Kurt Villsen, Gaït Archambaud-Suard, Emese Meglécz, Simon Blanchet, Jean-Pierre Balmain, Mathilde Bertrand, Rémi Chappaz, Vincent Dubut, Emmanuel Corse
{"title":"Disentangling the Effects of Biotic and Abiotic Dimensions of Ecological Opportunity on Individual Trophic Trait Variation.","authors":"Kurt Villsen, Gaït Archambaud-Suard, Emese Meglécz, Simon Blanchet, Jean-Pierre Balmain, Mathilde Bertrand, Rémi Chappaz, Vincent Dubut, Emmanuel Corse","doi":"10.1111/mec.70115","DOIUrl":"https://doi.org/10.1111/mec.70115","url":null,"abstract":"<p><p>Within-species individual trait variation (ITV) plays a critical role in ecological and evolutionary dynamics by influencing community structure, ecosystem functioning, and individual fitness. While the role of the biotic dimension of ecological opportunity (e.g., interspecific competition, prey availability) in shaping trophic ITV is now well established, the role of the abiotic dimension, and its interactions with biotic factors, remains critically overlooked, limiting our understanding of how individuals cope with changes in ecological opportunity. To address this knowledge gap, we investigated trophic ITV in the endangered riverine fish Zingel asper using a multi-faceted approach: (i) precise quantification of trophic ITV via faecal metabarcoding, (ii) fine-scale mapping of prey availability and habitat structure across seasons, and (iii) path analysis to assess the direct and indirect effects of prey, habitat, and their spatial heterogeneity in driving ITV. The individual niche width (INW) in Z. asper was largely determined by preferred prey availability, while between-individual variation (BIC) was largely determined by a combination of prey and habitat factors, with habitat exerting a direct effect (i.e., not mediated via prey) on trophic ITV. This study provides a mechanistic explanation of the processes underlying the shift from selective to opportunistic foraging strategies. Notably, we demonstrated that trophic ITV is altered by the interaction between predator life-history traits (in the present study, size) and four distinct dimensions of ecological opportunity: prey availability and their spatial distribution, habitat structure and seasonality.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70115"},"PeriodicalIF":3.9,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129738","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":"Patterns of Genomic Divergence and Introgression in Two Primulina Hybrid Zones.","authors":"Huiqin Yi, Lihua Yang, Ming Kang","doi":"10.1111/mec.70117","DOIUrl":"https://doi.org/10.1111/mec.70117","url":null,"abstract":"<p><p>Hybrid zones have long been promoted as natural laboratories for understanding the mechanisms of speciation. Multiple or replicated hybrid zones are particularly informative, as they allow for assessing the consistency of genomic divergence and introgression across different environmental contexts and demographic histories, thereby improving our understanding of the factors that drive or hinder speciation on a broader scale. Here, using whole-genome resequencing data, we compare the patterns of genomic divergence and introgression in two Primulina hybrid zones. We found that genomic divergence in both hybrid zones is largely shaped by neutral processes, with only a few genomic regions showing signatures of balancing or lineage-specific selection. Genomic cline analyses identified numerous SNPs that showed significantly steeper clines and biased centres than the genome-wide expectation in both hybrid zones, consistent with the existence of reproductive barriers. Within regions of restricted gene flow, we identified 21 genes shared between the two hybrid zones. Annotation of gene function revealed that several genes are involved in reproductive processes. In addition, many zone-specific outlier loci were linked to genes associated with pollen and flower development, suggesting that these barriers may contribute to reproductive isolation under localised ecological conditions. Overall, these findings suggest that while certain reproductive barriers remain consistent across independent hybrid zones, others may be contingent on local environmental contexts. Our results demonstrate that both general and zone-specific mechanisms contribute to reproductive isolation in Primulina, providing empirical evidence that some genomic barriers recur across independent hybrid zones while others arise through localised adaptation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70117"},"PeriodicalIF":3.9,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129759","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}
Emily C Giles, Romuald Laso-Jadart, Daniel Ortiz-Barrientos, Paulina Carimán Soto, Erwan Delrieu-Trottin, Marie Laure Guillemin, Stefano Mona, Xavier Pochon, Pablo Saenz-Agudelo
{"title":"Mapping Species Birth Across the Recombination Landscapes of Marine Snails.","authors":"Emily C Giles, Romuald Laso-Jadart, Daniel Ortiz-Barrientos, Paulina Carimán Soto, Erwan Delrieu-Trottin, Marie Laure Guillemin, Stefano Mona, Xavier Pochon, Pablo Saenz-Agudelo","doi":"10.1111/mec.70108","DOIUrl":"https://doi.org/10.1111/mec.70108","url":null,"abstract":"<p><p>Understanding the drivers of heterogeneous genomic divergence is essential for uncovering the mechanisms that generate and constrain biodiversity. The extent to which adaptation and speciation are facilitated by reorganisation of the recombination landscape remains untested in many systems. Marine ecosystems, with their dynamic and fluid habitats, offer a compelling context to investigate genomic divergence. In this study, we mapped genomic divergence and selection across recombination landscapes of parapatric marine snail sister species that we show have recently undergone secondary contact. Regions of reduced recombination were enriched for genes exhibiting signatures of negative selection, whereas regions of high recombination were associated with genes under putative positive selection. Notably, the recombination landscape of the population in parapatry of one species (Scurria viridula) differs markedly from that of the other population within this same species, highlighting the role of introgression in reshaping recombination landscapes. In the other species (Scurria zebrina), conservation of the recombination landscape and divergent selection among populations suggest trapping of beneficial allele combinations in regions of low recombination maintains the identity of this species. Among species, signals of divergence with gene flow consistently cluster within specific genomic regions characterised by high recombination rate variation among the populations of S. viridula. These results challenge traditional theoretical expectations of recombination evolution by showing that the causes of genomic divergence can be population-specific. This study demonstrates that recombination landscapes are key modulators of genomic divergence, with contemporary evolutionary shifts that could enable populations to adapt to distinct environments. Our findings provide new insights into the interplay between recombination, selection, and gene flow during speciation, underscoring the complexity of evolutionary trajectories in marine systems.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70108"},"PeriodicalIF":3.9,"publicationDate":"2025-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111593","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}
Filippo Nicolini, Sergey V Nuzhdin, Fabrizio Ghiselli, Andrea Luchetti, Liliana Milani
{"title":"Comparative Genomics of Sex-Determination-Related Genes Reveals Shared Evolutionary Patterns Between Bivalves and Mammals, but Not Fruit Flies.","authors":"Filippo Nicolini, Sergey V Nuzhdin, Fabrizio Ghiselli, Andrea Luchetti, Liliana Milani","doi":"10.1111/mec.70103","DOIUrl":"https://doi.org/10.1111/mec.70103","url":null,"abstract":"<p><p>The molecular basis of sex determination (SD), while being extensively studied in model organisms, remains poorly understood in many animal groups. Bivalves, a diverse class of molluscs with a variety of reproductive modes, represent an ideal yet challenging clade for investigating SD and the evolution of sexual systems. However, the absence of a comprehensive framework has limited progress in this field, particularly regarding the study of sex-determination-related genes (SRGs). In this study, we performed a genome-wide sequence evolutionary analysis of the Dmrt, Sox and Fox gene families in more than 40 bivalve species. For the first time, we provide an extensive and phylogenetically aware dataset of these SRGs, and we find support for the hypothesis that Dmrt-1L and Sox-H may act as primary sex-determining genes by showing their high levels of sequence diversity within the bivalve genomic context. To validate our findings, we studied the same gene families in two well-characterised systems, mammals and fruit flies (genus Drosophila). In the former, we found that the male sex-determining gene Sry exhibits a pattern of amino acid sequence diversity similar to that of Dmrt-1L and Sox-H in bivalves, consistent with its role as master SD regulator. In contrast, no such pattern was observed among genes of the fruit fly SD cascade, which is controlled by a chromosomic mechanism. Overall, our findings highlight similarities in the sequence evolution of some mammal and bivalve SRGs, possibly driven by a comparable architecture of SD cascades. This work underscores once again the importance of employing a comparative approach when investigating understudied and non-model systems.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70103"},"PeriodicalIF":3.9,"publicationDate":"2025-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111608","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}
Nozomu Muto, Yong-Chao Su, Harutaka Hata, Nguyen Van Quan, Veera Vilasri, Mazlan Abd Ghaffar, Ricardo P Babaran
{"title":"Homoploid Hybrid Speciation in a Marine Pelagic Fish.","authors":"Nozomu Muto, Yong-Chao Su, Harutaka Hata, Nguyen Van Quan, Veera Vilasri, Mazlan Abd Ghaffar, Ricardo P Babaran","doi":"10.1111/mec.70112","DOIUrl":"https://doi.org/10.1111/mec.70112","url":null,"abstract":"<p><p>Homoploid hybrid speciation (HHS) is an enigmatic evolutionary process where new species arise through hybridisation of divergent lineages without changes in chromosome number. Although increasingly documented in various taxa and ecosystems, convincing cases of HHS in marine fishes have been lacking. This study presents a possible case of HHS in a pelagic marine fish based on comprehensive genomic, morphological, and ecological analyses. Population genomics, species tree estimation, and tests of introgression and admixture identified three sympatric clusters in Megalaspis cordyla in the western Pacific and the admixed nature of one cluster between the others. Moreover, model-based demographic inference favoured a hybrid speciation scenario over introgression for the origin of the admixed cluster. While contemporary gene flow suggested partial reproductive isolation, examination of occurrence data and ecologically relevant morphological characters suggested ecological differences between the clusters, potentially contributing to the reproductive isolation and niche partitioning in sympatry. The clusters are also morphologically distinguishable and thus can be taxonomically recognised as separate species. The hybrid cluster is restricted to the coasts of Taiwan and Japan, where all three clusters coexist. The parental clusters are additionally found in lower latitudes, where they display non-overlapping distributions. Given the geographical distributions, estimated times of species formation, and patterns of historical demographic changes, we propose that the Pleistocene glacial cycles were the primary driver of HHS in this system. We also develop an ecogeographic model of HHS in marine coastal ecosystems, including a novel hypothesis to explain the initial stages of HHS.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70112"},"PeriodicalIF":3.9,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084723","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}
Shuang Han, Jie Wang, Taixing Lin, Jingping Zhang, Adelino V M Canario, Qigen Liu, Liangbiao Chen
{"title":"Adaptive Evolution for Freshwater Adaptation in Coilia nasus by Directional Selection on Osmoregulation Genes.","authors":"Shuang Han, Jie Wang, Taixing Lin, Jingping Zhang, Adelino V M Canario, Qigen Liu, Liangbiao Chen","doi":"10.1111/mec.70104","DOIUrl":"https://doi.org/10.1111/mec.70104","url":null,"abstract":"<p><p>The molecular mechanisms underlying the adaptation to freshwater habitats in fish of marine origin remain unclear. Grenadier anchovies, such as Coilia nasus, originate from marine environments and include both anadromous and freshwater-resident conspecifics, making them ideal for studying adaptive evolution from marine to freshwater habitats. We conducted a comparative population genomic and transcriptome analysis of two distinct C. nasus lineages, one anadromous and the other freshwater-resident, collected from mainstream and estuarine regions of the Yangtze River, China. By genome-wide genotyping of the anadromous and the freshwater-resident populations, we observed significant divergence in osmoregulation, energy metabolism, and immune response pathways associated with ecological adaptation and energy expenditure for migration. Some ion transport genes such as CAMK1, ATP1α3, KCNJ1 and SLC30A2 were identified that may contribute to freshwater adaptation. Notably, numerous mineralocorticoid signalling genes (e.g., NR3C2, SGK1, ATP1α3, KCNJ1) exhibit dynamic change between the anadromous and freshwater populations, suggesting an important role for the hormone cortisol in regulating salinity acclimation in euryhaline fish. Among these genes, the ion channel ATP1α3 experienced adaptive amino acid substitutions (Val317Ile and Thr329Ser), which appear to be evolutionary hotspots across migratory species based on ortholog comparisons. These variants may facilitate sodium/potassium transport and highlight salinity tolerance as a key driver of divergence in anadromous fish transitioning to freshwater. These results enhance our understanding of the genetic basis underlying freshwater adaptation for an anadromous fish across osmotic boundaries.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70104"},"PeriodicalIF":3.9,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079072","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}
Devin P Bendixsen, Ciaran Gilchrist, Chloé Haberkorn, Karl Persson, Cecilia Geijer, Jonas Warringer, Rike Stelkens
{"title":"Reproductive Isolation due to Divergent Ecological Selection Is Accompanied by Vast Genomic Instability in Experimentally Evolved Yeast Populations.","authors":"Devin P Bendixsen, Ciaran Gilchrist, Chloé Haberkorn, Karl Persson, Cecilia Geijer, Jonas Warringer, Rike Stelkens","doi":"10.1111/mec.70110","DOIUrl":"https://doi.org/10.1111/mec.70110","url":null,"abstract":"<p><p>Populations evolving independently in divergent environments accumulate genetic differences and potentially evolve reproductive isolation as a by-product of divergence. The speed and mechanisms underlying this process are difficult to investigate because we rarely get the opportunity to witness them in natural settings, and histories of selection and gene flow between populations are often unknown. Here, we experimentally evolved yeast for 1000 generations of evolution in both divergent and parallel environments. At regular time points during experimental evolution, we made crosses between parallel- and divergent-evolving populations to measure postzygotic reproductive isolation (gamete viability). We used whole genome population sequencing to determine the mutational load, the number and types of structural variation, and other genomic features of the parent, F1 and F2 intraspecific hybrids. We found evidence for large-scale phenotypic and genome-wide differentiation in response to divergent laboratory selection. Divergent-selected populations produced hybrids with reduced gamete viability-a classic signature of postzygotic reproductive isolation in the form of hybrid breakdown. Parallel-selected populations, on the other hand, remained more reproductively compatible (with exceptions). We found that F2 hybrid genomes contained vast genomic instability, that is, new structural variants (especially insertions, deletions and interchromosomal translocations) that were not observed in parent and F1 genomes, which is likely a result of chromosome missegregation and recombination errors in hybrid meiosis. Our results provide phenotypic and genomic evidence that partial reproductive isolation evolved due to adaptation to divergent environments, consistent with predictions of ecological speciation theory.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70110"},"PeriodicalIF":3.9,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074217","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}
Nemo V Robles, Benjamin M Moran, María José Rodríguez Barrera, Gaston I Jofre, Theresa Gunn, Erik N K Iverson, Sofia Beskid, John J Baczenas, Alisa Sedghifar, Peter Andolfatto, Daniel L Powell, Yaniv Brandvain, Justin C Havird, Gil G Rosenthal, Molly Schumer
{"title":"Admixture Mapping Reveals Evidence for Multiple Mitonuclear Incompatibilities in Swordtail Fish Hybrids.","authors":"Nemo V Robles, Benjamin M Moran, María José Rodríguez Barrera, Gaston I Jofre, Theresa Gunn, Erik N K Iverson, Sofia Beskid, John J Baczenas, Alisa Sedghifar, Peter Andolfatto, Daniel L Powell, Yaniv Brandvain, Justin C Havird, Gil G Rosenthal, Molly Schumer","doi":"10.1111/mec.70106","DOIUrl":"10.1111/mec.70106","url":null,"abstract":"<p><p>How barriers to gene flow arise between closely related species is one of the oldest questions in evolutionary biology. Classic models in evolutionary biology predict that negative epistatic interactions between variants in the genomes of diverged lineages, known as hybrid incompatibilities, will reduce viability or fertility in hybrids. The genetic architecture of these interactions and the evolutionary paths through which they arise have profound implications for the efficacy of hybrid incompatibilities as barriers to gene flow between species. While these questions have been studied using theoretical approaches for several decades, only recently has it become possible to genetically map larger numbers of hybrid incompatibilities. Here, we use admixture mapping in natural hybrid populations of swordtail fish (Xiphophorus) to identify hybrid incompatibilities involving genetic interactions between the mitochondrial and nuclear genomes. We find that at least nine regions of the genome are involved in mitonuclear incompatibilities. These incompatibilities involve interactions between the nuclear genome and the X. malinche mitochondria, the X. birchmanni mitochondria, or both. Moreover, they vary in the strength of selection they experience and the degree to which they limit gene flow in natural hybrid populations. Our results build a deeper understanding of the complex architecture of selection against incompatibilities in naturally hybridising species and highlight an important role of mitonuclear interactions in the evolution of reproductive barriers between closely related species.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70106"},"PeriodicalIF":3.9,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074222","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}
Rebecca von Hellfeld, Rebecca Konietzny, Philip D Charles, Roman Fischer, Benedikt M Kessler, Stuart Wigby, Irem Sepil, Juliano Morimoto
{"title":"The Developmental Environment Mediates Adult Seminal Proteome Allocation in Male Drosophila melanogaster.","authors":"Rebecca von Hellfeld, Rebecca Konietzny, Philip D Charles, Roman Fischer, Benedikt M Kessler, Stuart Wigby, Irem Sepil, Juliano Morimoto","doi":"10.1111/mec.70101","DOIUrl":"https://doi.org/10.1111/mec.70101","url":null,"abstract":"<p><p>Early life conditions can have long-lasting effects on fitness. In insects, larval crowding increases intraspecific competition, shaping adult phenotypes and influencing male reproductive success in pre- and post-mating competition. Although some larval crowding effects on seminal fluid protein (Sfp) allocation are known, studies often focus on a small subset of Sfps and overlook male-female interactions. A comprehensive understanding of how male and female larval environments interact to influence seminal proteome composition and transfer is still lacking. Here, we manipulated Drosophila melanogaster larval crowding (low vs. high) to generate large and small adults and mated individuals in a fully factorial design. We then measured Sfp production, composition and transfer. Large males produced relatively higher quantities of Sfps. However, small males transferred greater quantities of a subset of Sfps. When examining proteins individually, 10 Sfps were transferred at significantly higher abundances by small males than large males. Our findings suggest that small males invest more per mating, potentially due to fewer mating opportunities or cues of high larval density influencing reproductive strategies. This study provides new insights into early life effects on ejaculate allocation in D. melanogaster, highlighting physiological and behavioural responses to developmental conditions. Understanding these mechanisms offers valuable perspectives on reproductive strategies and fitness trade-offs in insects.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70101"},"PeriodicalIF":3.9,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145063032","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":"Adaptation of the Cyst Nematode Globodera pallida to the Colinear Potato Resistant QTLs GpaV<sub>vrn</sub> and GpaV<sub>spl</sub> Involved Distinct Genomic Regions and Absence of Cross-Virulence.","authors":"Océane Lechevalier, Magali Esquibet, Mathieu Gautier, Rachel Fourdin, Eric Grenier, Sylvain Fournet, Josselin Montarry","doi":"10.1111/mec.70105","DOIUrl":"https://doi.org/10.1111/mec.70105","url":null,"abstract":"<p><p>The use of alternative methods to control cyst nematode populations has accelerated since the ban of chemical nematicides in Europe. The resistant QTL GpaV<sub>vrn</sub>, derived from the wild species Solanum vernei, is widely present in resistant European potato cultivars and provides strong protection against Globodera pallida populations although a risk of resistance breakdown has already been demonstrated in both experimental evolution studies and field populations. The wild relative S. sparsipilum, harbouring the resistant QTL GpaV<sub>spl</sub>, would be an interesting alternative source of resistance to control virulent G. pallida. The goal of the present study was to understand the genomics of adaptation of the nematode to these two colinear resistant QTLs. Starting with two natural populations, an experimental evolution approach allowed, after 10 generations on resistant potato genotypes, selecting independent nematode lineages adapted to each QTL. These virulent lineages were analysed through a combination of phenotyping and genome scans approaches. Phenotyping enabled the quantification of virulence levels and confirmed resistance breakdowns. Pool-Seq whole genome sequencing followed by genome scan analyses identified genomic regions under selection, potentially involved in the adaptive mechanisms to each resistance factor. Candidate genes within these regions provided insights into the genetic basis of adaptation, revealing effectors known to suppress plant immunity. As genome scans highlighted distinct genomic regions for the adaptation to both resistant factors, we were able to predict and phenotypically confirm the absence of cross-virulence between nematode lineages evolving on GpaV<sub>vrn</sub> and GpaV<sub>spl</sub>. These findings have significant implications for the design of effective and sustainable resistance management strategies.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70105"},"PeriodicalIF":3.9,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145051560","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}