Molecular biology and evolution最新文献

{"title":"Largest-Scale Genomic Resource Reconstructing the Genetic Origin, Population Structure, and Biological Adaptations of the Hui People.","authors":"Guanglin He, Jing Chen, Shuhan Duan, Qingxin Yang, Bowen Li, Lintao Luo, Jie Zhong, Qiuxia Sun, Fengxiao Bu, Renkuan Tang, Hongliang Lu, Haibing Yuan, Huijun Yuan, Chao Liu, Mengge Wang","doi":"10.1093/molbev/msaf225","DOIUrl":"10.1093/molbev/msaf225","url":null,"abstract":"<p><p>Historical and archaeological records indicate that the Maritime and Land Silk Roads played a pivotal role in facilitating Trans-Eurasian migrations and cultural exchanges. However, the extent to which population movements or the spread of ideas shape Chinese Hui populations remains debated. We present the largest genomic resource to date, including 2,280 Hui individuals sequenced or genotyped from 30 diverse regions, to examine the genetic origins, population structure, and biological adaptations of this underrepresented group in global human genome research. We identified a detailed population structure characterized by five distinct genetic lineages of the Hui, influenced by geography and varying gene flow. The admixture history and demographic events suggest that the northwestern and northern Hui lineages emerged from demic diffusion during the Tang and Yuan Dynasties via the Land Silk Road. In contrast, the southern and island Hui lineages reflect cultural diffusion along the Maritime Silk Road, while the mixed southern-northern lineage likely developed through a combination of demic and cultural diffusion. Our findings support a hybrid model for Hui formation, indicating that both demographic processes and sociocultural transmissions contributed to their population history. We identified east-west highly differentiated variants and pre- and post-admixture adaptations in Hui genomes, demonstrating that admixture-driven adaptive or neutral variants impacted susceptibility to cardiovascular diseases and immune- and diet-related traits. These adaptive signatures include post-admixture signals of SLC24A5 and ECHDC1 in the Hui, as well as pre-admixture signals of the HLA region, BCL2A1, and KCNH8 in the East Asian source. Overall, our study suggests that Han-related genetic components helped the Hui population rapidly adapt to new local environments. Additionally, the frequency spectrum of clinically essential variants differed significantly between Hui and Han individuals, emphasizing the importance of including underrepresented populations in genomic research to promote health equity.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 10","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12497895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotype by Environment Interactions in Gene Regulation Underlie the Response to Soil Drying in the Model Grass Brachypodium distachyon.","authors":"Jie Yun, Angela C Burnett, Alistair Rogers, David L Des Marais","doi":"10.1093/molbev/msaf218","DOIUrl":"https://doi.org/10.1093/molbev/msaf218","url":null,"abstract":"<p><p>Gene expression is a quantitative trait under the control of genetic and environmental factors and their interaction, so-called genotype and environment (G × E). Understanding the mechanisms driving G × E is fundamental for ensuring stable crop performance across environments and for predicting the response of natural populations to climate change. Gene expression is regulated through complex molecular networks, yet the interactions between genotype and environment in gene regulation are rarely considered, particularly at the genome scale. Current frameworks and experimental designs often lack power to explicitly test network rewiring or to systematically compare regulatory networks. Here, we leverage a highly replicated RNA-sequencing dataset to model genome-scale gene expression variation between two natural accessions of the model grass Brachypodium distachyon and their response to soil drying. We first identified genotypic, environmental, and G × E effects on physiological, metabolic, and gene expression traits. We identify patterns of conservation-or variation-in gene coexpression networks and link these coexpression features to physiological traits. We further develop predictions of gene-gene interactions using causal inference and screen for interactions specific to-or with higher affinity in-a single genotype, treatment, or their interaction, G × E. Our analyses identify variation in candidate gene regulatory networks that may shape the evolution of environmental response in B. distachyon. We highlight the environmentally dependent regulatory control of several metabolic traits shown previously to play a role in drought acclimation. The framework presented here provides a scalable approach for more complex comparisons, particularly with the growing availability of large datasets from technologies such as single-cell transcriptomics.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 10","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From Binding to Catalysis: Emergence of a Rudimentary Enzyme Conferring Intrinsic Antibiotic Resistance.","authors":"Claudèle Lemay-St-Denis, Stella Cellier-Goetghebeur, Maxime St-Aubin, Keigo Ide, Janine N Copp, Soichiro Tsuda, Nir Ben-Tal, Rachel Kolodny, Joelle N Pelletier","doi":"10.1093/molbev/msaf215","DOIUrl":"10.1093/molbev/msaf215","url":null,"abstract":"<p><p>How does enzymatic activity emerge? To shed light on this fundamental question, we study type B dihydrofolate reductases (DfrB), which were discovered for their role in antibiotic resistance. These rudimentary enzymes are evolutionarily distinct from the ubiquitous, monomeric FolA dihydrofolate reductases targeted by the antibiotic trimethoprim. DfrB is unique: it homotetramerizes to form a highly symmetrical central tunnel that accommodates its substrates in close proximity and the right orientation, thus promoting the metabolically essential production of tetrahydrofolate. It is the only known enzyme built from the ancient Src Homology 3 fold, typically a binding module. Strikingly, by studying the evolution of this enzyme family, we observe that no active-site residues are conserved across catalytically active homologs. Integrating experimental and computational analyses, we identify an intricate relationship between homotetramerization and catalytic activity, where formation of a tunnel featuring positive electrostatic potential proves to be a powerful predictor of activity. We demonstrate that the DfrB enzymes have not evolved in response to the synthetic antibiotic to which they confer strong resistance, and propose that DfrB domains evolved the capacity for rudimentary catalysis from a binding capacity. That (rudimentary) catalysis can emerge from the homotetramerization of a binding domain, and that it has been recently recruited by pathogenic bacteria, manifests the opportunistic nature of evolution.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12486381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiomic Analyses Reveal the Molecular Mechanisms of Arid Adaptation in a Desert Rodent Species.","authors":"Shuai Yuan, Rong Zhang, Yongling Jin, Xin Li, Linlin Li, Dong Zhang, Yu Ling, Kaijian Zhang, Xiaodong Wu, Xueying Zhang, Heping Fu","doi":"10.1093/molbev/msaf230","DOIUrl":"10.1093/molbev/msaf230","url":null,"abstract":"<p><p>Organisms living in desert habitats face multiple simultaneous pressures, such as high temperatures and arid, and the population dynamics and community diversity of small rodents are strongly affected by climate extremes. However, the potential mechanisms by which desert rodents adapt to arid remain largely unexplored. Here, we assembled a 3.18 Gb genome, including 25,812 protein-encoding genes, for Orientallactaga sibirica, which is widely distributed across both arid and semihumid environments in Eurasia. Orientallactaga sibirica has longer ears and hind limbs to enhance heat dissipation, which may be related to the positively selected genes, such as Fgf10, Fgf11, Hoxc4, Hoxd1, and Bmp4. The renal transcriptome revealed increased fat and carbohydrate metabolism for metabolic water production in O. sibirica residing in arid habitats. Pathways such as material metabolism, oxidative stress response, osmoregulation, and water and salt reabsorption were enriched in candidate genes, such as Avp, Ang, and Ace, under positive selection in O. sibirica. Moreover, amino acid replacement was observed in the protein sequences of seven candidate genes, including Aldh7a1, Lnpep, Wnk4, C1qc, and Awat2, and these specific amino acid replacements of genes such as Umod and Scnn1a were related to unique osmoregulation, osmotic protection, and water retention compensation mechanisms. Water deprivation under laboratory conditions induced the upregulation of Umod and Aldh7a1 expression, further supporting the results observed in the wild population. These findings demonstrate that the positively selected genes related to limb development and specific amino acid replacements in the genes Umod and Scnn1a for unique osmoregulation in the renal vascular system may contribute to arid adaptation in the desert rodent species O. sibirica. This study provides novel insights into the adaptive evolution of desert small mammals and can serve as a reference for future research on renal damage-related diseases, such as human kidney stones and salt-sensitive hypertension.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12502661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seasonal Influenza Viruses Show Distinct Adaptive Dynamics During Growth in Chicken Eggs.","authors":"Kathryn Kistler, Trevor Bedford","doi":"10.1093/molbev/msaf227","DOIUrl":"10.1093/molbev/msaf227","url":null,"abstract":"<p><p>Human influenza viruses are grown in chicken eggs for vaccine production. Sequences of these egg-passaged viruses give us the opportunity to examine the evolution that occurs when these human viruses are subjected to the selective pressure of growing in chicken eggs, which (among other things) express different sialic acid receptors. The repetition of this evolutionary experiment in hundreds of strains over the past several decades allows us to identify mutations that adapt the virus to eggs and epistatic constraints that influence them. We analyze influenza A/H3N2, A/H1N1pdm, B/Vic, and B/Yam sequences that were passaged in eggs and find that almost all of the adaptive mutations are located around the receptor-binding pocket of hemagglutinin (HA). We observe epistatic interactions both between adaptive mutations and between these mutations and the continually evolving human influenza HA background sequence. Our results show that this background dependence is greatest for influenza A/H3N2, and then A/H1N1pdm, with B/Vic and B/Yam showing little-to-no background dependence. We find that the total number of adaptive mutations and the length of adaptive walk also follow the same pattern between the influenza subtypes, suggesting that background dependence, number of adaptive mutations, and extent of additive versus epistatic interactions may all be related features of the fitness landscape.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Arthropod Pax Gene Evolution: A Role for Vanessa Cardui Twin of Eyeless in Eye Development.","authors":"Ximena Gutiérrez Ramos, Leslie Pick","doi":"10.1093/molbev/msaf220","DOIUrl":"10.1093/molbev/msaf220","url":null,"abstract":"<p><p>Pax genes encode transcription factors involved in diverse processes. First identified in Drosophila, they have been found throughout the animal kingdom, suggesting highly conserved functions. Pax proteins are defined by a DNA-binding PRD domain along with variable presence of a homeodomain and octapeptide motif. Although some Pax genes have been studied in selected arthropod groups, less is known about phylogenetic relationships among arthropod Pax genes. Here, we analyzed their distribution and classification and established the painted lady butterfly, Vanessa cardui, to study Pax gene expression and function. Our phylogenetic analysis grouped arthropod Pax genes into 6 clades: Pax3/7, Pax1/9, Poxn, Pax6-like/eyg, Pax2/5/8, and Pax4/6. This large-scale analysis confirmed that the Pax3/7 gene paired was lost in Lepidoptera, which retain other Pax3/7 family members as well as all other Pax groups. Expression of Vcar-Pax genes during Vanessa embryonic development was largely similar to previous reports for Drosophila. To test functional conservation, we focused on the eye development master regulator, twin of eyeless (toy). Vcar-toy was expressed in the head lobes and embryonic RNA interference resulted in loss of larval eyes. In addition, Vcar-ey, a candidate downstream target of toy, was downregulated after Vcar-toy knockdown. Ectopic expression of Vcar-toy in Drosophila resulted in ectopic, Drosophila-like adult eyes, supporting the notion that gene regulatory networks regulating larval and adult eyes are conserved and also shared between Vanessa and Drosophila. Overall, these results suggest that Pax genes are highly conserved in arthropods and provide a butterfly model to study eye regulatory networks in Lepidoptera.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12486386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Examination of germline and somatic intercellular bridges in Hydra vulgaris reveals insights into the evolutionarily conserved mechanism of intercellular bridge formation.","authors":"Kari L Price, Dyuthi M Tharakan, Will Salvenmoser, Kathleen Ayers, Jasmine Mah, Casey Dunn, Bert Hobmayer, Lynn Cooley","doi":"10.1093/molbev/msaf248","DOIUrl":"10.1093/molbev/msaf248","url":null,"abstract":"<p><p>Incomplete cytokinesis results in the formation of stable intercellular bridges that have been extensively studied in bilaterians, where they play essential roles in cell-cell communication and coordination of differentiation. However, little is known about their structure and molecular composition in non-bilaterian animals. This study characterizes germline and somatic intercellular bridges in the cnidarian Hydra vulgaris, providing insights into their evolutionary origins and functional significance. We identified key conserved components, including KIF23, F-actin, and phosphotyrosine epitopes. Notably, we observed microtubule localization within Hydra ring canals, suggesting previously unrecognized functions for this cytoskeletal component in intercellular bridge formation. Bioinformatic analyses confirmed the conserved expression of Kif23 and suggested its role as a molecular marker for identifying ring canal-associated components. EdU incorporation during DNA replication demonstrated that cells connected by ring canals exhibit synchronized cell cycles, which may be critical for the coordination of division and differentiation. Our findings reveal that the molecular and structural features of intercellular bridges in Hydra are conserved across evolutionary lineages, highlighting their ancient origins and functional significance in cellular connectivity. The presence of synchronized cell cycles in ring canal-connected cells underscores their role in promoting coordinated cellular behaviors, processes fundamental to multicellular organization. This study provides new perspectives on the evolution of incomplete cytokinesis and establishes a framework for comparative investigations into the diversity and conservation of intercellular bridge mechanisms across metazoans.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High conservation of translation-enabling RNA editing sites in hyper-editing ferns implies they are not selectively neutral.","authors":"Farley M Kwok van der Giezen, Rose McDowell, Owen Duncan, Simon Zumkeller, Catherine Colas des Francs-Small, Ian Small","doi":"10.1093/molbev/msaf241","DOIUrl":"https://doi.org/10.1093/molbev/msaf241","url":null,"abstract":"<p><p>RNA editing is essential for processing transcripts in plant chloroplasts and mitochondria. Levels of RNA editing vary between lineages but some hornworts, lycophytes and ferns have an extraordinary abundance of RNA editing. A feature of 'hyper-editing' species is the prevalence of RNA editing events that promote translation by creating start codons or removing stop codons via C-to-U or U-to-C editing respectively. These 'translation-enabling' RNA editing events may play roles in regulating organelle gene expression. To investigate the importance of translation-enabling RNA editing events, we generated DNA and RNA sequence libraries for four Salviniales water ferns: Azolla rubra, Azolla pinnata, Marsilea mutica and Salvinia molesta. We assembled chloroplast genomes, mitochondrial genes and transcriptomes, and identified RNA editing sites and candidate RNA editing factors. We re-analysed sequence data of Azolla filiculoides and conducted a comparative analysis of RNA editing in chloroplasts and mitochondrial transcripts. Estimates of pyrimidine transition rates show that translation-enabling RNA editing sites are more conserved than other nonsynonymous editing sites, suggesting an emergent role in organelle gene expression that is not selectively neutral. This makes these events rare examples of RNA editing conferring adaptive advantage, in contrast to the prevailing view that RNA editing arises via constructive neutral evolutionary processes. Shotgun proteomics of Marsilea mutica chloroplast thylakoid fractions verified the expected consequences of RNA editing on translation of chloroplast transcripts and implies that mechanisms exist to avoid translation of partially edited transcripts. Start codon editing may be one of those mechanisms.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145192098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Resolving the stasis-dynamism paradox: Genome evolution in tree ferns.","authors":"Zuoying Wei, Hengchi Chen, Chao Feng, Zengqiang Xia, Yves Van de Peer, Ming Kang, Jing Wang","doi":"10.1093/molbev/msaf247","DOIUrl":"https://doi.org/10.1093/molbev/msaf247","url":null,"abstract":"<p><p>The paradox of evolutionary stasis and dynamism-how morphologically static lineages persist through deep geological periods despite environmental fluctuations-remains unresolved in evolutionary biology. Here, we present chromosome-scale genomes for three ecologically divergent species (including both arborescent and non-arborescent growth forms) within Cyatheaceae, an ancient tree fern family characterized by morphological conservation dating back to the Jurassic era. Our results revealed substantial yet cryptically regulated genomic dynamism. A shared Jurassic whole-genome duplication (∼154 Ma) conferred dual adaptive advantages: initially buffering tree ferns against Late Jurassic climatic extremes through retention of stress-response genes, and subsequently facilitating niche diversification and phenotypic innovation via lineage-specific repurposing of duplicate genes. Arborescent lineages preferentially retained duplicates involved in cell wall biogenesis, essential for structural reinforcement and lignification, while non-arborescent forms conserved paralogs linked to metabolic resilience and defense. Alongside slow substitution rates, we detected cryptic genome dynamism mediated primarily by bursts of transposable elements, leading to genome size variations, chromosomal rearrangements, and localized innovation hotspots with elevated evolutionary rates. The concerted expansion and expression of lignification-related genes, coordinated with light signaling components, suggest a potential evolutionary mechanism integrating light perception with shade-adaptation and lignification, facilitating arborescent adaptation in angiosperm-dominated understories. Our findings redefine evolutionary stasis as a dynamic equilibrium, sustained by regulatory plasticity and localized genomic innovation within a conserved morphological framework. This study offers a novel genomic perspective on the long-term persistence and evolution of ancient plant lineages, demonstrating how regulated genomic dynamism enables adaptive diversification while sustaining morphological conservatism.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145150125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spread of a single superclone drives insecticide resistance in Acyrthosiphon kondoi across an invasive range.","authors":"Joshua A Thia, Benjamin J Hunt, Shuchao Wang, Bartlomiej J Troczka, Evatt Chirgwin, Courtney J Brown, Rumi Sakamoto, Monica Stelmach, Kelly Richardson, Leonhard S Arinanto, Ashritha P S Dorai, Chinmayee Joglekar, Qiong Yang, Marielle Babineau, Chris Bass, Paul A Umina, Ary A Hoffmann","doi":"10.1093/molbev/msaf246","DOIUrl":"https://doi.org/10.1093/molbev/msaf246","url":null,"abstract":"<p><p>Populations under similar selection pressures may adapt via parallel evolution or dispersal of advantageous alleles. Here, we investigated insecticide resistance in the invasive blue-green aphid, Acyrthosiphon kondoi, which reproduces clonally in Australia and has rapidly developed resistance across geographic locations. Using genomic, transcriptomic, and experimental approaches, we explored the evolutionary origins and molecular mechanisms of resistance. We developed the first nuclear genome assembly for A. kondoi (443.8 Mb, 28,405 annotated genes, BUSCO score 97.5%) and a partial mitochondrial assembly (11,598 bp). All resistant strains shared a common ancestor, supporting the spread of a resistant 'superclone' lineage that is distinct from susceptible strains. Resistance was associated with over-expression of an esterase gene that was homologous to E4/FE4 esterases in other aphid pests that are linked to resistance. Functional experiments in Drosophila melanogaster confirmed a causal role of this E4-like esterase in resistance to organophosphates, carbamates, and pyrethroids. These findings highlight how clonal dispersal and insecticide overuse can transform local adaptation into a widespread pest management issue. Our results suggest a parallel macroevolutionary response to insecticide selection in A. kondoi and other aphid species at the gene family level, but with a distinct regulatory mechanism in A. kondoi. Given the rapid spread of the resistant superclone, alternative management strategies, including expanded chemical control options and enhanced biological control, are urgently needed to mitigate this growing pest problem.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145176823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}