Colin Vullioud, Diana Geweiler, Joerg Melzheimer, Sonja Heinrich, Jörns Fickel, Bettina Wachter, Alexandra Weyrich
{"title":"Epigenetic Changes Associated With a Phenotypic Transition in Namibian Cheetahs.","authors":"Colin Vullioud, Diana Geweiler, Joerg Melzheimer, Sonja Heinrich, Jörns Fickel, Bettina Wachter, Alexandra Weyrich","doi":"10.1111/mec.70527","DOIUrl":"https://doi.org/10.1111/mec.70527","url":null,"abstract":"<p><p>In populations with low genetic diversity, the capacity to adapt to environmental change is limited. While epigenetic mechanisms can generate phenotypic plasticity, their role in mediating adaptive life-history transitions in the wild is largely unknown. Here, we show that in adult Namibian cheetahs (Acinonyx jubatus jubatus), a species with remarkably low genetic diversity, the transition from a floater to a male holding a territory is associated with widespread DNA methylation changes, with a predominance of hypermethylation in territorial males. Using paired blood samples collected from the same individuals before and after becoming territorial, we identified differentially methylated genes which function in pathways related to anatomical and head development, brain development and neurodevelopment, cAMP biosynthesis and ion channel transport, consistent with the observed phenotypic shifts in morphology, spatial movement and aggressive behaviour. These findings suggest that DNA methylation mediates this life-history transition at the molecular level. More broadly, they provide rare evidence that epigenetic regulation is relevant in phenotypic diversity within species with low genetic diversity, potentially supporting adaptive potential at the population level.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 17","pages":"e70527"},"PeriodicalIF":3.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148899973","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":"Correction to \"Evidence of an Additional Centre of Apple Domestication in Iran, With Contributions From the Caucasian Crab Apple Malus orientalis Uglitzk. to the Cultivated Apple Gene Pool\".","authors":"","doi":"10.1111/mec.70538","DOIUrl":"10.1111/mec.70538","url":null,"abstract":"","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 17","pages":"e70538"},"PeriodicalIF":3.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13527276/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148862956","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}
Evgenii Potapenko, David Schwarts, Tali Mandel, Nimrod Ashkenazy, Dana Fuerst, Guy Atsmon, Sagi Snir, Abraham B Korol, Michael B Kantar, Avi Bar-Massada, Sariel Hübner
{"title":"Haplotype Blocks Are Associated With Rapid Local Adaptation to Environmental Shifts in Wild Barley.","authors":"Evgenii Potapenko, David Schwarts, Tali Mandel, Nimrod Ashkenazy, Dana Fuerst, Guy Atsmon, Sagi Snir, Abraham B Korol, Michael B Kantar, Avi Bar-Massada, Sariel Hübner","doi":"10.1111/mec.70540","DOIUrl":"10.1111/mec.70540","url":null,"abstract":"<p><p>Genomic mechanisms of local adaptation must be highly responsive in geographic regions where climate is changing rapidly. The Levant region is a critical biodiversity hotspot and the distribution edge for many species, including the wild ancestor of domesticated barley. This region is under an accelerated desertification process, thus enforcing a rapid genomic response to the projected environmental changes. To elucidate the genomic basis of rapid local adaptation, we studied wild barley populations using an ecological-genetic sampling design that decouples environmental variation from demographic background. We collected and sequenced 300 wild barley individuals and evaluated the phenotypes of 3600 progeny plants over 3 years. Our genomic analyses revealed that local adaptation is associated with clusters of candidate genes forming haplotype blocks. These clusters are enriched with environment and stress responsive genes, including flowering time regulators, drought and heat responsive genes. We identified six candidate adaptive haplotype blocks which span 1-8 Mbp and are distributed across chromosomes 1H, 2H, 4H and 5H, each segregating as two major haplotypes. Additionally, we integrated over 2600 occurrence records into ecological and evolutionary modelling to assess the genomic vulnerability of populations to projected future climates. Our study identifies candidate genomic regions and environmental drivers of local adaptation in wild barley and highlights the advantage of haplotype blocks architecture in orchestrating an efficient response to rapid environmental change. We highlight the ecological factors most strongly associated with the observed evolutionary responses and provide insights and guidelines for biodiversity conservation and implementation of crop wild relatives in breeding.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 17","pages":"e70540"},"PeriodicalIF":3.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13531266/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148862894","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 Jeanne, Julien Prunier, Richard Hogue, Arnaud Droit
{"title":"An Interpretable Machine Learning Approach to Ecologically Characterize Soil Carbon and Structure From Multi-Kingdom Microbiome, Texture and Climate.","authors":"Thomas Jeanne, Julien Prunier, Richard Hogue, Arnaud Droit","doi":"10.1111/mec.70535","DOIUrl":"10.1111/mec.70535","url":null,"abstract":"<p><p>Soil physical structure is a critical determinant of agricultural landscape resilience, yet standard pedotransfer functions estimate soil hydraulic and structural properties using static abiotic variables, often overlooking the biological mechanisms that actively organize soil structure. This study evaluates the predictive power of multi-kingdom microbiome data (prokaryotes, fungi and microeukaryotes) for three key soil functions: soil organic carbon (SOC) stock, mean weight diameter (MWD) and macroporosity. Using a dataset of 2251 agricultural soil samples from Quebec, Canada, we benchmarked four machine learning algorithms (HGBR, RFR, XGBoost, SVR) and four data aggregation strategies. The integration of microbiome data with texture and climate variables achieved high peak predictive accuracy ( <math> <mrow><msup><mi>R</mi> <mn>2</mn></msup> </mrow> </math> range: 0.70-0.82). Methodologically, high-resolution compositional approaches (ASV-level centered log-ratio) and kingdom-balanced absolute abundances consistently outperformed taxonomic or functional aggregations. The loss of predictive power at the family level indicates that traits governing soil physical modification are phylogenetically shallow and strain-specific. Interpretability analysis using Shapley Additive Explanations (SHAP) revealed a clear functional hierarchy in soil assembly. Specific prokaryotic and fungal features drove biochemical stabilization and physical scaffolding via the microbial carbon pump and structural enmeshment dynamics. In contrast, the architectural openness of macroporosity was fundamentally constrained by abiotic physical limits (e.g., texture). Within this physical framework, specific microbial taxa, including anaerobic bacteria and microeukaryotic amoebae, functioned not as active engineers, but as high-sensitivity bio-indicators of the resulting aeration and hydrological connectivity. These results define soil physical organization as a biologically mediated hierarchy rather than a passive geological byproduct. Consequently, we propose shifting from static pedotransfer functions to a dynamic biotransfer framework that leverages multi-kingdom omic signatures to monitor soil physical resilience and crop adaptation potential.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 17","pages":"e70535"},"PeriodicalIF":3.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13531267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148862872","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}
Vitor A C Pavinato, Erin H Penton-Michel, Saima Shahid, Jacob A Wenger, R Keith Slotkin, Andy Michel
{"title":"Adaptation to Plant Defence in an Agricultural Insect Pest: Integrating Genome Scans and Gene Expression in the Soybean Aphid Reveals Multi-Genic Pathways.","authors":"Vitor A C Pavinato, Erin H Penton-Michel, Saima Shahid, Jacob A Wenger, R Keith Slotkin, Andy Michel","doi":"10.1111/mec.70536","DOIUrl":"https://doi.org/10.1111/mec.70536","url":null,"abstract":"<p><p>In agroecosystems, intense selection pressures cause species to adapt and spread, often leading to the evolution and persistence of pests. Understanding how pests rapidly adapt can help develop sustainable strategies for their management and improve agroecosystem health. Pest adaptation involves stable variations in DNA sequence, as well as dynamic shifts in gene expression, often mediated by non-coding regulatory elements. We examined adaptation to plant defences in the soybean aphid, Aphis glycines, in which virulent aphids have overcome plant defences and avirulent aphids have not. Previous data with laboratory colonies suggested that virulent aphids have higher overall gene expression, including transposable elements, some of which influence gene regulation. However, we lack information on how genetic variation in natural populations impacts adaptation and potentially gene regulation. We integrated population genome scans of field-collected, soybean aphid populations with gene expression profiles of virulent and avirulent laboratory colonies to uncover connections between genetic differentiation and gene regulation for virulence. Genome scan methods found 2144 single nucleotide polymorphisms (SNPs) with significant genetic differentiation (i.e., outliers) in field-collected populations. These SNPs were near 1004 genes, representing 5.16% of the effective number of genes. Based on previous RNA-Seq data with laboratory colonies, we found 3160 genes and 147 long non-coding RNAs (lncRNAs) with differential expression among virulent and avirulent biotypes. By integrating both data sets, we identified 16 genes and 5 long non-coding RNAs with differential expression and that were associated with an outlier SNP (within 10 kbp). We validated SNPs with additional field collected aphids and found an aphid clone with stronger virulence than our laboratory virulent colony, surviving on 2 different aphid-resistant soybean varieties. This new virulent clone had fixed allele differences at 9 SNPs compared to our avirulent and other virulent colony. Field collected soybean aphids matching the phenotype of this new virulent clone had significant genetic differentiation with 3 outlier SNPs near genes related to zinc transport and lachesin compared to field collected avirulent aphids. Our entire data reinforced the importance of a potential multi-genetic response to overcome plant defence and generates new insights into complex genetic and regulatory mechanisms involved in insect-plant interactions.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 17","pages":"e70536"},"PeriodicalIF":3.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148899931","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}
Tunç Dabak, Jeffrey D Lozier, Cecil Smith, Brandon Meadows, Jonathan Berenguer Uhuad Koch, Heather M Hines
{"title":"A Cis-Regulatory Duplication in a Hox Hotspot Implicated in Mimetic Convergence in the Bumble Bee Bombus flavifrons.","authors":"Tunç Dabak, Jeffrey D Lozier, Cecil Smith, Brandon Meadows, Jonathan Berenguer Uhuad Koch, Heather M Hines","doi":"10.1111/mec.70539","DOIUrl":"https://doi.org/10.1111/mec.70539","url":null,"abstract":"<p><p>Several species of North American bumble bees spanning the Pacific Coastal and Rocky Mountain regions converge onto distinct mimetic abdominal colour forms for each region by switching abdominal coloration from black to red. Previous genome-wide association studies (GWAS) of red and black transitions in two mimics (Bombus melanopygus and Bombus vancouverensis) revealed that black forms were generated by independently deleting a portion of the same cis-regulatory region near the Hox gene Abdominal-B (Abd-B). Here, we test the genetic basis of these mimetic colour forms in a third co-mimic, Bombus flavifrons, that has continuous variation in red and black that is shifted posteriorly one segment compared to its co-mimics. Using genome-wide association of red and black forms, we identified a structural variant < 50 bp away from the deletions in B. melanopygus and B. vancouverensis that was strongly associated with the colour phenotype. Sequencing across mimicry zones and closely related taxa revealed that all red forms of B. flavifrons and monomorphic red close relative Bombus centralis have a 319 bp tandem duplication at this locus that has extensive modification to the duplicated copy. Black forms of B. flavifrons from the Cascades also have this duplication but without the modifications, while black forms in the western Rockies mostly lack this duplication, similar to ancestral black forms. This suggests independent mechanisms may regulate the black phenotypes in different populations and that ancestral sorting of variation and/or adaptive introgression generated these phenotypes. This study strengthens support for this Abd-B cis-regulatory region being a hotspot for regulating abdominal coloration in bumble bees, and features the role of regulatory region duplication in creating novel phenotypes.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 17","pages":"e70539"},"PeriodicalIF":3.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148899962","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 C Thomas, Jenny C Dunn, Helen Hipperson, Antony J Morris, Philip V Grice, Keith C Hamer, Simon J Goodman
{"title":"Multiple Strains of Trichomonas gallinae are Widespread in Reservoir Hosts and Environmental Resources in UK Farmland.","authors":"Rebecca C Thomas, Jenny C Dunn, Helen Hipperson, Antony J Morris, Philip V Grice, Keith C Hamer, Simon J Goodman","doi":"10.1111/mec.70520","DOIUrl":"10.1111/mec.70520","url":null,"abstract":"<p><p>Understanding transmission routes of parasites and pathogens is critical for the development of control measures and mitigation of impacts on host populations. Trichomonas gallinae is a widespread parasite in columbids worldwide, and has emerged as a lethal disease in passerines, particularly finches. The postulated transmission route from columbids to passerines via spillover at shared resources has not yet been empirically tested. Here, we screen 363 birds (261 columbids and 102 non-columbids) in the UK and France for the presence and strain identity of T. gallinae. To quantify potential environmental transmission, we also screened 51 food and water resources common in farmland, at 12 sites over a 2-year period. We isolated T. gallinae parasites from 79% of columbids, 36% of non-columbids, and 39% of environmental resources. Prevalence of the Type A strain was more than double in birds sampled at fed sites compared to those at unfed sites. Strain composition was mirrored in columbids, passerines, and shared food and water resources, providing compelling evidence that T. gallinae, especially the Type A strain, is transmitted via these shared resources. T. gallinae was isolated from high density feeding resources (where supplementary food was provided) nearly three times as often as low density resources (natural areas of seed-providing vegetation), meaning that careful management of supplementary resources has the potential to reduce T. gallinae prevalence in wild bird populations. Further work needs to test practical means of achieving this, but ensuring any supplementary feeding is provided at low density is likely to be critical to reducing parasite transmission.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 17","pages":"e70520"},"PeriodicalIF":3.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13542872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148885940","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}
Mary Kathleen Hickox, Ben A Wasserman, Alan Garcia-Elfring, Eric P Palkovacs, Andrew P Hendry, Rowan D H Barrett
{"title":"The Spatial and Temporal Repeatability of Genomic Responses to Natural Selection as Demonstrated in Stickleback Populations Experiencing Highly Dynamic Environments.","authors":"Mary Kathleen Hickox, Ben A Wasserman, Alan Garcia-Elfring, Eric P Palkovacs, Andrew P Hendry, Rowan D H Barrett","doi":"10.1111/mec.70528","DOIUrl":"10.1111/mec.70528","url":null,"abstract":"<p><p>The evolution of genotypic parallelism under shared environmental conditions provides strong evidence for the role of natural selection. However, analyses typically examine genomic signatures of selection long after the putative selection event and only assess the repeatability of responses across spatial population replicates. This impedes our ability to attribute a particular response to a given selection pressure and to distinguish non-parallel responses caused by stochastic processes from those caused by local selection. As such, the consistency of natural selection over space and time is unknown, and the role of persistent local selection pressures is unclear. Here, we leveraged the natural bar-built estuary system of Santa Cruz, California, to examine the repeatability of seasonal genomic change in threespine stickleback (Gasterosteus aculeatus) over space and time. By comparing allele-frequency shifts that are shared across locations (spatial repeatability) with those that are shared across years within locations (temporal repeatability), we identified both spatially shared and local components of putative selection. We found that repeated seasonal outlier responses occurred more often than expected under a neutral null model. Although repeatability declined as the number of estuaries sharing an outlier increased, enrichment above neutral expectations increased with broader spatial sharing, particularly for outliers repeated across both years. While the precise outlier SNPs varied across years, estuary-specific patterns of responses were broadly consistent, suggesting an important role for local conditions. Together, our findings show that temporal sampling can reveal components of putative selection that would be missed from spatial comparisons alone. More broadly, they highlight the importance of examining repeatability over both space and time to understand the parallel and non-parallel components of adaptive genomic change.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 17","pages":"e70528"},"PeriodicalIF":3.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13545515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890511","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}
Kevin P Mulder, André Lourenço, Ivan Gomez-Mestre, Miguel Carneiro, David Buckley, Iñigo Martínez-Solano, Robert C Fleischer, Rayna C Bell, Guillermo Velo-Antón
{"title":"Comparative Transcriptomic Analyses Identify Candidate Genes for Convergent Reproductive Shifts in a Bimodal Viviparous Amphibian.","authors":"Kevin P Mulder, André Lourenço, Ivan Gomez-Mestre, Miguel Carneiro, David Buckley, Iñigo Martínez-Solano, Robert C Fleischer, Rayna C Bell, Guillermo Velo-Antón","doi":"10.1111/mec.70499","DOIUrl":"10.1111/mec.70499","url":null,"abstract":"<p><p>Shifts in reproductive mode represent key evolutionary innovations that shape species' life histories and evolutionary trajectories. Species showing bimodal reproductive strategies with multiple independent origins offer a rare opportunity to gain insights into the adaptive processes and mechanisms underlying convergent traits. The fire salamander, Salamandra salamandra, is the only amphibian exhibiting intraspecific variation in reproductive mode across multiple independent reproductive shifts, enabling investigation of the transition between larviparity (females give birth to aquatic larvae) and pueriparity (females give birth to fully developed terrestrial juveniles) within a single species and across different timescales. Pueriparity is an adaptive innovation that skips the aquatic larval stage, allowing individuals to exploit habitats with no available water bodies. The fire salamander is larviparous across most of its range, but pueriparity has evolved independently at least three times: once in the early Pleistocene within S. s. bernardezi in the mountains of northern Spain, and more recently on two land-bridge islands (NW Spain) inhabited by S. s. gallaica. To identify candidate genes associated with these distinct reproductive modes, we compared gene expression profiles of the uterus and oviduct of pregnant females across two independent evolutionary transitions using RNA-sequencing. We detected shared changes in maternal gene expression among pueriparous S. s. bernardezi and S. s. gallaica relative to their larviparous counterparts, in addition to differences unique to each independent evolutionary transition. Functional enrichment analyses indicated that differentially expressed genes were associated with reproductive timing, angiogenesis, and maternal signalling, consistent with the phenotypic differences observed in the uterine environment and embryonic development between the two reproductive modes. This study represents an important first step towards understanding the genomic basis of the evolution of pueriparity in a remarkable bimodal reproductive system, and provides transcriptomic resources and candidate genes for future research into the genomic architecture underlying this poorly understood adaptive trait.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 17","pages":"e70499"},"PeriodicalIF":3.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13545552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890531","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}
Julia C Clarke, Rebecca S Taylor, Micheline Manseau
{"title":"Runs of Homozygosity Predict Inbreeding Depression Across Taxa: A Systematic Review and Meta-Analysis.","authors":"Julia C Clarke, Rebecca S Taylor, Micheline Manseau","doi":"10.1111/mec.70541","DOIUrl":"10.1111/mec.70541","url":null,"abstract":"<p><p>Measuring inbreeding via runs of homozygosity (ROH) captures realized autozygosity and can infer inbreeding timing through ROH length. A growing body of literature links the proportion of the genome in ROH (F<sub>ROH</sub>) to fitness outcomes across taxa, yet systematic synthesis has been lacking. Here, we conduct a systematic review and meta-analysis to quantify F<sub>ROH</sub>-fitness associations, identify drivers of variation and derive conservation-relevant recommendations. Narrative synthesis of 44 studies revealed that inbreeding depression operates through multiple interconnected pathways (survival, maternal effects, disease susceptibility, reproduction). Critically, purging cannot be relied upon to eliminate inbreeding depression as substantial fitness costs persist even in historically small populations. Meta-analysis of 62 effect sizes revealed a significant negative association between genomic inbreeding and fitness across taxa (Fisher's z = -0.103, r = -0.10, p < 0.0001). Study group, whether wildlife, livestock or humans, explained 22.5% of variance, with wildlife showing strongest effects (6-fold stronger than humans). Survival traits showed the greatest sensitivity to the effects of ROH (r = -0.22). Additionally, ROH detection methodology significantly influenced effect sizes: comprehensive approaches (all ROH lengths) detected stronger depression (r = -0.18) than long-ROH-only analyses (r = -0.08, p = 0.008), indicating cumulative genetic load matters. Overall, results indicate significant but variable fitness associations with ROH, with effect magnitude depending on biological context and methodological approach. Comprehensive ROH-based approaches show promise as conservation monitoring tools, but limited wildlife studies, particularly for non-mammalian taxa, highlight an urgent need for standardized protocols and expanded empirical research.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 17","pages":"e70541"},"PeriodicalIF":3.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13531397/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148862930","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}