Hong-Fan Chen, Ryan Andrew Folk, Ya-Li Wang, Wen-Jing Wang, Guo-Jun Shao, Mei-Yuan Huang, Xiang-Qin Yu, Li Li, Jian-Li Zhao
{"title":"Extensive Introgression Failed to Erode Species Boundaries Among Multiple Sympatric Closely Related Species of Roscoea","authors":"Hong-Fan Chen, Ryan Andrew Folk, Ya-Li Wang, Wen-Jing Wang, Guo-Jun Shao, Mei-Yuan Huang, Xiang-Qin Yu, Li Li, Jian-Li Zhao","doi":"10.1111/mec.70083","DOIUrl":"10.1111/mec.70083","url":null,"abstract":"<div>\u0000 \u0000 <p>How species boundaries are maintained among sympatric closely related species experiencing gene flow is a puzzling question in evolutionary biology. Although introgression is commonly documented, the dynamics and gene function of introgression have rarely been explored to probe why frequent introgression does not necessarily destroy species boundaries in sympatry. In this study, we employ whole-genome resequencing data to examine introgression among five closely related species of <i>Roscoea</i> that coexist in a ‘sky island’ with seventeen distinct morphological traits. Our findings reveal that introgression has led to the phylogenomic discordance between nuclear and chloroplast genomes among these morphologically distinct species. Additionally, introgression is predominantly asymmetrical in both intensity and gene function, particularly concerning recombination. Notably, the majority of gene functions associated with introgressed loci are unrelated to reproductive processes. Our results suggest that closely related species with incomplete allele assortment can coexist despite theoretical predictions, highlighting the semipermeable nature of species boundaries as reproductive isolation develops. This provides a critical conceptual framework for understanding the interplay between introgression and species persistence. Our finding offers insights into how related sympatric species boundaries can be maintained in the face of frequent asymmetrical gene introgression.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 19","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144854083","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}
Drew R Schield, Javan K Carter, Megan G Alderman, Keaka Farleigh, Dylan K Highland, Rebecca J Safran
{"title":"Recombination Rate and Recurrent Linked Selection Shape Correlated Genomic Landscapes Across a Continuum of Divergence in Swallows.","authors":"Drew R Schield, Javan K Carter, Megan G Alderman, Keaka Farleigh, Dylan K Highland, Rebecca J Safran","doi":"10.1111/mec.70074","DOIUrl":"https://doi.org/10.1111/mec.70074","url":null,"abstract":"<p><p>Disentangling the drivers of genomic divergence during speciation is essential to our broader understanding of the generation of biological diversity. Genetic changes accumulate at variable rates across the genome as populations diverge, leading to heterogenous landscapes of genetic differentiation. The 'islands of differentiation' that characterise these landscapes harbour genetic signatures of the evolutionary processes that led to their formation, providing insight into the roles of these processes in adaptation and speciation. Here, we study swallows in the genus Hirundo to investigate genomic landscapes of differentiation between species spanning a continuum of evolutionary divergence. Genomic differentiation spans a wide range of values (F<sub>ST</sub> = 0.01-0.8) between species, with substantial heterogeneity in genome-wide patterns. Genomic landscapes are strongly correlated among species (ρ = 0.46-0.99), both at shallow and deep evolutionary timescales, with broad evidence for the role of linked selection together with recombination rate in shaping genomic differentiation. Further dissection of genomic islands reveals patterns consistent with a model of 'recurrent selection', wherein differentiation increases due to selection in the same genomic regions in ancestral and descendant populations. Finally, we use measures of the site frequency spectrum to differentiate between alternative forms of selection, providing evidence that genetic hitchhiking due to positive selection has contributed substantially to genomic divergence. Our results demonstrate the pervasive role of recurrent linked selection in shaping genomic divergence despite a history of gene flow and underscore the importance of non-neutral evolutionary processes in predictive frameworks for genomic divergence in speciation genomics studies.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70074"},"PeriodicalIF":3.9,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144843938","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}
Dolph Schluter, Thor Veen, Ken A Thompson, Greg L Owens, Diana J Rennison
{"title":"Coexistence in Sympatry With Gene Flow Before Speciation Has Completed.","authors":"Dolph Schluter, Thor Veen, Ken A Thompson, Greg L Owens, Diana J Rennison","doi":"10.1111/mec.70079","DOIUrl":"https://doi.org/10.1111/mec.70079","url":null,"abstract":"<p><p>Incipient species often coexist in sympatry before complete reproductive isolation has evolved between them. How do they persist in the face of hybridization and gene flow? The challenge is more acute than ordinary ecological coexistence not only because gene flow erodes and recombines genetic differences, but also because selection against hybrids can destabilise population sizes. We estimated gene flow and selection against hybrid genotypes between sympatric limnetic and benthic species of threespine stickleback in two British Columbia lakes. First-generation hybrids are present at a rate of about 2%. To estimate selection, we compared the frequency distribution of ancestry proportions between juvenile and adult samples. We also used genomic simulation with assortative mating in an ecological model to determine how much selection is required to reproduce observed genotype frequencies. Results from the two approaches were comparable and yielded estimated selection coefficients S against the least fit ancestry proportion (within backcross range) between 0.5 and 0.6. Surprisingly, selection was found to be only slightly weaker than that leading readily to collapse and fusion in our simulations, suggesting that sympatric stickleback species are close to a coexistence boundary. Moderately strong selection appears to be required for coexistence with even low levels of gene flow. We suggest that larger niche differences are required to stabilise coexistence with gene flow than without gene flow. This helps to explain why successful sympatric species that hybridise often show conspicuous ecological and phenotypic differences.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70079"},"PeriodicalIF":3.9,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833541","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}
Lua Lopez, Patricia L M Lang, Stephanie Marciniak, Logan Kistler, Sergio M Latorre, Asnake Haile, Eleanna Vasquez Cerda, Diana Gamba, Yuxing Xu, Patrick Woods, Mistire Yifru, Jeffrey Kerby, John K McKay, Christopher G Oakley, Jon Ågren, Tigist Wondimu, Collins Bulafu, George H Perry, Hernán A Burbano, Jesse R Lasky
{"title":"Museum Genomics Reveals Temporal Genetic Stasis and Global Genetic Diversity in Arabidopsis thaliana.","authors":"Lua Lopez, Patricia L M Lang, Stephanie Marciniak, Logan Kistler, Sergio M Latorre, Asnake Haile, Eleanna Vasquez Cerda, Diana Gamba, Yuxing Xu, Patrick Woods, Mistire Yifru, Jeffrey Kerby, John K McKay, Christopher G Oakley, Jon Ågren, Tigist Wondimu, Collins Bulafu, George H Perry, Hernán A Burbano, Jesse R Lasky","doi":"10.1111/mec.70081","DOIUrl":"10.1111/mec.70081","url":null,"abstract":"<p><p>Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in population genetic composition. At individual loci, migration, drift and selection (among other processes) may affect allele frequencies. Museum specimens of widely distributed species offer a unique window into the genetics of understudied populations and changes over time. Here, we sequenced genomes of 130 herbarium specimens and 91 new field collections of Arabidopsis thaliana and combined these with published genomes. We sought a broader view of genomic diversity across the species and to test if population genomic composition is changing through time. We documented extensive and previously uncharacterised diversity in a range of populations in Africa, populations that are under threat from anthropogenic climate change. Through time, we did not find dramatic changes in genomic composition of populations. Instead, we found a pattern of genetic change every 100 years of the same magnitude seen when comparing Eurasian populations that are 185 km apart, potentially due to a combination of drift and changing selection. We found only mixed signals of polygenic adaptation at phenology and physiology QTL. We did find that genes conserved across eudicots show altered levels of directional allele frequency change, potentially due to variable purifying and background selection. Our study highlights how museum specimens can reveal new dimensions of population diversity and show how wild populations are evolving in recent history.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70081"},"PeriodicalIF":3.9,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833544","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}
Jialiang Li, Shiyang Wang, Georg Miehe, Lars Opgenoorth, Heng Yang, Dayu Wu, Kangshan Mao
{"title":"Ecological Selection as Drivers During Early Speciation: Insights From Two Allopatric Cypress Species in the Himalaya.","authors":"Jialiang Li, Shiyang Wang, Georg Miehe, Lars Opgenoorth, Heng Yang, Dayu Wu, Kangshan Mao","doi":"10.1111/mec.70072","DOIUrl":"https://doi.org/10.1111/mec.70072","url":null,"abstract":"<p><p>Understanding the factors driving speciation is fundamental to evolutionary biology. While geographic isolation has long been considered a primary factor, the role of ecological selection during early speciation stages is poorly understood. The Himalaya, a biodiversity hotspot, offers a unique opportunity to study these processes. We investigated two closely related conifer species, Cupressus torulosa and C. cashmeriana, which are geographically separated yet exhibit distinct ecological adaptations. Using target-capture sequencing of 52 C. cashmeriana samples from Bhutan and 46 C. torulosa samples from Nepal, we surveyed their genetic diversity, demographic history and adaptive evolution. Genomic analyses revealed moderate genetic differentiation between them yet confirmed they are genetically distinct sister species. Demographic modelling indicated their divergence began around 6.57 million years ago, with strong gene flow persisting until approximately 2.08 million years ago, shortly after the initiation of Quaternary climate oscillations. Ecological niche modelling showed low niche overlap, reflecting adaptations to different climatic conditions-C. cashmeriana to warmer, wetter habitats and C. torulosa to colder, drier habitats. We identified positively selected genes related to environmental stress responses, highlighting the crucial role of ecological selection. Genotype-environment association and partial redundancy analysis emphasised that ecological factors significantly drive genetic variation. Although overall genomic vulnerability is low, both species show increased offset under future warming, especially C. torulosa, suggesting a need for focused conservation efforts. Our findings underscore the importance of ecological selection in initiating speciation despite strong gene flow and have significant implications for managing mountain biodiversity in the face of climate change.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70072"},"PeriodicalIF":3.9,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833542","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}
Christopher B. Wall, Madeline G. Perreault, Margaret Y. Demmel, Evelyn M. Diaz, Joshua H. Dominguez, Jonathan B. Shurin
{"title":"Geography and Host Identity Shape Intraseasonal Variation of Free-Living and Zooplankton Associated Microbial Communities in Alpine Lakes","authors":"Christopher B. Wall, Madeline G. Perreault, Margaret Y. Demmel, Evelyn M. Diaz, Joshua H. Dominguez, Jonathan B. Shurin","doi":"10.1111/mec.70069","DOIUrl":"10.1111/mec.70069","url":null,"abstract":"<p>Microbes contribute to aquatic ecosystem function and the fitness of macroscopic organisms, including zooplankton. Many factors affect the taxonomic compositions of free-living (bacterioplankton) and zooplankton-associated microbial communities in lakes; yet how these communities vary seasonally and among lakes remains poorly understood. Here, we investigate how free-living bacterial communities and those associated with different crustacean zooplankton hosts change in response to fluctuations in their natural environment across time and space. We repeatedly sampled bacterioplankton, zooplankton communities, zooplankton microbiomes, and water chemistry parameters of six lakes in the eastern Sierra Nevada mountains of California across a summer season. 16S rRNA gene sequencing revealed clear differences in the community composition and relative abundance of bacterial taxa between bacterioplankton and zooplankton microbiomes, which was best explained by lake and host identity rather than intraseasonal sampling times. Bacterioplankton communities were highly conserved across the summer season and showed higher alpha diversity, but lower species turnover, than zooplankton microbiomes, which were more variable and largely partitioned by host taxa and phylogenetics (Copepoda vs. Cladocera). Spatial and local environmental context (drainage basin, home-lake habitat) interacted secondarily with community types (free-living, host-associated) and zooplankton host identity to shape bacterial community composition. These results show that deterministic processes related to host filtering, host taxonomy, and spatial/environmental variation among lakes drive changes in microbial communities more than temporal changes within lakes. Higher beta diversity among zooplankton-associated microbes suggests dispersal limitation and/or local selection play stronger roles for zooplankton microbiomes than for free-living bacterioplankton.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 19","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70069","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833543","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}
James R M Bickerstaff, Bjarte H Jordal, Markus Riegler
{"title":"Biogeography and Social Family Structure Contribute to Cryptic Genomic Divergence in the Only Obligate Eusocial Beetle Species, Austroplatypus incompertus (Curculionidae: Platypodinae).","authors":"James R M Bickerstaff, Bjarte H Jordal, Markus Riegler","doi":"10.1111/mec.70076","DOIUrl":"https://doi.org/10.1111/mec.70076","url":null,"abstract":"<p><p>Eusociality in insects has arisen multiple times independently in Hymenoptera (bees, wasps and ants), Blattodea (termites) and Coleoptera (beetles). In Hymenoptera and Blattodea, the evolution of eusociality led to species proliferation. In the hyperdiverse Coleoptera, obligate eusociality evolved only once, in the ancient Australian ambrosia beetle Austroplatypus incompertus (Curculionidae: Platypodinae). This species occurs patchily in mesic eucalypt forests of eastern Australia, from Victoria to northern New South Wales, and has a low dispersal capacity. Based on individuals collected from the southern and northern edges of its distribution, it was initially described as two distinct species. However, the names were later synonymised as no morphological differences were found throughout the species' distribution. Recent mitochondrial analyses revealed substantial latitudinal divergence across populations. To address this disparity between morphological and molecular data, we sequenced and analysed a SNP panel of over 6656 biallelic markers from 187 individuals from 11 sites across 1000 km of this species' range. Our data indicate that eusocial demographic processes such as limited dispersal and reliance on few reproductive individuals, together with habitat fragmentation, contributed to the genetic structuring of this species into northern, central and southern lineages. We further identified low levels of introgression between the highly diverged central and northern lineages at a site close to the Hunter Valley biogeographic barrier, possibly due to secondary contact. Our results highlight the interplay of biogeography and life history on the genomic divergence in this unique ambrosia beetle lineage of important standing in the evolution of eusociality in insects.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70076"},"PeriodicalIF":3.9,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833540","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}
Jason A Toy, Arthur Oulès, Gary Longo, H Bradley Shaffer, Giacomo Bernardi
{"title":"Population Genomics, Local Adaptation and Cryptic Speciation in a Temperate Reef Fish, the Black Surfperch, Embiotoca jacksoni, Using Genome-Wide Resequencing.","authors":"Jason A Toy, Arthur Oulès, Gary Longo, H Bradley Shaffer, Giacomo Bernardi","doi":"10.1111/mec.70073","DOIUrl":"https://doi.org/10.1111/mec.70073","url":null,"abstract":"<p><p>The black surfperch, Embiotoca jacksoni , exhibits limited dispersal due to its lack of a pelagic larval stage and offers a unique model for studying local adaptation and potential cryptic speciation in marine species. This study employs medium-coverage whole genome resequencing to explore population structure, local adaptation, and genetic divergence across a latitudinal gradient from central California to Baja California, Mexico, including offshore islands. We identify strong genetic differentiation between five distinct groups: a coastal group and four island groups (Santa Catalina Island, San Clemente Island, Isla Guadalupe, and Isla San Jerónimo), from Principal Components Analysis (PCA), Fst estimation, ancestry (sNMF), and phylogenetic analyses. For coastal populations, genetic structure correlates with geographic distance, following isolation-by-distance (IBD) expectations. Further, we identify numerous outlier loci associated with adaptive traits, particularly genes linked to reproductive isolation, such as Spermine oxidase, Izumo sperm-egg fusion protein 1, and SPAG1, which are involved in fertilisation success. These loci suggest that reproductive barriers are contributing to divergence among genetic groups. The presence of signatures of both genetic drift and selective pressures, particularly in genes governing fertilisation, indicates that these distinct populations may represent incipient or cryptic species. Our findings highlight the role of low dispersal in fostering local adaptation and speciation in marine systems and underscore the potential for rapid evolutionary responses to environmental gradients. This research provides insights into the complex processes of speciation in marine vertebrates, particularly those with limited gene flow, and offers a baseline for monitoring genetic shifts in response to climate change.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70073"},"PeriodicalIF":3.9,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144815422","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}
Ellika Faust, Julie Conrads, Marco Giulio, Claudio Ciofi, Chiara Natali, Philine G D Feulner, Alexandra A-T Weber
{"title":"Beyond Genetic Indicators: How Reproductive Mode and Hybridisation Challenge Freshwater Mussel Conservation.","authors":"Ellika Faust, Julie Conrads, Marco Giulio, Claudio Ciofi, Chiara Natali, Philine G D Feulner, Alexandra A-T Weber","doi":"10.1111/mec.70066","DOIUrl":"https://doi.org/10.1111/mec.70066","url":null,"abstract":"<p><p>Genetic diversity is a fundamental aspect of biodiversity, yet it is rarely assessed and monitored in conservation practice. Unionid freshwater mussels exemplify the dramatic loss of biodiversity in freshwater ecosystems, yet genomic data for these ecologically important species remain scarce. Here, we conducted a high-resolution population genomics study of all Anodonta species in Switzerland, with a focus on two species with contrasting reproductive strategies. After generating draft genomes of the hermaphroditic Anodonta cygnea and the gonochoric Anodonta anatina, we performed whole-genome resequencing of 421 individuals collected in 31 localities. While A. anatina populations followed a metapopulation structure shaped by catchment areas, genetic diversity correlated positively with waterbody size, suggesting greater vulnerability in small ponds compared with large lakes. Inbreeding levels were low; however, effective population sizes were consistently below 100, indicating serious extinction risks. Strong divergence between A. anatina populations north and south of the Alps suggests a putative undescribed Anodonta species in the Ticino area. Furthermore, we detected hybridisation between A. cygnea and A. exulcerata, indicating genomic permeability between these species. In addition, genomic data suggested facultative selfing in A. cygnea, leading to a marked reduction in genetic diversity, increased population structure and inbreeding and a decline in effective population size compared to the outcrossing A. anatina. Our study underscores that reproductive strategy fundamentally shapes genetic indicators of biodiversity and influences extinction risk; conservation targets should therefore be adapted to the biology of the species of interest. To conclude, we advocate for integrating reproductive mode and genomic data into conservation planning to more accurately assess vulnerability and guide effective action.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70066"},"PeriodicalIF":3.9,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144815419","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":"Bumble Bees and Honey Bees on Islands Harbour Reduced Viral Species Richness, Yet Honey Bee Populations Are Dominated by a Deformed Wing Virus Recombinant.","authors":"Jana Dobelmann, Lena Wilfert","doi":"10.1111/mec.70070","DOIUrl":"https://doi.org/10.1111/mec.70070","url":null,"abstract":"<p><p>Pollinators harbour diverse RNA viromes that play a vital role in their health. Yet, factors that shape viral communities are often unclear. The European honey bee (Apis mellifera) is experiencing a viral epidemic since the emergence of the parasitic mite Varroa destructor (varroa) introduced vector-borne transmission, which has also been linked to increased viral spillover into wild pollinator communities. Varroa-free island populations provide natural laboratories to study the effect of varroa, while also allowing us to ask how islands affect viral communities. Barriers that restrict the dispersal of wild pollinators and their pathogens to islands may be overcome by human-mediated transport in managed honey bees. Here we used islands with and without varroa and matched mainland populations of honey bees (A. mellifera) and bumble bees (Bombus terrestris) from 2015 and 2021 to explore how varroa presence and island location affect the virome of managed and wild bees. We find lower viral richness on islands in both species. Bumble bees harbour a distinct viral community that was not affected by varroa but geographically structured. In honey bees, however, varroa-present populations contained more viral reads driven by a high abundance of deformed wing virus (DWV). Within the 6 years between the sampling events, DWV underwent a shift from mostly DWV-B towards a mix of DWV-B and recombinant strains. Surprisingly, these shifts appeared independent of varroa. Viewing pollinator virome composition within an ecological framework provides valuable insights into the barriers to virus spread and could help to predict drivers of disease emergence.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70070"},"PeriodicalIF":3.9,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144815420","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}