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| Open AccessOrigin and dispersal history of Hepatitis B virus in Eastern Eurasia
Hepatitis B virus is an ancient human pathogen that dates back more than 10,000 years. Here, the authors investigate the evolutionary history of the virus in Eastern Eurasia by sequencing 34 genomes dating from approximately 400–5,000 years ago and comparing them with other contemporary sequences.
- Bing Sun
- , Aida Andrades Valtueña
- & Yinqiu Cui
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Article
| Open AccessEarly detection of emerging viral variants through analysis of community structure of coordinated substitution networks
Rise of new viral strains is a major public health challenge, demanding advanced detection and forecasting methods. This study shows how examining communities within networks of viral mutations enables early detection of emerging strains.
- Fatemeh Mohebbi
- , Alex Zelikovsky
- & Pavel Skums
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Article
| Open AccessThe Miocene primate Pliobates is a pliopithecoid
Pliobates cataloniae is a small-bodied Miocene catarrhine primate with unclear systematic status. Here, the authors present additional dental remains from this species, conducting cladistic analyses that indicate it is a pliopithecoid convergent with apes in elbow and wrist morphology.
- Florian Bouchet
- , Clément Zanolli
- & David M. Alba
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Article
| Open AccessHigh temperature delays and low temperature accelerates evolution of a new protein phenotype
The effect of temperature fluctuations on the evolution of new phenotypes is largely unknown. Using experimental evolution of fluorescent protein in E. coli, this study shows that a cooling environment can accelerate, and a warming environment decelerate, the evolution of a new protein phenotype.
- Jia Zheng
- , Ning Guo
- & Andreas Wagner
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Article
| Open AccessAnaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution
Here, Pratt et al identify a community of deep-branching anaerobic fungi in tortoise feces. Multiple characteristics underpinning their success in tortoise, as opposed to scarcity in mammalian alimentary tracts, are presented.
- Carrie J. Pratt
- , Casey H. Meili
- & Noha H. Youssef
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Article
| Open AccessMethyl transfer in psilocybin biosynthesis
The natural hallucinogen psilocybin — produced by so-called magic mushrooms — holds promise for the treatment of depression and other mental health conditions. Here, the authors provide a structural and biochemical analysis of the Psilocybe methyl transferase PsiM that provides mechanistic insight into the last step of psilocybin biosynthesis.
- Jesse Hudspeth
- , Kai Rogge
- & Sebastiaan Werten
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Article
| Open AccessBee-pollination promotes rapid divergent evolution in plants growing in different soils
In nature, soil, pollinators, and herbivores are the main drivers of plant adaptation and diversification. This study reveals that the interaction between soil and biotic pollination causes divergent evolution where pollinators play a key role, leading to strong divergence among plants in different soils.
- Thomas Dorey
- & Florian P. Schiestl
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Article
| Open AccessNaked mole-rats have distinctive cardiometabolic and genetic adaptations to their underground low-oxygen lifestyles
The naked mole-rat exhibits extreme longevity, resistance to hypoxia and absence of cardiovascular disease. Here, Faulkes et al. identify mechanisms behind these traits by comparing cardiac metabolomes and transcriptomes of naked more-rats to other African mole-rat genera and evolutionary divergent mammals.
- Chris G. Faulkes
- , Thomas R. Eykyn
- & Dunja Aksentijevic
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Article
| Open AccessTrade-offs shaping transmission of sylvatic dengue and Zika viruses in monkey hosts
Hanley et al show that transmission of dengue and Zika virus from Old and New World monkeys is shaped by an immunologically-mediated trade-off between magnitude and duration of replication. Patterns of Zika transmission suggests high risk of spillback into neotropical monkeys.
- Kathryn A. Hanley
- , Hélène Cecilia
- & Shannan L. Rossi
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Article
| Open AccessMacroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages
Correspondence between genome and organismal complexity over macroevolutionary time is poorly understood. Here the authors show that multicellular eukaryotes increasingly simplify their genomes and suggest that the concept of functional outsourcing, via ecological interactions, could explain this paradoxical complexity decoupling.
- Mirjana Domazet-Lošo
- , Tin Široki
- & Tomislav Domazet-Lošo
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Article
| Open AccessSynthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose
Pseudomonas putida is becoming a host of choice for the valorization of lignocellulosic substrates. Here, the authors provide insight into the adaptation of this bacterium to the non-native substrate D-xylose, enabled by metabolic engineering and adaptive laboratory evolution.
- Pavel Dvořák
- , Barbora Burýšková
- & Martin Benešík
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Article
| Open AccessThe 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 AccessPlasmid-mediated phenotypic noise leads to transient antibiotic resistance in bacteria
In this work, authors combine computational models with single-cell and population-level data showing the variability in plasmid copy number within bacterial populations leads to phenotypic diversity. They reveal how multicopy plasmids contribute to bacterial transient antibiotic resistance.
- J. Carlos R. Hernandez-Beltran
- , Jerónimo Rodríguez-Beltrán
- & Rafael Peña-Miller
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Article
| Open AccessPredictive evolutionary modelling for influenza virus by site-based dynamics of mutations
Seasonal influenza vaccine effectiveness depends on including virus strains in the vaccine that closely match those circulating in the upcoming season. In this study, the authors develop a computational model of influenza virus evolution to predict future circulating strains and therefore support vaccine strain selection.
- Jingzhi Lou
- , Weiwen Liang
- & Maggie Haitian Wang
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Article
| Open AccessAn evolutionary mechanism to assimilate new nutrient sensors into the mTORC1 pathway
Unmet expectations, a previously uncharacterized fly protein, is a SAM sensor for the mTORC1 pathway. Tracing the evolution of Unmet reveals that the pathway uses the GATOR2 complex to capture and repurpose ancestral enzymes as nutrient sensors.
- Grace Y. Liu
- , Patrick Jouandin
- & David M. Sabatini
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Article
| Open AccessDynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry
Subgenome dominance is widely observed in allopolyploid species, but the molecular mechanisms remain unclear. Here, the authors generate genome-wide map of accessible chromatin regions (ACRs) in allo-octoploid cultivated strawberry and reveal that dynamics of the ACRs play an important role in its subgenome dominance.
- Chao Fang
- , Ning Jiang
- & Jiming Jiang
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Article
| Open AccessThe evolutionary origin of naturally occurring intermolecular Diels-Alderases from Morus alba
Diels-Alderases (DAs), enzymes catalyzing [4 + 2] cycloaddition reactions, are of high interest, but insights into their evolution are lacking. Here, the authors investigate the evolutionary origins of the intermolecular DAs in the biosynthesis of Moraceae plant-derived Diels-Alder-type secondary metabolites, suggesting they evolved from an ancestor functioning as a flavin adenine dinucleotide-dependent oxidocyclase.
- Qi Ding
- , Nianxin Guo
- & Xiaoguang Lei
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Article
| Open AccessSingle cell atlas of Xenoturbella bocki highlights limited cell-type complexity
Recent phylogenetic analyses have identified orphan clades, including Xenacoelomorphs, that can offer insights into bilaterian evolution. Here they generate a cell type atlas of Xenoturbella bockithat highlights cellular diversity in the nervous system and other tissues, reinforcing the idea of parallel evolution of cell types across animals.
- Helen E. Robertson
- , Arnau Sebé-Pedrós
- & Heather Marlow
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Article
| Open AccessEvolutionary origin of Hoxc13-dependent skin appendages in amphibians
Hair is the main skin appendage of mammals. Here, the authors show that claws of clawed frogs and hair contain homologous keratins and depend on the same transcription factor, Hoxc13, suggesting a common evolutionary origin of these skin appendages.
- Marjolein Carron
- , Attila Placido Sachslehner
- & Leopold Eckhart
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Article
| Open AccessTemporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids
Wei et al. report a unique interspecific ascidian hybrid system and single-cell RNA sequencing to reveal the temporal hierarchy, spatial heterogeneity, and allele-specific expression of zygotic genome activation in urochordates.
- Jiankai Wei
- , Wei Zhang
- & Bo Dong
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Article
| Open AccessClearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation
There is limited data on immune factors contributing to SARS-CoV-2 viral clearance in people living with HIV. Here, the authors show that re-emergence of the neutralizing antibody response may be key to clearing persistent SARS-CoV-2 infection in ART-mediated recovery from immunosuppression in advanced HIV disease.
- Farina Karim
- , Catherine Riou
- & Alex Sigal
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Article
| Open AccessDivergent 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 AccessInter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis
Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection closely related to Streptococcus pyogenes. Here the authors investigate the degree of genomic similarity between the two species and assess implications for development of vaccines.
- Ouli Xie
- , Jacqueline M. Morris
- & Mark R. Davies
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Article
| Open AccessNew estimates indicate that males are not larger than females in most mammal species
The narrative that larger males are the norm in mammals has predominated for over a century. An analysis of body mass dimorphism across mammals, sampling families by their species richness, indicates that males are not larger than females in most mammals and that monomorphism is almost as prevalent.
- Kaia J. Tombak
- , Severine B. S. W. Hex
- & Daniel I. Rubenstein
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Article
| Open AccessDependency on host vitamin B12 has shaped Mycobacterium tuberculosis Complex evolution
Campos-Pardos et al show that the virulence of Mycobacterium tuberculosis is dependent on sufficient uptake of exogenous vitamin B12 from host serum and this phenotype is not conserved in environmental, opportunistic and ancestral lineages.
- Elena Campos-Pardos
- , Santiago Uranga
- & Jesús Gonzalo-Asensio
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Article
| Open AccessThe 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 AccessBet hedging in a unicellular microalga
Bet hedging is an evolutionary strategy facilitating survival in randomly fluctuating environments. Here, the authors report bet hedging in the unicellular microalga Haematococcus pluvialis, undergoing reversible diversification into mobile and non-mobile cells.
- Si Tang
- , Yaqing Liu
- & Zhonghua Cai
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Article
| Open AccessBiosensor and machine learning-aided engineering of an amaryllidaceae enzyme
Amaryllidaceae alkaloids, such as the Alzheimer’s medication galantamine, are currently extracted from low-yielding daffodils. Here, authors pair biosensor-assisted screening with machine learning-guided protein design to rapidly engineer an improved Amaryllidaceae enzyme in a microbial host.
- Simon d’Oelsnitz
- , Daniel J. Diaz
- & Andrew D. Ellington
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Article
| Open AccessKey homeobox transcription factors regulate the development of the firefly’s adult light organ and bioluminescence
Adult firefly light organs exhibit flashing signals important for courtship, though how these organs form during development is largely unknown. Here the authors demonstrate that homeobox transcription factors play a patterning role in the development of the adult light organs.
- Xinhua Fu
- & Xinlei Zhu
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Article
| Open AccessExtensive DNA methylome rearrangement during early lamprey embryogenesis
DNA methylation plays a major role in establishing cell identity, but the dynamics of DNA methylation patterns are highly variable across species. Here, the authors discover extensive DNA methylation reprogramming during embryonic development of the sea lamprey, a jawless fish with a distinctive, highly disordered methylome.
- Allegra Angeloni
- , Skye Fissette
- & Ozren Bogdanovic
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Article
| Open AccessWidespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and ORF features
By developing computational algorithms, the authors annotated translated open reading frames in five eukaryotes and found many stable peptides are encoded by putative ‘noncoding’ regions of genomes.
- Haiwang Yang
- , Qianru Li
- & Zhe Ji
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Article
| Open AccessGlobal conservation status of the jawed vertebrate Tree of Life
Extinction threatens to erode the Tree of Life. Here, the authors calculate extinction risk for jawed vertebrates, predicting a loss of 86–150 billion years (11–19%) of evolutionary history through the next 50–500 years and indicating that cartilaginous fish, ray-finned fish, and turtles are most at risk from a phylogenetic perspective.
- Rikki Gumbs
- , Oenone Scott
- & James Rosindell
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Article
| Open AccessThe evolutionary impact of childhood cancer on the human gene pool
Pathogenic germline variants associated with childhood cancer risk could be subject to evolutionary constraints. Here, the authors analyse publicly available germline data in large cohorts and observe that paediatric cancer predisposition syndrome genes are highly constrained in the general population.
- Ulrik Kristoffer Stoltze
- , Jon Foss-Skiftesvik
- & Kjeld Schmiegelow
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Article
| Open AccessDispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean
Genomic surveillance has been important for tracking the evolution and spread of SARS-CoV-2. Here, the authors analyse ~300,000 SARS-CoV-2 genomes from two years of sequencing in the Latin America and Caribbean regions and describe the emergence and spread of different lineages over time.
- Tiago Gräf
- , Alexander A. Martinez
- & Juliana Almeida Leite
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Article
| Open AccessJapanese wolves are most closely related to dogs and share DNA with East Eurasian dogs
The evolutionary origin of the domestic dog is uncertain. Here, the authors sequence the whole genomes of 9 extinct Japanese wolves and 11 modern Japanese dogs, applying a phylogenetic analysis to show that dogs may have originated in East Asia from a common ancestor with the Japanese wolf.
- Jun Gojobori
- , Nami Arakawa
- & Yohey Terai
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Article
| Open AccessDipterocarpoidae 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 AccessEvolution and expression patterns of the neo-sex chromosomes of the crested ibis
The evolutionary trajectory of avian sex chromosomes may be more intricate than previously understood. In this study, sequencing and analysis of the neo-sex chromosomes and genome of the Crested Ibis suggests a multidirectional evolution of sex chromosomes in core waterbirds.
- Lulu Xu
- , Yandong Ren
- & Gang Li
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Article
| Open AccessPredator selection on phenotypic variability of cryptic and aposematic moths
Selection is expected to act differently on aposematic and cryptic species. Analysis of wing images revealed that camouflaged moths exhibit higher wing pattern variability than aposematic moths, supporting the theory that camouflaged species display more variability, consistent with anti-predator strategy.
- Ossi Nokelainen
- , Sanni A. Silvasti
- & Johanna Mappes
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Article
| Open AccessGenomic evidence for rediploidization and adaptive evolution following the whole-genome triplication
Polyploidization-rediploidization process plays an important role in plant adaptive evolution. Here, the authors assemble the genomes of mangrove species Sonneratia alba and its inland relative Lagerstroemia speciosa, and reveal genomic evidence for rediploidization and adaptive evolution after the whole-genome triplication.
- Xiao Feng
- , Qipian Chen
- & Ziwen He
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Article
| Open AccessGlobal evaluation of lineage-specific human papillomavirus capsid antigenicity using antibodies elicited by natural infection
Human Papillomaviruses (HPV) are classified in lineages based on their sequence. Here, the authors test neutralizing activity of sera from naturally infected women against vaccine-preventable HPV variants, delineating lineage-specific antibody responses.
- Gathoni Kamuyu
- , Filomeno Coelho da Silva
- & Simon Beddows
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Article
| Open AccessPorous 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 AccessQuantifying 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 AccessRecurrent evolutionary switches of mitochondrial cytochrome c maturation systems in Archaeplastida
Cytochrome c maturation (CCM) is the process of covalent attachment of a heme group to the conserved cysteines to form the holocytochrome. Here, the authors report that the non-adaptive convergent evolution at the pathway level leads to mosaic distribution of CCM systems I and III among Archaeplastida species.
- Huang Li
- , Soujanya Akella
- & Jeffrey P. Mower
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Article
| Open AccessSea lamprey enlightens the origin of the coupling of retinoic acid signaling to vertebrate hindbrain segmentation
Retinoic acid signaling is involved in patterning the embryonic antero-posterior axis, and also regulates hindbrain segmentation in jawed vertebrates. Here they show that retinoic acid signaling plays important roles in hindbrain segmentation in a jawless vertebrate, the lamprey, thus indicating this feature of hindbrain development is conserved in all vertebrates.
- Alice M. H. Bedois
- , Hugo J. Parker
- & Robb Krumlauf
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Article
| Open AccessPhage-plasmids promote recombination and emergence of phages and plasmids
Phage-plasmids are mobile genetic elements that transfer horizontally between bacterial cells as viruses, and vertically within bacterial lineages as plasmids. Here, Pfeifer & Rocha show that phage-plasmids can mediate gene transfer across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.
- Eugen Pfeifer
- & Eduardo P. C. Rocha
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Article
| Open AccessDuplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria
Mobile genetic elements can promote the duplication of antibiotic resistance genes which may in turn accelerate the evolution of resistance to new drugs. Here, the authors show that duplicated antibiotic resistance genes are enriched in bacterial isolates from environments associated with rampant antibiotic use.
- Rohan Maddamsetti
- , Yi Yao
- & Lingchong You
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Article
| Open AccessArticular surface interactions distinguish dinosaurian locomotor joint poses
Criteria for evaluating joint articulation in vertebrates are lacking. Here, the authors propose an approach for combining measurements of 3D articular overlap, symmetry, and congruence into a single metric, and apply this to examine the walking stride of Deinonychus antirrhopus.
- Armita R. Manafzadeh
- , Stephen M. Gatesy
- & Bhart-Anjan S. Bhullar
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Article
| Open AccessDiversity and evolution of the vertebrate chemoreceptor gene repertoire
Chemoreception - the ability to smell and taste - relies on diverse receptor genes. Examining 1,527 vertebrate genomes, this study explores the dynamic evolution, lineage-specific expansions and losses of chemoreceptor genes as well as ecological and morphological factors associated with these.
- Maxime Policarpo
- , Maude W. Baldwin
- & Walter Salzburger
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Article
| Open AccessExperimental evidence for cancer resistance in a bat species
Bats have been suggested to be resistant to cancer due to mechanisms related to their evolved longevity, but the associated molecular drivers are still understudied. Here, the authors examine cancer resistance mechanisms across seven bat species using in vitro and in vivo models, and identify HIF1A, COPS5, and RPS3 as related genes.
- Rong Hua
- , Yuan-Shuo Ma
- & Zhen Liu
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