基于环境DNA-宏条形码技术的底栖动物监测及水质评价研究进展

底栖动物是淡水生态系统中物种多样性最高的类群,也是应用最广泛的水质监测指示生物之一。传统的底栖动物监测以形态学为基础,耗时费力,无法满足流域尺度大规模监测的需求。环境DNA-宏条形码技术是一种新兴的生物监测方法,其与传统方法相比优势在于采样方法简单、低成本、高灵敏度,不受生物样本和环境状况的影响,不依赖分类专家和鉴定资料,能够快速准确地对多个类群进行大规模、高通量的物种鉴定。然而,在实际应用中该方法的效果受诸多因素的影响,不同的方法、流程往往会产生差异较大的结果。鉴于此,着重分析总结了应用环境DNA-宏条形码技术监测底栖动物的关键影响因素,包括样品采集与处理流程、分子标记选择、引物设计、PCR偏好性、参考数据库的完整性及相应的优化。并基于此探讨了提高环境DNA-宏条形码技术在底栖动物监测效率和准确率的途径,以期为底栖动物环境DNA-宏条形码监测方案的制定提供可靠的参考。最后对该技术在底栖动物监测和水质评价中的最新发展方向进行了展望。     

Recommendations for the forensic diagnosis of sex and age from skeletons.

In both diagnostic fields a two-stage strategy is recommended: to first use "field" methods that are quick and easy but more imprecise and then "laboratory" methods that are time consuming but more precise. In preparing skeletal work, individuality of a skeleton should be checked, traces of diseases sought and time since death assessed. For sexing non-adults, the field methods are tooth mineralisation, long bone length and a few morphological skull and pelvis characteristics, for adults it is the morphology of pelvis and skull, and for both age groups the advanced laboratory method is molecular biology. For ageing non-adults the methods are mineralisation of teeth, long bone length and epiphysis development. For ageing adults the advanced laboratory method is aspartic acid racemisation. Less accurate laboratory methods are cement ring counts and histology of bones and teeth. Quick morphological methods using the pubic symphysis and other traits in combinations follow. Finally, cranial sutures and tooth number give a quick and rough impression. For the selection of a method and the assessment of its value the stochastic error produced for the reference sample is the decisive criterion; it should also be used to assess the reliability of a single diagnosis. Prerequisites for all work with skeletons are not only a complete knowledge of the relevant biology as well as specific techniques but also initial detailed instructions and with forensic applications, personal experience.     

Trait‐based climate vulnerability assessments in data‐rich systems: An application to eastern Bering Sea fish and invertebrate stocks

Trait‐based climate vulnerability assessments based on expert evaluation have emerged as a rapid tool to assess biological vulnerability when detailed correlative or mechanistic studies are not feasible. Trait‐based assessments typically view vulnerability as a combination of sensitivity and exposure to climate change. However, in some locations, a substantial amount of information may exist on system productivity and environmental conditions (both current and projected), with potential disparities in the information available for data‐rich and data‐poor stocks. Incorporating this level of detailed information poses challenges when conducting, and communicating uncertainty from, rapid vulnerability assessments. We applied a trait‐based vulnerability assessment to 36 fish and invertebrate stocks in the eastern Bering Sea (EBS), a data‐rich ecosystem. In recent years, the living marine resources of the EBS and Aleutian Islands have supported fisheries worth more than US $1 billion of annual ex‐vessel value. Our vulnerability assessment uses projections (to 2039) from three downscaled climate models, and graphically characterizes the variation in climate projections between climate models and between seasons. Bootstrapping was used to characterize uncertainty in specific biological traits and environmental variables, and in the scores for sensitivity, exposure, and vulnerability. The sensitivity of EBS stocks to climate change ranged from “low” to “high,” but vulnerability ranged between “low” and “moderate” due to limited exposure to climate change. Comparison with more detailed studies reveals that water temperature is an important variable for projecting climate impacts on stocks such as walleye pollock (Gadus chalcogrammus), and sensitivity analyses revealed that modifying the rule for determining vulnerability increased the vulnerability scores. This study demonstrates the importance of considering several uncertainties (e.g., climate projections, biological, and model structure) when conducting climate vulnerability assessments, and can be extended in future research to consider the vulnerability of user groups dependent on these stocks.     

An overview of methods used to assess vegetation condition at the scale of the site

Summary   Rapid, on-ground assessments of vegetation condition are frequently used as a basis for landholder education, development applications, distributing incentive funds, prescribing restoration treatments and monitoring change. We provide an overview of methods used to rapidly assess vegetation condition for these purposes. We encourage those developing new approaches to work through the steps we have presented here, namely define management objectives and operational constraints; develop an appropriate conceptual framework for the ecosystems under consideration; select an appropriate suite of indicators; and consider the options available for combining these into an index. We argue that information must be gained from broader scales to make decisions about the condition of individual sites. Remote sensing and spatial modelling might be more appropriate methods than on-ground assessments for obtaining this information. However, we believe that spatial prediction of vegetation condition will only add value to on-ground assessments rather than replace them. This is because the current techniques for spatially predicting vegetation condition cannot capture all of the information in a site assessment or at the required level of accuracy, and maps cannot replace the exchange of information between assessors and land managers that is an important component of on-ground assessment. There is scope for more sophistication in the way on-ground assessments of vegetation condition are undertaken, but the challenge will be to maintain the simplicity that makes rapid on-ground assessment a popular vehicle for informing natural resource management. We encourage greater peer review and publishing in this field to facilitate greater exchange of ideas and experiences.     

Lessons for stock assessment from the northern cod collapse

Fisheries assessment scientists can learn at least three lessons from the collapse of the northern cod off Newfoundland: (1) assessment errors can contribute to overfishing through optimistic long-term forecasts leading to the build-up of overcapacity or through optimistic assessments which lead to TACs being set higher than they should; (2) stock size overestimation is a major risk when commercial catch per effort is used as an abundance trend index, so there is continued need to invest in survey indices of abundance trend no matter what assessment methodology is used; and (3) the risk of recruitment overfishing exists and may be high even for very fecund species like cod. This implies that harvest rate targets should be lower than has often been assumed, especially when stock size assessments are uncertain. In the end, the high cost of information for accurate stock assessment may call for an alternative approach to management, involving regulation of exploitation rate via measures such as large-scale closures (refuges) that directly restrict the proportion of fish available to harvest. Development of predictive models for such regulatory options is a major challenge for fisheries assessment science.     

Evaluating the use of roving diver and transect surveys to assess the coral reef fish assemblage off southeastern Hispaniola

The relatively little-studied fish fauna off southeastern Hispaniola was rapidly assessed using a combination of visual survey techniques including transects and roving diver surveys. It was found that when combined, both methods provided a more complete overall species assessment than either method was able to provide in isolation. Being able to conduct rapid species assessments is becoming increasingly more important as a conservation tool. Data on species composition, sighting frequency, and abundance of all fishes were collected using both methods. Abundance was recorded in four logarithmic-based categories (roving diver method) while the number of fishes were counted within 40-m² transects (transect method). Both methods were similar in recording the most abundant species, while a greater number of rare species (especially fishery-targeted species) were recorded with the roving diver method. The most abundant groupers were Cephalopholis cruentata and C. fulva. The most abundant parrotfishes were Scarus taeniopterus, Sparisoma aurofrenatum, and Scarus iserti. The most conspicuous differences between fishes off southeastern Hispaniola and elsewhere in the tropical western Atlantic were the low abundance and smaller size of harvested species such as groupers, snappers (Fam. Lutjanidae), and grunts (Fam. Haemulidae). With the roving diver method, more time could be spent surveying (instead of placing transect lines), resulting in a greater number of species being recorded. Additionally, well-trained volunteers can adopt the roving diver method as part of their regular diving program. Transect surveys were able to provide information such as length (biomass) and actual density measures that were not recorded in roving diver surveys. Thus, these methods were complementary and should be used in conjunction when conducting rapid assessments of fish assemblages, especially to detect the effects of overfishing.     

Design and implementation of rapid assessment approaches for water resource monitoring using benthic macroinvertebrates

Abstract Benthic macroinvertebrates are the group of organisms most widely used for assessment of water resources. Rapid assessment approaches are intended to be efficient and cost effective; savings are found in reduced sampling and more efficient data analysis. Rapid bioassessment programmes have been quickly accepted and now cover most of the United States (US) and equivalent programmes cover all of the United Kingdom (UK). Rapid bioassessment programmes are designed to screen large regions, pinpointing trouble spots worthy of more detailed attention. Fundamental to all rapid bioassessment methods is the classification of streams so that comparisons can be made between reference areas and areas of concern, or test sites with similar characteristics. Both the UK and US approaches assess habitat characteristics. These characteristics are used to predict the fauna expected at a test site in the UK approach; in the US they are used as an aid to classification and interpretation of aquatic faunal data. Habitat assessments in the US are also used to determine whether poor water quality or degraded habitat are stressing the invertebrate communities. This is a major development in approaches to water resource assessment. In the UK, a model developed using multivariate statistics uses a few environmental variables thought to be unaffected by human activities to predict the fauna expected at a test site. The US approaches analyse data using several indices (or metrics) presumed to represent ecological features of interest. These indices have a range of sensitivities to different kinds of stress and must be calibrated for the area of interest. The two approaches have been developed in isolation but may have much to offer each other. Developing programmes are advised to consider both. Future needs include: development of procedures that can be applied to large rivers and to lakes; further refinement of ecological principles underlying metric choice; the inclusion of chemical criteria and toxicity tests to establish thresholds that indicate impairment; and development of criteria indicating the necessity for implementation of quantitative assessment studies.     

Human body burdens of chemicals used in plastic manufacture

In the last decades, the availability of sophisticated analytical chemistry techniques has facilitated measuring trace levels of multiple environmental chemicals in human biological matrices (i.e. biomonitoring) with a high degree of accuracy and precision. As biomonitoring data have become readily available, interest in their interpretation has increased. We present an overview on the use of biomonitoring in exposure and risk assessment using phthalates and bisphenol A as examples of chemicals used in the manufacture of plastic goods. We present and review the most relevant research on biomarkers of exposure for phthalates and bisphenol A, including novel and most comprehensive biomonitoring data from Germany and the United States. We discuss several factors relevant for interpreting and understanding biomonitoring data, including selection of both biomarkers of exposure and human matrices, and toxicokinetic information.     

The Intersection of Independent Lies: Increasing Realism in Ecological Risk Assessment

In 1966, Levins presented a philosophical discussion on making inference about populations using clusters of models. In this article we provide an overview of model inference in ecological risk assessment, discuss the benefits and trade-offs of increasing model realism, show the similarities and differences between Levins' model clusters and those used in ecological risk assessment, and present how risk assessment models can incorporate Levins' ideas of truth through independent lies. Two aspects of Levins' philosophy are directly relevant to risk assessment. First, confidence in our interpretation of risk is increased when multiple risk assessments yield similar qualitative results. Second, model clusters should be evaluated to determine if they maximize precision, generality, or realism or a mix of the three. In the later case, the evaluation of each model will differ depending on whether it is more general, precise, or realistic relative to the other models used. We conclude that risk assessments can be strengthened using Levins' idea, but that Levins' caution that model outcome should not be mistaken for truth is still applicable.     

水中病原微生物分子检测技术研究进展

基于PCR方法的多种分子检测技术已广泛的应用于水体病原微生物的检测中。而以DNA芯片为代表的微型化、快速化手段将是未来检测技术的发展方向,可实现对病原微生物实时和快速的检测。新检测技术的发展有利于建立水体污染早期预警机制,同时,可靠的病原微生物检测方法可降低有害微生物对人类健康的影响。对水体病原微生物分子检测方法及其在水污染相关疾病风险控制中所扮演的重要角色进行阐述。     

Rapid assessment in conservation research: a critique of avifaunal assessment techniques illustrated by Ecuadorian and Madagascan case study data

The urgency of conservation concerns in the tropics, linked with the limitations imposed on research efforts by the tropical environment has resulted in the development of methods for rapid assessment of biological communities. One such method, the MacKinnon list technique, has been increasingly applied in avifaunal surveys worldwide. Using paired tropical bird data sets from Ecuadorian cloud forest and Madagascan littoral forest, we compare the performance of the MacKinnon list with that of the more standard method of point counts in indicating when a site has been adequately surveyed, estimating the magnitude of species richness, quantifying relative species abundance, and providing an α‐index of diversity. In species‐rich Ecuadorian cloud forest, neither method produced data indicating adequate survey effort, despite extensive sampling, whereas in the relatively species‐poor Madagascan littoral forests, data collected by both methods indicated that the area had been sufficiently surveyed with comparable sampling effort. Species richness estimates generated from MacKinnon list data provided a more accurate estimate of the magnitude of the species richness for the Ecuadorian avifauna, whereas estimates for the Madagascan avifauna stabilised with relatively few samples using either method. Data collected by each method reflected different patterns of relative abundance among the five most abundant species, with MacKinnon list data showing a bias towards solitary and territorial species and against monospecific flocking species relative to the point count data. As a consequence of this bias, MacKinnon list data also fail to reflect accurately the structure of communities as quantified by an index of community evenness. Point counts, on the other hand, failed to capture the full species complement of the species‐rich Ecuadorian study area. As techniques for the rapid assessment of unsurveyed areas, both methods are subject to biases that limit their value, if used alone, in collecting data of scientific and management value. We propose a hybrid rapid assessment methodology that capitalises on the strengths of both techniques while compensating for their weaknesses.     

Ammonium retention and whole-stream metabolism in cave streams

The influence of sampling technique on the characterization of benthic macroinvertebrate communities on boulder-cobble substrate in two shallow freshwater ponds was analysed. Sweep-net and rock-bag sampling techniques were used to collect macroinvertebrates from two ponds in Newfoundland, Canada. Abundance and diversity of macroinvertebrates were compared in relation to the nature of the substrate and the technique. The two sampling techniques provided different estimates of diversity and density of the benthos. Neither method truly represented the benthic community as neither collected all taxa and each method typically over- or under-estimated the abundance of taxa. The difficulty of interpreting such data is discussed, with special reference to the rapid assessment of water quality in biomonitoring studies.     

What Biomonitoring Can and Cannot Tell Us about Causality in Human Health and Ecological Risk Assessments

Biomonitoring can provide exposure and effects information on various stressors (chemical or biological) that can be useful for human health and ecological risk assessments. It has been applied over the years where harmful changes in human health or the environment were observed and which may have warranted more detailed investigation. Sometimes biomonitoring programs may have been useful in determining the significance and/or cause of these harmful observations. These data can help to infer, but not confirm, causality as exemplified in classical studies conducted in humans and wildlife. However, in most cases we note that additional work was needed to provide the information necessary to support or refute causality. Today modern technology provides the ability to measure a wide variety of parameters in environmental media, plants, animals, and humans. Finding a chemical in an environmental medium or biological tissue may be helpful in understanding potential exposure (and perhaps to begin estimating hazard) to humans and ecological receptors, but mere presence does not necessarily help to establish effects or assign causality. In this article we evaluate the strengths and weaknesses, in a risk assessment context, of the use of biomonitoring data to support a determination of causality.     

A Tale of Two Forest Carbon Assessments in the Eastern United States: Forest Use Versus Cover as a Metric of Change

The dynamics of land-use practices (for example, forest versus settlements) is often a major driver of changes in terrestrial carbon (C). As the management and conservation of forest land uses are considered a means of reducing future atmospheric CO₂ concentrations, the monitoring of forest C stocks and stock change by categories of land-use change (for example, croplands converted to forest) is often a requirement of C monitoring protocols such as those espoused by the Intergovernmental Panel on Climate Change (that is, Good Practice Guidance and Guidelines). The identification of land use is often along a spectrum ranging from direct observation (for example, interpretation of owner intent via field visits) to interpretation of remotely sensed imagery (for example, land cover mapping) or some combination thereof. Given the potential for substantial differences across this spectrum of monitoring techniques, a region-wide, repeated forest inventory across the eastern U.S. was used to evaluate relationships between forest land-use change (derived from a forest inventory) and forest cover change (derived from Landsat modeling) in the context of forest C monitoring strategies. It was found that the correlation between forest land-use change and cover change was minimal (<0.08), with an increase in forest land use but a net decrease in forest cover being the most frequent observation. Cover assessments may be more sensitive to active forest management and/or conversion activities that can lead to confounded conclusions regarding the forest C sink (for example, decreasing forest cover but increasing C stocks in industrial timberlands). In contrast, the categorical nature of direct land-use field observations reduces their sensitivity to forest management activities (for example, clearcutting versus thinning) and recent disturbance events (for example, floods or wildfire) that may obscure interpretation of C dynamics over short time steps. While using direct land-use observations or cover mapping in forest C assessments, they should not be considered interchangeable as both approaches possess idiosyncratic qualities that should be considered when developing conclusions regarding forest C attributes and dynamics across large scales.     

Fifty millennia of catastrophic extinctions after human contact

Debate continues to rage between enthusiasts for climate change versus humans as a cause of the catastrophic faunal extinctions that have occurred in the wake of human arrival in previously uninhabited regions of the world. A global pattern of human arrival to such landmasses, followed by faunal collapse and other ecological changes, appears without known exception. This strongly suggests to some investigators that a more interesting extinction debate lies within the realm of potential human-caused explanations and how climate might exacerbate human impacts. New observations emerging from refined dating techniques, paleoecology and modeling suggest that the megafaunal collapses of the Americas and Australia, as well as most prehistoric island biotic losses, trace to a variety of human impacts, including rapid overharvesting, biological invasions, habitat transformation and disease.     

Applicability of macrobenthos indexes in health assessment upstream of a large river: A case study in the Babian River of the Red River Basin,China

Biological assessment is an important component of river health assessments. With the thorough growth of river health assessment in China, the scientific verification and screening of straightforward, easily quantifiable, and widely used bio-assessment indexes has emerged as a significant scientific challenge that needs to be resolved immediately in river health assessment. In 2019, 28 sections of the Babian River were examined for water quality, macrobenthos, status of the riparian zone and societal value. Based on the presence of macrobenthos in river health assessments, the applicability of 17 indexes was analyzed. The indexes that could differentiate between reference sites and impaired sites were B-IBI, S₂, S₃, and BMWP, which had good correlation with environmental factors. Although there was no significant link with riparian conditions, B-IBI, S₂, S₃, and BMWP had strong negative correlations with total ammoniacal nitrogen, total nitrogen, and total phosphorus but S₂, S₃, and BMWP are effective alternatives for B-IBI in river health assessment since their results were comparable to those of B-IBI, which covered all the assessment grades. Moreover, when constructing and selecting a bio-assessment index, more attention should be paid to the role of dominant and rare species, as well as the appropriate condition of indexes. In addition, riparian condition is a necessary aspect of river health assessment, but it is challenging to reflect the influence of land components on river health because of the small scale of riparian investigation. Therefore, it is necessary to introduce basin-scale indexes to optimize river health assessment systems. By doing this, watershed system management and overall governance will be supported more effectively.     

A novel approach to determining violence risk in schizophrenia: developing a stepped strategy in 13,806 discharged patients

Clinical guidelines recommend that violence risk be assessed in schizophrenia. Current approaches are resource-intensive as they employ detailed clinical assessments of dangerousness for most patients. An alternative approach would be to first screen out patients at very low risk of future violence prior to more costly and time-consuming assessments. In order to implement such a stepped strategy, we developed a simple tool to screen out individuals with schizophrenia at very low risk of violent offending. We merged high quality Swedish national registers containing information on psychiatric diagnoses, socio-demographic factors, and violent crime. A cohort of 13,806 individuals with hospital discharge diagnoses of schizophrenia was identified and followed for up to 33 years for violent crime. Cox regression was used to determine risk factors for violent crime and construct the screening tool, the predictive validity of which was measured using four outcome statistics. The instrument was calibrated on 6,903 participants and cross-validated using three independent replication samples of 2,301 participants each. Regression analyses resulted in a tool composed of five items: male sex, previous criminal conviction, young age at assessment, comorbid alcohol abuse, and comorbid drug abuse. At 5 years after discharge, the instrument had a negative predictive value of 0.99 (95% CI = 0.98–0.99), meaning that very few individuals who the tool screened out (n = 2,359 out of original sample of 6,903) were subsequently convicted of a violent offence. Screening out patients who are at very low risk of violence prior to more detailed clinical assessment may assist the risk assessment process in schizophrenia.     

A modular assessment tool for managing introduced fishes according to risks of species and their populations,and impacts of management actions

A modular assessment scheme for assisting the risk management of introduced fishes is described, with its recent application to England and Wales demonstrated. The initial module prioritises the introduced fishes in the risk assessment area according to their potential invasiveness and current distribution. The second module then assesses populations of the prioritised species in relation to the character of their receiving waters and the potential risks posed by their population in that circumstance; the output is a suggested management action for each population. The third module evaluates the suggested management action in relation to its potential impacts in the environment and how these impacts may be mitigated. The final module assesses the estimated cumulative cost of the selected management action relative to an alternative action. To demonstrate its potential value for managing extant populations of introduced fish, three eradication case-studies from England were assessed retrospectively using the scheme. This revealed eradication of two topmouth gudgeon Pseudorasbora parva populations was commensurate with their levels of ecological risk in the environment. By contrast, initial assessment of the eradication of a feral population of fathead minnow Pimephales promelas suggested control and containment was the commensurate management action due to a relatively low risk of natural dispersal. Application of the scheme elsewhere in the world and to other faunal groups should enable more objective decision-making in management programmes and enhance conservation outcomes.     

Effective sociodemographic population assessment of elusive species in ecology and conservation management

Wildlife managers are urgently searching for improved sociodemographic population assessment methods to evaluate the effectiveness of implemented conservation activities. These need to be inexpensive, appropriate for a wide spectrum of species and straightforward to apply by local staff members with minimal training. Furthermore, conservation management would benefit from single approaches which cover many aspects of population assessment beyond only density estimates, to include for instance social and demographic structure, movement patterns, or species interactions. Remote camera traps have traditionally been used to measure species richness. Currently, there is a rapid move toward using remote camera trapping in density estimation, community ecology, and conservation management. Here, we demonstrate such comprehensive population assessment by linking remote video trapping, spatially explicit capture–recapture (SECR) techniques, and other methods. We apply it to three species: chimpanzees Pan troglodytes troglodytes, gorillas Gorilla gorilla gorilla, and forest elephants Loxodonta cyclotis in Loango National Park, Gabon. All three species exhibited considerable heterogeneity in capture probability at the sex or group level and density was estimated at 1.72, 1.2, and 1.37 individuals per km² and male to female sex ratios were 1:2.1, 1:3.2, and 1:2 for chimpanzees, gorillas, and elephants, respectively. Association patterns revealed four, eight, and 18 independent social groups of chimpanzees, gorillas, and elephants, respectively: key information for both conservation management and studies on the species' ecology. Additionally, there was evidence of resident and nonresident elephants within the study area and intersexual variation in home range size among elephants but not chimpanzees. Our study highlights the potential of combining camera trapping and SECR methods in conducting detailed population assessments that go far beyond documenting species diversity patterns or estimating single species population size. Our study design is widely applicable to other species and spatial scales, and moderately trained staff members can collect and process the required data. Furthermore, assessments using the same method can be extended to include several other ecological, behavioral, and demographic aspects: fission and fusion dynamics and intergroup transfers, birth and mortality rates, species interactions, and ranging patterns.     

Faunal standards for the restoration of terrestrial ecosystems: a framework and its application to a high-profile case study

Assessments of ecosystem restoration have traditionally focused on soil and vegetation, often with little consideration of fauna. It is critical to include fauna in such assessments, not just because of their intrinsic biodiversity value but also because of the many ecological roles that animals play in restoration processes. However, a widely accepted framework for specifying faunal standards for restoration is lacking. Here we present such a framework, incorporating: (1) the identification of appropriate reference conditions; (2) the taxa to be targeted for assessment; (3) the attributes of these taxa to be measured; (4) acceptable similarity with reference conditions; and (5) robust sampling methodologies for reliable assessment. We illustrate this framework using the restoration program at Ranger Uranium Mine in the Australian seasonal tropics, which aims to establish an environment similar to the surrounding World Heritage-listed Kakadu National Park, corresponding to “full recovery” according to Society for Ecosystem Restoration's standards. Our case study has especially high restoration standards, but our framework has wide applicability to the specification of faunal standards for ecosystem restoration.