Molecular Ecology最新文献

{"title":"Prevalent Hybridisation Between Highly Divergent Iberian Chub Species Produces Contrasting Outcomes Across Different Geographic and Time Scales.","authors":"Sofia L Mendes, Catarina Bernardo, Silvia Perea, João M Moreno, Ignacio Doadrio, Philine G D Feulner, Carla Sousa Santos, Vitor C Sousa","doi":"10.1111/mec.70009","DOIUrl":"10.1111/mec.70009","url":null,"abstract":"<p><p>Genomic data has revealed hybridisation is common in nature. Highly divergent allopatric species are often overlooked in our efforts to characterise the prevalence and consequences of hybridisation in natural systems, presumably because they are viewed as less likely to hybridise. Yet, such species are models to investigate later stages of the speciation continuum. Here, we study such a system-the Iberian chubs (Squalius spp.), a group of primary fish species with allopatric distributions across distinct environments and river catchments. Throughout their evolutionary history, the rivers inhabited by these species suffered quite dramatic changes, potentially allowing for multiple periods of isolation and secondary contact. To investigate if such a history left traces, we generated low-coverage whole-genome resequencing data for 125 individuals from eight Iberian chub species. Our results showed high levels of inter (0.44 ≤ F_ST ≤ 0.88) and intra-specific (0 ≤ F_ST ≤ 0.61) genetic differentiation. We uncovered four contrasting cases of potential hybridisation, spanning different geographical and time scales. First, we found evidence of ancient hybridisation on a species now inhabiting a whole river catchment. Second, we uncover recent hybridisation restricted to a localised stream, with introgression of nuclear and mitochondrial DNA. Third, we detected, at a regional scale, a case with nuclear introgression but no detectable mitochondrial DNA introgression. Finally, we uncover a case where two very distinct mitochondrial lineages persist at balanced frequencies in a putative hybrid population, despite no detectable nuclear introgression. Our findings suggest hybridisation and introgression led to assimilation or local exclusion of one or both parental species.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70009"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144566862","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":"Low but significant evolutionary potential for growth, phenology and reproduction traits in European beech.","authors":"Marjana Westergren, Juliette Archambeau, Marko Bajc, Rok Damjanić, Adélaïde Theraroz, Hojka Kraigher, Sylvie Oddou-Muratorio, Santiago C González-Martínez","doi":"10.1111/mec.17196","DOIUrl":"10.1111/mec.17196","url":null,"abstract":"<p><p>Local survival of forest tree populations under climate change depends on existing genetic variation and their adaptability to changing environments. Responses to selection were studied in European beech (Fagus sylvatica) under field conditions. A total of 1087 adult trees, seeds, 1-year-old seedlings and established multiyear saplings were genotyped with 16 nuSSRs. Adult trees were assessed for phenotypic traits related to growth, phenology and reproduction. Parentage and paternity analyses were used to estimate effective female and male fecundity as a proxy of fitness and showed that few parents contributed to successful regeneration. Selection gradients were estimated from the relationship between traits and fecundity, while heritability and evolvability were estimated using mixed models and the breeder's equation. Larger trees bearing more fruit and early male flowering had higher total fecundity, while trees with longer growth season had lower total fecundity (directional selection). Stabilizing selection on spring phenology was found for female fecundity, highlighting the role of late frosts as a selection driver. Selection gradients for other traits varied between measurement years and the offspring cohort used to estimate parental fecundity. Compared to other studies in natural populations, we found low to moderate heritability and evolvability for most traits. Response to selection was higher for growth than for budburst, leaf senescence or reproduction traits, reflecting more consistent selection gradients across years and sex functions, and higher phenotypic variability in the population. Our study provides empirical evidence suggesting that populations of long-lived organisms such as forest trees can adapt locally, even at short-time scales.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17196"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92152055","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":"Naturally Occurring Epialleles and Their Roles in Response to Climate Change in Birch.","authors":"Bowei Chen, Tianxu Zhang, Yile Guo, Lesheng Cao, Xu Zhang, Shahid Ali, Renyi Ma, Linan Xie, Jiang Wang, Gaurav Zinta, Shanwen Sun, Guifeng Liu, Qingzhu Zhang","doi":"10.1111/mec.70031","DOIUrl":"10.1111/mec.70031","url":null,"abstract":"<p><p>Epigenetics has been proposed to be an important mechanism that enables plant species to respond and adapt to environmental and climatic fluctuations and is sometimes entirely uncoupled from genetic variation. Nevertheless, the extent of this uncoupling and the contribution of epigenetics to plant responses to global climate change have not been well studied, particularly in forest trees. Here, we generated a high-quality genome assembly for Betula platyphylla, a key pioneer species in temperate and boreal forest ecosystems, one of the most sensitive areas to global warming. Extensive multi-omics sequencing of naturally white birch across the 48 provenances captured their full scope of temperate/boreal forests in Northeast China. Using a genome-wide association study (GWAS), it was shown that over 55% of differentially methylated regions (DMRs) were spontaneous, independent of genetic factors. More than 30% of the spontaneous DMRs were significantly associated with gene expression, that is, potential epialleles, which are primarily involved in metabolism and responses to abiotic stresses; and 1819 of these epialleles were significantly associated with bio-climatic variables (i.e., climatic epialleles, cEpialleles). Integrating these cEpialleles into a gradient modelling framework revealed that the natural populations of Asian white birch at high altitude/latitude might be most vulnerable to future climates. Our findings highlight the importance of integrating epigenomic and climatic data sets to forecast the adaptive capacity of a key forest species to rapid climate change.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70031"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673541","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":"The Way to a Generalist Herbivore's Heart Is Through Its Chemosensory Receptors: Using Multiple Approaches to Map the Genetic Basis of Adaptation in a Non-Model Organism.","authors":"Tiago da Silva Ribeiro, Rodrigo Cogni","doi":"10.1111/mec.70017","DOIUrl":"10.1111/mec.70017","url":null,"abstract":"","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70017"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329619/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590043","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":"Genomic Evaluation of Assisted Gene Flow Options in an Endangered Rattlesnake.","authors":"Samarth Mathur, H Lisle Gibbs","doi":"10.1111/mec.70014","DOIUrl":"10.1111/mec.70014","url":null,"abstract":"<p><p>Assisted gene flow is used to counteract genetic erosion in small populations of endangered species, yet an evaluation of genetic compatibility of potential donor populations and recipient populations is rare. We developed new metrics for assessing the genetic impact of genetic augmentation based on genotype identity of functional variants between donor and recipient genomes and used these metrics to evaluate options for assisted gene flow in Eastern Massasauga rattlesnake (Sistrurus catenatus) populations in Ohio, USA. We used putatively deleterious variants and genetic variants likely under positive selection (termed 'adaptive' variants) as the two components of functional variation. For potential donor and recipient populations, we estimated three key aspects of genetic compatibility: (a) introduction of novel variants, (b) masking or unmasking of existing deleterious variants and (c) potential for outbreeding depression through disruption of local adaptation. The main impact of augmentation from diverse donor populations was to introduce novel deleterious variants and to a lesser extent novel adaptive variants into each recipient population. Both donor populations had a similar minor impact in terms of masking existing deleterious variants. Finally, only ~7% of adaptive variants show evidence for local adaptation, arguing that the negative effect of outbreeding depression would be small. These results draw attention to the importance of considering the potential impact of both deleterious and adaptive genetic variants in augmentation efforts and suggest that in the case of these endangered rattlesnakes, the net effect of proposed assisted gene flow may lead to an increase in absolute levels of mutation load.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70014"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144574567","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":"Pathways to Recovery: Genomics and Resistance Assays for Tree Species Devastated by the Myrtle Rust Pathogen.","authors":"Stephanie H Chen, Jia-Yee S Yap, Veronica Viler, Craig Stehn, Karanjeet S Sandhu, Julie Percival, Geoff S Pegg, Tracey Menzies, Ashley Jones, Karina Guo, Fiona R Giblin, Joel Cohen, Richard J Edwards, Maurizio Rossetto, Jason G Bragg","doi":"10.1111/mec.70030","DOIUrl":"10.1111/mec.70030","url":null,"abstract":"<p><p>Myrtle rust is a plant disease caused by the invasive fungal pathogen Austropuccinia psidii (G. Winter) Beenken, which has a global host list of 480 species. It was detected in Australia in 2010 and has caused the rapid decline of native Myrtaceae species, including rainforest trees Rhodamnia rubescens (Benth.) Miq. (scrub turpentine) and Rhodomyrtus psidioides (G.Don) Benth. (native guava). Ex situ collections of these species have been established, with the goal of preserving remaining genetic variation. Analysis of reduced representation sequencing (DArTseq; n = 444 for R. rubescens and n = 301 for R. psidioides) showed genetic diversity is distributed along a latitudinal gradient across the range of each species. A panel of samples of each species (n = 27 for R. rubescens and n = 37 for R. psidioides) was resequenced at genome scale, revealing large historical effective population sizes, and little variation among individuals in inferred levels of deleterious load. In Rhodamnia rubescens, experimental assays (n = 297) identified individuals that are putatively resistant to myrtle rust. This highlights two important points: there are tangible pathways to recovery for species that are highly susceptible to rust via a genetically informed breeding programme, and there is a critical need to act quickly before more standing diversity is lost.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70030"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329637/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144599011","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":"Whole Genome Resequencing Reveals Origins and Global Invasion Pathways of the Japanese Beetle Popillia japonica.","authors":"Rebecca Funari, Elahe Parvizi, Claudio Cucini, Sara Boschi, Elena Cardaioli, Daniel A Potter, Shin-Ichiro Asano, Duarte Toubarro, Luca Jelmini, Francesco Paoli, Antonio Carapelli, Angela McGaughran, Francesco Frati, Francesco Nardi","doi":"10.1111/mec.70008","DOIUrl":"10.1111/mec.70008","url":null,"abstract":"<p><p>Invasive species are an increasing global threat given their ability to rapidly spread and adapt to novel environments. The adverse ecological and economic impacts of invasive species highlight the critical need to understand the mechanisms that underpin invasion processes and success. The Japanese beetle, Popillia japonica, is an invasive pest of remarkable interest, as it feeds on hundreds of economically valuable plant species. It has been expanding outside of its native range in Japan since the first decades of the 20th century, colonising large areas of North America and, more recently, Europe. Here, we compared whole-genome resequencing data from individuals encompassing the entire species distribution to study the geographic differentiation of P. japonica populations and reconstruct expansion routes from Japan to the USA and Europe. We found six genomically distinguishable clusters, corresponding to the approximate colonisation areas at a continental scale. Our analysis supported an ancestral divergence between South and North/Central Japan, with the latter being the source of the initial invasion to the USA. Coalescent simulations supported independent bridgehead events from the USA to the Azores and Italy. We also investigated possible signals of selection to better understand the adaptive mechanisms that underlie the invasion success of P. japonica. However, the absence of strong selection signatures suggested that the beetle's adaptive ability might be embedded in pre-existing genomic features. Our comprehensive genome-wide dataset allowed a detailed inference of the invasion process and may be useful in determining the origin of P. japonica individuals in future invasion events.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70008"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329639/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537597","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":"Population Divergence in the Eastern North American Boreal Forests: Extensive Gene Flow Characterises a Hybrid Zone Between Palm Warbler Subspecies (Parulidae: Setophaga palmarum).","authors":"Gihyun Yoo, Jason T Weir","doi":"10.1111/mec.70032","DOIUrl":"10.1111/mec.70032","url":null,"abstract":"<p><p>Pleistocene glaciations have shaped much of the population divergence events in the coniferous forests of North America. However, unlike in western North America, the evidence for forest fragmentation and population divergence associated with glacial cycles is less clear in the boreal forests of eastern North America. Here, we present the first genomic analysis of an avian hybrid zone in the eastern North American boreal forest between two subspecies of Palm Warblers (Setophaga palmarum). Using both genomic and plumage datasets, we characterise the divergence history of the two subspecies and relate our findings to the larger biogeographic history of the region. We find the Palm Warbler subspecies to have diverged in the mid-Pleistocene (~831 KYA) and have experienced near-continuous gene flow since initial splitting, resulting in a wide hybrid zone and little evidence of reproductive isolation. Coalescent modelling further indicates that the divergence of these two subspecies is congruent with the effects of glacial cycles and suggests a shared biogeographic history with the sole other known example of avian divergence in the region. However, in addition to the general paucity of such events, both of the known divergence events in the eastern boreal forests are characterised by low differentiation at present. This suggests that the conditions in the proposed eastern glacial refugia may not have been sufficient in establishing strong reproductive isolation, which perhaps explains why speciation events have been relatively rare in the eastern boreal forests of North America.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70032"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144657982","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":"Multiple Origins of Sex Chromosomes in Nothobranchius Killifishes.","authors":"Monika Hospodářská, Pablo Mora, Anna Chung Voleníková, Ahmed Al-Rikabi, Marie Altmanová, Sergey A Simanovsky, Nikolas Tolar, Tomáš Pavlica, Karolína Janečková, Jana Štundlová, Kseniya Bobryshava, Marek Jankásek, Matyáš Hiřman, Thomas Liehr, Martin Reichard, Eugene Yu Krysanov, Petr Ráb, Christoph Englert, Petr Nguyen, Alexandr Sember","doi":"10.1111/mec.70029","DOIUrl":"10.1111/mec.70029","url":null,"abstract":"<p><p>Sex chromosomes have evolved repeatedly across eukaryotes. The emergence of a sex-determining (SD) locus is expected to progressively restrict recombination, driving convergent molecular differentiation. However, evidence from taxa like teleost fishes, representing over half of vertebrate species with unmatched diversity in SD systems, challenges this model. Teleost sex chromosomes are often difficult to detect as they experience frequent turnovers, resetting the differentiation process. Nothobranchius killifishes, which include the XY system shared by N. furzeri and N. kadleci and X₁X₂Y systems in six other species, offer a valuable model to study sex chromosome turnovers. We characterised X₁X₂Y systems in five killifish species and found that sex chromosomes evolved at least four times independently. Sex-determining regions resided near centromeres or predicted chromosome rearrangement breakpoints in N. brieni and N. guentheri, suggesting recombination cold spots may facilitate sex chromosome evolution. Chromosomes representing the XY system in N. furzeri/N. kadleci were sex-linked also in the outgroup Fundulosoma thierryi, with several genes, including gdf6, residing in the region of differentiation. Although the X₁X₂Y systems of N. guentheri, N. lourensi (both Coastal clade), and N. brieni (Kalahari clade) involved different chromosomes, they shared a potential SD region. We uncovered two sex-linked evolutionary strata of distinct age in N. guentheri. However, its potential SD gene amhr2 was located in the younger stratum and is hence unlikely to be the ancestral SD gene in this lineage. Our findings suggest recombination landscapes shape sex chromosome turnover and that certain synteny blocks are repeatedly co-opted as sex chromosomes in killifishes.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70029"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697220","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":"Independent Genetic Mapping Experiments Identify Diverse Molecular Determinants of Host Adaptation in a Generalist Herbivore.","authors":"Ernesto Villacis-Perez, Femke De Graeve, Berdien De Beer, Seham Ali Alshami, Rick De Jong, Tim De Meyer, Thomas Van Leeuwen","doi":"10.1111/mec.17618","DOIUrl":"10.1111/mec.17618","url":null,"abstract":"<p><p>Interactions between plants and herbivores promote evolutionary change. Studying the evolution of herbivore mechanisms aimed to cope with different host plant species is a critical intersection between evolutionary biology and sustainable pest management. Generalist herbivores are of particular interest, as hybridization between genetically distinct populations can increase the standing genetic variation and therefore the adaptive potential of the species. Tetranychus urticae is a generalist arthropod known for its adaptive potential, evidenced in its immense host range and ability to develop metabolic resistance to xenobiotics. However, the molecular underpinnings associated with the potential of host adaptation and the consequences of host adaptation in this, and many other pests remain elusive. Here, we use two independent, empirical approaches to identify and map the genetic basis of host plant performance and adaptation in genetically distinct populations of T. urticae. In the first approach, we subject a genetically diverse mite population to tomato selection and map genomic regions linked to the phenotypic evolution of increased reproductive performance. In the second approach, we map genomic regions responsible for performance on tomato by comparing the genomes of pooled individuals from an F2 backcross between populations with high and low reproductive performance. Both approaches revealed specific and shared genomic regions associated with host plant performance and adaptation and key candidate genes were identified. Our findings highlight the power of spider mite genetic approaches to identify the complex genetic basis of host adaptation in generalist herbivores.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17618"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142826824","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}