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Article
| Open AccessFunctional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia
Functional divergence of CYP76AK subfamily, accompanied by oxidation variations at C-20, leads to diverse abietane-type diterpenoids in Salvia species. Enzyme activity loss contributes to this unique chemical diversity within the lineage.
- Jiadong Hu
- , Shi Qiu
- & Wansheng Chen
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Article
| Open AccessPatrilocality 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 AccessClade density and the evolution of diversity-dependent diversification
common assumption of evolution is that of an ecological limit to species diversity. This study tests whether sympatry with closely-related species leads to decreasing speciation rates. They find that, for terrestrial vertebrates, the probability of speciation seems to be unaffected by the number of other species of that lineage already present
- Marcio R. Pie
- , Raquel Divieso
- & Fernanda S. Caron
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Article
| Open AccessPreventing antimalarial drug resistance with triple artemisinin-based combination therapies
Triple artemisinin-based combination therapies have shown high efficacy for treatment of malaria in preliminary studies. Here, the authors use mathematical modelling to assess whether these therapies could also delay the emergence and spread of antimalarial drug resistance when compared against frontline therapies.
- Tran Dang Nguyen
- , Bo Gao
- & Ricardo Aguas
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Article
| Open AccessRapid gene content turnover on the germline-restricted chromosome in songbirds
Songbirds have an extra chromosome with unknown function found only in their germline. This study assembles and compares this chromosome in two closely related nightingale species, finding large differences in genetic content and only one conserved gene with probable essential function.
- Stephen A. Schlebusch
- , Jakub Rídl
- & Radka Reifová
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Article
| Open AccessIntra-gastric phytoliths provide evidence for folivory in basal avialans of the Early Cretaceous Jehol Biota
Birds exhibit extensive close ecological interactions with flowering plants, but the evolutionary origins of those relationships remain unclear. Plant phytolith analysis of stomach contents of the Early Cretaceous long-tailed bird Jeholornis reveals the earliest example of leaf eating by birds.
- Yan Wu
- , Yong Ge
- & Zhonghe Zhou
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Article
| Open AccessMammalian maxilloturbinal evolution does not reflect thermal biology
The maxilloturbinal, an area of the mammalian nasal cavity, has been proposed to play a pivotal role in body temperature maintenance. Here, the authors use computed tomographic data to show that neither corrected basal metabolic rate nor body temperature significantly correlate with the relative surface area of the maxilloturbinal.
- Quentin Martinez
- , Jan Okrouhlík
- & Pierre-Henri Fabre
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Article
| Open AccessIncreased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil
Chikungunya virus is endemic in Brazil and cases have been rapidly increasing in recent years. Here, the authors describe the expansion of a genomic surveillance program across the country allowing them to characterise the emergence and dispersal of two distinct subclades mainly seeded from the north eastern region.
- Joilson Xavier
- , Luiz Carlos Junior Alcantara
- & Marta Giovanetti
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Article
| Open AccessComparative genomics reveals a unique nitrogen-carbon balance system in Asteraceae
Asteraceae is the largest family of flowering plants. Here, the authors assemble the genomes of stem lettuce (within Asteraceae) and beach cabbage (within Goodeniaceae) for evolutionary genomics analyses and reveal the absence of the core regulatory gene of nitrogen and carbon assimilation in Asteraceae.
- Fei Shen
- , Yajuan Qin
- & Xiaozeng Yang
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Article
| Open AccessC. elegans ageing is accelerated by a self-destructive reproductive programme
Caenorhabditis elegans is used as a model species to investigate ageing, yet has a very high degree of plasticity in lifespan. This study argues that ageing in C. elegans is driven by suicidal reproductive effort, unlike many other organisms.
- Carina C. Kern
- , Shivangi Srivastava
- & David Gems
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Article
| Open AccessHerbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history
Herbarium collections are an important source of historical DNA, whose analysis can shed light on the evolutionary history of plant pathogens. Here, Campos et al. reconstruct historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri from citrus herbarium specimens, estimating that the pathogen originated in Southern Asia ~11,500 years ago and diversified during the beginning of the 13th century.
- Paola E. Campos
- , Olivier Pruvost
- & Lionel Gagnevin
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Article
| Open AccessAncient 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 AccessIntegrating full and partial genome sequences to decipher the global spread of canine rabies virus
Although pathogen whole genome sequencing is becoming more common, for many pathogens far more partial sequences are available. In this study, the authors develop a phylogenetic pipeline to efficiently combine whole and partial viral genome sequences and demonstrate its application using rabies virus sequences.
- Andrew Holtz
- , Guy Baele
- & Anna Zhukova
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Article
| Open AccessComplementarity in Allen’s and Bergmann’s rules among birds
Birds can adapt to temperature gradients by changing body size (Bergmann’s rule) or bill size (Allen’s rule), but many groups don’t conform to these patterns. Here the authors show that most bird families show subtle and complementary changes in bill and body size, while also being constrained by feeding ecology.
- Justin W. Baldwin
- , Joan Garcia-Porta
- & Carlos A. Botero
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Article
| Open AccessThe effect of environmental information on evolution of cooperation in stochastic games
In stochastic games, there is a feedback loop between a group’s social behaviors and its environment. Kleshnina et al. show that groups are often more cooperative when they know the exact state of their environment, although there are also intriguing cases when ignorance is beneficial.
- Maria Kleshnina
- , Christian Hilbe
- & Martin A. Nowak
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Article
| Open AccessDecoding 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
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Article
| Open AccessMixed strain pathogen populations accelerate the evolution of antibiotic resistance in patients
Here, Caballero et al. provide an in depth characterisation of patients colonized with single or mixed strains of Pseudomonas aeruginosa to demonstrate the impact of within-host diversity on the development of antibiotic resistance.
- Julio Diaz Caballero
- , Rachel M. Wheatley
- & R. Craig MacLean
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Article
| Open AccessGroup size and mating system predict sex differences in vocal fundamental frequency in anthropoid primates
Sexual dimorphism in the fundamental frequency of primate vocalizations is variable. Here, the authors examine 1914 vocalizations from 37 anthropoid species to find that fundamental frequency dimorphism increased with larger group size and polygyny, due to sexual selection.
- Toe Aung
- , Alexander K. Hill
- & David A. Puts
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Article
| Open AccessTransmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States
The SARS-CoV-2 virus has been documented to transmit between humans and animals, providing opportunities for viral reservoirs. Here, the authors show SARS-CoV-2 lineages in free-ranging white-tailed deer across the United States, long after the lineages had declined in human populations.
- Aijing Feng
- , Sarah Bevins
- & Xiu-Feng Wan
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Article
| Open AccessRapid expansion and visual specialisation of learning and memory centres in the brains of Heliconiini butterflies
Changes in the abundance and diversity of neural cell types provide the substrate for behavioral evolution. This study provides evidence of extensive, mosaic expansion of an integration brain center, among closely related Heliconiini butterflies, associated with increased neuron number, visual processing and long term memory.
- Antoine Couto
- , Fletcher J. Young
- & Stephen H. Montgomery
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Article
| Open AccessA mid-Cambrian tunicate and the deep origin of the ascidiacean body plan
Our understanding of the origins of tunicates, an important group of filter-feeding marine invertebrate chordates, is limited due to a poor fossil record. Here, the authors present a 500 million year old tunicate fossil, demonstrating that the modern tunicate body plan was established shortly after the Cambrian Explosion.
- Karma Nanglu
- , Rudy Lerosey-Aubril
- & Javier Ortega-Hernández
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Article
| Open AccessCharacterizing the evolution and phenotypic impact of ampliconic Y chromosome regions
A major part of the human Y chromosome consists of palindromes with multiple copies of genes primarily expressed in testis. Here, the authors investigate copy number variation in these palindromes based on whole genome sequence data from 11,527 Icelandic men.
- Elise A. Lucotte
- , Valdís Björt Guðmundsdóttir
- & Kari Stefansson
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Article
| Open AccessRAS-independent ERK activation by constitutively active KSR3 in non-chordate metazoa
ERK signalling is a core developmental pathway that is canonically activated by RTKs through activated RAS. Here they show that the process of ERK activation in skeletogenic precursors of the sea urchin embryo is growth factor and RAS-independent, uncovering a new mode of ERK signalling in non-chordate metazoa.
- Aline Chessel
- , Noémie De Crozé
- & Thierry Lepage
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Article
| Open AccessParallel and convergent genomic changes underlie independent subterranean colonization across beetles
The genomic underpinnings of cave-related phenotypes are underexplored. Here, the authors investigate adaptation to underground life in cave beetle lineages using transcriptomic and genomic data, finding both parallel and convergent changes in six independent episodes of subterranean colonization.
- Pau Balart-García
- , Leandro Aristide
- & Rosa Fernández
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Article
| Open AccessSequence variants affecting the genome-wide rate of germline microsatellite mutations
Microsatellites are tandem repeats of short DNA motifs and represent some of the most polymorphic sites in the genome. Here, the authors report that the human germline microsatellite mutation rate is, in part, under genetic control.
- Snaedis Kristmundsdottir
- , Hakon Jonsson
- & Kari Stefansson
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Article
| Open AccessCoexisting ecotypes in long-term evolution emerged from interacting trade-offs
Previous, a long-term evolution experiment in E.coli resulted in spontaneous emergence of ecotypes that coexisted for more than 14,000 generations. Here, the authors show that the emergence and persistence of this phenomenon results from two interacting trade-offs, rooted in biochemical constraints.
- Avik Mukherjee
- , Jade Ealy
- & Markus Basan
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Article
| Open AccessDiploid and tetraploid genomes of Acorus and the evolution of monocots
Acorales is sister to all other monocots and contains only one family with just one genus, Acorus. Here, the authors assemble the genome of the diploid Ac. gramineus and the tetraploid Ac. calamus, reconstruct an ancestral monocot karyotype and gene toolkit, and discuss the origin and evolution of the two species and other monocots.
- Liang Ma
- , Ke-Wei Liu
- & Zhong-Jian Liu
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Article
| Open AccessThe genome of Acorus deciphers insights into early monocot evolution
Monocots are one of the most diverse and dominant clades of flowering plants. Here, the authors assemble the genome of Acorus gramineus, confirm its phylogenetic position as sister to the rest of monocots and reveal the absence of tau (τ) whole-genome duplication observed in the majority of monocot clades.
- Xing Guo
- , Fang Wang
- & Huan Liu
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Article
| Open AccessEvolvability-enhancing mutations in the fitness landscapes of an RNA and a protein
Whether evolvability itself can be a product of adaptive Darwinian evolution is a debated question. This study proposes that adaptive landscapes harbor mutations that enhance the evolvability of evolving molecules and help populations of these molecules to evolve high fitness.
- Andreas Wagner
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Article
| Open AccessCancer genomes tolerate deleterious coding mutations through somatic copy number amplifications of wild-type regions
Most of the mutations accumulated in cancer cells are deleterious, and it is unclear how such alterations are tolerated. Here, the authors propose that copy number amplifications could increase the tolerance to deleterious mutations, and analyse the features that could determine the underlying selection process.
- Fabio Alfieri
- , Giulio Caravagna
- & Martin H. Schaefer
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Article
| Open AccessSexual selection for both diversity and repetition in birdsong
Birdsong is simultaneously repetitive and highly diverse. Sierro et al. resolve this apparent paradox through experiments in blue tits showing that consistent repetition is a fitness indicator, while song diversity reduces habituation during singing displays.
- Javier Sierro
- , Selvino R. de Kort
- & Ian R. Hartley
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Article
| Open AccessBacteria evolve macroscopic multicellularity by the genetic assimilation of phenotypically plastic cell clustering
Diverse bacteria exhibit phenotypically plastic multicellular clustering. Here the authors show that a single mutation can genetically assimilate ancestrally inducible multicellularity by modulating plasticity at multiple levels of organization to make E. coli grow constitutively as macroscopic multicellular clusters.
- Yashraj Chavhan
- , Sutirth Dey
- & Peter A. Lind
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Article
| Open AccessPhylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru
The second SARS-CoV-2 wave in Peru had a high case fatality rate with Lambda and Gamma causing most cases. Using phylodynamics, the authors here show that Lambda most likely originated in Peru from where it spread to other South American countries and that the center of Peru played a key role in transmission to other regions.
- Santiago Justo Arevalo
- , Carmen Sofia Uribe Calampa
- & Joao Renato Rebello Pinho
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Article
| Open AccessDivergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries
The egg membrane protein Bouncer is an important mediator of gamete interaction and prevents cross-fertilisation between medaka and zebrafish. This study demonstrates unique functional and structural differences in Bouncer proteins of these and other distantly related fish species which may determine which species can hybridize.
- Krista R. B. Gert
- , Karin Panser
- & Andrea Pauli
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Article
| Open AccessEarly presence of Homo sapiens in Southeast Asia by 86–68 kyr at Tam Pà Ling, Northern Laos
Here the authors report new human fossils from Tam Pà Ling cave, Laos, consisting of a cranial and a tibial fragment, dated to 68–86 thousand years ago. This find confirms that Homo sapiens were present in Southeast Asia by this time and the shape of the fossils indicates they may have descended from non-local populations.
- Sarah E. Freidline
- , Kira E. Westaway
- & Fabrice Demeter
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Article
| Open AccessCoordinated adaptations define the ontogenetic shift from worm- to fish-hunting in a venomous cone snail
Challenges rearing juvenile cone snails have limited our understanding of their developmental biology. This study cultured Conus magus cone snails and revealed how complex morphological, behavioural and molecular changes facilitate the ontogenetic shift from juvenile worm-hunters to fish-hunting adults.
- Aymeric Rogalski
- , S. W. A. Himaya
- & Richard J. Lewis
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Article
| Open AccessGenomics of cold adaptations in the Antarctic notothenioid fish radiation
The notothenioid radiation is a remarkable group of fish adapted to life in the icy waters of the Southern Ocean. This study investigates the evolutionary history of this group and the basis of their adaption to cold environments through genomic analysis of 24 new genome assemblies.
- Iliana Bista
- , Jonathan M. D. Wood
- & Richard Durbin
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Article
| Open AccessQuorum sensing as a mechanism to harness the wisdom of the crowds
Bacteria release and respond to autoinducers in a process known as quorum sensing. While classically viewed as a strategy to coordinate cell behaviour, Moreno-Gámez et al. demonstrate using modelling that quorum sensing may also be used to sense the environment as a collective by pooling information at relevant scales and harnessing the wisdom of the crowds.
- Stefany Moreno-Gámez
- , Michael E. Hochberg
- & G. S. van Doorn
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Article
| Open AccessDirected natural evolution generates a next-generation oncolytic virus with a high potency and safety profile
Compromised killing effects of oncolytic viruses due to attenuation of virulence remains a challenge. Here, the authors use a directed natural evolution approach to increase the oncolytic effect of the oncolytic virus M1 attributed to mutations in the E2 and nsP3 genes.
- Li Guo
- , Cheng Hu
- & Yuan Lin
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Article
| Open AccessBreakdown of self-incompatibility due to genetic interaction between a specific S-allele and an unlinked modifier
Breakdown of self-incompatibility in plants is often attributed to S-locus mutations. Here, by crossing between populations of Arabidopsis lyrate that differ in their breeding system, the authors propose that a modifier unlinked to the S-locus causes self-compatibility by disrupting S-locus function.
- Yan Li
- , Ekaterina Mamonova
- & Marc Stift
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Article
| Open AccessThe monoaminergic system is a bilaterian innovation
Monoamines act as neuromodulators in the nervous system, but their evolutionary origins are unclear. Here, the authors examine the evolution of genes involved in monoamine production, and processing suggesting that the monoaminergic system evolved in the bilaterian stem-group.
- Matthew Goulty
- , Gaelle Botton-Amiot
- & Roberto Feuda
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Article
| Open AccessDynamic pathogen detection and social feedback shape collective hygiene in ants
Cooperative disease defense is part of group-level collective behavior. Here, the authors explore individual decisions, finding that garden ants increase grooming highly infectious individuals when they perceive a high pathogen load and suppress grooming after having been groomed by nestmates.
- Barbara Casillas-Pérez
- , Katarína Boďová
- & Sylvia Cremer
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Article
| Open AccessSequential intrahost evolution and onward transmission of SARS-CoV-2 variants
There is limited understanding of SARS-CoV-2 intra-host evolution and subsequent transmission and adaptations in the context of persistent infection. Here, the authors describe sequential persistent SARS-CoV-2 infections that led to the emergence, transmission and further evolution of a novel Omicron BA.1.23 lineage.
- Ana S. Gonzalez-Reiche
- , Hala Alshammary
- & Harm van Bakel
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Article
| Open AccessSerine ADP-ribosylation in Drosophila provides insights into the evolution of reversible ADP-ribosylation signalling
In the DNA damage response, ADP-ribosylation is an essential signaling pathway. Here the authors utilize a multidisciplinary approach to establish its molecular basis in fruit flies and provide evidence for Drosophila’s suitability as model organism.
- Pietro Fontana
- , Sara C. Buch-Larsen
- & Ivan Ahel
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Article
| Open AccessIdentification of a covert evolutionary pathway between two protein folds
Protein secondary structures–α-helices and β-sheets–are generally assumed to be fixed over evolutionary history. By leveraging sequence information and sensitive statistical techniques, this work proposes that secondary structures in naturally occurring DNA-binding proteins switched in response to stepwise mutation.
- Devlina Chakravarty
- , Shwetha Sreenivasan
- & Lauren L. Porter
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Article
| Open AccessTelomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals
Using data from the Tara Pacific expedition, this study shows that a key driver of variation in coral telomere DNA length across the Pacific Ocean is the history of water temperature. The telomere lengths of short-lived, stress-sensitive Pocillopora colonies are more sensitive to seasonal temperature variations than those of long-lived and stress-resistant Porites colonies.
- Alice Rouan
- , Melanie Pousse
- & Eric Gilson
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Article
| Open AccessTransposon signatures of allopolyploid genome evolution
Assigning assembled chromosomes to subgenome in allopolypoid genome analysis is challenging. Here, the authors report a statistical formwork for identifying evolutionarily coherent subgneomes relying on transposable elements to group chromosomes into sets with shared ancestry and apply it in cyprinids, false flax and strawberry.
- Adam M. Session
- & Daniel S. Rokhsar
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Article
| Open AccessYersinia pestis genomes reveal plague in Britain 4000 years ago
An extinct prehistoric plague lineage of Yersinia pestis has been documented from Central Europe to Asia during the Late Neolithic and Bronze Age. Here, Swali et al. show that this lineage spread to Europe’s northwestern periphery by sequencing three ~4000 year-old Yersinia pestis genomes from Britain.
- Pooja Swali
- , Rick Schulting
- & Pontus Skoglund
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Article
| Open AccessRapid evolution of A(H5N1) influenza viruses after intercontinental spread to North America
Highly pathogenic avian influenza A(H5N1) viruses of clade 2.3.4.4b underwent an explosive geographic expansion in 2021 among wild birds and domestic poultry. Here, Kandeil et al. show that the Western movement of this clade was followed by reassortment with viruses circulating in wild birds in North America which resulted in different genotypes exhibiting a wide range of disease severity in mammal models (mice, ferrets, chicken) ranging from asymptomatic disease to severe neurological pathology.
- Ahmed Kandeil
- , Christopher Patton
- & Richard J. Webby
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