Yu-Chi Chen, Nikolas Vellnow, Justin J. S. Wilcox, Sahar Javaheri Tehrani, Toni I. Gossmann
{"title":"Opinion: Why Sex-Based Genomic Differentiation Should Not Be Overlooked in Population Genetics","authors":"Yu-Chi Chen, Nikolas Vellnow, Justin J. S. Wilcox, Sahar Javaheri Tehrani, Toni I. Gossmann","doi":"10.1111/mec.70061","DOIUrl":"10.1111/mec.70061","url":null,"abstract":"<p>Sex-specific genomic differentiation is a crucial yet frequently overlooked factor in population genetics. In this opinion piece, we leverage the substantial genomic resources available for the great tit (<i>Parus major</i>), including population-scale data sets from many European populations, to investigate genomic differentiation between males and females. Unlike in some other species, where high-quality genome assemblies exist but broad population sampling is lacking, the great tit offers a unique opportunity to study sex-based differentiation at both the genomic and population level. We identify significant differentiation at an autosomal locus on chromosome 5, which we hypothesise originates from sex-linked variation present on the sex chromosomes (Z and potentially W). By referencing genomic data from other songbirds with well-assembled sex chromosomes, we illustrate how autosomal loci may exhibit high sequence similarity to sex-linked regions. Our analyses demonstrate that uneven sex ratios in sampled populations can substantially bias differentiation metrics (e.g., <i>F</i><sub><i>ST</i></sub>), potentially resulting in false-positive interpretations of adaptive differentiation. To mitigate such issues, we stress the importance of sex-aware study designs, including balanced sex sampling and explicitly incorporating sex as a covariate. Furthermore, while optimal study designs would include high-quality reference genomes from both sexes, we recommend, as a pragmatic and cost-effective alternative for labs with limited resources, generating a reference genome from the heterogametic sex (females in birds) to ensure both sex chromosomes are represented in mapping and analysis. Finally, we emphasise the need for rigorous validation of candidate loci to ensure accurate and biologically meaningful outcomes in evolutionary genomic studies.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70061","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144793101","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}
Dabao Sun Lu, Ine-Susanne Hopland Methlie, Jørn-Henrik Sønstebø, Anneli Andersen, David Peris, Sundy Maurice, Håvard Kauserud, Inger Skrede
{"title":"Postglacial History of a Widespread Wood-Decaying Fungus in Europe Suggests Migration out of Multiple Refugia Followed by Admixture.","authors":"Dabao Sun Lu, Ine-Susanne Hopland Methlie, Jørn-Henrik Sønstebø, Anneli Andersen, David Peris, Sundy Maurice, Håvard Kauserud, Inger Skrede","doi":"10.1111/mec.70053","DOIUrl":"https://doi.org/10.1111/mec.70053","url":null,"abstract":"<p><p>While postglacial migration patterns have been well-studied in plants and animals in Europe, the same is not true for microorganisms such as fungi, and it remains unclear whether fungi have followed the same postglacial migration trajectories. In this study, we infer the postglacial history of the widespread wood-decay fungus Trichaptum abietinum in Europe. We investigate whether this fungus resided in multiple glacial refugia, as observed in many plants and animals, and how it migrated following the retreat of the ice. Population genomic analyses of T. abietinum suggest at least two glacial refugia in Europe: a southern refugium extending from Portugal to the Caucasus (potentially formed by several earlier distinct refugia), an eastern refugium and a potential third western refugium. Expansion from these refugia followed by migration and secondary contact has led to a complex genomic pattern of what we call the Mediterranean, Boreal, Atlantic and Central European admixed groups. From the southern and potential western refugia there have likely been northwards expansions resulting in the Mediterranean and Atlantic groups, while the Boreal group probably expanded westwards from the eastern refugium. A contact zone is present in Central Europe, where the Mediterranean and Boreal groups are admixing. In these admixed individuals, the second half of their largest scaffold is entirely inherited from the Boreal group, indicating either strong selection or genomic incompatibilities. In Scandinavia, the Atlantic and Boreal groups are in close contact but with limited admixture. Tajima's D and analyses of linkage disequilibrium decay support a recent history of contraction and expansion of this fungus in Europe. We conclude that the postglacial migration patterns in T. abietinum resemble those observed in several plants and animals, suggesting multiple glacial refugia followed by admixture during northward and westward expansions.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70053"},"PeriodicalIF":3.9,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144793102","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":"Time-Series RNA-Seq of Acropora tenuis Reveals Molecular Waves Leading to Synchronous Mass Spawning of Scleractinian Corals.","authors":"Yuki Yoshioka, Go Suzuki, Yuji Fujikura, Satokuni Tashiro, Taiga Uchida, Eiichi Shoguchi, Noriyuki Satoh, Chuya Shinzato","doi":"10.1111/mec.70054","DOIUrl":"https://doi.org/10.1111/mec.70054","url":null,"abstract":"<p><p>Although mass, synchronised spawning of scleractinian corals is a well-known phenomenon, its underlying molecular mechanisms, especially those that achieve synchronous release of gametes, are still unknown. In the genus Acropora, the dominant scleractinian coral in shallow reefs, spawning timing is synchronised in any given location, but often varies among locations. Here, we report gene expression cascades potentially driving synchronous mass spawning, revealed through transcriptome monitoring of Acropora tenuis, tracking both daily and monthly dynamics during a year-long experiment that included two spawning events. We identified 236 genes in four waves of molecular events that culminated in spawning. First, receptor function and prostaglandin secretion became active 2 weeks before spawning and gradually decreased, but remained elevated until spawning, suggesting communication of maturation among colonies. Second, 1-2 weeks before spawning, TGF-β signalling and spermiogenesis involving kinases were activated. Third, sperm capacitation and preparation of egg-sperm bundle material commenced a week before spawning. Finally, activation of transcription factor ELF1 triggered a signal cascade that induced spawning. This moonlight-independent system may serve to fine-tune the timing of spawning and may explain the broad geographic distribution and ecological success of Acropora, making it the most diverse and abundant genus of scleractinian corals in reef ecosystems.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70054"},"PeriodicalIF":3.9,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144783111","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}
Martin N. Andersson, Twinkle Biswas, Jothi Kumar Yuvaraj
{"title":"Highly Expressed Odorant Receptor Orthologs Detect the Aggregation Pheromone Lineatin in Trypodendron Ambrosia Beetles","authors":"Martin N. Andersson, Twinkle Biswas, Jothi Kumar Yuvaraj","doi":"10.1111/mec.70064","DOIUrl":"10.1111/mec.70064","url":null,"abstract":"<p>Chemical communication using pheromones is crucial for the reproductive success of many insect species, including beetles (Coleoptera). Pheromones are detected by specialised odorant receptors (ORs), called pheromone receptors (PRs), in the sensory neurons of the antennae. The PRs in Coleoptera remain understudied, with only a few receptors being functionally characterised. This limits our understanding of their response specificities and evolutionary origins. To this end, we aimed to identify PRs in two species of ambrosia beetles (Curculionidae; Scolytinae), the conifer-attacking <i>Trypodendron lineatum</i> (‘Tlin’) and the congener <i>T. domesticum</i> (‘Tdom’), specialising in deciduous trees. Both species use the female-produced aggregation pheromone lineatin for host- and mate finding. To date, no OR has been functionally characterised in ambrosia beetles. We specifically aimed to investigate the response specificity of the candidate PRs and their evolutionary relationships with PRs in other curculionids. We annotated 53 ORs from a <i>T. domesticum</i> antennal transcriptome, whereas ORs from <i>T. lineatum</i> were reported previously. We reveal numerous conserved <i>Trypodendron</i> OR orthologs with high sequence identity, with one orthologous pair (TdomOR13/TlinOR13) having much higher expression than all other OR genes. Through functional characterisation in HEK293 cells, we show that these receptors respond exclusively to lineatin. We further show that the receptors are phylogenetically well separated from all other known beetle PRs, including those in other curculionid species. This is the first study to demonstrate functional conservation of PR orthologs in congeneric beetles, and our findings support a scenario in which coleopteran PRs have evolved on multiple independent occasions.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70064","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144774394","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}
Thomas James Ellis, David Luke Field, Nicholas H. Barton
{"title":"Joint Estimation of Paternity, Sibships and Pollen Dispersal in a Snapdragon Hybrid Zone","authors":"Thomas James Ellis, David Luke Field, Nicholas H. Barton","doi":"10.1111/mec.70051","DOIUrl":"10.1111/mec.70051","url":null,"abstract":"<p>Inferring genealogical relationships of wild populations is useful because it gives direct estimates of mating patterns and variance in reproductive success. Inference can be improved by including information about parentage shared between siblings, or by modelling phenotypes or population data related to mating. However, we currently lack a framework to infer parent–offspring relationships, sibships and population parameters in a single analysis. To address this, we here extend a previous method, Fractional Analysis of Paternity and Sibships, to include population data for the case where one parent is known. We illustrate this with the example of pollen dispersal in a natural hybrid zone population of the snapdragon <i>Antirrhinum majus</i>. Pollen dispersal is leptokurtic, with half of mating events occurring within 30 m, but with a long tail of mating events up to 859 m. Using simulations, we find that both sibship and population information substantially improve pedigree reconstruction, and that we can expect to resolve median dispersal distances with high accuracy.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70051","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144764241","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}
Molecular EcologyPub Date : 2025-08-01Epub Date: 2025-07-25DOI: 10.1111/mec.70027
Stephen J Sabatino, M Pilar Cabezas, Paulo Pereira, Susana Garrido, António M Santos, Miguel Carneiro, Paulo T Santos, Bruno Louro, Cymon J Cox, Adelino V M Canário, Ana Veríssimo
{"title":"Inversions Dominate Evolution in the European Sardine (Sardina pilchardus) Amid Strong Gene Flow.","authors":"Stephen J Sabatino, M Pilar Cabezas, Paulo Pereira, Susana Garrido, António M Santos, Miguel Carneiro, Paulo T Santos, Bruno Louro, Cymon J Cox, Adelino V M Canário, Ana Veríssimo","doi":"10.1111/mec.70027","DOIUrl":"10.1111/mec.70027","url":null,"abstract":"<p><p>Inversions can play key roles in the genetic architecture of adaptation, but the scale of their effects across different species remains poorly understood. Here, we use whole-genome sequencing and demographic modelling to investigate the influence of inversions on the population genomics of the r-selected European sardine (Sardina pilchardus). Allele frequency differences from millions of SNPs across 34 populations spanning the species' range were analysed. Genomic scans identified several extreme outlier regions overlapping large inversions (29-52 Mbp), collectively representing over half the genome. Our findings suggest these inversions correlate with locally adapted life-history strategies. First, SNPs within outlier regions containing inversions exhibited striking allele frequency differences between Atlantic and Mediterranean sardines, which differ in key adaptive life-history traits. In the Atlantic, inversion allele frequencies varied latitudinally, while in the Mediterranean, they shifted longitudinally, aligning with temperature and oceanographic features that influence sardine life-history strategies. Moreover, adjacent populations in contrasting environments exhibited pronounced differences in inversion allele frequencies, accompanied by a marked reduction in migration between them. In contrast, spatial patterns at neutral loci showed widespread gene flow, isolation by distance within basins, and population structure between Atlantic and Mediterranean basins (except for the Canary Islands). These results suggest that the inversions studied are under selection and demonstrate the capacity of large inversions to shape genome-wide patterns of genetic diversity and population structure in species characterized by widespread gene flow. Our work also offers crucial insights for stock delimitation and management of this commercially valuable species in the face of climate change.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70027"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144705897","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}
Molecular EcologyPub Date : 2025-08-01Epub Date: 2025-07-11DOI: 10.1111/mec.70023
Rachel Berg, Gastón Aguilera, Guillermo Goyenola, Ana C Petry, Axel Meyer, Julián Torres-Dowdall
{"title":"Peripheral Budding Following Range Expansion Explains Diversity and Distribution of One-Sided Livebearing Fish.","authors":"Rachel Berg, Gastón Aguilera, Guillermo Goyenola, Ana C Petry, Axel Meyer, Julián Torres-Dowdall","doi":"10.1111/mec.70023","DOIUrl":"10.1111/mec.70023","url":null,"abstract":"<p><p>Peripheral budding occurs when populations diverge from a widespread parental population and speciate along its periphery, facilitated by the interaction of ecological and geographic barriers. This phenomenon results in species that contrast in range size and ecological tolerance and can lead to confounding phylogenies. Here we examine patterns of peripheral budding in the Jenynsia lineata species complex using a genomic approach. The J. lineata species complex is a group of live-bearing fish in South America that shows signals of peripheral budding through asymmetric range sizes, J. lineata being widespread, and with a confounding and unresolved phylogeny. Our goal was to adequately classify the J. lineata species complex, delimit species within the complex, and identify signals of introgression to better understand the underlying evolutionary patterns. We collected 85 samples from the species complex for DNA extraction and performed RAD sequencing to generate genome-wide molecular markers for phylogenetic analyses. We found evidence of six distinct genetic groups within the complex and delimited at least five species, with a new species of Jenynsia in Northern Argentina along the periphery of J. lineata. Jenynsia lineata was recovered as the most recently diverged species in our phylogeny. This placement, along with observed patterns of introgression between species, suggests peripheral budding to have facilitated speciation in the J. lineata species complex, following a range expansion of a parental J. lineata. Our results show genomic patterns associated with peripheral budding and support the utility of using peripheral budding to better understand confounding phylogenetic patterns.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70023"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144606955","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}
Molecular EcologyPub Date : 2025-08-01Epub Date: 2025-07-19DOI: 10.1111/mec.70028
Léna Kläy, Léo Girardin, Vincent Calvez, Florence Débarre
{"title":"The Spatial Spread and the Persistence of Gene Drives Are Affected by Demographic Feedbacks, Density Dependence and Allee Effects.","authors":"Léna Kläy, Léo Girardin, Vincent Calvez, Florence Débarre","doi":"10.1111/mec.70028","DOIUrl":"10.1111/mec.70028","url":null,"abstract":"<p><p>Homing gene drive alleles bias their own transmission by converting wild-type alleles into drive alleles. If introduced in a natural population, they might fix within a relatively small number of generations, even if they are deleterious. No engineered homing gene drive organisms have been released in the wild so far, and modelling is essential to develop a clear understanding of the potential outcomes of such releases. We use deterministic models to investigate how different demographic features affect the spatial spread of a gene drive. Building on previous work, we first consider the effect of the intrinsic population growth rate on drive spread. We confirm that including demographic dynamics can change outcomes compared to a model ignoring changes in population sizes because changes in population density can oppose the spatial spread of a drive. Secondly, we study the consequences of including an Allee effect and find that it makes a population more prone to eradication following drive spread. Finally, we investigate the effects of the fitness component on which density dependence operates (fecundity or survival) and find that it affects the speed of drive invasion in space and can accentuate the consequences of an Allee effect. These results confirm the importance of checking the robustness of model outcomes to changes in the underlying assumptions, especially if models are to be used for gene drive risk assessment.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70028"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666659","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}
Molecular EcologyPub Date : 2025-08-01Epub Date: 2025-07-01DOI: 10.1111/mec.70010
Irene de Sosa, Marta Turon, Sergi Taboada, José Lorente-Sorolla, Rosa Fernández, Natasha Tilikj, Alberto Piris, Marta Novo, Patricia Álvarez Campos, Ana Riesgo
{"title":"No Mate, No Problem: Molecular Mechanisms Involved in Parthenogenesis in the Cosmopolitan Earthworm Aporrectodea trapezoides (Annelida, Clitellata).","authors":"Irene de Sosa, Marta Turon, Sergi Taboada, José Lorente-Sorolla, Rosa Fernández, Natasha Tilikj, Alberto Piris, Marta Novo, Patricia Álvarez Campos, Ana Riesgo","doi":"10.1111/mec.70010","DOIUrl":"10.1111/mec.70010","url":null,"abstract":"<p><p>Approximately, 40% of earthworm species can reproduce by parthenogenesis. This is the case for the cosmopolitan species, Aporrectodea trapezoides, although sexual forms have been described sporadically. We analyse the genotypes and microbiomes of 30 individuals from four localities where both forms appear in order to understand the evolutionary mechanisms related to parthenogenesis. In all sites, heterozygosity values were approximately 30% higher in parthenogenetic individuals. However, we detected a stronger genomic structuring due to reproduction than to the geographical setting only in the Algerian population, underpinned by 195 loci that were related to gametogenesis, symbiont-like processes, and nitrate reduction. Similarly, statistical differences in the abundance of ZOTUs were only found between the Algerian sexual and parthenogenetic earthworms, with 754 ZOTUs that included the genus Romboutsia, which is involved in the production of nitric oxide, which enhances sperm motility. In summary, significant genomic and microbiome differences were found only between sexual and parthenogenetic lineages in a single locality. We hypothesise that obligate parthenogenesis evolved early, leaving traces at the genomic and microbiome levels in the Algerian parthenogens that were the earliest splitting lineage. Such obligate parthenogenesis was lost secondarily and individuals in the Iberian sites were facultative parthenogens, with the potential to copulate and therefore erase the genomic and microbial traces of obligate parthenogenesis. Our results indicate a hybrid origin of parthenogenesis in A. trapezoides and shed light on the complex interplay between genomic, microbiome, and reproductive mechanisms in A. trapezoides.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70010"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525640","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}
Molecular EcologyPub Date : 2025-08-01Epub Date: 2025-07-09DOI: 10.1111/mec.70022
Logan S Billet, Obed Hernández-Gómez, David K Skelly
{"title":"Ranavirus Epizootics and Gut Bacteriome Dysbiosis in Tadpoles: Evidence for the Anna Karenina Principle?","authors":"Logan S Billet, Obed Hernández-Gómez, David K Skelly","doi":"10.1111/mec.70022","DOIUrl":"10.1111/mec.70022","url":null,"abstract":"<p><p>The microbiome plays a critical role in animal health, yet its responses to pathogens under natural conditions remain poorly understood. We investigated gut bacterial community (bacteriome) dynamics in wood frog (Rana sylvatica [Lithobates sylvaticus]) tadpoles during natural ranavirus outbreaks to understand how pathogen-induced disturbances shape the bacteriome. Using 16S rRNA sequencing, we compared the bacteriomes of tadpoles in ponds experiencing ranavirus die-offs with those from unaffected ponds before, during and after die-offs. Ranavirus infection significantly altered gut bacteriome composition and increased variability (dispersion), consistent with the Anna Karenina principle. Tadpoles with high infection intensities exhibited reduced bacterial diversity and shifts in community structure, including enrichment of some genera that have been linked previously to antiviral immunity. The predicted functional pathway analyses revealed shifts toward carbohydrate metabolism pathways during die-offs, suggesting microbial adaptation to altered host physiology under infection stress. Some bacteriome changes were detectable even before die-offs occurred, highlighting potential early indicators of infection in the gut bacteriome. In a pond that recovered after an epizootic, we observed partial recovery of some of the bacteria that shifted in relative abundance during the die-off, a pattern that may reflect microbial resilience within hosts, selective survival of tadpoles that never developed severe infections, or a combination of both mechanisms. Our findings demonstrate that ranavirus epizootics disrupt gut bacteriomes in amphibians while simultaneously eliciting potentially adaptive microbial responses. These insights underscore the complex interplay between immunity, microbiome dynamics, and environmental conditions during disease outbreaks, highlighting opportunities for microbiome-based interventions to support amphibian conservation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70022"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590032","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}