission advantage over other lineages.
- Erik Volz
- , Swapnil Mishra
- & Neil M. Ferguson
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Article |
Genomic insights into the formation of human populations in East Asia
Genome-wide data from 166 East Asian individuals dating to between 6000 bc and ad 1000 and from 46 present-day groups provide insights into the histories of mixture and migration of human populations in East Asia.
- Chuan-Chao Wang
- , Hui-Yuan Yeh
- & David Reich
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Article |
Million-year-old DNA sheds light on the genomic history of mammoths
Siberian mammoth genomes from the Early and Middle Pleistocene subepochs reveal adaptive changes and a key hybridization event, highlighting the value of deep-time palaeogenomics for studies of speciation and long-term evolutionary trends.
- Tom van der Valk
- , Patrícia Pečnerová
- & Love Dalén
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Article
| Open AccessSequencing of 53,831 diverse genomes from the NHLBI TOPMed Program
The goals, resources and design of the NHLBI Trans-Omics for Precision Medicine (TOPMed) programme are described, and analyses of rare variants detected in the first 53,831 samples provide insights into mutational processes and recent human evolutionary history.
- Daniel Taliun
- , Daniel N. Harris
- & Gonçalo R. Abecasis
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Article
| Open AccessGenomic mechanisms of climate adaptation in polyploid bioenergy switchgrass
The genome of the biofuel crop switchgrass (Panicum virgatum) reveals climate–gene–biomass associations that underlie adaptation in nature and will facilitate improvements of the yield of this crop for bioenergy production.
- John T. Lovell
- , Alice H. MacQueen
- & Jeremy Schmutz
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Article |
Patterns of de novo tandem repeat mutations and their role in autism
A bioinformatics pipeline to identify tandem repeat mutations is developed and used to characterize precise changes in repeat copy number associated with autism spectrum disorder.
- Ileena Mitra
- , Bonnie Huang
- & Melissa Gymrek
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Article |
A genetic history of the pre-contact Caribbean
Ancient DNA reveals genetic differences between stone-tool users and people associated with ceramic technology in the Caribbean and provides substantially lower estimates of population sizes in the region before European contact.
- Daniel M. Fernandes
- , Kendra A. Sirak
- & David Reich
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Article
| Open AccessThe barley pan-genome reveals the hidden legacy of mutation breeding
Chromosome-scale sequence assemblies of 20 diverse varieties of barley are used to construct a first-generation pan-genome, revealing previously hidden genetic variation that can be used by studies aimed at crop improvement
- Murukarthick Jayakodi
- , Sudharsan Padmarasu
- & Nils Stein
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Article
| Open AccessContrasting signatures of genomic divergence during sympatric speciation
Population genomic analyses of Midas cichlid fishes in young Nicaraguan crater lakes suggest that sympatric speciation is promoted by polygenic architectures.
- Andreas F. Kautt
- , Claudius F. Kratochwil
- & Axel Meyer
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Article |
High-depth African genomes inform human migration and health
Whole-genome sequencing analyses of African populations provide insights into continental migration, gene flow and the response to human disease, highlighting the importance of including diverse populations in genomic analyses to understand human ancestry and improve health.
- Ananyo Choudhury
- , Shaun Aron
- & Neil A. Hanchard
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Article
| Open AccessExome sequencing and characterization of 49,960 individuals in the UK Biobank
Exome sequences from the first 49,960 participants in the UK Biobank highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community.
- Cristopher V. Van Hout
- , Ioanna Tachmazidou
- & Aris Baras
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Article |
Population genomics of the Viking world
Ancient DNA analyses reveal that Viking Age migrations from Scandinavia resulted in differential influxes of ancestry to different parts of Europe, and the increased presence of non-local ancestry within Scandinavia.
- Ashot Margaryan
- , Daniel J. Lawson
- & Eske Willerslev
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Article |
Reverse and forward engineering of Drosophila corneal nanocoatings
The building blocks of the nanostructures observed on Drosophila corneas are determined, and then used to create artificial nanostructures with anti-reflective and anti-adhesive properties.
- Mikhail Kryuchkov
- , Oleksii Bilousov
- & Vladimir L. Katanaev
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Article |
Genome-wide detection of tandem DNA repeats that are expanded in autism
Genome-wide analysis of tandem DNA repeats in the genomes of individuals with autism spectrum disorder and control participants reveals a strong contribution of tandem repeat expansions to the genetic aetiology and phenotypic complexity of autism spectrum disorder.
- Brett Trost
- , Worrawat Engchuan
- & Ryan K. C. Yuen
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Article |
Native American gene flow into Polynesia predating Easter Island settlement
Genomic analyses of DNA from modern individuals show that, about 800 years ago, pre-European contact occurred between Polynesian individuals and Native American individuals from near present-day Colombia, while remote Pacific islands were still being settled.
- Alexander G. Ioannidis
- , Javier Blanco-Portillo
- & Andrés Moreno-Estrada
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Article |
Massive haplotypes underlie ecotypic differentiation in sunflowers
Resequencing analyses of three species of wild sunflower identify large non-recombining haplotype blocks that correlate with ecologically relevant traits, soil and climate characteristics, and that differentiate species ecotypes.
- Marco Todesco
- , Gregory L. Owens
- & Loren H. Rieseberg
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Article |
A dynastic elite in monumental Neolithic society
Skeletal remains from the Neolithic passage tomb at Newgrange (Ireland) represent the adult son of a first-degree incestuous union, suggesting that a politico-religious elite may have controlled the construction of Irish sites of this type.
- Lara M. Cassidy
- , Ros Ó Maoldúin
- & Daniel G. Bradley
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Article |
Insights into variation in meiosis from 31,228 human sperm genomes
Thousands of sperm genomes have been analysed with a new method called Sperm-seq, revealing interconnected meiotic variation at the single-cell and person-to-person levels, and suggesting chromosome compaction as a way to explain the relationships between diverse recombination phenotypes.
- Avery Davis Bell
- , Curtis J. Mello
- & Steven A. McCarroll
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Article
| Open AccessThe mutational constraint spectrum quantified from variation in 141,456 humans
A catalogue of predicted loss-of-function variants in 125,748 whole-exome and 15,708 whole-genome sequencing datasets from the Genome Aggregation Database (gnomAD) reveals the spectrum of mutational constraints that affect these human protein-coding genes.
- Konrad J. Karczewski
- , Laurent C. Francioli
- & Daniel G. MacArthur
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Article |
Mapping and characterization of structural variation in 17,795 human genomes
Structural variants in more than 17,000 human genomes are mapped and characterized using whole-genome sequencing, showing how this type of variation contributes to rare deleterious coding and noncoding alleles.
- Haley J. Abel
- , David E. Larson
- & Ira M. Hall
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Article |
A positively selected FBN1 missense variant reduces height in Peruvian individuals
In an ethnically diverse group of Peruvian individuals, the population-specific, missense variant in FBN1 (E1297G) is associated with lower height and shows evidence of positive selection within the Peruvian population.
- Samira Asgari
- , Yang Luo
- & Soumya Raychaudhuri
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Article |
The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes
Analysis of Icelandic genomes reveals chromosome fragments of Neanderthal and Denisovan origin, the latter of which occurred through Denisovan gene flow either into ancestors of the Neanderthals or directly into humans.
- Laurits Skov
- , Moisès Coll Macià
- & Kari Stefansson
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Article |
Ancient West African foragers in the context of African population history
Genome-wide ancestry profiles of four individuals, dating to 8,000 and 3,000 years before present, from the archaeological site of Shum Laka (Cameroon) shed light on the deep population history of sub-Saharan Africa.
- Mark Lipson
- , Isabelle Ribot
- & David Reich
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Article
| Open AccessThe GenomeAsia 100K Project enables genetic discoveries across Asia
Using whole-genome sequencing data from 1,739 individuals, the GenomeAsia 100K Project catalogues genetic variation, population structure and disease associations to facilitate genetic studies in Asian populations and increase representation in genetics studies worldwide.
- Jeffrey D. Wall
- , Eric W. Stawiski
- & Andrew S. Peterson
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Article |
High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast
A renewable barcoding system reveals the evolutionary dynamics of laboratory budding yeast, showing that fitness changes over time in a travelling wave of adaptation that can fluctuate owing to leapfrogging events.
- Alex N. Nguyen Ba
- , Ivana Cvijović
- & Michael M. Desai
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Letter |
Genetic analyses of diverse populations improves discovery for complex traits
Genetic analyses of ancestrally diverse populations show evidence of heterogeneity across ancestries and provide insights into clinical implications, highlighting the importance of including ancestrally diverse populations to maximize genetic discovery and reduce health disparities.
- Genevieve L. Wojcik
- , Mariaelisa Graff
- & Christopher S. Carlson
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Letter |
Mating preferences of selfish sex chromosomes
Population genetic modelling shows that mate preferences encoded on sex chromosomes can drive the evolution of extremely male-costly traits.
- Pavitra Muralidhar
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Letter |
Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America
DNA analysis of ancient individuals and modern populations suggests that the population history of North America can be explained by the admixture of two ancestral lineages—Palaeo-Eskimos and First Peoples.
- Pavel Flegontov
- , N. Ezgi Altınışık
- & Stephan Schiffels
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Article |
The population history of northeastern Siberia since the Pleistocene
Analyses of 34 ancient genomes from northeastern Siberia, dating to between 31,000 and 600 years ago, reveal at least three major migration events in the late Pleistocene population history of the region.
- Martin Sikora
- , Vladimir V. Pitulko
- & Eske Willerslev
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Article
| Open AccessImproved reference genome of Aedes aegypti informs arbovirus vector control
An improved, fully re-annotated Aedes aegypti genome assembly (AaegL5) provides insights into the sex-determining M locus, chemosensory systems that help mosquitoes to hunt humans and loci involved in insecticide resistance and will help to generate intervention strategies to fight this deadly disease vector.
- Benjamin J. Matthews
- , Olga Dudchenko
- & Leslie B. Vosshall
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Article
| Open AccessThe UK Biobank resource with deep phenotyping and genomic data
Deep phenotype and genome-wide genetic data from 500,000 individuals from the UK Biobank, describing population structure and relatedness in the cohort, and imputation to increase the number of testable variants to 96 million.
- Clare Bycroft
- , Colin Freeman
- & Jonathan Marchini
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Article |
137 ancient human genomes from across the Eurasian steppes
Sequences of 137 ancient and 502 modern human genomes illuminate the population history of the Eurasian steppes after the Bronze Age and document the replacement of Indo-European speakers of West Eurasian ancestry by Turkic-speaking groups of East Asian ancestry.
- Peter de Barros Damgaard
- , Nina Marchi
- & Eske Willerslev
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Brief Communications Arising |
Ghalambor et al. reply
- Cameron K. Ghalambor
- , Kim L. Hoke
- & Kimberly A. Hughes
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Brief Communications Arising |
Contesting the evidence for non-adaptive plasticity
- François Mallard
- , Ana Marija Jakšić
- & Christian Schlötterer
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Letter |
Dysregulation of expression correlates with rare-allele burden and fitness loss in maize
A multi-tissue gene expression resource representative of the genotypic and phenotypic diversity of modern inbred maize reveals the effect of rare alleles and evolutionary history on the regulation of gene expression.
- Karl A. G. Kremling
- , Shu-Yun Chen
- & Edward S. Buckler
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Article |
The genomic history of southeastern Europe
Genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe between 12000 and 500 bc reveals that the region acted as a genetic crossroads before and after the arrival of farming.
- Iain Mathieson
- , Songül Alpaslan-Roodenberg
- & David Reich