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| 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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| 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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| 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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| 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 AccessEvolution of T cells in the cancer-resistant naked mole-rat
Naked mole-rats are long-lived rodents with remarkable resistance to cancer. Here authors show that their T-cell compartment is different from that of mice in that they have a large population of circulating cytotoxic γδ T cells harboring a dominant clonotype, and the clonotypic diversity of their conventional cytotoxic αβ T cells is more modest than that of mice.
- Tzuhua D. Lin
- , Nimrod D. Rubinstein
- & Rochelle Buffenstein
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| Open AccessAdaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events
Endogenous retroviruses (ERVs) are remnants of ancient viruses embedded in animal DNA. This study found that the solitary long terminal repeats of ERVs in birds, particularly Passeriformes, have evolved to influence gene expression, potentially contributing to adaptive diversification of species.
- Guangji Chen
- , Dan Yu
- & Shaohong Feng
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| Open AccessAn adaptive biomolecular condensation response is conserved across environmentally divergent species
Cells must respond to environmental changes. In three fungal species adapted to different temperatures, cellular responses are conserved yet tuned to each organism’s thermal niche, including the formation of adaptive biomolecular condensates.
- Samantha Keyport Kik
- , Dana Christopher
- & D. Allan Drummond
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| Open AccessThe genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus
This study on respiratory syncytial virus (RSV) reveals global genomic gaps. Using INFORM-RSV data, it uncovers selection’s impact on RSVA and RSVB diversity. Analysing full genomes, it highlights non-neutral epidemic processes. The research emphasises air travel’s influence on global spread, underscoring the need for comprehensive RSV genomic surveillance.
- Annefleur C. Langedijk
- , Bram Vrancken
- & Shabir A. Madhi
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| 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 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 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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| 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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| 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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| 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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| 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 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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| Open AccessEvolutionary trajectory of pattern recognition receptors in plants
Plant cell-surface receptors perceive both self- and nonself-molecules to regulate biological processes. Here the authors show that a subclass of phytohormone and immune receptors share a common origin, which have diverged to perceive distinct ligands and activate differential downstream responses.
- Bruno Pok Man Ngou
- , Michele Wyler
- & Ken Shirasu
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| Open AccessThe origin and structural evolution of de novo genes in Drosophila
It is unclear whether naturally evolved de novo proteins have stable, folded structures. Here, through systematic identification and structural modeling of de novo genes, this study reveals that a small subset of these proteins may have well-folded structures, and were likely born with these structures.
- Junhui Peng
- & Li Zhao
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| Open AccessUltraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces
Bacterial viruses (phages) are generally recognised as rapidly evolving biological entities. Here, Rozwalak et al. analyse DNA sequence datasets generated from ancient palaeofaeces and identify 298 phage genomes from the last 5300 years, including a 1300-year-old phage genome nearly identical to a present-day virus that infects human gut bacteria.
- Piotr Rozwalak
- , Jakub Barylski
- & Andrzej Zielezinski
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| Open AccessUsing big sequencing data to identify chronic SARS-Coronavirus-2 infections
Chronic SARS-CoV-2 infections have been hypothesised to be sources of new variants. Here, the authors use large-scale genome sequencing data to identify mutations predictive of chronic infections, which may therefore be relevant in future variants.
- Sheri Harari
- , Danielle Miller
- & Adi Stern
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Article
| Open AccessConserved chromatin and repetitive patterns reveal slow genome evolution in frogs
Frogs are an ancient and ecologically diverse group of amphibians that include important model systems. This paper reports genome sequences of multiple frog species, revealing remarkable stability of frog chromosomes and centromeres, along with highly recombinogenic extended subtelomeres.
- Jessen V. Bredeson
- , Austin B. Mudd
- & Daniel S. Rokhsar
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| Open AccessEvolution of optimal growth temperature in Asgard archaea inferred from the temperature dependence of GDP binding to EF-1A
The archaeal ancestor of eukaryotes belonged to the phylum Asgardarchaeota, or Asgard archaea. Here, the authors use ancestral sequence reconstruction and experimentally determine the optimal GDP-binding temperature of a translation elongation factor from ancient and extant Asgard archaea, to infer optimal growth temperatures for eukaryotes’ ancestors.
- Zhongyi Lu
- , Runyue Xia
- & Meng Li
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| Open AccessSilica-associated proteins from hexactinellid sponges support an alternative evolutionary scenario for biomineralization in Porifera
Sponges, being early-diverging metazoans and the only animals to develop extensive skeletons of silica, have potential to inform about the evolutionary steps of metazoan traits, including biomineralization. Here, the authors characterize two proteins associated with the hexactinellid sponge silica.
- Katsuhiko Shimizu
- , Michika Nishi
- & Manuel Maldonado
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| Open AccessThe polyketide to fatty acid transition in the evolution of animal lipid metabolism
Much is still unknown of the evolution of animal metabolic enzymes. This study describes a new enzyme family bridging the production of polyketides and membrane lipids. This expands the known biochemical repertoire of animals for making ecologically and biomedically important natural products.
- Zhenjian Lin
- , Feng Li
- & Eric W. Schmidt
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Article
| Open AccessQuantifying negative selection in human 3ʹ UTRs uncovers constrained targets of RNA-binding proteins
Identifying functional genetic variants in non-coding regions of the human genome is challenging. Here the authors apply their iMAPS approach to 3ʹ untranslated regions, identifying thousands of variants that disrupt post-transcriptional gene regulation.
- Scott D. Findlay
- , Lindsay Romo
- & Christopher B. Burge
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| Open AccessPervasive epistasis exposes intramolecular networks in adaptive enzyme evolution
Here, the authors perform statistical analyses to demonstrate that epistasis is highly pervasive in adaptive evolutionary trajectories of enzymes. Using epistatic data, they expose higher-order rewiring of intramolecular amino acid networks.
- Karol Buda
- , Charlotte M. Miton
- & Nobuhiko Tokuriki
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| Open AccessMaternal dominance contributes to subgenome differentiation in allopolyploid fishes
Cyprinids fish species contain multiple subgenomes as a result of past duplications. Here, Xu et al. report new genomes of 21 cyprinid fish and conclude that observed subgenome dominance patterns are likely due to both maternal dominance and transposable element densities in each polyploid.
- Min-Rui-Xuan Xu
- , Zhen-Yang Liao
- & Hua-Hao Zhang
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| Open AccessUbiquitination-mediated Golgi-to-endosome sorting determines the toxin-antidote duality of fission yeast wtf meiotic drivers
Meiotic drivers of the wtf family kill progeny lacking the driver by producing a toxin and an antidote. Here, authors reveal that ubiquitination-mediated sorting of the antidote prevents it from becoming toxic and enables it to neutralize the toxin.
- Jin-Xin Zheng
- , Tong-Yang Du
- & Li-Lin Du
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| Open AccessTopological structures and syntenic conservation in sea anemone genomes
Slowly evolving cnidarians are useful models to study genome architecture. This study shows that sea anemones have a high degree of chromosomal macrosynteny, but poor microsynteny conservation. This is correlated with a small genome size and short distances of cis-regulatory elements to genes.
- Bob Zimmermann
- , Juan D. Montenegro
- & Ulrich Technau
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| Open AccessPhylogeny and molecular evolution of the first local monkeypox virus cluster in Guangdong Province, China
The first known local mpox outbreak in Guangdong Province, China occurred in June 2023. Here, the authors perform phylogenetic and molecular evolution analysis of ten mpox virus genome sequences from this outbreak, and place them in the context of other samples detected in surrounding regions.
- Jianhai Yu
- , Xin Zhang
- & Baisheng Li
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Article
| Open AccessQuorum-sensing synthase mutations re-calibrate autoinducer concentrations in clinical isolates of Pseudomonas aeruginosa to enhance pathogenesis
Simanek et al. discovered variants that arise in the protein responsible for synthesizing a molecule required for bacterial communication, which mediates the progression of virulence in the pathogen Pseudomonas aeruginosa.
- Kayla A. Simanek
- , Megan L. Schumacher
- & Jon E. Paczkowski
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| Open AccessCommon origin of sterol biosynthesis points to a feeding strategy shift in Neoproterozoic animals
Sterane molecular fossils are used to compliment evidence from the fossil record. Here, the authors use a molecular clock to explore the origins of the smt gene, tracing the loss of sterol synthesis to dietary shifts in animals at the end-Neoproterozoic.
- T. Brunoir
- , C. Mulligan
- & D. A. Gold
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| Open AccessWorldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change
Extinction of megafauna is a defining trend of the last 50,000 years. Here, the authors use genomic data to infer population histories of 139 extant megafauna, suggesting that their population decline is better explained by Homo sapiens expansion than by climate change.
- Juraj Bergman
- , Rasmus Ø. Pedersen
- & Jens-Christian Svenning
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| Open AccessHorizontal acquisition of a DNA ligase improves DNA damage tolerance in eukaryotes
Bdelloid rotifers can withstand a wide range of genotoxic stresses. Here the authors reveal that a DNA ligase of bacterial origin was acquired by horizontal gene transfer to confer high resistance to ionizing radiation in bdelloid rotifers and other organisms known for their extreme tolerance to stress.
- Emilien Nicolas
- , Paul Simion
- & Karine Van Doninck
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Article
| Open AccessLipases and carboxylesterases affect moth sex pheromone compounds involved in interspecific mate recognition
Moth sex pheromones, pivotal for mate attraction, are a classic model for sexual selection. Through introgression, transcriptomics and knocking out genes, this study identifies lipases and esterases that affect pheromone blend composition, offering insights into moth pheromone evolution.
- Arthur de Fouchier
- , Elise Fruitet
- & Astrid T. Groot
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Article
| Open AccessATP synthase evolution on a cross-braced dated tree of life
The timing of cellular evolution is poorly constrained. Here, the authors used improved molecular dating approaches to study the evolution of the ATP synthase in light of a dated tree of life thereby providing an absolute timescale for cellular evolution including eukaryotic origins.
- Tara A. Mahendrarajah
- , Edmund R. R. Moody
- & Anja Spang
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Article
| Open AccessGenomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae
Non-ammonia oxidising Thaumarachaeota lineages are common in acidic soils, but their evolution is unclear. Here, the authors assemble 15 genomes from deeply rooted Thaumarachaeota in topsoils and subsoils, investigating evolutionary divergence in the family Gagatemarchaeaceae.
- Paul O. Sheridan
- , Yiyu Meng
- & Cécile Gubry-Rangin
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Article
| Open AccessMultiple parallel origins of parasitic Marine Alveolates
The Marine Alveolates (MALVs) include important parasites of other protists/animals. Here, using new data from MALV-I, the psammosids, and a new group called the eleftherids, the authors show MALVs, and therefore parasitism in early dinoflagellates, evolved from two distinct free-living ancestors.
- Corey C. Holt
- , Elisabeth Hehenberger
- & Patrick J. Keeling
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Article
| Open AccessLow mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks
Mutations provide the genetic variability required for evolutionary change. Here, using pedigree-based whole genome sequencing, the authors determine that the Epaulette shark appears to have the lowest mutation rate identified in a vertebrate, providing a potential explanation for slow evolution in the shark lineage.
- Ashley T. Sendell-Price
- , Frank J. Tulenko
- & Manfred Schartl
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Article
| Open AccessSpatial and temporal dynamics of West Nile virus between Africa and Europe
West Nile virus is an animal pathogen that has spread rapidly in Europe in recent years, causing several human deaths. This study investigates the spatial and temporal dynamics of the virus circulation between Africa (its place of origin) and Europe.
- Giulia Mencattelli
- , Marie Henriette Dior Ndione
- & Giovanni Savini
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| Open AccessCharacterization of the horse chestnut genome reveals the evolution of aescin and aesculin biosynthesis
Horse chestnut (Aesculus chinensis) is a tree species that can produce medicinal compounds such as aescin and aesculin. Here, the authors assemble its genome, identify key genes involved in the biosynthesis of these two group of compounds, and achieve the de novo synthesis of aesculin in E. coli.
- Wei Sun
- , Qinggang Yin
- & Shilin Chen
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| Open AccessMutations that enhance evolvability may open doors to faster adaptation
A recent study demonstrated the existence of mutations that facilitate access to efficient evolutionary solutions. Here I discuss the implications of this finding and the potential to open a new chapter in the study of evolvability.
- C. Brandon Ogbunugafor
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Article
| Open AccessEvolution of lasR mutants in polymorphic Pseudomonas aeruginosa populations facilitates chronic infection of the lung
Chronic infection with the bacterium Pseudomonas aeruginosa often leads to coexistence of heterogeneous bacterial populations carrying diverse mutations. Here, Zhao et al. use genetic and multi-omics functional analyses to shed light on the multistage evolution of bacterial populations in the lungs of chronically infected patients.
- Kelei Zhao
- , Xiting Yang
- & Xikun Zhou
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| Open AccessA de novo evolved gene contributes to rice grain shape difference between indica and japonica
Genetic bases of grain shape differentiation between the two subspecies of Asian cultivated rice have not been fully elucidated. Here, the authors report GSE9, a de novo gene evolved from a non-coding region of wild rice through acquisition of start codon, contributes to the grain shape difference between the two subspecies.
- Rujia Chen
- , Ning Xiao
- & Zefeng Yang
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Article
| Open AccessA single-cell atlas of West African lungfish respiratory system reveals evolutionary adaptations to terrestrialization
The water-to-land transition of vertebrates is a landmark event in evolutionary history. This work utilizes single-cell RNA sequencing to explore the adaptations in African lungfish lungs and gills to terrestrialization.
- Ruihua Zhang
- , Qun Liu
- & Guangyi Fan
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| Open AccessEvolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies
The diverse Heliconius butterflies have evolved key innovations, including pollen feeding, and are a quintessential example of adaptive radiation. Using comparative genomics, Cicconardi et al. identify targets of selection at coding and non-coding loci during major ecological transitions in Heliconius.
- Francesco Cicconardi
- , Edoardo Milanetti
- & Stephen H. Montgomery