Featured
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| Open AccessA large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy
Extreme colour pattern variation in male Trinidadian guppies are influenced by natural selection and sexual selection. Here, the authors phenotype and genotype four guppy lineages finding that colour pattern is associated with a diverse haplotype on an autosome.
- Josephine R. Paris
- , James R. Whiting
- & Bonnie A. Fraser
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Article
| Open AccessAncient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors
Liu et al. report genome-wide data of 33 ancient individuals from the Himalayas, illuminating the deep genetic history of Tibetans and other Tibeto-Burman-speaking populations around the Tibetan Plateau in fine resolution.
- Chi-Chun Liu
- , David Witonsky
- & Choongwon Jeong
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| Open AccessWhole-genome sequencing of 1,171 elderly admixed individuals from Brazil
Whole genome sequencing (WGS) data on non-European and admixed individuals remains scarce. Here, the authors analyse WGS data from 1,171 admixed elderly Brazilians from a census cohort, characterising population-specific genetic variation and exploring the clinical utility of this expanded dataset.
- Michel S. Naslavsky
- , Marilia O. Scliar
- & Mayana Zatz
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| Open AccessAlternative splicing in seasonal plasticity and the potential for adaptation to environmental change
Little is known about how alternative splicing and other post-transcriptional molecular mechanisms impact plasticity. Steward et al. use transcriptomic and genomic data from the butterfly Bicyclus anynana, finding that splicing plasticity is likely to experience genetic constraints.
- Rachel A. Steward
- , Maaike A. de Jong
- & Christopher W. Wheat
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| Open AccessPopulation-level deficit of homozygosity unveils CPSF3 as an intellectual disability syndrome gene
While the consequences of homozygous loss of function variants have been studied, the effect of missense variants is less understood. Here, the authors identify pathogenic genotypes through an observed deficit of homozygous carriers of missense variants in a population, elucidating previously unexplained recessive disease and miscarriage.
- Gudny A. Arnadottir
- , Asmundur Oddsson
- & Kari Stefansson
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Article
| Open AccessAssortative mating biases marker-based heritability estimators
Methods for estimating heritability, the fraction of variance attributable to genetic factors, assume random mating. Here, the authors show that under assortative mating, when mate choice reflects phenotypic similarity, these methods produce overestimates.
- Richard Border
- , Sean O’Rourke
- & Matthew C. Keller
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| Open AccessThe formation of avian montane diversity across barriers and along elevational gradients
Islands and mountaintops are often considered evolutionary dead ends. Using whole genomic data of 18 bird species and demographic models, the authors show that populations become isolated at high elevations, but disjunct montane populations maintain gene flow and thus the capacity for further colonisation.
- José Martín Pujolar
- , Mozes P. K. Blom
- & Knud Andreas Jønsson
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| Open AccessThe genomes of 204 Vitis vinifera accessions reveal the origin of European wine grapes
Reports on the origin of European wine grapes are controversial. Here, the authors perform population genetics analyses on a large set of representative wine-making varieties and reveal a single domestication event at the origin of the entire germplasm followed by repeated introgression from wild populations.
- Gabriele Magris
- , Irena Jurman
- & Michele Morgante
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Article
| Open AccessSocial stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia
Little is known about the genetic landscape of people living in the Nile region prior to the Islamic migrations of the late 1st millennium CE. Here, the authors report genome-wide data for 66 ancient individuals to investigate the genetic ancestry of a Christian Period group from Kulubnarti.
- Kendra A. Sirak
- , Daniel M. Fernandes
- & David Reich
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Article
| Open AccessEstimating the strength of selection for new SARS-CoV-2 variants
Identifying new SARS-CoV-2 genetic variants of concern is important to inform public health strategies, but distinguishing those causing a significant threat is challenging. Here, the authors develop and evaluate two models for assessing the strength of selection for new variants.
- Christiaan H. van Dorp
- , Emma E. Goldberg
- & Ethan O. Romero-Severson
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Article
| Open AccessFine-scale population structure and demographic history of British Pakistanis
Little is known about the recent population history or the effects of endogamy on the Pakistani population. Here the authors examine the impact of the biraderi social stratification system on the population structure of individuals of British Pakistani ancestry in the Born in Bradford cohort.
- Elena Arciero
- , Sufyan A. Dogra
- & Hilary C. Martin
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Article
| Open AccessPopulation analysis of Legionella pneumophila reveals a basis for resistance to complement-mediated killing
The bacterium Legionella pneumophila can cause severe respiratory infection, but is typically a symbiont of free-living amoeba. Here, the authors analyse the genomes of 902 clinical and environmental isolates, and identify a bacterial gene that is strongly associated with human infection and confers resistance to complement-mediated killing.
- Bryan A. Wee
- , Joana Alves
- & J. Ross Fitzgerald
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Article
| Open AccessA supergene underlies linked variation in color and morphology in a Holarctic songbird
Trait genetic architecture influences how populations evolve and adapt. Genomic analysis finds that an inversion links genetic variation controlling redpoll finch color and bill shape, allowing the maintenance of latitudinal ecotypes despite a genome largely homogenized by gene flow.
- Erik R. Funk
- , Nicholas A. Mason
- & Scott A. Taylor
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Article
| Open AccessThe genetic architecture of DNA replication timing in human pluripotent stem cells
The genetic basis of how cells replicate their DNA is not well understood. Here, the authors identify >1000 genetic elements that control human replication and reveal a complex epigenetic system that regulates replication origin activities.
- Qiliang Ding
- , Matthew M. Edwards
- & Amnon Koren
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Article
| Open AccessRare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4
Genetic studies of eczema to date have mostly explored common genetic variation. Here, the authors perform a large meta-analysis for common and rare variants and discover 8 loci associated with eczema. Over 20% of the heritability of the condition is attributable to rare variants.
- Sarah Grosche
- , Ingo Marenholz
- & Young-Ae Lee
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| Open AccessStructural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation
Although many studies have characterized genetic variation in human populations, few have investigated structural variation and few have been in non-European populations. Here, the authors have performed long read sequencing on 405 Chinese individuals to identify structural variants and link them to phenotypes.
- Zhikun Wu
- , Zehang Jiang
- & Zhi Xie
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Article
| Open AccessDiscordant associations of educational attainment with ASD and ADHD implicate a polygenic form of pleiotropy
Autism Spectrum Disorder and Attention-Deficit/Hyperactivity Disorder are co-occurring neurodevelopmental conditions displaying strong, discordant polygenic associations with educational attainment. Here, the authors study genetic mechanisms underlying genome-wide correlation patterns across these traits.
- Ellen Verhoef
- , Jakob Grove
- & Beate St Pourcain
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| Open AccessThe history and geographic distribution of a KCNQ1 atrial fibrillation risk allele
Many rare high-impact variants have been associated with disease, but the origins and functional impact are not always explored. Here, the authors trace the ancestry of a rare high impact atrial fibrillation allele in KCNQ1, and use iPSC-derived cardiomyocytes to characterize the effect of the allele.
- Shannon Hateley
- , Angelica Lopez-Izquierdo
- & Martin Tristani-Firouzi
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Article
| Open AccessEstimating disease prevalence in large datasets using genetic risk scores
Estimating disease prevalence in biobanks is prone to error, especially for self-reported traits. Here, the authors propose a method to estimate the prevalence of a disease within a cohort based on genetic risk scores.
- Benjamin D. Evans
- , Piotr Słowiński
- & Nicholas J. Thomas
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| Open AccessMicroevolutionary dynamics show tropical valleys are deeper for montane birds of the Atlantic Forest
There are many hypotheses for why the tropics are more biodiverse than higher latitudes. Phylogenomic analyses of 21 montane birds finds that tropical birds disperse less and have more genetically structured populations than their counterparts at higher latitudes, possibly due to a larger elevational climate gradient in the tropics
- Gregory Thom
- , Marcelo Gehara
- & Fábio Raposo do Amaral
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| Open AccessRefining models of archaic admixture in Eurasia with ArchaicSeeker 2.0
Existing methods to identify the presence of DNA from other hominin species can be limited in the ability to accurately estimate introgression waves, or can only be applied to specific populations. Here, the authors have developed a generalizable method to identify introgression in multi-wave situations.
- Kai Yuan
- , Xumin Ni
- & Shuhua Xu
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| Open AccessRapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020
The true number of infections from SARS-Cov-2 is unknown and believed to exceed the reported numbers by several fold. National testing policies, in particular, can strongly affect the proportion of undetected cases. Here, the authors propose a method that reconstructs incidence profiles within minutes, solely from publicly available, time-stamped viral genomes.
- Maureen Rebecca Smith
- , Maria Trofimova
- & Max von Kleist
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| Open AccessThousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes
Arab populations are relatively understudied, especially their genetic architecture and historical relationship with early founders of the ancient Near East. Here, the authors examine 6,218 Qatari whole genomes, revealing insights on migration, population history and genetic structure of populations across the Middle Eastern region.
- Rozaimi Mohamad Razali
- , Juan Rodriguez-Flores
- & Younes Mokrab
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| Open AccessThe genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas
Indigenous populations, including in those in Mexico are underrepresented in genetic studies. Here, the authors perform a population genetics study of indigenous peoples in Mexico to explore demographic histories of the region in the context of geography and cultural influences.
- Humberto García-Ortiz
- , Francisco Barajas-Olmos
- & Lorena Orozco
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| Open AccessParental relatedness through time revealed by runs of homozygosity in ancient DNA
Little is known about how human parental relatedness varied across ancient populations. Runs of homozygosity (ROH) in the offspring’s genome can give clues. Here, the authors present a method to identify ROH in ancient genomes and infer low rates of close kin unions across most ancient populations.
- Harald Ringbauer
- , John Novembre
- & Matthias Steinrücken
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| Open AccessGenetic basis and adaptation trajectory of soybean from its temperate origin to tropics
How soybean, a temperate origin crop, adapted to a tropical environment remains unclear. Here, the authors report Tof16, an ortholog of LHY, and the previously identified J locus, control soybean yield under short-day condition and loss of function of these two genes contributes to the adaptation to tropics.
- Lidong Dong
- , Chao Fang
- & Baohui Liu
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Article
| Open AccessEstimating direct and indirect genetic effects on offspring phenotypes using genome-wide summary results data
Estimating direct and indirect effects of genotypes on phenotypes is important for genetic analyses such as Mendelian randomization. Here the authors compare five different methods to estimate direct and indirect genetic effects using summary results statistics that account for sample overlap.
- Nicole M. Warrington
- , Liang-Dar Hwang
- & David M. Evans
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| Open AccessDifferent historical generation intervals in human populations inferred from Neanderthal fragment lengths and mutation signatures
Historical interbreeding between Neanderthals and humans should leave signatures of historical demographics in modern human genomes. Analysing the size distribution of Neanderthal fragments in non-African genomes suggests consistent differences in the generation interval across Eurasia, and that this could explain mutational spectrum variation.
- Moisès Coll Macià
- , Laurits Skov
- & Mikkel Heide Schierup
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| Open AccessTranslating polygenic risk scores for clinical use by estimating the confidence bounds of risk prediction
The application of polygenic risk scores to individual-level disease susceptibility is challenging, as risk is evaluated at a group-level. Here, the authors describe a machine learning method, Mondrian Cross-Conformal Prediction, that reports disease status conditional probability value at the individual level.
- Jiangming Sun
- , Yunpeng Wang
- & Kasper Lage
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Article
| Open AccessParallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles
Relative contributions of pre-existing versus de novo genomic variation to adaptation remain unclear. Here, the authors address this problem by examining the adaptation of autotetraploid Arabidopsis arenosa to serpentine soils and find that both types of variations contribute to rapid adaptation.
- Veronika Konečná
- , Sian Bray
- & Filip Kolář
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Article
| Open AccessInteracting evolutionary pressures drive mutation dynamics and health outcomes in aging blood
Age-related clonal hematopoiesis is associated with risk for diseases like acute myeloid leukemia (AML), yet it is unclear why some individuals do not progress despite having AML driver mutations. Here, the authors use deep learning and population genetics models to investigate how the interplay of positive and negative selection influences AML progression.
- Kimberly Skead
- , Armande Ang Houle
- & Philip Awadalla
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Article
| Open AccessWhole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration
Schistosomiasis control strategies rely on mass drug administration (MDA) using praziquantel. Here, Berger et al. perform whole-genome sequencing of larvae from infected children across Ugandan regions with differing MDA histories. They find extensive gene flow with limited positive selection suggesting minimal change post MDA.
- Duncan J. Berger
- , Thomas Crellen
- & James A. Cotton
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Article
| Open AccessDiversification of mandarin citrus by hybrid speciation and apomixis
To explore the nature of wild and cultivated mandarins, the authors carry out genomic analysis of diverse east Asian citrus. The discovery of a wild species Citrus ryukyuensis native to the Ryukyu islands and a new population of wild mainland Asian mandarin explains the origin and diversity of mandarins and their ability to reproduce apomictically.
- Guohong Albert Wu
- , Chikatoshi Sugimoto
- & Daniel S. Rokhsar
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| Open AccessQuantifying the contribution of Neanderthal introgression to the heritability of complex traits
We lack a comprehensive understanding of how Neanderthal ancestry influences human traits. This study finds that regions with Neanderthal ancestry are broadly depleted of trait-associated variation; yet, introgressed variants likely contributed to human adaptation in a few traits, like skin color and immune response modulation.
- Evonne McArthur
- , David C. Rinker
- & John A. Capra
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| Open AccessContextualizing genetic risk score for disease screening and rare variant discovery
Genetic studies on complex traits have revealed a substantial role for common, small-effect polygenic burden and large-effect variants. Here, the authors investigate how these types of variation can inform disease risk stratification and prediction.
- Dan Zhou
- , Dongmei Yu
- & Eric R. Gamazon
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| Open AccessExtensive standing genetic variation from a small number of founders enables rapid adaptation in Daphnia
Standing genetic variation allows natural populations to evolve rapidly. Genome sequences of a resurrected Daphnia population show that genetic variation carried by only five founding individuals from the regional genotype pool is enough to fuel rapid evolution in response to strong selection pressures with no evidence of genetic erosion.
- Anurag Chaturvedi
- , Jiarui Zhou
- & Luc De Meester
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| Open AccessSignatures of mitonuclear coevolution in a warbler species complex
Little is known on how mitonuclear interactions influence genomic divergence among hybrid and parental lineages. A study of hybridizing wood warbler species complex finds a nuclear gene block with mitochondrial functions coevolves with mitochondrial genome, driven by climate-associated divergent selection underlying hybrid-parental population divergence.
- Silu Wang
- , Madelyn J. Ore
- & Darren Irwin
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Article
| Open AccessProfiling variable-number tandem repeat variation across populations using repeat-pangenome graphs
Variable number tandem repeats (VNTRs) are difficult to analyze by short-read sequencing in disease studies. Here, the authors describe a VNTR mapping strategy for short-read analyses using a repeat pangenome graph. This method will help elucidate the contribution of VNTRs to diversity and disease.
- Tsung-Yu Lu
- , Katherine M. Munson
- & Mark J. P. Chaisson
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| Open AccessPopulation genomics of apricots unravels domestication history and adaptive events
The evolutionary and domestication history of apricots is poorly understood. Here, the authors provide four apricot high-quality genome assemblies, the genomes of 578 accessions from natural and cultivated populations, and show that Chinese and European apricots constitute two different gene pools, resulting from independent domestication events.
- Alexis Groppi
- , Shuo Liu
- & Véronique Decroocq
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Article
| Open AccessEvidence of the interplay of genetics and culture in Ethiopia
Ethiopia is one of the most ethnically and culturally diverse countries. Here, the authors look at genetic and cultural variation in 1,214 Ethiopians to unravel the relationship between genetic admixture and cultural factors.
- Saioa López
- , Ayele Tarekegn
- & Garrett Hellenthal
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Article
| Open AccessRapid detection of identity-by-descent tracts for mega-scale datasets
Traditional methods to identify genomic regions identical-by-descent (IBD) do not scale well to biobank-level datasets. Here, the authors describe a new IBD algorithm, iLASH, which uses LocAlity-Sensitive Hashing to provide rapid IBD estimation when applied to the PAGE and UK Biobank datasets.
- Ruhollah Shemirani
- , Gillian M. Belbin
- & José Luis Ambite
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Article
| Open AccessLeveraging supervised learning for functionally informed fine-mapping of cis-eQTLs identifies an additional 20,913 putative causal eQTLs
Finding causal variants and genes from GWAS loci results remains a challenge. Here, the authors train a model to predict if a variant affects nearby gene expression, and apply the method to identify new possible causal eQTLs and mechanisms of GWAS loci.
- Qingbo S. Wang
- , David R. Kelley
- & Hilary K. Finucane
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Article
| Open AccessDistinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa
The genetic diversity of Plasmodium vivax strains in South Asia isn’t well described. Here, the authors sequence P. vivax from returning UK travelers and establish South Asian isolates as subpopulation distinct from East African and South East Asian isolates.
- Ernest Diez Benavente
- , Emilia Manko
- & Taane G. Clark
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Article
| Open AccessOffspring survival changes over generations of captive breeding
Captive breeding could prevent species extinctions, but selection for captivity may decrease fitness. Here the authors analyse pedigree data on 15 long-running vertebrate breeding programs and find generational fitness changes that processes such as inbreeding depression cannot explain.
- Katherine A. Farquharson
- , Carolyn J. Hogg
- & Catherine E. Grueber
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Matters Arising
| Open AccessReply to “Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin”
- David A. Marques
- , Kay Lucek
- & Ole Seehausen
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Matters Arising
| Open AccessRe-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin
- Daniel Berner
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Article
| Open AccessPopulation genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii
Mycobacterium kansasii can cause serious pulmonary disease. Here, the authors present a population genomics analysis of 358 environmental and clinical isolates from around the world, supporting the idea that municipal water is a main source of infection, and shedding light into the pathogen’s diversity and adaptation to the human host.
- Tao Luo
- , Peng Xu
- & Qian Gao
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| Open AccessGenomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations
Highly endangered species like the Sumatran rhinoceros are at risk from inbreeding. Five historical and 16 modern genomes from across the species range show mutational load, but little evidence for local adaptation, suggesting that future inbreeding depression could be mitigated by assisted gene flow among populations.
- Johanna von Seth
- , Nicolas Dussex
- & Love Dalén
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Article
| Open AccessGenetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions
Estimating the effects of non-pharmaceutical interventions for COVID-19 is challenging, partly due to variations in testing. Here, the authors use viral sequence data as an alternative means of inferring intervention effects, and show that delays in implementation resulted in more severe epidemics.
- Manon Ragonnet-Cronin
- , Olivia Boyd
- & Erik Volz