Molecular Ecology最新文献

{"title":"Population Genomics in a Biodiversity Hotspot: Methods and Cross-Kingdom Insights From the 2025 Workshop in Xishuangbanna Tropical Botanic Garden, China.","authors":"Hafiz Muhammad Wariss, Jie Gao","doi":"10.1111/mec.70585","DOIUrl":"https://doi.org/10.1111/mec.70585","url":null,"abstract":"<p><p>The 2025 Population Genomics Workshop at the Xishuangbanna Tropical Botanical Garden (XTBG) convened leading researchers, early-career scientists and students to explore rapid advancements and emerging priorities in population genomics. The workshop highlighted advances in pangenomics, demographic modelling, archaeogenomics, and the integration of population variation with functional and genomic insights. It also emphasised strengthening interdisciplinary collaborations to apply genomics findings to climate-resilient agriculture and biodiversity conservation. This report summarises key methodological discussions from the workshop and underscores their emerging relevance to plant population genomics, biodiversity conservation and climate adaptation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 19","pages":"e70585"},"PeriodicalIF":3.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149126155","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":"Advancing Marine Mammal Conservation Through Omics Tools and Integration of Indigenous Ecological Knowledge.","authors":"Isabella M Reeves, Gabrielle Genty, Alana Alexander, Diana Aguilar-Gómez, Kerstin Bilgmann, Ane Liv Berthelsen, Arial M Brewer, Emma L Carroll, Grace A Day, Eda M Dönmez, Franca Eichenberger, Fabricio Furni, Joseph I Hoffman, Steven Holmes, Keith M Hernandez, Karen K Martien, Svenja M Marfurt, Morgan L McCarthy, Phillip A Morin, Mariana F Nery, Sergio Nigenda-Morales, Éadin N O'Mahony, Erika Oteri, Danai Papageorgiou, Kim M Parsons, Nicolás Restrepo-Garzón, Lennart Schreiber, Ramari Oliphant Stewart, David L J Vendrami, Morten Tange Olsen, Ebru Unal, Catherine E Meyer, Sebastian Alvarez-Costes","doi":"10.1111/mec.70567","DOIUrl":"10.1111/mec.70567","url":null,"abstract":"<p><p>Conservation of biodiversity is a global priority as human-driven pressures continue to intensify and alter ecosystems worldwide. Marine mammals are vulnerable species, facing numerous escalating anthropogenic threats. Here, we evaluate how, as omics technologies become more accessible and affordable, established and emerging tools are advancing effective marine mammal research and conservation management. Assessments of genetic diversity, adaptive capacity, demographic history and local adaptation provide vital insights into how marine mammal populations respond to environmental change across contemporary and evolutionary timescales. Whole-genome sequencing, functional genomics, epigenetics and multi-omic integration enable deeper insights into the molecular basis of complex fitness-related traits. Approaches like epigenetics, ancient DNA and environmental DNA offer new opportunities to study cryptic, rare, or historical populations and evolutionary processes. Yet, effective marine mammal conservation management cannot rely exclusively on increased availability of omics tools and data. We emphasize the need and obligation for genuine collaboration and integration of Indigenous perspectives with marine mammal genomics approaches to foster ethical, inclusive and effective conservation, and suggest best practices for this. Additionally, we highlight that translating omics data into practical conservation outcomes remains challenging, requiring clear communication, collaboration and integration into management. Using marine mammal genomics to address conservation challenges in a changing world requires innovation, partnership and the integration of diverse knowledge systems, such as Indigenous Ecological Knowledge.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 19","pages":"e70567"},"PeriodicalIF":3.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13658925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149163780","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ecological Boundaries Shape Microbial Diversity and Microbiome Similarity Across Host Communities in Mixed Pastoral Systems","authors":"Linglong Wang,&nbsp;Shuixing Yu,&nbsp;Jianni Huang,&nbsp;Yanxia Meng,&nbsp;Caiquan Zhao,&nbsp;Yanzi Gan,&nbsp;Wei Hu,&nbsp;Yang Yang","doi":"10.1111/mec.70579","DOIUrl":"10.1111/mec.70579","url":null,"abstract":"<div>\u0000 \u0000 <p>Mixed pastoral ecosystems provide natural settings in which wildlife, livestock, humans and arthropod vectors interact, creating opportunities for microbial exchange across host communities. However, the ecological factors shaping microbial diversity and microbiome similarity across hosts remain poorly understood. We conducted field surveys and sampled 1527 individuals across 20 sites spanning pastures and natural grasslands. Metagenomic and metatranscriptomic sequencing generated over 30.5 million contigs, identifying 41 bacterial genera, 24 fungal genera, 28 parasitic genera and 174 viral species. Arthropod vectors and wild birds harboured the highest viral diversity, including 11 novel viruses. Virome analyses revealed viral sharing among host groups, particularly within mosquito- and bird-associated communities. Ecological network analyses revealed substantial cross-host microbiome similarity among phylogenetically distant hosts, especially involving arthropod vectors and resident birds. Generalized linear and additive models identified livestock density, habitat overlap and host traits as key predictors of microbial richness, relative microbial abundance and microbiome similarity. Random forest models further showed that host clusters and livestock density were among the strongest predictors of microbial connectivity. This study provides a system-wide view of microbial diversity and microbiome similarity in mixed pastoral systems. Arthropod vectors and resident birds occupied central positions in host-associated microbial networks and acted as ecological bridges linking otherwise distinct host communities. Together, our results demonstrate that ecological structure and livestock density are major determinants of microbial diversity and microbiome similarity across complex host communities.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 19","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149101495","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":"Turning Red to Green Repeatedly: Ancestral LWS Duplications Drive Convergent Visual Tuning in Teleost Fishes.","authors":"Fabio Cortesi, Daniel Escobar-Camacho, Gina Maria Sommer, Martin Luehrmann, Flurin Hidber, Xavier Deupi, Karen Carleton, Zuzana Musilova","doi":"10.1111/mec.70592","DOIUrl":"https://doi.org/10.1111/mec.70592","url":null,"abstract":"<p><p>Photopigments, formed by an opsin protein bound to a light-sensitive chromophore, underlie vertebrate vision. Long-wavelength-sensitive (LWS) opsins mediate red-light detection, and most teleosts retain a single functional LWS1. A shorter-shifted green-sensitive paralog (LWS2) is found only in a few lineages. By mining teleost genomes and sequencing retinal transcriptomes, we identify elopomorphs as an additional lineage retaining LWS2 (alongside characins and osteoglossomorphs). Surprisingly, we reveal a previously overlooked, shorter-shifted paralog, LWS3, restricted to gobies (Percomorpha) and arising from an ancestral duplication either in the teleost or in the percomorph ancestor. Structural modelling of twelve LWS opsins reveals convergent evolution at four key amino acid sites (214, 259, 261, 269) in the retinal-binding pocket, indicating convergent substitutions in human MWS (an old-world primate-specific duplicate of the vertebrate LWS1), teleost LWS2, and goby LWS3 relative to red-sensitive counterparts, consistent with repeated spectral shifts towards greener wavelengths. In several lineages, including characins, mormyrids, gobies, and primates, these shorter-shifted LWS opsins have at least partially replaced the canonical green-sensitive RH2-based visual pigment. Retinal transcriptomes revealed variable lws3 expression across adult gobies, either complementing lws1 in most species, or dominating the visual opsin expression profile as in the sicydiines. In situ hybridisation in the whitebarred goby (Amblygobius phalaena; Valenciennes, 1837) showed that lws1 and lws3 are expressed in separate double-cone members, analogous to rh2 expression in other fish species. Together, these results show that repeated convergence towards shorter LWS sensitivity in vertebrate evolution involves coordinated changes at the molecular, regulatory, and functional levels, providing a striking example of multilevel sensory adaptation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 20","pages":"e70592"},"PeriodicalIF":3.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149222886","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":"Host and Environmental Factors Outweigh Pathogen in Shaping Skin Microbiome of a Threatened Andean Amphibian Community.","authors":"Claudia Lansac, Ignacio De la Riva, Marta Miñarro, Amadeus Plewnia, Ana V Longo, Patricia A Burrowes","doi":"10.1111/mec.70586","DOIUrl":"10.1111/mec.70586","url":null,"abstract":"<p><p>The fungal pathogen Batrachochytrium dendrobatidis (Bd) has driven severe amphibian declines across the Neotropics, yet some species persist under enzootic pathogen conditions following epizootics. We investigated whether skin bacterial communities and host mucosome activity contributed to the persistence of seven amphibian species in a once megadiverse Chocó-Andean community that experienced drastic Bd-associated declines. Across dry and wet seasons, we characterized skin bacterial communities using 16S rRNA metabarcoding and assessed mucosome-mediated inhibition of a local Bd lineage using in vitro challenge assays. Host species identity was the strongest predictor of bacterial community composition, while season and reproductive mode, which were strongly associated with habitat use, also contributed to microbiome structure. Host phylogeny was associated with broad-scale bacterial community patterns, whereas Bd infection status and intensity explained little variation. Putative Bd-inhibitory bacteria were detected in all host species and occurred at greater relative abundance during the dry season and in species with aquatic larvae, but neither their richness nor abundance was associated with Bd infection or load. Mucosome assays showed little to no inhibition of Bd growth in most species; only Pristimantis laticlavius, one of the few species whose abundance increased following the historical Bd epizootic, exhibited slight inhibition. Overall, host identity, seasonality, and habitat-associated reproductive mode, rather than current Bd infection, were the principal drivers of amphibian skin bacterial community composition. The widespread occurrence of putative Bd-inhibitory bacteria and their enrichment in some persistent hosts are consistent with a potential microbiome-mediated response, but limited mucosome activity indicates that the microbiome alone is unlikely to explain host persistence. Integrating host immune traits, pathogen characteristics, and environmental conditions will be necessary to understand long-term host-pathogen coexistence in this threatened amphibian community.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 19","pages":"e70586"},"PeriodicalIF":3.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13653128/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acidogenic Bacteria Dominate Brood Pollen Provisions Across Diverse Bee Taxa.","authors":"Jordan G Kueneman, Magda Argueta-Guzmán, Quinn S McFrederick, Rachel L Vannette, Shawn A Steffan, Stephen L Buchmann, David W Roubik, William T Wcislo, Bryan N Danforth","doi":"10.1111/mec.70578","DOIUrl":"https://doi.org/10.1111/mec.70578","url":null,"abstract":"<p><p>Bacteria and fungi play vital roles in bee health and development, yet microbial communities associated with pollen provisions remain largely uncharacterized for most bee species, particularly ground-nesting taxa. Microbial communities may prevent pollen provision spoilage, liberate nutrients from pollen, supply direct nutrition and/or suppress pathogens, though these functions appear context-dependent and variable among hosts. To determine whether bee evolutionary history and ecological traits structure pollen provision microbiomes, we analyzed 345 'live' brood cell pollen provisions representing 39 species, 18 tribes and six bee families spanning diverse life histories, diet breadths, floral resource use and nesting substrates. Microbial composition was determined by amplicon sequencing of bacterial 16S rRNA (V5-V7) and fungal ITS (1 and 2) regions. Bacterial richness and community composition were strongly structured by bee taxonomy and were also associated with several ecological traits, while community composition was significantly associated with host phylogeny. Fungal richness also varied among bee taxa and ecological groups, whereas fungal community composition showed greater variability and weaker, though detectable, taxonomic structure, with comparatively small ecological-trait effects. Across phylogenetically distant bee tribes, pollen provisions were often dominated by lactic- or acetic acid-producing bacteria, indicating a strategy of microbial fermentation that reduces bacterial richness and may enhance food preservation. Together, these results reveal broad evolutionary and ecological patterns underlying the microbiome of solitary bee brood cells and suggest that acid-producing bacteria play a stabilizing role in the preservation and function of pollen provisions.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 19","pages":"e70578"},"PeriodicalIF":3.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149178246","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":"Multidimensional Trait Space of Soil Protists: Ecological Strategies and Environmental Responses.","authors":"Junneng Yao, Stefan Geisen, Saisai Cheng, Zhengkun Hu, Chongzhe Zhang, Xianping Li, Sibo Shi, Hui Guo, Nianpeng He, Manqiang Liu","doi":"10.1111/mec.70583","DOIUrl":"https://doi.org/10.1111/mec.70583","url":null,"abstract":"<p><p>Soil protists comprise vast eukaryotic diversity and play key roles in microbial food webs, yet their community assembly remains poorly understood from a trait-based perspective. Here, we address this gap by integrating 10 traits related to morphology, behaviour, life history and trophic strategy across broad environmental gradients. RLQ analysis combined with fourth-corner tests revealed two major dimensions of soil protist trait variation. Reduced precipitation drove trait composition towards slower, persistence-oriented strategies, including reduced mobility, narrower niche breadth and increased reliance on asexual reproduction. Nutrient and resource limitation shifted trophic structure away from heterotrophic consumer-related strategies towards autotrophic or mixotrophic energy acquisition. These dimensions were consistently detected in a large-scale field survey and broadly supported by an independent global-change manipulation experiment, indicating that they capture generalizable components of soil protist functional organization. Further functional diversity analyses indicated that environmental gradients primarily constrained the range of occupied trait space rather than consistently reshaping the internal dispersion or evenness of trait distributions. Our study provides a trait-based framework for predicting belowground community assembly and ecosystem functional responses to environmental change.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 19","pages":"e70583"},"PeriodicalIF":3.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149101511","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":"Phylogeographic Breaks With and Without Contemporary Barriers to Migration in the Lizard Acanthodactylus erythrurus.","authors":"Filipe Gomes de Almeida, Loïs Rancilhac, Laure Benoit, Anne Loiseau, Menad Beddek, Abdellah Bouazza, José Carlos Brito, Laghzaoui El-Mustapha, Aurélien Miralles, Philippe Geniez, Raphaël Leblois, Pierre-André Crochet","doi":"10.1111/mec.70555","DOIUrl":"10.1111/mec.70555","url":null,"abstract":"<p><p>Identifying phylogeographic breaks and deciphering the relative contributions of environmental extrinsic (e.g., geological barriers, ecological gradients) and organismal intrinsic (e.g., limited dispersal, reproductive incompatibilities) factors to their persistence remain challenging, especially in the absence of genomic data. Here, we address this issue using parapatric lineages of the lizard Acanthodactylus erythrurus in south-western Morocco. A previous study based on nine nuclear loci identified two phylogeographic units (coastal vs. inland) whose separation did not align with landscape features preventing migration. The coastal lineage was inferred to evolve under isolation by distance (IBD, the regular increase of genetic differentiation with geographic distance), despite the presence of large rivers across its range. This suggests either that phylogeographic breaks do not align with landscape features, or that the restricted marker set prevented an accurate inference of phylogeographic breaks. We tested these hypotheses using RADseq data and recovered three lineages, each separated by phylogeographic breaks and narrow contact zones with restricted admixture. Coastal populations that had been previously identified to evolve under IBD actually included two lineages separated by a major, permanent river, reducing migration. The inland phylogeographic break, correctly identified by the previous study, is located in a continuously distributed habitat. Neither of the breaks aligned with steep changes in bioclimatic variables, suggesting a negligible contribution of local adaptation. We conclude that intrinsic reproductive barriers, as evidenced by narrow clines in allele frequencies at multiple loci spread over the genome, play a major role in maintaining these phylogeographic breaks. Our results also highlight the difficulty of identifying phylogeographic breaks from pre-genomic molecular data.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 19","pages":"e70555"},"PeriodicalIF":3.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13648158/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149134418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-Wide Analyses Reveal Spatially Structured Genetic Diversity in Indian Rice Shaped by Ancestry, Geography and Environment.","authors":"Somnath Roy, Puranjoy Sar, Sonal Gupta, Shreyasi Gupta Choudhury, Amrita Banerjee, Nimai Prasad Mandal, Gautam Talukdar, Arunava Pattanayak, Kailash Chander Bansal","doi":"10.1111/mec.70604","DOIUrl":"https://doi.org/10.1111/mec.70604","url":null,"abstract":"<p><p>India is a major centre of rice diversity, where long-term cultivation across contrasting environments has generated substantial genomic and phenotypic variation. We analysed genome-wide SNP variation in 313 Indian rice accessions to resolve ancestry structure, regional diversity, spatial genetic processes, environmental associations and haplotype variation at key domestication and adaptation genes. Population structure analyses resolved eight ancestry groups corresponding to indica, aus, aromatic and japonica lineages. Ancestry explained substantially more genomic differentiation than biogeographic regionalization, while there is extensive historical connectivity among lineages and regions. Genetic diversity considerably varied across biogeographic zones. After balanced resampling, the Himalayan region showed the highest standardized allelic diversity and private-allele richness, whereas the North-East region retained high observed heterozygosity and broad ancestry representation. Isolation-by-distance was weak overall but strongly lineage- and region-dependent. Spatial principal component analysis identified significant ancestry-independent broad-scale genetic gradients, demonstrating geography-influenced structure beyond lineage composition. Redundancy analysis detected significant genome-environment associations (F = 3.07, p = 0.001), with climate explaining more independent genomic variation (2.7%) than soil (0.9%). District-level tribal population proportion showed only a weak negative association with individual heterozygosity (Spearman ρ = -0.155, p = 0.006), although PTP classes exhibited low-to-moderate genetic differentiation. Haplotype analysis revealed strong locus-specific ancestry and geographic structuring at sd1, Wx, GS3 and DRO1. Together, the results show that Indian rice diversity is a reticulate genomic mosaic shaped by ancestry, geography, historical gene flow and environmental heterogeneity. This study provides a landscape-genomic framework for conservation and targeted germplasm utilization in breeding programmes.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 20","pages":"e70604"},"PeriodicalIF":3.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149222932","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":"Multi-Taxa Genome-Environment Associations With Contemporary and Historical Climate in the Brazilian Atlantic Forest","authors":"Laura D. Bertola,&nbsp;Mariana M. Vasconcellos,&nbsp;Roberta P. Damasceno,&nbsp;Ivan Prates,&nbsp;Marcelo Reginato,&nbsp;Gregory Thom,&nbsp;Andressa Nuss,&nbsp;Fabio Raposo do Amaral,&nbsp;Ana Beatriz da Silva Bueno,&nbsp;Cristina Yumi Miyaki,&nbsp;Gustavo S. Cabanne,&nbsp;Leonardo Campagna,&nbsp;Jacob S. Berv,&nbsp;Marcos Maldonado-Coelho,&nbsp;Sidnei Sampaio dos Santos,&nbsp;Karina Lucas Silva-Brandão,&nbsp;Luiza Moraes Magaldi,&nbsp;Daniel Michiute Carolino,&nbsp;André Victor Lucci Freitas,&nbsp;Miguel Trefaut Rodrigues,&nbsp;Fabián A. Michelangeli,&nbsp;Kyle McDonald,&nbsp;Ana C. Carnaval,&nbsp;Michael J. Hickerson","doi":"10.1111/mec.70545","DOIUrl":"10.1111/mec.70545","url":null,"abstract":"<div>\u0000 \u0000 <p>Multi-taxa genomic data offer valuable opportunities to assess the extent to which co-distributed taxa exhibit parallel responses to shared environmental regimes and climatic history. In this study, we use genome-environment associations (GEA) to examine how present and past climate may have shaped spatial patterns of adaptive genomic variation across 27 taxa in the Atlantic Forest biodiversity hotspot. Our sampling repurposes existing data from a wide array of taxonomic groups, including frogs, lizards, birds, butterflies, flowering plants, and a conifer, spanning multiple bioclimatic domains and representing variation in range size, niche volume, and niche marginality. Using these data, we explore two alternative hypotheses linking genomic adaptation to local environmental conditions with three species traits: range size, specialization (the inverse of niche volume), and niche marginality. The first hypothesis (H1) posits that taxa with large ranges, low specialization, and low niche marginality contain more climate-associated SNPs, as they are expected to harbor higher levels of standing genetic variation, forming a crude basis for genetic adaptation. An alternative hypothesis (H2) predicts that large-ranged species rely on other means of adaptation, such as phenotypic plasticity rather than on fixed genomic changes across environmental gradients and that stronger adaptive genomic responses happen in taxa with small ranges, high specialization, and high marginality. Our results show highly variable and species-specific genomic associations with climate, measured as the percentage of sampled SNPs correlated with environmental variables. There is no strong evidence that species' range size, specialization, or niche marginality consistently predict the proportion of climate-associated loci, rendering us unable to conclusively distinguish between H1 and H2. However, when the data are partitioned by taxonomic group, trend directionalities are more consistent with H2. Our findings highlight that the genomic basis of local adaptation varies substantially across taxa, underscoring the complexity of biodiversity patterns and dynamics, and the challenges of exploring alternative hypotheses through repurposing of existing data for multi-taxa inference. They also emphasize that conservation strategies should be prepared to account for taxon-specific responses rather than relying on generalized expectations across species. We hope that these results can inspire future studies of species' responses to climate in the Atlantic Forest and beyond, informing strategies for biodiversity monitoring and conservation.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 19","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149101542","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}