Molecular Ecology最新文献

{"title":"Conservation Arks: Genomic Erosion and Inbreeding in an Abundant Island Population of Koalas.","authors":"Katie Gates, Jonathan Sandoval-Castillo, Julian E Beaman, Karen Burke da Silva, Frédérik Saltré, Katherine Belov, Carolyn J Hogg, Corey J A Bradshaw, Luciano B Beheregaray","doi":"10.1111/mec.70097","DOIUrl":"https://doi.org/10.1111/mec.70097","url":null,"abstract":"<p><p>The persistence of many threatened species depends on isolated habitat patches such as conservation parks, fenced reserves, and islands. While these 'conservation arks' provide refuge from many contemporary threats, they can also pose risks of genetic diversity loss and inbreeding depression, further exacerbating extinction risk. A pertinent example is the Kangaroo Island koala population in South Australia that originated from a few translocated founding individuals in the 1920s but now sustains a large population with a low prevalence of infectious disease. We investigated the extent and consequences of founder effects on genomic diversity, inbreeding, and adaptive potential in Kangaroo Island koalas by comparing them with mainland Australian populations using high-coverage whole genomes. Our findings support sharp, recent declines in effective population sizes (N_e) in both mainland and Kangaroo Island populations. However, Kangaroo Island koalas had much lower individual and population-level diversity. Together with longer and more numerous runs of homozygosity and an increased proportion of homozygous genetic load, these results support the hypothesis that a severe bottleneck has contributed to inbreeding and maladaptation in Kangaroo Island koalas. While Kangaroo Island has the potential to conserve a viable population of koalas, we recommend genetic rescue to restore diversity and mitigate inbreeding depression in this isolated population. Our results emphasise the need for longitudinal genomic monitoring and genetic management to maintain long-term viability and resilience in potential conservation arks. Understanding the demographic history of such populations will help inform future conservation aimed at preventing genetic erosion and preserving biodiversity.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70097"},"PeriodicalIF":3.9,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058188","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 Role of Community Science in DNA-Based Biodiversity Monitoring","authors":"Carolina Corrales,&nbsp;Karolina Bacela-Spychalska,&nbsp;Elena Buzan,&nbsp;Torbjørn Ekrem,&nbsp;Sónia Ferreira,&nbsp;William Goodall-Copestake,&nbsp;Elaine van Ommen Kloeke,&nbsp;Peter M. Hollingsworth,&nbsp;Sarah J. Bourlat","doi":"10.1111/mec.70100","DOIUrl":"10.1111/mec.70100","url":null,"abstract":"<p>The mutual interest in nature by the general public and scientists has led to many collaborations, past and present. Community science shows great potential for monitoring species occurrences and distributions, especially in combination with scalable and (semi)-automated methods such as DNA-based monitoring, helping to obtain data from a broader geographic and temporal range than would be possible by the scientific community alone. Here, we present an overview of the complementarity between community science and DNA-based biomonitoring through examples from ongoing projects. The involvement of hobby experts is particularly crucial for building up the necessary species reference databases that enable DNA-based monitoring. Based on this overview, we identify some key points related to learning opportunities and participant recognition to maximise the success, impact and benefit of community participants in DNA-based monitoring.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 19","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70100","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145038752","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":"Male and Female Parent Birds Enhance Their Reproductive Success Using Different Strategies but the Same Optimal Pathway.","authors":"Ning-Ning Sun, Bi-Yun Jia, Rong-Yu Xu, Li-Fang Gao, Xue-Fei Guo, Rang Li, Yu-Jie Wang, Shu-Min Wang, Bo Du","doi":"10.1111/mec.70111","DOIUrl":"https://doi.org/10.1111/mec.70111","url":null,"abstract":"<p><p>Parental birds exhibit diverse alternative reproductive strategies; however, the pathways by which these alternative strategies enhance the reproductive success of parents remain poorly understood. Here, we used generalised linear mixed models (GLMMs) and structural equation modelling (SEM) to analyse a long-term dataset of multiple components of reproductive fitness in the azure-winged magpie (Cyanopica cyanus ), including incipient offspring number, extra-pair fertilisation (EPF), unhatched eggs, offspring preyed on by predators and conspecific raiders and offspring that starved. GLMM results revealed significant associations between these components and the first lay date. SEM further elucidated causal relationships among female/male breeding conditions, cooperative breeding, first lay date and the positive/negative effects on female/male reproductive success. SEM results revealed that both female and male reproductive success were mainly influenced by negative effects rather than positive effects. Specifically, negative effects were largely determined by unhatched eggs for females but by female EPF frequency for males. In contrast, positive effects were predominantly determined by the incipient offspring number for both sexes. Therefore, minimising negative effects was prioritised over enhancing positive effects to achieve reproductive success in both sexes. To modulate these effects, females and males employed different strategies. However, they achieved their respective goals through a shared pathway: reducing negative effects for social bonds formed with smaller-bodied males and enhancing positive effects for social bonds formed with larger-bodied males. Our multivariate analysis of various aspects of avian reproduction suggests that the formation of social bonds plays a more important role than alternative reproductive strategies in determining individual reproductive success.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70111"},"PeriodicalIF":3.9,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145051567","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":"Environmental Stress Shapes Bacterial Community Structure and Function Through Interactive Abiotic Effects.","authors":"Jessica R Bernardin, Erica B Young, Grace A Cagle, Zachary B Freedman, Leonora S Bittleston","doi":"10.1111/mec.70102","DOIUrl":"https://doi.org/10.1111/mec.70102","url":null,"abstract":"<p><p>Microbial communities play critical roles in ecosystem functioning across a wide range of environmental conditions. The physiological stress imposed by temperature, pH and resource levels can shape the structure and function of microbial communities; however, while often tested independently, factors influencing physiological stress on a community rarely occur in isolation from each other. Controlled experiments simultaneously testing multiple interactive stressors allow researchers to better assess the dynamical responses of microbial communities to rapidly changing environments. Using a full factorial, controlled experiment, we tested three hypotheses for how independent and interactive effects of abiotic stresses impact bacterial community composition, structure and function in a model system. We utilised an aquatic, pitcher plant-associated bacterial community in which microbial nutrient cycling is essential to the host plant and ecosystem. Temperature, pH and resource (food) concentration had strong independent and interactive effects on bacterial community composition, structure and function. Community functions did not respond to interactive stressors in the same way. Chitinase and protease enzymatic activities had opposite responses to temperature and pH changes, indicating that diverse functional measures are necessary for understanding the varied effects of interacting stressors. The most extreme abiotic stress combination (high temperature, lowest pH and excess food) resulted in the lowest enzyme activity and reduced species richness as compared to the other treatments. Stressful conditions, especially high temperature, strengthened correlations between community structure and function. Higher phylogenetic dispersion under abiotic extremes suggested selection for diverse taxa adapted to similar conditions through convergent evolution. These interactive effects highlight the often greater-than-additive impact of multiple stressors and demonstrate that environmental filtering and trait convergence shape microbial responses to stress.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70102"},"PeriodicalIF":3.9,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145038812","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":"Environmental Stresses Constrain Soil Microbial Community Functions by Regulating Deterministic Assembly and Niche Width.","authors":"Xiaojun Wang, Jie Wang, Ji Chen, T Martijn Bezemer, Zilin Song, Wolfgang Wanek, Guobin Liu, Chao Zhang","doi":"10.1111/mec.70096","DOIUrl":"https://doi.org/10.1111/mec.70096","url":null,"abstract":"<p><p>Increasing evidence indicates that the loss of soil microbial α-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial α-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal α- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal α-diversity declined under high environmental stress across three soil layers (0-20 cm, 20-40 cm and 40-60 cm). Metagenomic-based analyses showed that the diversity of functional genes decreased along the stress gradients. High stress enhanced the abundance of genes associated with broad functional categories (e.g., glycolysis/gluconeogenesis, TCA cycle, DNA replication/repair and cell growth/death) but reduced the abundance of genes linked to specialised functional categories (e.g., C, N, S and methane metabolism). Phylogenetic null models and niche analyses indicated that stochastic assembly processes predominated in high-diversity communities, in which bacterial and fungal taxa had a narrow ecological niche. However, in low-diversity communities, deterministic assembly processes were dominant, and taxa had wide niches, correlating with the reduction in gene abundance observed for broad and specialised functional categories. Given the essential role of the microbiome in regulating ecosystem functions, our findings suggest that low-diversity-induced deterministic community assembly processes and a wide niche under high environmental stress may regulate microbial functions. These findings emphasise the ecological mechanisms through which microbial biodiversity regulates terrestrial ecosystem functioning.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70096"},"PeriodicalIF":3.9,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028637","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":"Gene Expression Associated With Behaviour Manipulation in Wood Ants Infected With Larval Lancet Fluke, Dicrocoelium dendriticum.","authors":"Chen-Hua Li, Cameron P Goater, James D Wasmuth","doi":"10.1111/mec.70099","DOIUrl":"https://doi.org/10.1111/mec.70099","url":null,"abstract":"<p><p>Many ant species show dramatic shifts in behaviour when infected with parasites, but the molecular basis of these behavioural changes is not well understood. An example is the wood ant, Formica aserva, which serves as an intermediate host for the lancet liver fluke, Dicrocoelium dendriticum. Infected ants leave their nests during the cool hours of the day, ascend a flower and then attach themselves to a petal with their mandibles. Attached ants remain affixed to an inflorescence overnight, after which they detach, descend the plant and return to their nest. Unless eaten by a grazing mammal (the obligate next host), infected ants repeat this attach-and-detach cycle for the rest of the summer. We used transcriptomics to decipher the potential molecular mechanisms that underlie this reversible behaviour manipulation. Using naturally infected ants, we recreated the manipulation cycle in the laboratory and then evaluated messenger RNA from ant brains at four contrasting phases of manipulation. Among these phases, we found a total of 1349 transcripts differentially expressed between infected and uninfected ant brains. Many of these transcripts are involved in cell signalling pathways, including odorant, gustatory, vision, circadian rhythm and the production of biogenic monoamines and hormones. Metabolism, protein management and DNA repair functions might also play a role at different phases of manipulation. Our combined results are consistent with the idea that the mechanism(s) leading to the attach/detach/repeat sequence of behaviours of fluke-infected ants is multifaceted, involving much more than temperature-dependent contraction/relaxation of the mandibular muscles.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70099"},"PeriodicalIF":3.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Patterns of Genetic Diversity Within Three California Quail Species Are Best Explained by Climate and Landscape Changes.","authors":"Phred M Benham, Carla Cicero, Michelle M Davila, Erik D Enbody, Katherine S Miller, Allison J Shultz, Lydia L Smith, Michael W Nachman, Rauri C K Bowie","doi":"10.1111/mec.70093","DOIUrl":"https://doi.org/10.1111/mec.70093","url":null,"abstract":"<p><p>Many North American game animals experienced severe population declines during the 19th century due to market hunting. However, estimates of the timing and magnitude of these declines often rely on anecdotal evidence, which makes it difficult to understand the lasting impacts of hunting pressures versus climate or landscape changes on the genetic diversity of contemporary populations. Historical reports suggest the California quail (Callipepla californica) suffered more significant hunting pressure in the late 19th century relative to either Gambel's (Callipepla gambelii) or mountain quail (Oreortyx pictus). Genomic data can help illuminate the extent to which historical exploitation moulded the genetic health of modern quail populations. We compared whole genome sequences from these three quail species to evaluate whether reported differences in hunting pressure affected contemporary patterns of genetic diversity. Contrary to our expectations, California quail did not exhibit any evidence for population declines until the late 20th century, long after the era of market hunting ended. California quail also exhibited the highest levels of genetic diversity across most analyses with evidence for population expansion over the past 500,000 years. In contrast, the mountain quail exhibited a long-term population decline beginning in the middle of the last ice age 30-40 thousand years ago. The Gambel's quail appears to have suffered a more recent bottleneck in association with a major drought that impacted the desert southwest during the mid-20th century. Gambel's quail also exhibited increased realised genetic load for mild and moderately deleterious genetic variants. Together, our results demonstrate that market hunting had little lasting impact on the genetic diversity of these quail species, whereas landscape and climate changes have led to fluctuations in effective population size (Ne) and the buildup of genetic load.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70093"},"PeriodicalIF":3.9,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145013606","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":"Are We Witnessing a Speciation Continuum? Evidence From Current and Past Gene Flow in the Genus Oritrophium s.s. (Asteraceae) From the Tropical High Andes.","authors":"Juan Manuel Gorospe, Luciana Salomón, Jorge Armijos-Barros, Adam Kantor, Filip Kolář, Itziar Arnelas, Petr Sklenář, Roswitha Schmickl","doi":"10.1111/mec.70095","DOIUrl":"https://doi.org/10.1111/mec.70095","url":null,"abstract":"<p><p>Determining species boundaries is key for appropriately assessing biodiversity. However, the continuity of the speciation process makes delimiting species a difficult task, especially for recently diverged taxa. Furthermore, past introgression may leave traces that result in reticulate evolutionary patterns, challenging the estimation of species relationships. The fastest-evolving biodiversity hotspot on Earth is the Páramo. Its flora in the tropical high Andes is known for extraordinarily high species richness and endemism. However, the recent origin, fast diversification and complex taxonomy of many genera challenge species delimitation and phylogenetic reconstruction. In this study, we reconstructed phylogenetic relationships and addressed the role of introgression in the diversification of Oritrophium s.s. (Asteraceae) based on phylogenomic data. We combined genomic, phenotypic and ecological data to test species boundaries and compared trajectories across the speciation continuum within the taxonomically complex 'O. peruvianum group'. We found that historical introgression played an important role in the evolution of Oritrophium s.s., and many of the taxa within the 'O. peruvianum group' are at various stages of speciation. These results highlight the importance of testing for introgression to understand the diversification of recently evolved groups. Likewise, they suggest that heterogeneous speciation trajectories associated with geographic isolation and secondary contact, possibly during the Pleistocene, contributed to plant diversity in the tropical high Andes.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70095"},"PeriodicalIF":3.9,"publicationDate":"2025-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145013623","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":"Heat Stress Drives Rapid Viral and Antiviral Innate Immunity Activation in Hexacorallia.","authors":"Ton Sharoni, Adrian Jaimes-Becerra, Magda Lewandowska, Reuven Aharoni, Christian R Voolstra, Maoz Fine, Yehu Moran","doi":"10.1111/mec.70098","DOIUrl":"https://doi.org/10.1111/mec.70098","url":null,"abstract":"<p><p>The class Hexacorallia, encompassing stony corals and sea anemones, plays a critical role in marine ecosystems. Coral bleaching, the disruption of the symbiosis between stony corals and zooxanthellate algae, is driven by seawater warming and further exacerbated by pathogenic microbes. However, how pathogens, especially viruses, contribute to accelerated bleaching remains poorly understood. Here the model sea anemone Nematostella vectensis is used to explore these dynamics by creating a transgenic line with a reporter gene regulated by sequences from two RIG-I-like receptor genes involved in antiviral responses. Under heat stress, the reporter genes showed significant upregulation. Further, transcriptomes from N. vectensis, Exaiptasia diaphana and the stony coral Stylophora pistillata were analysed to reveal stress-induced activation of a set of bona fide immune-related genes conserved between the three species. Population-specific differences in stress-induced transcriptional responses of immune-related genes were evident in both Nematostella and Stylophora, depending on geographic origin. In Exaiptasia, the presence of zooxanthellae also influenced stress-induced immune gene expression. To test whether the viruses themselves contribute to this immune response under stress, we subjected N. vectensis to heat stress and measured the transcription dynamics of resident viruses as well as selected antiviral genes. While the antiviral genes responded within hours of heat stress, viral gene expression was already upregulated within 30 min, suggesting that their increase might be contributing to the elevated immune response under stress, and consequentially, the further demise of organismal homeostasis. These findings highlight the interplay between environmental stress, viruses, immune responses and symbiotic states in Hexacorallia.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70098"},"PeriodicalIF":3.9,"publicationDate":"2025-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145013556","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":"Characterisation of the Historic Demographic Decline of the British European Polecat Population.","authors":"R Shaw, J MacPherson, A C Kitchener, G J Etherington, W Haerty","doi":"10.1111/mec.70091","DOIUrl":"https://doi.org/10.1111/mec.70091","url":null,"abstract":"<p><p>The European polecat (Mustela putorius) has a widespread distribution across many countries of mainland Europe but is documented to be declining within these ranges. In Britain, direct persecution led to a severe decline of the polecat population during the 19th century. Unlike European mainland populations, it is now recovering across much of its former British range. The genomic and conservation implications of such a severe demographic decline, followed by the current recovery, have still to be characterised in the European polecat in Britain. Here we carry out population-level whole-genome analyses of 65 polecats from Britain (Wales and England) and the European mainland. Our analyses reveal that Welsh polecats show genetic variability from both English and European polecats, while British polecats as a whole exhibit signs of genetic isolation from mainland European populations. We also reconstructed the demographic history of the Welsh polecat to quantify the magnitude of the bottleneck. Our analyses confirmed the drastic decline of the Welsh polecat's effective population size, with a severe genetic bottleneck around 30-40 generations ago (1854-894). We investigated whether whole-genome diversity reflected this demographic event and found that Welsh polecats had significantly less genetic diversity than English polecats, but not European polecats. Runs of homozygosity and genetic load present in Welsh and English polecat genomes also indicated recent historic inbreeding. Our findings suggest that the increase in the British polecat population size may be attributed to admixture events. Additionally, we demonstrate that the Welsh polecat constitutes a genetically distinct population, which could be crucial for the overall conservation of European polecats by preserving unique genetic diversity.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70091"},"PeriodicalIF":3.9,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144991067","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}