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| Open Access
Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data
- Vivak Soni
- , John W. Terbot II
- & Jeffrey D. Jensen
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Article
| Open Access
Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations
The evolutionary genetics of a keystone savannah species the blue wildebeest, and the related black wildebeest, remain largely unexplored. This study finds evidence for archaic introgression of black wildebeest to blue wildebeest and detrimental effects of human activities on migratory populations.
- Xiaodong Liu
- , Long Lin
- & Rasmus Heller
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Article
| Open Access
Allopolyploid origin and diversification of the Hawaiian endemic mints
Hawaiian endemic mints represent the second largest plant radiation in the archipelago. Here, the authors present a reference genome and numerous resequenced individuals to uncover evidence for polyploidy, geographic speciation and localized hybridization underlying diversification in this lineage
- Crystal M. Tomlin
- , Sitaram Rajaraman
- & Charlotte Lindqvist
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Article
| Open Access
Exome-wide analysis implicates rare protein-altering variants in human handedness
Left-handedness is a common and partly heritable trait. Here, the authors perform a genome-wide screen for rare, protein-altering genetic variants associated with handedness in over 350,000 people, and implicate the tubulin gene TUBB4B.
- Dick Schijven
- , Sourena Soheili-Nezhad
- & Clyde Francks
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Article
| Open Access
An analysis of the accuracy of retrospective birth location recall using sibling data
Many surveys ask participants to retrospectively record their location of birth. Here, the authors find misreporting in retrospective birth location data in UK Biobank using data from siblings, which can lead to bias in estimates of the impact of location-based exposures.
- Stephanie von Hinke
- & Nicolai Vitt
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Article
| Open Access
The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal
The timing and chronology of the movement of Homo sapiens after migration out of Africa remains unclear. Here, the authors combine a genetic approach with a palaeoecological model to estimate that the Persian Plateau could have been a hub for migration out of Africa, suggesting the environment may have been suitable for population maintenance.
- Leonardo Vallini
- , Carlo Zampieri
- & Luca Pagani
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Article
| Open Access
Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum
Identity-by-descent (IBD) is used to infer malaria parasite population demography, but positive selection imposed by drug pressure can bias IBD estimates. This study shows that strong selection distorts IBD distributions impacting downstream inferences and presents an approach to correct these biases.
- Bing Guo
- , Victor Borda
- & Shannon Takala-Harrison
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Article
| Open Access
Divergent dynamics of sexual and habitat isolation at the transition between stick insect populations and species
Speciation may not be a mechanistically or temporally uniform process. We show divergent evolution of sexual versus habitat isolation and flat versus linear accumulation of the latter for within- versus between-species comparisons, revealing a critical role for species.
- Patrik Nosil
- , Zachariah Gompert
- & Daniel J. Funk
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Article
| Open Access
The global speciation continuum of the cyanobacterium Microcoleus
The relative importance of the various mechanisms that can drive microbial speciation is poorly understood. Here, Stanojković et al. explore the diversification of the soil cyanobacterium Microcoleus, showing that this genus represents a global speciation continuum of at least 12 lineages, with lineage divergence driven by selection, geographical distance, and the environment.
- Aleksandar Stanojković
- , Svatopluk Skoupý
- & Petr Dvořák
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Article
| Open Access
Dipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests
Dipterocarp trees are iconic but severely threatened species in Asian rainforests. This study assembles high-quality genomes of seven dipterocarp species to reveal the molecular basis of key adaptations and identifies a recent sharp population decline coinciding with local human activity.
- Rong Wang
- , Chao-Nan Liu
- & Xiao-Yong Chen
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Article
| Open Access
Porous borders at the wild-crop interface promote weed adaptation in Southeast Asia
Genome-wide evidence to support that wild rice can contribute to weedy rice evolution by hybridization and adaptive introgression is very limited. Here, the authors sequence the weedy rice genomes and show reproductively compatible wild rice can contribute to weedy rice evolution.
- Lin-Feng Li
- , Tonapha Pusadee
- & Kenneth M. Olsen
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Article
| Open Access
Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking
Here, the authors characterize the fine-scale dynamics of genome-wide insertion libraries across four human Bacteroides strains in gnotobiotic mice, revealing rapid adaptation and fitness tradeoffs when commensal gut bacteria adapt to a new host.
- Daniel P. G. H. Wong
- & Benjamin H. Good
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Article
| Open Access
Assessing emergence risk of double-resistant and triple-resistant genotypes of Plasmodium falciparum
Emergence of malaria parasites resistant to artemisinin has prompted the need for new drug regimens to ensure effective treatment. In this simulation study, the authors evaluate the risk of multidrug resistance under regimens with either concurrent or cyclic use of different first-line therapies.
- Eric Zhewen Li
- , Tran Dang Nguyen
- & Maciej F. Boni
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Article
| Open Access
Natural selection and genetic diversity maintenance in a parasitic wasp during continuous biological control application
Parasitoid wasps are reared and released as biocontrol agents to manage aphids and protect crops. Here, the authors use genomes from 542 wasps to show that, in spite of wide scale release of low-diversity captive individuals, diversity in wild populations is maintained.
- Bingyan Li
- , Yuange Duan
- & Hu Li
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Article
| Open Access
A method to estimate the contribution of rare coding variants to complex trait heritability
The contribution of rare variants to complex traits has not been well studied. Here, the authors present RARity, a method to assess rare variant heritability without assuming a particular genetic architecture and enabling both gene-level and exome-wide heritability estimation of continuous traits.
- Nazia Pathan
- , Wei Q. Deng
- & Guillaume Paré
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Article
| Open Access
Predicting the risk and speed of drug resistance emerging in soil-transmitted helminths during preventive chemotherapy
Resistance to chemotherapy for soil-transmitted helminth infection has been detected in veterinary settings but not yet in human infections. Here, the authors investigate the risk of resistance in humans and how it may change as a result of scaling-up preventative deworming programs.
- Luc E. Coffeng
- , Wilma A. Stolk
- & Sake J. de Vlas
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Article
| Open Access
Anti-CRISPR Anopheles mosquitoes inhibit gene drive spread under challenging behavioural conditions in large cages
CRISPR-based gene drives have the potential to spread within populations and are considered as promising vector control tools. Here the authors show an anti-drive mosquito strain that prevents the spread and collapse of a population suppression gene drive in laboratory Anopheles mosquito large cage trials in complex ecological and behavioral conditions.
- Rocco D’Amato
- , Chrysanthi Taxiarchi
- & Ruth Müller
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Article
| Open Access
A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm
Coffea arabica is an allotetraploid hybrid of C. eugenioides and C. canephora and contributes to approximately 60% of world coffee production. Here, the authors report its chromosome-level genome assembly and identify that chromosomal abnormalities and introgression from C. canephora may contribute to diversity and pathogen resistance.
- Simone Scalabrin
- , Gabriele Magris
- & Michele Morgante
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Article
| Open Access
A genome-wide association meta-analysis implicates Hedgehog and Notch signaling in Dupuytren’s disease
In this meta-analysis of the fibrotic hand disorder Dupuytren’s disease, the authors identify genetic risk variants, study them for their functional consequences and implicate two signaling pathways involved in the disease mechanism of this debilitating disorder.
- Sophie A. Riesmeijer
- , Zoha Kamali
- & Ilja M. Nolte
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Article
| Open Access
African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival
The evolutionary history of pigs in Africa is unclear. Here, the authors examine 67 whole genomes, finding incomplete speciation between bushpigs and red river hogs as well as evidence suggesting that humans brought bushpigs to Madagascar 1000-5000 years ago.
- Renzo F. Balboa
- , Laura D. Bertola
- & Rasmus Heller
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Article
| Open Access
Quantifying negative selection in human 3ʹ UTRs uncovers constrained targets of RNA-binding proteins
Identifying functional genetic variants in non-coding regions of the human genome is challenging. Here the authors apply their iMAPS approach to 3ʹ untranslated regions, identifying thousands of variants that disrupt post-transcriptional gene regulation.
- Scott D. Findlay
- , Lindsay Romo
- & Christopher B. Burge
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Article
| Open Access
Genomic portrait and relatedness patterns of the Iron Age Log Coffin culture in northwestern Thailand
Large log coffins placed on stilts in natural caves characterize the Iron Age of northwestern Thailand. Here, the authors conduct archaeogenetic analyses of 33 individuals, identifying a large, well-connected community, where genetic relatedness played a significant role in the mortuary ritual.
- Selina Carlhoff
- , Wibhu Kutanan
- & Johannes Krause
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Article
| Open Access
Tandem gene duplications contributed to high-level azole resistance in a rapidly expanding Candida tropicalis population
Candida tropicalis is a cause of invasive candidiasis infection in humans that has been increasingly associated with azole drug resistance. In this study, the authors investigate the genetic basis for azole resistance through analysis of whole-genome sequencing and multilocus sequence typing data.
- Xin Fan
- , Rong-Chen Dai
- & Meng Xiao
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Article
| Open Access
Structural variants involved in high-altitude adaptation detected using single-molecule long-read sequencing
Here, the authors use single-molecule long-read sequencing to decipher the role of structural variations in high-altitude adaptation, finding evidence that an intergenic deletion down-regulates EPAS1 by disrupting a super-enhancer.
- Jinlong Shi
- , Zhilong Jia
- & Kunlun He
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Article
| Open Access
The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes
The bacterium Helicobacter pylori, often found in the human stomach, can be classified into distinct subpopulations associated with the geographic origin of the host. Here, the authors provide insights into H. pylori population structure by collecting over 1,000 clinical strains from 50 countries and generating and analyzing high-quality bacterial genome sequences.
- Kaisa Thorell
- , Zilia Y. Muñoz-Ramírez
- & Charles S. Rabkin
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Article
| Open Access
Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome
The butterfly Parnassius glacialis experienced vast environmental transition when it dispersed out of the Qinghai-Tibet plateau. Here, the authors find that P. glacialis has an unusually large genome with rapid accumulation of transposable elements possibly facilitating its evolutionary adaptation.
- Youjie Zhao
- , Chengyong Su
- & Jiasheng Hao
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Article
| Open Access
The formation of the Indo-Pacific montane avifauna
The mechanisms generating montane biodiversity remain incompletely understood. Here, the authors study the passerine avifauna of Indo-Pacific island mountains, finding that Eurasian-origin species colonized directly from other mountains, while Australo-Papuan-origin species made upslope range shifts from the lowlands.
- Andrew Hart Reeve
- , Jonathan David Kennedy
- & Knud Andreas Jønsson
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Article
| Open Access
Whole genomes from Angola and Mozambique inform about the origins and dispersals of major African migrations
African human genome variation remains under-sampled. Here, the authors present a collection of 350 whole genome sequences from Angola and Mozambique and model the timing and extent of significant demographic events in African history.
- Sam Tallman
- , Maria das Dores Sungo
- & Sandra Beleza
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Article
| Open Access
A computational framework for resolving the microbiome diversity conundrum
The microbiome is thought to be important for its host’s wellbeing, but it varies much among individuals. We offer a solution to this conundrum, showing that factors like the form of microbes’ contribution to hosts’ fitness and host population size may be preventing natural selection from operating effectively.
- Itay Daybog
- & Oren Kolodny
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Article
| Open Access
Haplotype-based inference of recent effective population size in modern and ancient DNA samples
The authors introduce a new computational method, HapNe, for inferring the recent effective size of human populations. HapNe does not require high-quality genotype data, making it suitable for the study of ancient DNA samples.
- Romain Fournier
- , Zoi Tsangalidou
- & Pier Francesco Palamara
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Article
| Open Access
Local adaptation and future climate vulnerability in a wild rodent
A species’ response to anthropogenic climate change may depend on its adaptations to past climate changes. Here, the authors use whole-genome resequencing and genetic-environment association to identify genes important for local adaptation and project adaptation under future climate scenarios across bank vole populations in Britain.
- Silvia Marková
- , Hayley C. Lanier
- & Petr Kotlík
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Article
| Open Access
Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing
Indicine cattle make up half of all cattle populations worldwide. Using a large genomic dataset, this study finds historic migrations and extensive introgression with domestic and wild bovine species has facilitated this species physiological adaptation to extreme environments.
- Ningbo Chen
- , Xiaoting Xia
- & Chuzhao Lei
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Article
| Open Access
Ancient diversity in host-parasite interaction genes in a model parasitic nematode
Host-parasite interactions can lead to negative frequency-dependent selection. Here, the authors sequence the genomes of H. bakeri and H. polygyrus, parasites of house and wood mice, respectively, and find that proteins that interact with the host immune response are often highly diverse.
- Lewis Stevens
- , Isaac Martínez-Ugalde
- & Mark Blaxter
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Article
| Open Access
Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change
Extinction of megafauna is a defining trend of the last 50,000 years. Here, the authors use genomic data to infer population histories of 139 extant megafauna, suggesting that their population decline is better explained by Homo sapiens expansion than by climate change.
- Juraj Bergman
- , Rasmus Ø. Pedersen
- & Jens-Christian Svenning
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Article
| Open Access
The metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban Malawi
Pneumococcal vaccination has been shown to promote emergence of non-vaccine S. pneumoniae serotypes. Here, the authors use data from Malawi to investigate whether vaccine introduction also results in changes in metabolic, virulence, and antimicrobial resistance profiles of circulating strains.
- Uri Obolski
- , Todd D. Swarthout
- & Robert S. Heyderman
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Article
| Open Access
Candidate genes under selection in song sparrows co-vary with climate and body mass in support of Bergmann’s Rule
Ecogeographic rules link spatial patterns in phenotype and environment, potentially reflecting adaptation. This study identifies nine genes associated with body mass variation in song sparrow populations, supporting Bergmann’s Rule and highlighting the role of natural selection in local adaptation.
- Katherine Carbeck
- , Peter Arcese
- & Jennifer Walsh
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Article
| Open Access
Ancestry-specific polygenic risk scores are risk enhancers for clinical cardiovascular disease assessments
Polygenic risk scores have been proposed as useful to refine cardiovascular risk assessments. Here, the authors validate polygenic risk scores in multiple ancestries and demonstrate their utility to more accurately assess 10 year risk.
- George B. Busby
- , Scott Kulm
- & Giordano Bottà
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Article
| Open Access
Clinical utility of polygenic scores for cardiometabolic disease in Arabs
Arabs account for 5% of the world population and have a high burden of cardiometabolic disease. Here, the authors optimize polygenic scores for 10 cardiometabolic traits in 5399 Arabs, achieving a performance on par with that among European-ancestry individuals.
- Injeong Shim
- , Hiroyuki Kuwahara
- & Akl C. Fahed
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Article
| Open Access
The parasitic nematode Strongyloides ratti exists predominantly as populations of long-lived asexual lineages
Nematodes are important parasites of people and animals. Here, the authors study the population structure of a nematode parasite of wild rats finding that it consists of mixtures of mainly asexual lineages widely dispersed across the host population.
- Rebecca Cole
- , Nancy Holroyd
- & Mark Viney
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Article
| Open Access
Evolutionary origin of genomic structural variations in domestic yaks
Yaks have been subject to natural selection, human domestication and interspecific introgression during their evolution. Here, the authors have identified genomic structural variations and the linked genes involved in these processes in domestic yaks, to reveal new insight into genetic basis of phenotypic diversity.
- Xinfeng Liu
- , Wenyu Liu
- & Jianquan Liu
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Article
| Open Access
The genomic footprint of whaling and isolation in fin whale populations
Industrial whaling drove several species to near extinction. From an analysis of 50 whole-genomes from fin whale populations, this study shows that the fin whale population in the Eastern North Pacific was reduced 99% during whaling but has maintained genomic diversity, whereas the Gulf of California population remained small and isolated, resulting in increased genetic load.
- Sergio F. Nigenda-Morales
- , Meixi Lin
- & Robert K. Wayne
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Article
| Open Access
Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation
Existing genetics and genomics studies of peppers mainly focus on single species. Here, the authors report a pepper graph pan-genome and a genome variation map of 500 accessions from five domesticated species and close wild relatives to reveal their domestication, introgression and population differentiation.
- Feng Liu
- , Jiantao Zhao
- & Xuexiao Zou
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Article
| Open Access
Global determinants of insect mitochondrial genetic diversity
This study presents a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences. From over 2 million mtDNA sequences, they find a negative quadratic latitudinal gradient in genetic diversity evenness, peaking in the subtropics and correlating with hot, stable environments.
- Connor M. French
- , Laura D. Bertola
- & Michael J. Hickerson
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Article
| Open Access
Hepatic SREBP signaling requires SPRING to govern systemic lipid metabolism in mice and humans
Hendrix et al show that absence of hepatic Spring dramatically lowers levels of lipids in the liver and plasma in mice, and protects from development of diet-induced steatosis. In line, genetic variation in SPRING is associated with lipid levels in humans.
- Sebastian Hendrix
- , Jenina Kingma
- & Noam Zelcer
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Article
| Open Access
The genomic history of the indigenous people of the Canary Islands
Here, the authors use paleogenomic data from the indigenous people of the Canary Islands to shed light on the Prehistory of North Africa, and on how insularity and resources availability shaped the genetic composition of this isolated population.
- Javier G. Serrano
- , Alejandra C. Ordóñez
- & Rosa Fregel
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Article
| Open Access
Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age
By analysing 91 Bronze Age genomes from East-Central Europe, the authors discovered that Middle Bronze Age populations were formed by an admixture event involving hunter-gatherers and that the social structure of resulting population was primarily patrilocal.
- Maciej Chyleński
- , Przemysław Makarowicz
- & Helena Malmström
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Article
| Open Access
Genetic erosion reduces biomass temporal stability in wild fish populations
Experimental evidence indicates that genetic diversity can promote biomass stability, but does this process occur in wild populations? Focusing on three freshwater fish species from two river basins in southwestern France, this study shows that the biomass of genetically diversified populations has been more stable in recent decades than populations that have suffered from genetic erosion.
- Jérôme G. Prunier
- , Mathieu Chevalier
- & Simon Blanchet
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Article
| Open Access
Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
The chronology and mode of parallel evolution remain unclear. Here, the authors compare mid-Holocene and contemporary bottlenose dolphin adaptations between pelagic and coastal ecosystems with paleogenomics, finding rapid adaptation to newly emerged habitat from standing genetic variation.
- Marie Louis
- , Petra Korlević
- & Andrew D. Foote
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Article
| Open Access
Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile
Detection of resistance to the antibiotic metronidazole in C. difficile often requires the presence of heme in the media, for unclear reasons. Here, the authors show that most metronidazole-resistant strains carry a mutation that promotes expression of a heme-dependent enzyme that degrades nitroimidazoles, and the mutation often co-occurs with an amino-acid substitution in DNA gyrase that confers resistance to another class of antibiotics, fluoroquinolones.
- Abiola O. Olaitan
- , Chetna Dureja
- & Julian G. Hurdle
Patrilineal segmentary systems provide a peaceful explanation for the post-Neolithic Y-chromosome bottleneck