Featured
-
-
Article
| Open AccessMalaria protection due to sickle haemoglobin depends on parasite genotype
A strong association has been found between three regions of the Plasmodium falciparum genome and sickle haemoglobin in children with severe malaria, suggesting parasites have adapted to overcome natural host immunity.
- Gavin Band
- , Ellen M. Leffler
- & Dominic P. Kwiatkowski
-
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
-
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
-
Article
| Open AccessGenomic reconstruction of the SARS-CoV-2 epidemic in England
A study of the evolution of the SARS-CoV-2 virus in England between September 2020 and June 2021 finds that interventions capable of containing previous variants were insufficient to stop the more transmissible Alpha and Delta variants.
- Harald S. Vöhringer
- , Theo Sanderson
- & Moritz Gerstung
-
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
-
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
-
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
-
Article
| Open AccessA high-quality bonobo genome refines the analysis of hominid evolution
A high-quality bonobo genome assembly provides insights into incomplete lineage sorting in hominids and its relevance to gene evolution and the genetic relationship among living hominids.
- Yafei Mao
- , Claudia R. Catacchio
- & Evan E. Eichler
-
Article
| Open AccessTowards complete and error-free genome assemblies of all vertebrate species
The Vertebrate Genome Project has used an optimized pipeline to generate high-quality genome assemblies for sixteen species (representing all major vertebrate classes), which have led to new biological insights.
- Arang Rhie
- , Shane A. McCarthy
- & Erich D. Jarvis
-
Article
| Open AccessUniversal nomenclature for oxytocin–vasotocin ligand and receptor families
A revised, universal nomenclature for the vertebrate genes that encode the oxytocin and vasopressin–vasotocin ligands and receptors will improve our understanding of gene evolution and facilitate the translation of findings across species.
- Constantina Theofanopoulou
- , Gregory Gedman
- & Erich D. Jarvis
-
Article
| Open AccessEvolutionary and biomedical insights from a marmoset diploid genome assembly
A trio-binning approach is used to produce a fully haplotype-resolved diploid genome assembly for the common marmoset, providing insight into the heterozygosity spectrum and the evolution of the sex-differentiation region.
- Chentao Yang
- , Yang Zhou
- & Guojie Zhang
-
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
-
Article
| Open AccessThe structure, function and evolution of a complete human chromosome 8
The complete assembly of human chromosome 8 resolves previous gaps and reveals hidden complex forms of genetic variation, enabling functional and evolutionary characterization of primate centromeres.
- Glennis A. Logsdon
- , Mitchell R. Vollger
- & Evan E. Eichler
-
Article |
Climate-driven flyway changes and memory-based long-distance migration
The routes and lengths of migrations of Eurasian Arctic peregrine falcons have probably been shaped by climate change across the Last Glacial Maximum–Holocene transition and by selection for long-term memory acting on ADCY8, respectively.
- Zhongru Gu
- , Shengkai Pan
- & Xiangjiang Zhan
-
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
-
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
-
Review Article |
Origins of modern human ancestry
A Review describes the three key phases that define the origins of modern human ancestry, and highlights the importance of analysing both palaeoanthropological and genomic records to further improve our understanding of our evolutionary history.
- Anders Bergström
- , Chris Stringer
- & Pontus Skoglund
-
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
-
Perspective |
Lessons from the host defences of bats, a unique viral reservoir
Unique biological traits of bats and adaptive evolution associated with flight confer immunotolerance of viral infection that may help to make bats special reservoir hosts for viruses.
- Aaron T. Irving
- , Matae Ahn
- & Lin-Fa Wang
-
Article
| Open AccessGiant lungfish genome elucidates the conquest of land by vertebrates
A chromosome-quality genome of the lungfish Neoceratodus fosteri sheds light on the development of obligate air-breathing and the gain of limb-like gene expression in lobed fins, providing insights into the water-to-land transition in vertebrate evolution.
- Axel Meyer
- , Siegfried Schloissnig
- & Manfred Schartl
-
Article |
Dire wolves were the last of an ancient New World canid lineage
Dire wolves split from living canids around 5.7 million years ago and originated in the New World isolated from the ancestors of grey wolves and coyotes, which evolved in Eurasia and colonized North America only relatively recently.
- Angela R. Perri
- , Kieren J. Mitchell
- & Laurent A. F. Frantz
-
Article
| Open AccessPlatypus and echidna genomes reveal mammalian biology and evolution
New reference genomes of the two extant monotreme lineages (platypus and echidna) reveal the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution.
- Yang Zhou
- , Linda Shearwin-Whyatt
- & Guojie Zhang
-
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
-
Article |
Widespread endogenization of giant viruses shapes genomes of green algae
The authors show that large endogenous viral elements derived from giant viruses are prominent components of green algal genomes.
- Mohammad Moniruzzaman
- , Alaina R. Weinheimer
- & Frank O. Aylward
-
Article |
A molecular cell atlas of the human lung from single-cell RNA sequencing
Expression profiling on 75,000 single cells creates a comprehensive cell atlas of the human lung that includes 41 out of 45 previously known cell types and 14 new ones.
- Kyle J. Travaglini
- , Ahmad N. Nabhan
- & Mark A. Krasnow
-
Article |
Dense sampling of bird diversity increases power of comparative genomics
A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
- Shaohong Feng
- , Josefin Stiller
- & Guojie Zhang
-
Article |
A yeast living ancestor reveals the origin of genomic introgressions
A yeast clonal descendant of an ancient hybridization event is identified and sheds light on the early evolution of the Saccharomyces cerevisiae Alpechin lineage and its abundant Saccharomyces paradoxus introgressions.
- Melania D’Angiolo
- , Matteo De Chiara
- & Gianni Liti
-
Analysis
| Open AccessA comparative genomics multitool for scientific discovery and conservation
A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal—including 131 previously uncharacterized species—from the Zoonomia Project provides data that support biological discovery, medical research and conservation.
- Diane P. Genereux
- , Aitor Serres
- & Elinor K. Karlsson
-
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
-
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
-
Article |
The major genetic risk factor for severe COVID-19 is inherited from Neanderthals
Risk of severe COVID-19 is conferred by a genomic segment that is inherited from Neanderthals and is carried by around 50% and 16% of people in south Asia and Europe, respectively.
- Hugo Zeberg
- & Svante Pääbo
-
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
-
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
-
Article |
Origin of complexity in haemoglobin evolution
Experimental analysis of reconstructed ancestral globins reveals that haemoglobin’s complex tetrameric structure and oxygen-binding functions evolved by simple genetic and biophysical mechanisms.
- Arvind S. Pillai
- , Shane A. Chandler
- & Joseph W. Thornton
-
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
-
Article |
The dental proteome of Homo antecessor
Analyses of the proteomes of dental enamel from Homo antecessor and Homo erectus demonstrate that the Early Pleistocene H. antecessor is a close sister lineage of later Homo sapiens, Neanderthal and Denisovan populations in Eurasia.
- Frido Welker
- , Jazmín Ramos-Madrigal
- & Enrico Cappellini
-
Article |
Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins
SARS-CoV-2-related coronaviruses are identified in Malayan pangolins (Manis javanica); these pangolin-associated coronaviruses belonged to two sub-lineages of SARS-CoV-2-related coronaviruses, including one that exhibits strong similarity in the receptor-binding domain to SARS-CoV-2.
- Tommy Tsan-Yuk Lam
- , Na Jia
- & Wu-Chun Cao
-
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
-
Article |
Human origins in a southern African palaeo-wetland and first migrations
Analyses of mitochondrial genomes from populations in southern Africa provide evidence of a southern African origin of anatomically modern humans and a sustained occupation of the homeland before the first migrations of people appear to be driven by regional climate shifts.
- Eva K. F. Chan
- , Axel Timmermann
- & Vanessa M. Hayes
-
Letter |
Genome editing retraces the evolution of toxin resistance in the monarch butterfly
CRISPR–Cas9 engineering of the Drosophila Atpα gene (encoding the α-subunit of the sodium pump) is used to study the ability of mutations that evolved independently in several insect orders to confer resistance to keystone plant toxins.
- Marianthi Karageorgi
- , Simon C. Groen
- & Noah K. Whiteman
-
Letter |
Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny
Palaeoproteomic analysis of dental enamel from an Early Pleistocene Stephanorhinus resolves the phylogeny of Eurasian Rhinocerotidae, by enabling the reconstruction of molecular evolution beyond the limits of ancient DNA preservation.
- Enrico Cappellini
- , Frido Welker
- & Eske Willerslev
-
Letter |
Natural selection on the Arabidopsis thaliana genome in present and future climates
The predicted increase in frequency of droughts and rising temperatures in Europe will lead core populations of a temperate plant to an evolutionary dead-end unless they acquire genetic alleles that are present only in extreme edge Mediterranean, Scandinavian, or Siberian populations.
- Moises Exposito-Alonso
- , Moises Exposito-Alonso
- & Detlef Weigel
-
Article |
Gene expression across mammalian organ development
The transcriptomes of seven major organs across developmental stages from several mammalian species are used for comparative analyses of gene expression and evolution across organ development.
- Margarida Cardoso-Moreira
- , Jean Halbert
- & Henrik Kaessmann
-
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
-
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
-
Letter |
Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia
A single-cell approach is used to follow the heritable stochastic changes to DNA methylation that occur in primary chronic lymphocytic leukaemia and healthy B cells, allowing the tracing of cell lineage histories and evolution during treatment with ibrutinib.
- Federico Gaiti
- , Ronan Chaligne
- & Dan A. Landau
-
Letter |
A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau
Fossil evidence indicates that Denisovans occupied the Tibetan Plateau in the Middle Pleistocene epoch and successfully adapted to this high-altitude hypoxic environments long before the regional arrival of modern Homo sapiens.
- Fahu Chen
- , Frido Welker
- & Jean-Jacques Hublin
-
Letter |
Heterozygous mutations cause genetic instability in a yeast model of cancer evolution
Repeated selection for adaptive mutations in a diploid yeast model results in increased genetic instability and sheds light on mechanisms of genetic instability that might contribute to tumorigenesis.
- Miguel C. Coelho
- , Ricardo M. Pinto
- & Andrew W. Murray
-
Article |
Age-related remodelling of oesophageal epithelia by mutated cancer drivers
In physiologically normal epithelia, age-related expansion of clones that carry mutations in NOTCH1 and other driver genes is accelerated by risk factors for developing oesophageal squamous cell carcinoma, such as alcohol consumption or smoking.
- Akira Yokoyama
- , Nobuyuki Kakiuchi
- & Seishi Ogawa