Molecular Ecology最新文献

{"title":"Repeatable Genomic Outcomes Along the Speciation Continuum: Insights From Pine Hybrid Zones (Genus Pinus).","authors":"Bartosz Łabiszak, Sebastian Szczepański, Witold Wachowiak","doi":"10.1111/mec.70137","DOIUrl":"https://doi.org/10.1111/mec.70137","url":null,"abstract":"<p><p>Hybridization is a widespread evolutionary process and a key source of evolutionary novelty. Despite intensive study, the extent to which hybridization is deterministic and repeatable, particularly in recurrent contact events involving the same species under varying ecological conditions, remains unclear. Here, we investigated three replicated contact zones between Scots pine (Pinus sylvestris) and dwarf mountain pine (Pinus mugo) in Central Europe: two occurring in peatland habitats and one in a contrasting sandstone outcrop. Using genome-wide SNP genotyping of over 1300 individuals, we analysed genomic structure, diversity, and ancestry patterns across these zones. All sites revealed pervasive hybridization, dominated by later-generation hybrids and a notable scarcity of pure P. mugo. Across environments, hybrid populations exhibited strikingly consistent genomic compositions, with asymmetric introgression strongly biased toward P. mugo ancestry, suggesting that hybrid genome structure may follow predictable patterns under similar ecological conditions and could be shaped by cytonuclear incompatibilities. Nonetheless, we also detected site-specific differences in hybrid diversity and phenotype, highlighting the influence of local environmental selection on shared hybrid genomic backgrounds. We provide genomic evidence that Pinus uliginosa, a morphologically distinct peat bog pine traditionally regarded as a relict and endangered species is instead a partially stabilised hybrid lineage. Its genome reflects incomplete hybridization and ecological filtering, yet it lacks sufficient genetic divergence to be recognised as a distinct species. Together, these results provide evidence for the repeatability of hybridization processes, which result in the formation of phenotypes reflecting a species continuum subjected to strong environmental pressures. The findings support the simplification of taxonomic nomenclature within the Pinus mugo complex, informing adaptive conservation strategies and the genetic management of hybrid lineages.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70137"},"PeriodicalIF":3.9,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145278548","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":"Habitat Differences in Resource Density and Distribution Affect Ecology and Life History of a Landscape-Modifying Fish.","authors":"Aneesh P H Bose, Boyd Dunster, Jonathan Henshaw, Lukas Koch, Jacqueline Grimm, Kristina M Sefc, Alex Jordan","doi":"10.1111/mec.70145","DOIUrl":"https://doi.org/10.1111/mec.70145","url":null,"abstract":"<p><p>Resource heterogeneity is a widespread phenomenon, as resources are rarely spaced evenly across a landscape. Variation in resource density and distribution can have a myriad of behavioural, ecological, and evolutionary consequences for populations, yet clarifying these effects is still challenging. We combine both novel and previously published data on genetic parentage, relatedness, life history, and predation to present a comprehensive field study of a shell bed in Lake Tanganyika. Here, a wild population of the cichlid fish Neolamprologus multifasciatus is naturally subdivided into habitat regions that differ immensely in shelter density and distribution, as well as in the capacity for the fish to physically rearrange their shelters into clusters (i.e., engage in niche construction). Shelters were evenly, densely, and continuously spaced in one habitat, while they were highly clustered in the other habitat. We expected the environmental potential for polygyny to be greater in the clustered habitat relative to the continuous habitat. Predation regimes and life history traits differed, with N. multifasciatus in the evenly distributed habitat experiencing higher predation threats, earlier maturation, and slower growth than those in the clustered habitat. Metrics of selection, however, were surprisingly consistent between the two habitats, as were patterns of dispersal. Overall, our research leverages the natural subdivision of a wild population into distinct habitats to investigate the ecological and evolutionary implications of resource heterogeneity and habitat modification.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70145"},"PeriodicalIF":3.9,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145278551","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":"Sex-Chromosome-Dependent Ageing in Female Heterogametic Methylomes.","authors":"Marianthi Tangili, Joanna Sudyka, Fabricio Furni, Per J Palsbøll, Simon Verhulst","doi":"10.1111/mec.70147","DOIUrl":"https://doi.org/10.1111/mec.70147","url":null,"abstract":"<p><p>Recent research in humans and both model and non-model animals has shown that DNA methylation (DNAm), an epigenetic modification, is one of the mechanisms underlying the ageing process. DNAm-based indices predict mortality and provide valuable insights into biological ageing mechanisms. Although sex-dependent differences in lifespan are ubiquitous and sex chromosomes are thought to play an important role in sex-specific ageing, they have been largely ignored in epigenetic ageing studies. We characterised the genome-wide distribution of age-related CpG (Cytosine-phosphate-Guanine) sites from longitudinal samples in two avian species (zebra finch and jackdaw), including for the first time the avian sex chromosomes (Z and the female-specific, haploid W). In both species, we find a small fraction of the CpG sites to show age-related changes in DNAm with the majority of them being located on the haploid, female-specific W chromosome, where DNAm levels predominantly decrease with age. Age-related CpG sites were over-represented on the zebra finch but under-represented on the jackdaw Z chromosome. Our results highlight distinct age-related changes in sex chromosome DNAm compared to the rest of the genome in two avian species, suggesting this previously understudied feature of sex chromosomes may be instrumental in sex-dependent ageing. Moreover, studying the DNAm of sex chromosomes might be particularly useful in ageing research, facilitating the identification of shared (sex-dependent) age-related pathways and processes between phylogenetically diverse organisms.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70147"},"PeriodicalIF":3.9,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145278524","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":"250 Million Years of Convergent Evolution and Functional Divergence of Glycoside Hydrolase Family 28 Genes in Xylophagous Beetles (Cerambycidae and Buprestidae): Insights Into Horizontal Gene Transfer, Gene Dynamics, Synteny and Adaptive Divergence.","authors":"Na Ra Shin, Mataya Duncan, Richard Adams, Duane D McKenna","doi":"10.1111/mec.70131","DOIUrl":"https://doi.org/10.1111/mec.70131","url":null,"abstract":"<p><p>Wood-feeding beetles harbour diverse gene families involved in plant cell wall degradation, including glycoside hydrolase family 28 (GH28) genes, which function as polygalacturonases. These genes are believed to have originated from microbial donors via horizontal gene transfers (HGT), followed by gene duplications. However, the evolutionary history of GH28 genes across independently evolved wood-feeding beetle lineages remains unclear. Here, we investigate the distribution, origin and diversification of GH28 genes in two xylophagous beetle groups, Cerambycidae: Lamiinae and Buprestidae: Agrilinae, which diverged over 250 million years ago. Phylogenetic analyses reveal that both groups possess GH28 genes most likely derived from ascomycete fungi, which are distinct from the 'ancestral-type' GH28 genes found in other Cerambycidae. Thus, Lamiinae and Agrilinae acquired similar 'new-type' GH28 genes via convergent HGT events. Comparative genomic analyses show conserved synteny around GH28 loci within each beetle subfamily, but not between them, consistent with independent acquisitions and endogenous retention. Subsequent lineage-specific duplications resulted in the expansion of GH28 gene copies, with protein structural modelling revealing divergent active sites and substrate-binding regions, suggesting functional differentiation and adaptation to distinct ecological contexts. Signatures of positive selection further support adaptive evolution of GH28 enzymes in both groups. Our findings demonstrate convergent acquisition and diversification of GH28 genes in distantly related xylophagous beetles, highlighting the roles of HGT, gene duplication and structural divergence in driving functional innovation. These results underscore how plant cell wall-degrading enzymes have contributed to trophic specialisation and the evolutionary success of specialised phytophagous beetles.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70131"},"PeriodicalIF":3.9,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145278586","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 Transcriptomics Reveal Reduction in Defence-Reproduction Trade-Offs During Coinfection.","authors":"Ian Will, Emily J Stevens, Kayla C King, Kieran A Bates","doi":"10.1111/mec.70124","DOIUrl":"https://doi.org/10.1111/mec.70124","url":null,"abstract":"<p><p>During infection, hosts may shift resources away from reproduction towards immune defence. It is unclear to what degree these costly trade-offs can be alleviated during protective coinfections, whereby antagonism between parasites reduces disease severity. We used transcriptomics to assess the extent to which host gene expression reflected the effect of protection and whether reducing or increasing investment in immunity carried costs to reproduction. Virulent infections by Leucobacter musarum bacteria elicited greater trade-offs in nematode hosts compared to the naturally coinfecting 'protective parasite' Leucobacter celer. We further found that coinfection attenuated host investment in pro-immune trade-offs, without significantly changing which host genes were involved. We then sought to understand if this attenuated host response would be consistent with possible mechanisms of inter-parasite competition. Our chromosome length genome assemblies for both parasite species revealed that protective coinfection may operate by competition for public goods, such as siderophore-mediated uptake of metal ions (e.g., iron) or colonisation of the host cuticle. Ultimately, we show that competition between coinfecting parasites can complement endogenous host defences and ease the reproductive costs of fighting harmful infection.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70124"},"PeriodicalIF":3.9,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145278570","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":"Habitat Specialisation Impacts Clownfish Demographic Resilience to Pleistocene Sea-Level Fluctuations.","authors":"Alberto García-Jiménez, Marion Talbi, Lucy M Fitzgerald, A Heim, Anna Marcionetti, Sarah Schmid, Joris Bertrand, Abigail Shaughnessy, Carl Santiago, Ploypallin Rangseethampanya, Phurinat Ruttanachuchote, Wiphawan Aunkhongthong, Sittiporn Pengsakun, Makamas Sutthacheep, Milan Malinsky, Bruno Frédérich, Fabio Cortesi, Marc Kochzius, Thamasak Yeemin, Théo Gaboriau, Nicolas Salamin","doi":"10.1111/mec.70134","DOIUrl":"https://doi.org/10.1111/mec.70134","url":null,"abstract":"<p><p>Habitat fragmentation and loss are key threats to biodiversity, yet their impacts on marine species remain poorly understood. Clownfishes, which rely on sea anemones for shelter and reproduction, provide an interesting model to explore how ecological specialisation mediates species responses to habitat perturbations. We used whole-genome data from 382 individuals across 10 species with varying host specialisations to reconstruct demographic histories and infer spatial genetic structure to assess the impact of Pleistocene sea-level fluctuations. Generalist species, associated with multiple hosts, maintained stable effective population sizes ( <math> <semantics> <mrow><msub><mi>N</mi> <mi>e</mi></msub> </mrow> <annotation>$$ {N}_e $$</annotation></semantics> </math> ) and population connectivity during habitat fragmentation, reflecting resilience to environmental instability. In contrast, specialists experienced severe <math> <semantics> <mrow><msub><mi>N</mi> <mi>e</mi></msub> </mrow> <annotation>$$ {N}_e $$</annotation></semantics> </math> declines and genetic structuring, driven by their dependence on specific hosts, without signs of population recovery following habitat reconnection. Spatial genomic analyses identified the Indonesian Through-Flow as a key dispersal corridor and the Coral Triangle as a critical hub of genetic diversity, while continental shelves and extensive open ocean regions appeared as barriers to gene flow. Our findings reveal how host specialisation shapes clownfish population dynamics, emphasising the importance of incorporating ecological dependencies into conservation assessments and deepening our understanding of species responses to ecological constraints and environmental changes over evolutionary timescales.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70134"},"PeriodicalIF":3.9,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145278595","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":"Inter-Caste Comparison Reveals a Unique Bioenergetic Signature in Long-Lived Ant Queens.","authors":"Maïly Kervella, Fabrice Bertile, Alexandra Granger-Farbos, Benoît Pinson, Claire Villette, Dimitri Heintz, Alain Schmitt, Martin Quque, Frédéric Bouillaud, François Criscuolo","doi":"10.1111/mec.70127","DOIUrl":"https://doi.org/10.1111/mec.70127","url":null,"abstract":"<p><p>Within the same species of eusocial insects, individuals of different castes typically display widely different life-history traits: sterile workers live for a few months, while queens can live for decades. Ageing theories emphasise the importance of metabolism and oxidative stress in explaining longevity, with mitochondrial bioenergetics standing at the crossroads of energy and reactive oxygen species production. The study of mitochondrial functioning is therefore of great relevance in determining the nature of the mechanisms that explain the contrasting longevities between insect social castes. We addressed this question in the eusocial black garden ant Lasius niger. Our findings reveal that caste differences in mitochondrial bioenergetics and the oxidative balance only partially align with oxidative stress theory predictions. Long-lived queens display lower metabolic rates and mitochondrial density, yet maintain higher cellular energy availability, as reflected by a high adenylate energy charge (AEC). This may result from enhanced mitochondrial maintenance processes and potentially a specific recourse to the purine salvage pathway, promoting ATP availability while limiting oxidative cost. Our study highlights so far unrevealed bioenergetic adaptations that might contribute to the queens' remarkable lifespan.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70127"},"PeriodicalIF":3.9,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145273268","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":"Landscape and Climate-Associated Selection in the Native and Widespread Bumblebee, Bombus terrestris.","authors":"Cecilia Kardum Hjort, Rachael Y Dudaniec, Peter Olsson, Johan Ekroos, Henrik G Smith","doi":"10.1111/mec.70141","DOIUrl":"https://doi.org/10.1111/mec.70141","url":null,"abstract":"<p><p>Anthropogenic land-use and climate change pose novel selection pressures on bees, yet their evolutionary responses in terms of morphological or physiological adaptations remain unclear. While adaptive responses are expected, these may be constrained by gene flow when changes in selection pressures are spatially heterogeneous. The buff-tailed bumblebee (Bombus terrestris) is a widespread species that copes well with anthropogenic land-use and climate change, suggesting high adaptive capacity or phenotypic plasticity. Here, we genotyped populations of native B. terrestris in south and central Sweden using RADseq to investigate genetic structure and local adaptation across a paired design of agricultural landscapes with high and low land-use complexity along a geographic climate gradient. We expected to find genetic structure reflective of regional barriers to gene flow, and molecular evidence for local adaptation to differing landscape and climate conditions. We found genetic structure separating southern Sweden from more northern regions, with a negative Tajima's D indicating a potential population expansion, likely northwards and inland into forested areas, consistent with observational data indicating a range shift. We found weak but significant evidence for local adaptation to climate and land use, specifically to agricultural land cover, including genes under putative selection linked to insecticide resistance. Signatures of selection were also identified in relation to latitude, temperature, and urban land cover, with other candidate SNPs associated with olfaction and immune response. Our results suggest that B. terrestris successfully responded to anthropogenic land-use and climate changes, likely due to its generalist traits, enabling phenotypic adaptation to changing environments.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70141"},"PeriodicalIF":3.9,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249109","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":"Ancient Introgression Explains Mitochondrial Genome Capture and Mitonuclear Discordance Among South American Collared Tropidurus Lizards.","authors":"Matheus M A Salles, André L G Carvalho, Adam D Leaché, Nicolas Martinez, Frederick Bauer, Martha Motte, Viviana Espínola, Miguel T Rodrigues, Carla Piantoni, Marcio R Pie, André Olivotto, Guarino R Colli, Erik L Choueri, Fernanda P Werneck, Fabricius M C B Domingos","doi":"10.1111/mec.70130","DOIUrl":"https://doi.org/10.1111/mec.70130","url":null,"abstract":"<p><p>Mitonuclear discordance-evolutionary discrepancies between mitochondrial and nuclear DNA phylogenies-can arise from various factors, including introgression, incomplete lineage sorting, recent or ancient demographic fluctuations, sex-biased dispersal asymmetries, among others. Understanding this phenomenon is crucial for accurately reconstructing evolutionary histories, as failing to account for discordance can lead to misinterpretations of species boundaries, phylogenetic relationships, and historical biogeographic patterns. We investigate the evolutionary drivers of mitonuclear discordance in the Tropidurus spinulosus species group, which contains nine species of lizards inhabiting open tropical and subtropical environments in South America. Using a combination of population genetic and phylogenomic approaches applied to mitochondrial and nuclear data, we identified different instances of gene flow that occurred in ancestral lineages of extant species. Our results point to a complex evolutionary history marked by prolonged isolation between species, demographic fluctuations, and potential episodes of secondary contact with genetic admixture. These conditions likely facilitated mitochondrial genome capture while diluting signals of nuclear introgression. Furthermore, we found no strong evidence supporting incomplete lineage sorting or natural selection as primary drivers of the observed mitonuclear discordance. Therefore, the unveiled patterns are most consistent with neutral demographic processes, coupled with ancient mitochondrial introgression, as the main factors underlying the mismatch between nuclear and mitochondrial phylogenies in this system. Future research could further explore the role of other demographic processes, such as asymmetric sex-biased dispersal, in shaping these complex evolutionary patterns.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70130"},"PeriodicalIF":3.9,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249182","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":"Nearly Synchronous Speciation in the Mexican Highlands: Did the Juniperus deppeana Complex Diverge Under Peripatry?","authors":"Rodrigo Martínez de León, Melania Vega, David S Gernandt, Juan Pablo Jaramillo-Correa, Alejandra Moreno-Letelier","doi":"10.1111/mec.70132","DOIUrl":"https://doi.org/10.1111/mec.70132","url":null,"abstract":"<p><p>Speciation is a central focus in evolutionary biology, yet the processes driving diversification in montane regions remain incompletely understood. The Mexican highlands, a hotspot of conifer diversity characterised by complex topography and pronounced climatic heterogeneity, offer a unique setting to study these dynamics. Here, we investigated the genetic and taxonomic diversity within the Juniperus deppeana species complex, a group that exhibits notable cryptic variation. Using multiple species delimitation methods and Approximate Bayesian Computation, we identified at least four distinct evolutionary lineages that diverged largely without gene flow, likely influenced by geographic barriers and climatic differences. Our study enhances the understanding of how environmental heterogeneity and historical factors contribute to lineage diversification in montane conifers, offering new insights into the remarkable origins and resilience of biodiversity in the Mexican highlands. We present the J. deppeana complex as a compelling example of peripatric speciation and a valuable model system for understanding conifer diversification.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70132"},"PeriodicalIF":3.9,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249130","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}