Featured
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Article
| Open AccessRapid response of fly populations to gene dosage across development and generations
While developmental phenotypes are often multigenic and involve environmental inputs, most research approaches involve perturbation of small numbers of genes. Here they use a synthetic evolution approach in Drosophila to show that adding extra copies of bicoid leads to rapid, system-wide phenotypic responses, potentiated by highly polygenic traits such as embryo size.
- Xueying C. Li
- , Lautaro Gandara
- & Justin Crocker
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Article
| Open AccessSmall body size is associated with increased evolutionary lability of wing skeleton proportions in birds
Birds vary in body mass by many orders of magnitude, but how this effects the evolution of their skeletal proportions is unclear. This study shows that small body size is associated with decreased evolutionary integration between wing bone sizes, facilitating increased evolutionary lability.
- Andrew Orkney
- & Brandon P. Hedrick
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Article
| Open AccessCrykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater
Wastewater surveillance has the potential to be used for early detection of new SARS-CoV-2 lineages. Here, the authors present Crykey, a computational method for detecting cryptic SARS-CoV-2 mutations in wastewater that co-occur on the same sequencing read, potentially representing new lineages.
- Yunxi Liu
- , Nicolae Sapoval
- & Lauren B. Stadler
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Article
| Open AccessShifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants
Kates et al. propose that nitrogen-fixing symbiosis between bacteria and angiosperms has been gained and lost multiple times, based on ancestral reconstructions of nodulation across a deeply sampled, 13,000-species phylogeny, in contrast to a single origin with many losses.
- Heather R. Kates
- , Brian C. O’Meara
- & Ryan A. Folk
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Article
| Open AccessEnhanced surface colonisation and competition during bacterial adaptation to a fungus
Bacterial-fungal interactions can stimulate the production of specialised microbial metabolites. Here, Richter et al. use co-culture experimental evolution to show that the presence of a fungus selects for increased surfactin production in the bacterium Bacillus subtilis, which inhibits fungal growth and facilitates the competitive success of the bacterium.
- Anne Richter
- , Felix Blei
- & Ákos T. Kovács
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Article
| Open AccessPhylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae
Lichen symbiosis between chlorophyte algae and fungi is a key player in ecosystems but our understanding of its evolution and genetic regulation in algae remains limited. This study finds that lichen symbiosis evolved at least three times in algae through gene family expansion and horizontal gene transfers
- Camille Puginier
- , Cyril Libourel
- & Jean Keller
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Article
| Open AccessConvergent evolution of fern nectaries facilitated independent recruitment of ant-bodyguards from flowering plants
Some plants use nectar to attract ant bodyguards. Here, the authors use a cross-kingdom phylogenetic approach to find that ferns and angiosperms evolved nectaries in the Cretaceous, coinciding with ant evolution, and that ferns recruited ant-bodyguards from existing ant-angiosperm partnerships.
- Jacob S. Suissa
- , Fay-Wei Li
- & Corrie S. Moreau
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Article
| Open AccessEnvironment modulates protein heterogeneity through transcriptional and translational stop codon readthrough
This study unveils that stop codon readthrough is prevalent in E. coli, particularly under stress conditions. It highlights the influence of stop codon type and genetic context, with both transcriptional and translational origins.
- Maria Luisa Romero Romero
- , Jonas Poehls
- & Agnes Toth-Petroczy
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Article
| Open AccessIlluminating the function of the orphan transporter, SLC22A10, in humans and other primates
Orphan transporters can be found in over 20 families in the SLC superfamily. Here, the authors show that human SLC22A10 is a unitary pseudogene due to a fixed missense mutation, P220; while in great apes, its orthologs transport sex steroid conjugates.
- Sook Wah Yee
- , Luis Ferrández-Peral
- & Kathleen M. Giacomini
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Article
| Open AccessAbrupt onset of intensive human occupation 44,000 years ago on the threshold of Sahul
Archaeological and genetic evidence suggest differing scenarios for human migration out of Africa. Here, the authors present archaeological evidence of intense occupation in Wallacea from 44 thousand years ago, suggesting that this occupation obscured genetic evidence of earlier dispersals.
- Ceri Shipton
- , Mike W. Morley
- & Sue O’Connor
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Article
| Open AccessEnvironmental conditions associated with initial northern expansion of anatomically modern humans
Past global human migration was the result of environmental and cultural factors. Here, the authors develop a statistical approach that combines archaeological, genetic, and palaeoclimate data to identify regional environmental conditions facilitating population expansion routes in northern Eurasia and the Americas.
- Frédérik Saltré
- , Joël Chadœuf
- & Corey J. A. Bradshaw
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Article
| Open AccessCellular structure of dinosaur scales reveals retention of reptile-type skin during the evolutionary transition to feathers
The evolution of feathers is associated with the evolution of related skin microstructures. Here, the authors demonstrate that Psittacosaurus, a non-avian feathered dinosaur, retained scaled skin like its ancestors in body regions lacking feathers.
- Zixiao Yang
- , Baoyu Jiang
- & Maria E. McNamara
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Article
| Open AccessA systematic review and meta-analysis of unimodal and multimodal predation risk assessment in birds
Animal behavioural response to predation risk could depend on the type and number of cues. This global metaanalysis shows that providing multiple cues of predation risk reduces variance in the behavioural responses of birds.
- Kimberley J. Mathot
- , Josue David Arteaga-Torres
- & Shinichi Nakagawa
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Article
| Open AccessInvariant γδTCR natural killer-like effector T cells in the naked mole-rat
Naked mole-rats are long-lived rodents known to be resistant to the development of cancer, yet their immune system remains poorly explored. Here, the authors identify natural killer-like effector γδ T cells that express a dominant γδ T cell receptor and may serve a role in tumour immunosurveillance.
- Guillem Sanchez Sanchez
- , Stephan Emmrich
- & David Vermijlen
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Article
| Open AccessDeepDive: estimating global biodiversity patterns through time using deep learning
Estimates of palaeodiversity are biased by the incompleteness of the fossil record. Here, the authors develop DeepDive, a deep learning approach that infers richness while accounting for record heterogeneity, and test it with two empirical datasets.
- Rebecca B. Cooper
- , Joseph T. Flannery-Sutherland
- & Daniele Silvestro
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Article
| Open AccessGenomic insights unveil the plasmid transfer mechanism and epidemiology of hypervirulent Klebsiella pneumoniae in Vietnam
Hypervirulent Klebsiella pneumoniae (hvKp) is a significant cause of severe community-acquired infection, primarily in Asia. Here, the authors characterise the genetic profile, phylogenetic structure, and plasmid features of hvKp in Vietnam.
- Quynh Nguyen
- , Nguyen Yen Thi Phuong
- & Duy Thanh Pham
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Article
| Open AccessConserved regulatory switches for the transition from natal down to juvenile feather in birds
Natal downs adapted for heat conservation transition to juvenile feathers that support simple flight during bird development. Here the authors characterize gene expression networks and epigenetic changes and use functional perturbations to characterize evolutionarily conserved regulatory switches that control this transition in birds.
- Chih-Kuan Chen
- , Yao-Ming Chang
- & Wen‐Hsiung Li
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Article
| Open AccessMacro-scale relationship between body mass and timing of bird migration
Clarifying migration timing and how it links with underlying drivers is essential to understanding bird migration. This study finds body mass affects the timing of both spring and autumn migration, while environmental factors mainly affect the timing of spring migration.
- Xiaodan Wang
- , Marius Somveille
- & Zhijun Ma
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Article
| Open AccessProteome partitioning constraints in long-term laboratory evolution
Adaptive laboratory evolution provides a real-time record of physiological change. In bacteria adapted to glucose over 40 000 generations, this study finds an apparent increase in enzyme efficiency consistent with increased substrate saturation due to loss of a flux sensing mechanism early in adaptation.
- Matteo Mori
- , Vadim Patsalo
- & Matthew Scott
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Article
| Open AccessThe greenbeard gene tgrB1 regulates altruism and cheating in Dictyostelium discoideum
Greenbeards encode perceptible signals, signal recognition ability, and altruism towards others displaying the signal. This study shows that activation of the greenbeard receptor gene tgrB1 increases altruism and inactivation causes kin-specific cheating in the social amoeba Dictyostelium discoideum.
- Mariko Katoh-Kurasawa
- , Peter Lehmann
- & Gad Shaulsky
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Article
| Open AccessFused in sarcoma (FUS) inhibits milk production efficiency in mammals
Efficient milk production in mammals confers advantages by facilitating the transmission of energy from mother to offspring. However, the factors for establishing the efficiency in mammals are unknown. Here, the authors identify FUS as a regulator of efficient milk production in mammals.
- Haili Shao
- , Jipeng Huang
- & Baowei Jiao
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Article
| Open AccessUnveiling the A-to-I mRNA editing machinery and its regulation and evolution in fungi
A-to-I editing in animals is catalyzed by enzymes of the Adenosine Deaminase Acting on RNA family, orthologues of which do not exist in fungi. Here, Feng et al. characterise the enzymes involved in A-to-I mRNA editing in Fusarium graminearum.
- Chanjing Feng
- , Kaiyun Xin
- & Huiquan Liu
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Article
| Open AccessLower Ordovician synziphosurine reveals early euchelicerate diversity and evolution
Here, the authors describe an early synziphosurine from the Lower Ordovician Fezouata Shale of Morocco, which exhibits traits that elucidate the long-contentious relationships between crown euchelicerates and their sister taxa, and also clarifies euchelicerate body plan evolution.
- Lorenzo Lustri
- , Pierre Gueriau
- & Allison C. Daley
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Article
| Open AccessMutation characteristics and molecular evolution of ovarian metastasis from gastric cancer and potential biomarkers for paclitaxel treatment
‘Gastric cancer metastasis to the ovary is difficult to treat and is not fully understood. Here, the authors characterized mutations in a cohort of matched primary and metastatic disease, and found mutations, including in CLDN18, could predict treatment response to paclitaxel.
- Pengfei Yu
- , Can Hu
- & Xiangdong Cheng
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Article
| Open AccessTiming the evolution of phosphorus-cycling enzymes through geological time using phylogenomics
Phosphorus is an essential nutrient which may have influenced Earth’s early biosphere. This study interrogates genomic records, finding potentially phosphate depleted conditions toward the end of the Archean when enzymes for scavenging reduced phosphorus compounds spread throughout the tree of life.
- Joanne S. Boden
- , Juntao Zhong
- & Eva E. Stüeken
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Article
| Open AccessThe gene “degrees of kevin bacon” (dokb) regulates a social network behaviour in Drosophila melanogaster
The structure of a social network is thought to be heritable in many animals, including humans. Here, Rooke and colleagues identify a gene, which they name “degrees of kevin bacon (dokb)”, that is expressed in the central nervous system of Drosophila melanogaster and regulates the structure of social networks.
- Rebecca Rooke
- , Joshua J. Krupp
- & Joel D. Levine
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Article
| Open AccessEvolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages
In this work, Yang et al. provide evidence of triclosan exposure resulting in increased evolvability of K. pneumoniae in experimental evolution studies. They utilize sequencing and transcriptomics to explore the chromosomally and horizontally acquired antimicrobial resistance mechanisms.
- Qiu E. Yang
- , Xiaodan Ma
- & Timothy R. Walsh
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Article
| Open AccessPositive selection in the genomes of two Papua New Guinean populations at distinct altitude levels
This study explores selection signals of Papua New Guinean highlanders and lowlanders using 128 new whole genome sequences. It highlights two genetic variants associated with blood traits that also influence the heart rate of these populations.
- Mathilde André
- , Nicolas Brucato
- & François-Xavier Ricaut
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Article
| Open AccessNew Late Pleistocene age for the Homo sapiens skeleton from Liujiang southern China
Here the authors provide new radiocarbon, U-series, and OSL dates for Homo sapiens fossils from Tongtianyan cave, southern China, placing them at 33-23 thousand years ago and indicating widespread presence of Homo sapiens across eastern Asia in the Late Pleistocene.
- Junyi Ge
- , Song Xing
- & Qingfeng Shao
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Perspective
| Open AccessEngineering is evolution: a perspective on design processes to engineer biology
Evolutionary and rational design approaches are commonly used to engineer biological systems but are typically seen at odds with each other. In this perspective the authors argue for the concept of an evolutionary design spectrum to help unify and compare these design methodologies to support more effective biological engineering.
- Simeon D. Castle
- , Michiel Stock
- & Thomas E. Gorochowski
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Article
| Open AccessClimate-forced Hg-remobilization associated with fern mutagenesis in the aftermath of the end-Triassic extinction
This study provides evidence for long-term effects of volcanic emissions of large quantities of gaseous mercury (Hg) and plant mutagenesis by recording high abundances of malformed fern spores across the Triassic-Jurassic boundary and Early Jurassic.
- Remco Bos
- , Wang Zheng
- & Bas van de Schootbrugge
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Article
| Open AccessThe airborne transmission of viruses causes tight transmission bottlenecks
Genomic analyses have indicated that a small number of virus particles usually found new infections. Here, the authors use a mathematical model to show that this small transmission bottleneck is a result of the physical processes of airborne virus emission, diffusion, and inhalation.
- Patrick Sinclair
- , Lei Zhao
- & Christopher J. R. Illingworth
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Article
| Open AccessTravel surveillance uncovers dengue virus dynamics and introductions in the Caribbean
Dengue is a major public health concern in the Americas, and the Caribbean can be a source for reintroduction and spread. Here, the authors use travel surveillance data and genomic epidemiology to reconstruct Dengue epidemic dynamics in the Caribbean from 2009-2022.
- Emma Taylor-Salmon
- , Verity Hill
- & Nathan D. Grubaugh
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Article
| Open AccessFunctional synergy of a human-specific and an ape-specific metabolic regulator in human neocortex development
Cell metabolism has emerged as a major factor implicated in human brain evolution. Here, the authors show that an ape-specific enzyme enhances the ability of a human-specific enzyme to increase glutaminolysis and therefore expand the size of the human neocortex.
- Lei Xing
- , Vasiliki Gkini
- & Takashi Namba
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Article
| Open AccessGoal-directed and flexible modulation of syllable sequence within birdsong
Birdsong contains strings of syllables and is essential for their communication. Using a new song decoder to annotates song in a quasi-real-time manner, and rewarding specific syllable sequences, this study shows Bengalese finches can flexibly modify the content of their song in a goal-directed way.
- Takuto Kawaji
- , Mizuki Fujibayashi
- & Kentaro Abe
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Article
| Open AccessEmergence of enhancers at late DNA replicating regions
Here the authors report that enhancers appear more often in late-replicating DNA regions and are enriched for mutations affecting TF binding. This relationship with DNA replication time is seen in species evolution and cancer, suggesting a fundamental principle of genome evolution.
- Paola Cornejo-Páramo
- , Veronika Petrova
- & Emily S. Wong
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Article
| Open AccessA genomic basis of vocal rhythm in birds
Little is known about the genetic basis of the rhythmic component of bird song, an important trait in sexual selection and species recognition. By studying a system with innate vocalizations, the Pogoniulus tinkerbirds, this study finds candidate genes that underlie differences in speed in vocal rhythm in this system.
- Matteo Sebastianelli
- , Sifiso M. Lukhele
- & Alexander N. G. Kirschel
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Article
| Open AccessPhysiography, foraging mobility, and the first peopling of Sahul
The speed and route by which Homo sapiens colonised Sahul is an ongoing topic of research. Here, the authors model the physical environment as it changes through time in combination with Lévy walk foraging patterns to suggest a wave of dispersal following coastlines and rivers.
- Tristan Salles
- , Renaud Joannes-Boyau
- & Manon Lorcery
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Article
| Open AccessDeviations in RSV epidemiological patterns and population structures in the United States following the COVID-19 pandemic
Non-pharmaceutical interventions for COVID-19 also impacted the transmission of other viruses including respiratory syncytial virus (RSV). Here the authors describe the changing epidemiology, clinical severity, and genetic diversity of RSV in Chicago, Illinois, from July 2010 to April 2023.
- Estefany Rios-Guzman
- , Lacy M. Simons
- & Judd F. Hultquist
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Article
| Open AccessMonkeypox virus genomic accordion strategies
The 2023 monkeypox outbreak was caused by a subclade IIb monkeypox virus (MPXV). Here, using advanced sequencing techniques, the authors identify variations on low-complexity regions of the MPXV genome and describe their potential as evolutionary drivers.
- Sara Monzón
- , Sarai Varona
- & Gustavo Palacios
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Article
| Open AccessThe genetic landscape of a metabolic interaction
Reynolds and colleagues examine a biochemically-mediated epistatic interaction between metabolic enzymes involved in folate metabolism and show that biochemical coupling shapes the range of enzyme activities sufficient to rescue cell growth.
- Thuy N. Nguyen
- , Christine Ingle
- & Kimberly A. Reynolds
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Article
| Open AccessRapid evolutionary change in trait correlations of single proteins
Trait correlations impact evolvability as selection on one trait can influence others. Here, the authors examine trait correlation in two proteins, a fluorescent protein & an antibiotic resistance enzyme, observing rapid evolution of trait correlations through changes in the biophysical properties of these proteins.
- Pouria Dasmeh
- , Jia Zheng
- & Andreas Wagner
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Article
| Open AccessPhylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages
Grasses share a whole-genome duplication called rho, but the adaptive implications are unclear. Here, the authors conduct phylogenomic and phylotranscriptomic analyses of 363 grasses, identifying additional whole-genome duplications and finding that duplicates are implicated in environmental adaptations or morphogenesis.
- Taikui Zhang
- , Weichen Huang
- & Hong Ma
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Matters Arising
| Open AccessPopulation 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 AccessUnexpectedly uneven distribution of functional trade-offs explains cranial morphological diversity in carnivores
Functional trade-offs can affect phenotypic variation. Here, the authors examine trade-offs between bite force and speed in 132 carnivore species, finding that optimising for velocity can be obtained in more ways than optimising for force, and this may impact morphological variability.
- Gabriele Sansalone
- , Stephen Wroe
- & Carmelo Fruciano
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Matters Arising
| Open AccessReply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data
- Chase W. Nelson
- , Leo L. M. Poon
- & Haogao Gu
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Article
| Open AccessPositive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution
SARS-CoV-2 constantly evolves but the roles of resulting mutations are not always clear. In this study, the authors report that ORF8 knockout confers a fitness advantage to SARS-CoV-2 using genomic surveillance data, highlighting how different types of adaptations across the SARS-CoV-2 genome can drive variant fitness.
- Cassia Wagner
- , Kathryn E. Kistler
- & Trevor Bedford
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Article
| Open AccessAnnelid adult cell type diversity and their pluripotent cellular origins
The cellular atlas of Pristina leidyi reveals cell type diversity in adult annelids by single cell transcriptomics, discovering several novel cell types and suggesting a pluripotent stem cell signature associated with adult cell type differentiation
- Patricia Álvarez-Campos
- , Helena García-Castro
- & Jordi Solana
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Article
| Open AccessIntrogression 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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