环境DNA技术在鱼类生态学中的应用研究进展

全球渔业衰退是21世纪人类面临的重要挑战之一。为了有效地遏制鱼类资源的衰退,精确的鱼类生态调查是其首要任务。传统的鱼类监测以渔获物采集与形态学鉴定为主,往往耗时耗力且效果不佳,已无法满足现阶段大尺度上的精确调查。环境DNA （eDNA）技术作为一种近年来新兴的鱼类生态调查方法,其与传统方法相比具有灵敏度高、经济高效、采样受限小且对生态系统无干扰的优势,目前其已被广泛地应用于鱼类物种监测、多样性调查、生物量评估以及繁殖活动监测等方面的研究。然而,eDNA技术在鱼类生态学研究的具体应用中暴露出的一些问题将会影响其监测结果的精确性,诸如操作流程的不规范、基因数据库的不完善以及eDNA在环境中生态学过程的不明确等。鉴于上述原因,首先对eDNA技术的发展历程、分析流程以及eDNA技术在鱼类生态学研究领域中的研究进展进行了综述,而后着重分析了eDNA技术的发展当前所面临的困难与挑战,并提出了相应的解决方案,最后对eDNA技术未来在鱼类生态学研究领域中的发展趋势做出了展望。通过本研究,以期能够为eDNA技术在鱼类生态学领域中的准确应用提供理论基础。     

Relationships among map resolution, fish assemblages, and habitat variables in a coral reef ecosystem

Benthic maps are broad-scale characterizations that lack the detailed environmental attributes which have been the focus of most prior empirical studies linking reef fish and habitat. We used multivariate analyses to quantify correlations among fish assemblages, local habitat variables, and reef types depicted in benthic maps. Benthic maps of a study system in the U.S. Virgin Islands with high (100 m² minimum mapping unit) and low (4,048 m² minimum mapping unit) spatial resolution, respectively, were evaluated. Benthic maps depicted six reef types and two shelf positions (lagoon vs. shelf). Fish assemblages and local environmental variables were quantified at random sites throughout the landscape by diver surveys. Multivariate ordination based on either fish assemblages or environmental data did not result in well-separated groups of sites. Mapped reef types were not associated with distinct values of either local environmental variables or fish assemblages. Reef types exhibited substantial overlap in ordination plots based on benthic characteristics with groupings based on fish assemblages showing even greater overlap. Ordination patterns involving reef type were largely the same for both low- and high-resolution maps. In contrast, sites showed clear groups for lagoon and shelf in ordinations based on both environmental variables and fish assemblage composition, respectively. These results suggest that knowledge of the overall fish assemblage or fine-scale environmental characteristics could not be used to predict reef type depicted in benthic maps or vice versa. In contrast, reef zone could be used to predict fish assemblage or fine-scale environmental variables and vice versa.     

The effect of a large-scale irrigation scheme on the fish community structure and integrity of a subtropical river system in South Africa

Large scale irrigation schemes are vitally important for food security in developing countries. This is especially relevant in subtropical countries where there is pressure on their water resources. However, the potential impacts on the fish communities of the rivers associated with these irrigation systems are extensive and potentially devastating. Therefore, the aim of the study was to evaluate the impact of the Vaalharts Irrigation Scheme (VHIS) on the fish community of two rivers (Harts and Vaal rivers) in the subtropical region of South Africa. The fish community was assessed during a three year period from 2007 to 2009 together with environmental and habitat quality parameters. A multivariate approach together with a local biotic index was used to determine the present ecological state and the environmental drivers responsible for the fish community structure. The results indicated that the fish community was in a largely natural state at the start of the VHIS and increasingly became modified due to various environmental parameters being affected by the irrigation scheme. Annual variation in the fish community structures was high while nitrate, zinc and sulphates corresponded with changes in the fish community. The outcome of the study highlighted that a lack of long term monitoring of fish community structures together with environmental and habitat parameters are a major challenge in many developing countries that can potentially affect management of irrigation schemes and the fish communities associated with the aquatic ecosystems.     

The role of environmental and spatial processes in structuring native and non‐native fish communities across thousands of lakes

Quantifying the role of spatial patterns is an important goal in ecology to further understand patterns of community composition. We quantified the relative role of environmental conditions and regional spatial patterns that could be produced by environmental filtering and dispersal limitation on fish community composition for thousands of lakes. A database was assembled on fish community composition, lake morphology, water quality, climatic conditions, and hydrological connectivity for 9885 lakes in Ontario, Canada. We utilized a variation partitioning approach in conjunction with Moran's Eigenvector Maps (MEM) and Asymmetric Eigenvector Maps (AEM) to model spatial patterns that could be produced by human‐mediated and natural modes of dispersal. Across 9885 lakes and 100 fish species, environmental factors and spatial structure explained approximately 19% of the variation in fish community composition. Examining the proportional role of spatial structure and environmental conditions revealed that as much as 90% of the explained variation in native species assemblage composition is governed by environmental conditions. Conversely on average, 67% of the explained variation in non‐native assemblage composition can be related to human‐mediated dispersal. This study highlights the importance of including spatial structure and environmental conditions when explaining patterns of community composition to better discriminate between the ecological processes that underlie biogeographical patterns of communities composed of native and non‐native fish species.     

A comparison between two GAM models in quantifying relationships of environmental variables with fish richness and diversity indices

Various regression methods can be used to quantify the relationships between fish populations and their environment. Strong correlations often existing between environmental variables, however, can cause multicollinearity, resulting in overfitting in modeling. This study compares the performance of a regular generalized additive model (GAM) with raw environmental variables as explanatory variables (regular GAM) and a GAM based on principal component analysis (PCA-based GAM) in modeling the relationship between fish richness and diversity indices and environmental variables. The PCA-based GAM tended to perform better than the regular GAM in cross-validation tests, showing a higher prediction precision. The variables identified being significant in modeling differed between the two models, and differences between the two models were also found in the scope and range of predicted richness and diversity indices for demersal fish community. This implies that choices between these two statistical modeling approaches can lead to different ecological interpretations of the relationships between fish communities and their habitats. This study suggests that the PCA-based GAM is a better approach than the original GAM in quantifying the relationship between fish richness and diversity indices and environmental variables if the environmental variables are highly correlated.     

Imperfect detection and the determination of environmental flows for fish: challenges,implications and solutions

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Fish–environment Associations in the Coastal Waters of Andros Island, The Bahamas

Synopsis We surveyed fish communities and corresponding environmental conditions at three broadly similar coastal sites of eastern Andros Island, The Bahamas over a summer–winter–summer sequence to assess the relationship between detailed environmental features and fish species patterns. Environmental variables included covers of various benthic flora components, benthic flora diversity, floral canopy height, micro-crustacean diversity and density, water temperature, extent of destructive land-use and extent of invasion by human-introduced exotic terrestrial plants. Correspondence analysis (CA) indicated that spatial (site) differences in environmental characteristics were greater than temporal (seasonal) differences. Detrended canonical correspondence analysis (DCCA) was used to assess the strength of relationships between the environmental characteristics and the distribution patterns of 25 fish species. Environmental features deemed to be most important in influencing fish species patterns included benthic flora canopy height, extent of invasion by exotic terrestrial plants, cover of Batophora oerstedii, cover of Thalassia testudinum, turf cover, water temperature, micro-crustacean diversity, and micro-crustacean density. Based upon similarities in distribution patterns, fish species formed four clusters which, ultimately, reflected similarities in species’ feeding habits and preferences for habitats that likely maximize foraging success. We conclude that fish distribution patterns are related to environmental characteristics, and that anthropogenic coastal activity, by influencing coastal benthic characteristics, may influence the distribution and abundances of fish species in coastal habitats.     

Linking environmental variability and fish performance: integration through the concept of scope for activity

Investigating the biological mechanisms linking environmental variability to fish production systems requires the disentangling of the interactions between habitat, environmental adaptation and fitness. Since the number of environmental variables and regulatory processes is large, straightening out the environmental influences on fish performance is intractable unless the mechanistic analysis of the 'fish-milieu' system is preceded by an understanding of the properties of that system. While revisiting the key points in our currently poorly integrated understanding of fish ecophysiology, we have highlighted the explanatory potential contained within Fry's (Fry 1947 Univ. Toronto Stud. Biol. Ser. 55, 1-62) concept of metabolic scope and categorization of environmental factors. These two notions constitute a pair of powerful tools for conducting an external (at the emerging property level) analysis of the environmental influences on fish, as well as an internal (mechanistic) examination of the behavioural, morphological and physiological processes involved. Using examples from our own and others work, we have tried to demonstrate that Fry's framework represents a valuable conceptual basis leading to a broad range of testable ecophysiological hypotheses.     

Fish Communities and Their Associations with Environmental Variables, Lower San Joaquin River Drainage, California

Twenty sites in the lower San Joaquin River drainage, California, were sampled from 1993 to 1995 to characterize fish communities and their associations with measures of water quality and habitat quality. The feasibility of developing an Index of Biotic Integrity was assessed by evaluating four fish community metrics, including percentages of native fish, omnivorous fish, fish intolerant of environmental degradation, and fish with external anomalies. Of the thirty-one taxa of fish captured during the study, only 10 taxa were native to the drainage. Multivariate analyses of percentage data identified four site groups characterized by different groups of species. The distributions of fish species were related to specific conductance, gradient, and mean depth; however, specific conductance acted as a surrogate variable for a large group of correlated variables. Two of the fish community metrics – percentage of introduced fish and percentage of intolerant fish – appeared to be responsive to environmental quality but the responses of the other two metrics – percentage of omnivorous fish and percentage of fish with anomalies – were less direct. The conclusion of the study is that fish communities are responsive to environmental conditions, including conditions associated with human-caused disturbances, particularly agriculture and water development. The results suggest that changes in water management and water quality could result in changes in species distributions. Balancing the costs and benefits of such changes poses a considerable challenge to resource managers.     

Trangenic fish as models in environmental toxicology

Historically, fish have played significant roles in assessing potential risks associated with exposure to chemical contamination in aquatic environments. Considering the contributions of transgenic rodent models to biomedicine, it is reasoned that the development of transgenic fish could enhance the role of fish in environmental toxicology. Application of transgenic fish in environmental studies remains at an early stage, but recent introduction of new models and methods demonstrates progress. Rapid advances are most evident in the area of in vivo mutagenesis using fish carrying transgenes that serve as recoverable mutational targets. These models highlight many advantages afforded by fish as models and illustrate important issues that apply broadly to transgenic fish in environmental toxicology. Development of fish models carrying identical transgenes to those found in rodents is beneficial and has revealed that numerous aspects of in vivo mutagenesis are similar between the two classes of vertebrates. Researchers have revealed that fish exhibit frequencies of spontaneous mutations similar to rodents and respond to mutagen exposure consistent with known mutagenic mechanisms. Results have demonstrated the feasibility of in vivo mutation analyses using transgenic fish and have illustrated their potential value as a comparative animal model. Challenges to development and application of transgenic fish relate to the needs for improved efficiencies in transgenic technology and in aspects of fish husbandry and use. By taking advantage of the valuable and unique attributes of fish as test organisms, it is anticipated that transgenic fish will make significant contributions to studies of environmentally induced diseases.     

Environmental and spatial effects on coastal stream fishes in the Atlantic rain forest

Contemporary and historical factors influence assemblage structure. The environmental and spatial influences acting on fish organization of rain forest coastal streams in the Atlantic rain forest of Brazil were examined. Fish (and functional traits such as morphology, diet, velocity preference, body size), environmental variables (pH, water conductivity, dissolved oxygen, temperature, stream width, flow, depth, substrate), and altitude were measured from 59 stream reaches. Asymmetric eigenvector maps were used to model the spatial structure considering direction of fish movements. Elevation played an important role—fish abundance, biomass, and richness all decrease with increasing elevation. Fish communities are influenced by both environmental and spatial factors, but downstream movements were shown to be more important in explaining the observed spatial variation than were bidirectional and upstream movements. Spatial factors, as well as environmental variables influenced by the spatial structure, explained most of the variation in fish assemblages. The strong spatial structuring is probably attributable to asymmetric dispersal limitation along the altitudinal profile: Dispersal is likely to be more limiting moving upstream than downstream. These fish assemblages reflect scale-dependent processes: At the stream-reach scale, fish respond to local environmental filters (habitat structure, water chemistry, and food supply), which are in turn influenced by a larger scale, namely the altitudinal gradient expected in steep coastal mountains. Thus, environmental drivers are not independent of spatial factors, and the effects of local factors can be confounded across the altitudinal gradient. These results may have implications for conservation, because downstream reaches are often neglected in management and conservation plans.     

Environmentally adaptive fish or no-fish classification for river video fish counters using high-performance desktop and embedded hardware

Automated fish counters featuring robust, real-time computer vision capabilities can provide a cost-effective means to count migrating freshwater fish. In this work, we propose a four-stage process for automatically sorting videos with and without fish. Underwater fish counter videos provide a challenging range of environmental conditions including clear water, biofilm growth, bubbles, turbidity, low light and overexposure. To address this, our method also includes the automated classification of these six environmental conditions. The proposed methods are computationally efficient and can be implemented on servers, high-performance desktop computers and low-cost, energy-efficient embedded hardware. The models were trained, tested, and validated using a collection of 3000 videos taken from underwater fish counter installations in several alpine and lowland European rivers provided by commercial and governmental collaborators. This work demonstrates a fast, accurate, and robust computer vision workflow for large-scale automated freshwater fish counting systems.     

淡水鱼类功能生态学研究进展

在全球变化和人类活动的影响下,生物多样性正以前所未有的速度丧失,全球生物正经受第六次生物多样性危机。淡水生态系统是最脆弱的生态系统之一。淡水鱼类作为淡水生态系统的重要组成部分,承受着日趋严重的气候变化、栖息地退化、生物入侵和过度捕捞等压力,面临巨大的威胁。在此背景下,如何准确评估鱼类种群和群落对环境变化的响应,以及鱼类群落结构和功能的变化对生态系统功能的影响是淡水鱼类多样性和淡水生态系统保护的关键问题。近年来,淡水鱼类功能生态学的快速发展为解答这一问题提供了一个框架。系统地介绍了淡水鱼类功能生态学主要研究内容、方法、进展及其应用,并着重介绍了淡水鱼类功能特征及其与环境的关系、环境变化下的功能生态学响应研究。据此提出了淡水鱼类功能生态学未来的重点研究方向,指出了其在鱼类多样性保护和资源利用等领域的应用前景。     

Development of a fish-based index to assess the eutrophication status of European lakes

The use of the CEN (European Committee for Standardization) standard method for sampling fish in lakes using multi-mesh gillnets allowed the collection of fish assemblages of 445 European lakes in 12 countries. The lakes were additionally characterised by environmental drivers and eutrophication proxies. Following a site-specific approach including a validation procedure, a fish index including two abundance metrics (catch per unit effort expressed as fish number and biomass) and one functional metric of composition (abundance of omnivorous fish) was developed. Correlated with the proxy of eutrophication, this index discriminates between heavily and moderately impacted lakes. Additional analyses on a subset of data from Nordic lakes revealed a stronger correlation between the new fish index and the pressure data. Despite an uneven geographical distribution of the lakes and certain shortcomings in the environmental and pressure data, the fish index proved to be useful for ecological status assessment of lakes applying standardised protocols and thus supports the development of national lake fish assessment tools in line with the European Water Framework Directive.     

Dispersal abilities of riverine freshwater mussels influence metacommunity structure

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环境雌激素实验室模拟暴露方法

从实验鱼类、暴露系统、暴露方式、评价指标四个方面对国内外环境雌激素的实验室暴露研究方法进行了介绍,为环境雌激素的暴露机制、毒性机理及雌激素效应的研究提供了理论依据和实验指导。     

长江中游干流鱼类群落构建机制分析

研究选取长江中游5个采样点(宜昌、枝江、荆州、汉南、湖口)为代表,采用系统发育群落结构方法分析了不同空间尺度下长江中游鱼类群落的构建机制。结果表明:(1)空间聚类分析显示,在65%的相似性水平上,所有样点可以划分为3个Group:GroupⅠ(宜昌)、GroupⅡ(枝江+荆州)和GroupⅢ(汉南+湖口);在55%的相似性水平上,所有样点可以划分为2个Group:Group A(宜昌)和Group B(枝江+荆州+汉南+湖口),且聚类分析结果与采样点的空间分布相符合。(2)在不同空间尺度下,鱼类群落构建机制存在差异:从地区采样点尺度来看,荆州江段鱼类群落表现为竞争作用主导群落构建,其余采样点鱼类群落均为环境过滤作用;从区域尺度来看,宜昌江段鱼类群落表现为环境过滤作用的建群机制,其余4个采样点在扩大空间尺度后,即分为Group A和Group B的情况下,其鱼类群落构建机制转变为物种间竞争作用。因此,长江中游干流鱼类群落构建机制表现了地区环境和空间尺度的共同作用。由于水流湍急,宜昌始终表现为环境过滤作用。其他江段在采样点尺度多数表现了环境过滤作用,但是在宏观的空间尺度上,却由于空间异质性...     

Detecting and managing fisheries-induced evolution

Exploitation of fish populations can induce evolutionary responses in life histories. For example, fisheries targeting large individuals are expected to select for early maturation at smaller sizes, leading to reduced fecundity and thus also reduced fisheries yield. These predicted phenotypic shifts have been observed in several fish stocks, but disentangling the environmental and genetic causes behind them has proved difficult. Here, we review recent studies investigating phenotypic shifts in exploited populations and strategies for minimizing fisheries-induced evolution. Responses to selective harvesting will depend on species-specific life-history traits, and on community-level and environmental processes. Therefore, the detection of fisheries-induced evolution and successful fish stock management requires routine population monitoring, and a good understanding of genetics, relevant ecological processes and changing environmental conditions.     

Macroecology of a host-parasite relationship

The larvae of freshwater mussels are obligate ectoparasites on fishes while adults are sedentary and benthic. Dispersal of mussels is dependent on the movement of fish hosts, a regional process, but growth and reproduction should be governed by local processes. Thus, mussel assemblage attributes should be predictable from the regional distribution and abundance of fishes. At a broad spatial scale in the Red River drainage, USA, mussel species richness and fish species richness were positively associated; maximum mussel richness was limited by fish richness, but was variable beneath that constraint. Measured environmental variables and the associated local fish assemblages each significantly accounted for the regional variation in mussel assemblages. Furthermore, mussel assemblages showed strong spatial autocorrelation. Variation partitioning revealed that pure fish effects accounted for 15.4% of the variation in mussel assemblages; pure spatial and environmental effects accounted for 16.1% and 7.8%, respectively. Shared variation among fish, space and environmental variables totaled 40%. Of this shared variation, 36.8% was associated with the fish matrix. Thus, the variation in mussel assemblages that was associated with the distribution and abundance of fishes was substantial (> 50%), indicating that fish community structure is an important determinant of mussel community structure. Although animals commonly disperse plants and, thus, influence the structure of plant communities, our results show a strong macroecological association between two disparate animal groups with one strongly affecting the assemblage structure of the other.