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1.
两栖动物是我国受威胁程度最高的动物类群,加强两栖动物资源调查和多样性监测,是开展两栖动物保护和濒危物种拯救行动的关键性基础工作。传统的两栖动物监测主要以形态学和声学为基础,耗时费力,且难以发现一些隐蔽性较强的稀有物种。基于环境DNA(environmental DNA, eDNA)的调查方法以其快速、灵敏、高效、无创等独特优势,为两栖动物多样性监测及保护提供了新的工具。综述了eDNA在两栖动物多样性监测、外来入侵和珍稀濒危物种调查、物种丰度或生物量估测等研究领域的应用进展,分析了两栖动物eDNA产生、扩散、迁移和降解的动态变化特征及其关键影响因子,探讨了eDNA应用于两栖动物监测研究的局限性并提出了优化建议,同时对未来的研究方向进行了展望,以充分挖掘eDNA在两栖动物监测中的应用潜力,为两栖动物多样性保护和管理提供新的思路。  相似文献   

2.
    
Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90–0.99) vs. 0.58 (CI = 0.50–0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA‐based approach has the potential to become the next‐generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.  相似文献   

3.
    
Rapid management responses against invasive species soon after their establishment are the most efficient way to limit their biological and economic impacts. Early detection and reliable monitoring is however challenging when cryptic taxa are involved. Here we show how environmental DNA (eDNA) metabarcoding of water samples efficiently unveiled an emerging invasion of Italian crested newts (Triturus carnifex), one of the most successful amphibian invaders in Europe. We compared and validated an eDNA survey by multilocus population genetics of wild-caught individuals. Both approaches consistently mapped a localized T. carnifex invasion in northwestern Switzerland, most likely following imports from the Italian Po Plain. We found evidence of gene flow with the indigenous and endangered Triturus cristatus in nearby populations, suggesting a potential expansion. Yet the currently small invasive range should be efficiently contained by future eradication programs. This textbook case emphasizes the implementation of eDNA metabarcoding to screen aquatic communities for exotic species, from which targeted studies can be designed on emerging biological invasions.  相似文献   

4.
    
A variety of challenges arise when monitoring wildlife populations for disease. Sampling tissues can be invasive to hosts, and obtaining sufficient sample sizes can be expensive and time‐consuming, particularly for rare species and when pathogen prevalence is low. Environmental DNA (eDNA)‐based detection of pathogens is an alternative approach to surveillance for aquatic communities that circumvents many of these issues. Ranaviruses are emerging pathogens of ectothermic vertebrates linked to die‐offs of amphibian populations. Detecting ranavirus infections is critical, but nonlethal methods have the above issues and are prone to false negatives. We report on the feasibility and effectiveness of eDNA‐based ranavirus detection in the field. We compared ranavirus titres in eDNA samples collected from pond water to titres in wood frog (Lithobates sylvaticus; n = 5) tadpoles in sites dominated by this one species (n = 20 pond visits). We examined whether ranavirus DNA can be detected in eDNA from pond water when infections are present in the pond and if viral titres detected in eDNA samples correlate with the prevalence or intensity of ranavirus infections in tadpoles. With three 250 mL water samples, we were able to detect the virus in all visits with infected larvae (0.92 diagnostic sensitivity). Also, we found a strong relationship between the viral eDNA titres and titres in larval tissues. eDNA titres increased prior to observed die‐offs and declined afterwards, and were two orders of magnitude higher in ponds with a die‐off. Our results suggest that eDNA is useful for detecting ranavirus infections in wildlife and aquaculture.  相似文献   

5.
伴随城市人口快速聚集及人类活动加剧,城市生态环境质量及其对人类社会经济发展的支撑能力正在受到严重挑战,城市生态系统及其变化的研究越来越受到重视,国内外涌现出大量城市生态学长期监测工作,但相关监测方法的讨论还很少。在分析城市生态学长期监测类型和实践经验基础上,从城市面临的环境胁迫和建设管理需求出发,构建了城市生态学长期监测的\"胁迫+需求-生态系统响应\"总体思路框架;从科学上最基本和社会上最关心的城市生态系统要素、格局和过程着眼,提出城市生态学长期监测的7项内容(土地覆盖与利用、人居环境质量、生物多样性、生物质生产、水文过程、生物地球化学循环和物质代谢);并分析了城市生态学长期监测的4种方法(遥感监测、仪器监测、调查监测、公众科学监测),分析了城市生态学长期监测单元及其空间布局及监测频率。这将为我国城市生态学长期监测工作开展提供方法论基础和实践参考。  相似文献   

6.
    
In this article, we describe ednaoccupancy , an r package for fitting Bayesian, multiscale occupancy models. These models are appropriate for occupancy surveys that include three nested levels of sampling: primary sample units within a study area, secondary sample units collected from each primary unit and replicates of each secondary sample unit. This design is commonly used in occupancy surveys of environmental DNA (eDNA). ednaoccupancy allows users to specify and fit multiscale occupancy models with or without covariates, to estimate posterior summaries of occurrence and detection probabilities, and to compare different models using Bayesian model‐selection criteria. We illustrate these features by analysing two published data sets: eDNA surveys of a fungal pathogen of amphibians and eDNA surveys of an endangered fish species.  相似文献   

7.
    
Our research shows that environmental features are important predictors of bovine tuberculosis (bTB) in British cattle herds in high-prevalence regions. Data from 503 case and 808 control farms included in the randomized badger culling trial (RBCT) were analysed. bTB risk increased in larger herds and on farms with greater areas of maize, deciduous woodland and marsh, whereas a higher percentage of boundaries composed of hedgerows decreased the risk. The model was tested on another case–control study outside RBCT areas, and here it had a much smaller predictive power. This suggests that different infection dynamics operate outside high-risk areas, although it is possible that unknown confounding factors may also have played a role.  相似文献   

8.
1. Within a community, different host species often exhibit broad variation in sensitivity to infection and disease. Because such differences can influence the strength and outcome of community interactions, it is essential to understand differential disease patterns and identify the mechanisms responsible. 2. In North American wetlands, amphibian species often exhibit extraordinary differences in the frequency of limb malformations induced by the digenetic trematode, Ribeiroia ondatrae. By coupling field studies with parasite exposure experiments, we evaluated whether such patterns were due to differences in (i) parasite encounter rate, (ii) infection establishment, or (iii) parasite persistence within hosts. 3. Field results underscored the broad variation in malformations and infection between host species; while nearly 60% (n = 618) of emerging American toads exhibited severe limb deformities such as bony triangles, skin webbings and missing limbs, fewer than 4% (n = 251) of Eastern gray treefrogs from the same pond were abnormal. Despite similarities in the phenology and larval development period of these species, they differed sharply in Ribeiroia infection. On average, toads supported 75x more metacercariae than did metamorphic treefrogs. 4. Experimental exposures of larval toads and treefrogs to a realistic range of Ribeiroia cercariae revealed strong differences in the sensitivity of these species to infection; exposed toads suffered elevated mortality (up to 95%), delayed metamorphosis, and severe limb malformations consistent with field observations. Treefrogs, in contrast, exhibited limited mortality and no malformations, regardless of exposure level. Ribeiroia cercariae were substantially less successful in locating and infecting Hyla versicolor larvae. 5. Our results indicate that the observed differences in infection and malformations owe to a lower ability of Ribeiroia cercariae to both find and establish within larval treefrogs, possibly stemming from a heightened immune response to infection. Because Ribeiroia is a highly pathogenic parasite with negative effects on larval and metamorphic amphibian survival, variation in infection resistance among species could have important implications for understanding patterns of species co-occurrence, competition, and community diversity.  相似文献   

9.
    
Management of wildlife populations often requires reliable estimates of population size or distribution. Estimating abundance can be logistically difficult, and occupancy models have been used as a less expensive proxy for abundance estimation. Another alternative is to use independent estimates of home-range size and mean group size to directly scale occupancy estimates up to abundance. We used simulations to explore when scaling occupancy up to abundance is reliable, and as an example we applied an occupancy approach to estimate abundance of wolves (Canis lupus) from roadside snow-tracking surveys in northern Wisconsin, USA, in 2016 and 2018. Estimates of wolf abundance were plausible and compared favorably with independent estimates produced by territory mapping, and snow-tracking data requirements were lower than for territory mapping. Simulation results suggested that reasonable abundance estimates could be obtained under some conditions but also that severe positive bias could result under other conditions, especially when populations were small and dispersed, home range size was small, and areal sampling units were large. Positive bias in abundance estimates occurs because of closure assumption violations when tracks from a single wolf or pack are detected in >1 sample unit, and the sum of the sample unit areas where tracks were detected exceed the sum of the home range areas. Bias was minimized when sampling units were small relative to home range size or when sampling units were route segments that approximate point sample units, and when home ranges were highly aggregated. We conclude that, although caution is warranted when scaling occupancy estimates up to abundance, scaled occupancy models can provide feasible and reliable estimates of abundance, assuming home range size and mean group size are accurately known or estimated, sampling units are appropriately chosen, and covariates that aggregate home ranges can be used to accurately predict occupancy probability. © 2021 The Authors. The Journal of Wildlife Management published by Wiley Periodicals LLC on behalf of The Wildlife Society.  相似文献   

10.
    
Surveying biodiversity has taken a quantum leap with environmental DNA (eDNA) metabarcoding, an immensely powerful approach lauded for its efficiency, sensitivity, and non-invasiveness. This approach emerges as a game-changer for the elusive realm of endangered and rare species—think nocturnal, environmentally elusive amphibians. Here, we have established a framework for constructing a reliable metabarcoding pipeline for amphibians, covering primer design, performance evaluation, laboratory validation, and field validation processes. The Am250 primer, located on the mitochondrial 16S gene, was optimal for the eDNA monitoring of amphibians, which demonstrated higher taxonomic resolution, smaller species amplification bias, and more extraordinary detection ability compared to the other primers tested. Am250 primer exhibit an 83.8% species amplification rate and 75.4% accurate species identification rate for Chinese amphibians in the in silico PCR and successfully amplified all tested species of the standard samples in the in vitro assay. Furthermore, the field-based mesocosm experiment showed that DNA can still be detected by metabarcoding even days to weeks after organisms have been removed from the mesocosm. Moreover, field mesocosm findings indicate that eDNA metabarcoding primers exhibit different read abundances, which can affect the relative biomass of species. Thus, appropriate primers should be screened and evaluated by three experimental approaches: in silico PCR simulation, target DNA amplification, and mesocosm eDNA validation. The selection of a single primer set or multiple primers' combination should be based on the monitoring groups to improve the species detection rate and the credibility of results.  相似文献   

11.
    
Environmental DNA (eDNA) is DNA that has been isolated from field samples, and it is increasingly used to infer the presence or absence of particular species in an ecosystem. However, the combination of sampling procedures and subsequent molecular amplification of eDNA can lead to spurious results. As such, it is imperative that eDNA studies include a statistical framework for interpreting eDNA presence/absence data. We reviewed published literature for studies that utilized eDNA where the species density was known and compared the probability of detecting the focal species to the sampling and analysis protocols. Although biomass of the target species and the volume per sample did not impact detectability, the number of field replicates and number of samples from each replicate were positively related to detection. Additionally, increased number of PCR replicates and increased primer specificity significantly increased detectability. Accordingly, we advocate for increased use of occupancy modelling as a method to incorporate effects of sampling effort and PCR sensitivity in eDNA study design. Based on simulation results and the hierarchical nature of occupancy models, we suggest that field replicates, as opposed to molecular replicates, result in better detection probabilities of target species.  相似文献   

12.
    
The decline of biodiversity, particularly among amphibians, is strongly associated with habitat loss and fragmentation. Vernal pools are a critical ecosystem for many pool-breeding amphibians, but they are often overlooked in wetland protection guidelines. Mitigation efforts include vernal pool creation and restoration, but these efforts have varying success in replacing lost functions. This study investigates the success of created vernal pools through long-term environmental monitoring of wood frogs and spotted salamanders (2014–2023) and integrates population genetics to assess the local population health of the wood frog. First, we monitored and compared environmental parameters and reproductive success of indicator species between natural and created pools in a Pennsylvania state park. We then used microsatellite loci to assess within- and between-pool measures of genetic diversity, population structuring, and gene flow for wood frogs. We found two carefully designed created pools positively contributed to local amphibian population persistence by maintaining similar measures of genetic diversity as compared to natural pools. On the other hand, one poorly created pool was genetically distinct and acted as a population sink. Although our findings offer valuable insights, they are based on a limited sample and may not fully represent the broader landscape. However, by integrating genetic information into long-term monitoring datasets, our interdisciplinary approach enhances our understanding of amphibian population dynamics in vernal pool ecosystems. Our findings imply that the most important factors for restoration practitioners to consider when creating or restoring vernal pools are hydroperiod (12–35 weeks), volume (> 50 m3), depth (≥ 30 cm), and surrounding forest land cover (> 60%). These variables are better predictors of indicator species success than pool type (i.e., natural or created). Ultimately, this study emphasizes the need to accompany restoration efforts with long-term monitoring programs that can be used to make adaptive management decisions in an era of extreme environmental change.  相似文献   

13.
    
Although DNA metabarcoding is an attractive approach for monitoring biodiversity, it is often difficult to detect all the species present in a bulk sample. In particular, sequence recovery for a given species depends on its biomass and mitome copy number as well as the primer set employed for PCR. To examine these variables, we constructed a mock community of terrestrial arthropods comprised of 374 species. We used this community to examine how species recovery was impacted when amplicon pools were constructed in four ways. The first two protocols involved the construction of bulk DNA extracts from different body segments (Bulk Abdomen, Bulk Leg). The other protocols involved the production of DNA extracts from single legs which were then merged prior to PCR (Composite Leg) or PCR‐amplified separately (Single Leg) and then pooled. The amplicons generated by these four treatments were then sequenced on three platforms (Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5). The choice of sequencing platform did not substantially influence species recovery, although the Miseq delivered the highest sequence quality. As expected, species recovery was most efficient from the Single Leg treatment because amplicon abundance varied little among taxa. Among the three treatments where PCR occurred after pooling, the Bulk Abdomen treatment produced a more uniform read abundance than the Bulk Leg or Composite Leg treatment. Primer choice also influenced species recovery and evenness. Our results reveal how variation in protocols can have substantial impacts on perceived diversity unless sequencing coverage is sufficient to reach an asymptote.  相似文献   

14.
We tested two hypotheses about boundary units and seven about environmental control of species diversity in order to explain geographical trends in the richness of amphibian species in the Mediterranean watershed of the southern coast of the Iberian Peninsula. The number of amphibian species tends to decrease from west to east. The longitudinal trend in the richness of amphibian species actually occurs on passing from one basin to another, but there is not any longitudinal trend within the basins. Multivariate analyses confirmed that the disturbances of episodic river-basin floodings were the principal factor which controls the richness of amphibian species. They explained 94.8% of the observed variations in the richness of amphibian species in this area, according to the intermediate disturbance hypothesis.We propose hydrographic basins as suitable geographical units for further biogeographical analysis and for considering the role of disturbances produced by floods in the environmental control of species diversity.  相似文献   

15.
Ectomycorrhizal (ECM) fungi play major ecological roles in temperate and tropical ecosystems. Although the richness of ECM fungal communities and the factors controlling their structure have been documented at local spatial scales, how they vary at larger spatial scales remains unclear. In this issue of Molecular Ecology, Tedersoo et al. (2012) present the results of a meta‐analysis of ECM fungal community structure that sheds important new light on global‐scale patterns. Using data from 69 study systems and 6021 fungal species, the researchers found that ECM fungal richness does not fit the classic latitudinal diversity gradient in which species richness peaks at lower latitudes. Instead, richness of ECM fungal communities has a unimodal relationship with latitude that peaks in temperate zones. Intriguingly, this conclusion suggests the mechanisms driving ECM fungal community richness may differ from those of many other organisms, including their plant hosts. Future research will be key to determine the robustness of this pattern and to examine the processes that generate and maintain global‐scale gradients of ECM fungal richness.  相似文献   

16.
    
A gold rush is currently going on in microbial ecology, which is powered by the possibility to determine the full complexity of microbial communities through next‐generation sequencing. Accordingly, enormous efforts are underway to describe microbiomes worldwide, in humans, animals, plants, soil, air and the ocean. While much can be learned from these studies, only experiments will finally unravel mechanisms. One of the key questions is how a microbial community is assembled from a pool of bacteria in the environment, and how it responds to change – be it the increase in CO2 concentration in the ocean, or antibiotic treatment of the gut microbiome. The study by Zhang et al. ( 2016 ) in this issue is one of the very few that approaches this problem experimentally in the natural environment. The authors selected a habitat which is both extremely interesting and difficult to access. They studied the Thuwal Seep in the Red Sea at 850 m depth and used a remotely operated vehicle (ROV) to place a steel frame carrying substrata for biofilm growth into the brine pool and into the adjacent normal bottom water (NBW). Biofilms were allowed to develop for 3 days, and then those that had been growing in the brine pool were transported to normal bottom water and stayed there for another 3 days, and vice versa. The ‘switched’ biofilms were then compared with their source communities by metagenome sequencing. Strikingly, both ‘switched’ biofilms were now dominated by the same two species. These species were able to cope with conditions in both source ecosystems, as shown by assembly of their genomes and detection of expression of key genes. The biofilms had adapted to environmental change, rather than to brine pools or NBW. The study shows both the resilience and adaptability of biofilm communities and has implications for microbial ecology in general and even for therapeutic approaches such as transplantation of faecal microbiomes.  相似文献   

17.
18.
The integration of the social sciences into long-term ecological research is an urgent priority. To address this need, a group of social, earth, and life scientists associated with the National Science Foundations (NSF) Long-Term Ecological Research (LTER) Network have articulated a conceptual framework for understanding the human dimensions of ecological change for the LTER Network. This framework explicitly advocates that what is often divided into natural and human systems be considered a single, complex social-ecological system (SES). In this paper, we propose a list of core social science research areas, concepts, and questions; identify the need for multiscale investigatory frameworks crucial for implementing integrated research; and suggest practical approaches for integration. In sum, this paper is a general outline for empirical and cross-site research projects where investigators agree that bringing together social, biological, and earth scientists can lead to synthetic approaches and a unified understanding of the mechanisms regulating SES. Although the motivation for this goal is specific to the LTER Network and similar projects, we believe that the issues and ideas presented here are widely applicable to other interdisciplinary SES studies.  相似文献   

19.
    
Arbuscular mycorrhizal fungi (AMF) represent an important soil microbial group playing a fundamental role in many terrestrial ecosystems. We explored the effects of deterministic (soil characteristics, host plant life stage, neighbouring plant communities) and stochastic processes on AMF colonization, richness and community composition in roots of Knautia arvensis (Dipsacaceae) plants from three serpentine grasslands and adjacent nonserpentine sites. Methodically, the study was based on 454‐sequencing of the ITS region of rDNA. In total, we detected 81 molecular taxonomical operational units (MOTUs) belonging to the Glomeromycota. Serpentine character of the site negatively influenced AMF root colonization, similarly as higher Fe concentration. AMF MOTUs richness linearly increased along a pH gradient from 3.5 to 5.8. Contrary, K and Cr soil concentration had a negative influence on AMF MOTUs richness. We also detected a strong relation between neighbouring plant community composition and AMF MOTUs richness. Although spatial distance between the sampled sites (c. 0.3–3 km) contributed to structuring AMF communities in K. arvensis roots, environmental parameters were key factors in this respect. In particular, the composition of AMF communities was shaped by the complex of serpentine conditions, pH and available soil Ni concentration. The composition of AMF communities was also dependent on host plant life stage (vegetative vs. generative). Our study supports the dominance of deterministic factors in structuring AMF communities in heterogeneous environment composed of an edaphic mosaic of serpentine and nonserpentine soils.  相似文献   

20.
    
Fungi are very abundant and functionally pivotal in Arctic terrestrial ecosystems. Yet, our understanding of their community composition, diversity and particularly their environmental drivers is superficial at the very best. In this issue of Molecular Ecology, Timling et al. ( 2014 ) describe perhaps one of the most comprehensive and geographically ambitious molecular studies on Arctic fungal communities to date. The results highlight the potential sensitivity of the fungal communities to plant communities, environmental conditions and therefore to environmental change. Thus, these studies lay a foundation to educated speculation on the fungal community migration northwards as a result of predicted climate change.  相似文献   

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