To pool or not to pool? Guidelines for pooling samples for use in surveillance testing of infectious diseases in aquatic animals

Samples from multiple animals may be pooled and tested to reduce costs of surveillance for infectious agents in aquatic animal populations. The primary advantage of pooling is increased population‐level coverage when prevalence is low (<10%) and the number of tests is fixed, because of increased likelihood of including target analyte from at least one infected animal in a tested pool. Important questions and a priori design considerations need to be addressed. Unfortunately, pooling recommendations in disease‐specific chapters of the 2018 OIE Aquatic Manual are incomplete and, except for amphibian chytrid fungus, are not supported by peer‐reviewed research. A systematic review identified only 12 peer‐reviewed aquatic diagnostic accuracy and surveillance studies using pooled samples. No clear patterns for pooling methods and characteristics were evident across reviewed studies, although most authors agreed there is a negative effect on detection. Therefore, our purpose was to review pooling procedures used in published aquatic infectious disease research, present evidence‐based guidelines, and provide simulated data examples for white spot syndrome virus in shrimp. A decision tree of pooling guidelines was developed for use by peer‐reviewed journals and research institutions for the design, statistical analysis and reporting of comparative accuracy studies of individual and pooled tests for surveillance purposes.     

Reporting standards for biofilter performance studies

The development of standardized rating and design procedures for biological filters will require that filter performance be evaluated and reported in a standardized manner. This article recommends draft reporting standards for biofilter performance studies. It is important that critical parameters are defined and reported in a standard manner, both in terms of definition, variable names, and units. Depending on the type and scale of an experiment, reporting of certain parameters will be either mandatory or optional. Basic principles of experimental design, statistical analysis, and randomization must be followed. Experimental protocols are recommended to ensure the accuracy of measured or computed parameters. The development of this reporting standard is being organized through the Standards and Reporting Committee of the Aquaculture Engineering Society (AES). It is anticipated that a revised version of these standards will be incorporated into the Guide to Authors for Aquacultural Engineering.     

Generic solutions for data‐limited fishery assessments are not so simple

The majority of the world's fisheries, by number, are data‐poor/limited, and there is a growing body of literature pertaining to approaches to estimate data‐limited stock status. There are at least two drivers for assessing the status of data‐limited fisheries. The first is to try to understand and report on the global or regional status of fisheries across many stocks. The second is to attempt to assess individual data‐limited stocks, for status reporting and/or guiding management decisions. These drivers have led to attempts to find simple, generic, low‐cost solutions, including the broad application of generically parameterised models, and the blanket application of a single, or limited number of possible, analytical approach(es). It is unclear that generic methods function as intended, especially when taken out of their original design context or used without care. If the intention is to resolve individual stock status for the purposes of management, there is concern with the indiscriminate application of a single method to a suite of stocks irrespective of the particular circumstances of each. We examine why caution needs to be exercised, and provide guidance on the appropriate application of data‐limited assessment methods (DLMs). We recommend: (a) obtaining better data, (b) using care in acknowledging and interpreting uncertainties in the results of DLMs, (c) embedding DLMs in harvest strategies that are robust to the higher levels of uncertainty in the output of DLMs by including precautionary management measures or buffers and (d) selecting and applying DLMs appropriate to specific species’ and fisheries’ data and context.     

Taxonomic versus functional diversity metrics: how do fish communities respond to anthropogenic stressors in reservoirs?

Biological indicators are frequently used to assess the effects of anthropogenic stressors on freshwater ecosystems. The structure of fish communities and their response to stressors have been commonly described by taxonomic richness, diversity and evenness. More recently, functional structure of communities has also been suggested to be a reliable indicator of disturbance. This article aimed at testing whether taxonomic and functional diversity metrics can provide comparable or complementary information on the response of fish communities to eutrophication and abundance of non‐native species in reservoirs. Comparison of the responses of taxonomic and functional diversities to biogeography, habitat and stressors was made in 112 French reservoirs. Widely observed effects of biogeographic and habitat variables on taxonomic and functional diversities were identified. Taxonomic and functional richness metrics notably increased with lake area and temperature respectively. Taxonomic diversity metrics did not respond to any stressor, while all functional diversity metrics were found to be impacted by non‐native species. Eutrophication was further found to decrease the impact of non‐native species on two functional diversity metrics: evenness and divergence. Our study therefore reveals that functional metrics are more sensitive than taxonomic metrics to anthropogenic stressors in the studied reservoirs. Still, the multiple linear regressions tested had overall low explanatory power. Further refinements will thus be needed to use this type of metrics in an impact assessment scheme.     

Developing a standard approach for assessing the hydromorphology of lakes in Europe

1. Methods for assessing the hydrology and morphology of lakes (‘hydromorphology’) are needed for reporting under national and international legislation, as well as to assist in lake management and restoration. Despite this, no consistent approaches have been developed around Europe for monitoring lake hydromorphology.
2. To address this need, representatives from 12 countries met at a series of workshops to develop two protocols for monitoring, published under the auspices of the European Committee for Standardization (CEN). The first standard (EN 16039) describes six categories for assessing lake hydromorphology: hydraulics, morphometry, bedforms/landforms and substrate, connectivity and continuity, and land cover. The second standard (EN 16870) sets out a scoring system for assessing the degree of modification of lake hydromorphology, which was designed, tested and refined using data from 127 lakes in seven European countries.
3. The CEN standards focus on four lake zones—riparian, shore, littoral, and open water—but recognize the importance of considering lakes within their wider catchment context. The field techniques described are based largely on Lake Habitat Survey but also rely on existing databases, maps and remote‐sensing data.
4. These standards are aimed at scientists, conservation bodies and environmental regulators, and are relevant not only for monitoring lakes under the Water Framework Directive, but also for contributing to programmes of lake conservation. For example, in the UK, parts of the CEN standards have been incorporated within the methods used for monitoring and reporting on the condition of Special Areas of Conservation (under the Habitats Directive) and Sites of Special Scientific Interest under national legislation.
5. It is hoped that this pan‐European approach will improve the ability to compare data across many countries, and ultimately ensure that the results of monitoring are translated into measures for improving the hydromorphological condition of lakes and the biological communities they contain .

     

Performance of regional fisheries management organizations: ecosystem‐based governance of bycatch and discards

A performance assessment was conducted of regional fisheries management organizations’ (RFMOs’) bycatch governance, one element of an ecosystem approach to fisheries management. Obtaining a mean score of 25%, with a 64% CV, collectively the RFMOs have large governance deficits. Individually, there has been mixed progress, with some RFMOs having made substantial progress for some governance elements. There has been nominal progress in gradually transitioning to ecosystem‐based fisheries management: controls largely do not account for broad or multispecies effects of fishing, and cross‐sectoral marine spatial planning is limited. Regional observers collect half of minimum information needed to assess the efficacy of bycatch measures. Over two‐thirds of RFMO‐managed fisheries lack regional observer coverage. International exchange of observers occurs in one‐third of programmes. There is no open access to research‐grade regional observer data. Ecological risk assessments focus on effects of bycatch removals on vulnerable species groups and effects of fishing on vulnerable benthic marine ecosystems. RFMOs largely do not assess or manage cryptic, generally undetectable sources of fishing mortality. Binding measures address about one‐third of bycatch problems. Eighty per cent of measures lack explicit performance standards against which to assess efficacy. Measures are piecemeal, developed without considering potential conflicts across vulnerable groups. RFMOs employ 60% of surveillance methods required to assess compliance. A lack of transparency and limited reporting of inspection effort, identified infractions, enforcement actions and outcomes further limits the ability to assess compliance. Augmented harmonization could help to fill identified deficits.     

Responsiveness of fish mass–abundance relationships and trophic metrics to flood disturbance,stream size,land cover and predator taxa presence in headwater streams

Characterisation of food webs, by summarising energy transfer and trophic relationships, allows more functional measurement of ecosystems and may reveal threats (e.g., land‐cover change) in sensitive environments that are not obvious from conventional biomonitoring. However, typical methods used to achieve this are time‐consuming and expensive. Therefore, we tested the usefulness of fish‐focused food‐web proxies as functional measures, specifically mass–abundance relationships of fish assemblages and stable isotope (SI)‐derived metrics in headwater stream reaches. These metrics have been trialled before for similar use in other settings, but have yielded varying results, and have not been employed in tandem in temperate freshwaters. Sampling reaches (N = 46) were spread across a variety of streams, and the effects of habitat predictors at multiple scales on metrics were assessed using model selection. We found that habitat size positively correlated with food‐chain lengths in streams, possibly because of increased abundance of fish at multiple trophic levels in habitats with more space. Additionally, flood disturbance was negatively associated with fish mass–abundance and carbon range, likely due to the harshness of flood‐prone streams. Riparian land‐cover variables were correlated with multiple metrics, indicating the importance of terrestrial–aquatic linkages. Additionally, variations in all metrics were influenced by the presence of native, predatory longfin eels. Overall, we conclude that mass–abundance relationships and SI‐derived metrics are sensitive to drivers of trophic organisation and likely reflect processes occurring at multiple spatial scales in freshwaters. Thus, these metrics could be an insightful monitoring tool for managers because they reflect functional measures of aquatic ecosystems.     

Development of fish-based assessment method for the ecological status of rivers in the Baltic region

Abstract  A fish-based assessment method for determining the ecological status of rivers in the southern part of the Baltic region was developed, classifying fish assemblages of near natural sites, and testing the response of a wide range of fish metrics to human pressure. However, the potential for developing a statistically robust method was limited because of insufficient data and the impact of fishery exploitation. A combination of expert judgement, historical data and spatially based methods were needed to establish reference conditions and classification criteria for fish metrics. The final list of metrics (6–9 metrics per six different river types) comprises five ecological guilds (feeding, overall tolerance, habitat, migration and spawning strategy) and three sentinel (dominant) species ( Salmo trutta L., Cottus gobio L. and Alburnoides bipunctatus [Bloch]). The method tends to underscore the ecological status of specific river types because the selected metrics probably do not account for all possible variability in fish community response to degradation, as some community-specific characteristics were poorly or not represented. Exploitation pressure might have considerable effects on functionality of fish metrics. Results suggest that the method needs modification to account for these limitations.     

Design and validation of a RT‐qPCR procedure for diagnosis and quantification of most types of infectious pancreatic necrosis virus using a single pair of degenerated primers

Infectious pancreatic necrosis virus (IPNV) is an important virus which affects the salmonid aquaculture industry worldwide; therefore, it is important to develop rapid and reliable methods of diagnosis to detect the disease at early stages. Nowadays, RT‐qPCR is replacing other methods because it provides additional information on the viral load, which is important to have a better understanding of the virus replication level and of the stage of the infection and its risk level. The main problem stems from the high diversity of this virus, which can compromise the reliability of the diagnosis. In this study, we have designed an RT‐qPCR procedure for diagnosis and quantification of IPNV based on a single pair of primers targeted to segment B. The procedure has been validated, in vitro and in vivo, testing two different types of standards against seven reference strains and 23 field isolates from different types. The procedure is reliable for the detection of any type, with a detection limit of 31 TCID₅₀ mL^?1, 50 pfu mL^?1 or 66 RNA copies mL^?1, depending on the standard. All the standard curves showed high reliability (R² > 0.95). The results support the high reliability of this new procedure for the diagnosis and quantification of IPNV.     

Development and evaluation of a high‐throughput single nucleotide polymorphism multiplex assay for assigning pedigrees in common carp

Accurate pedigree information is critical when managing animal breeding programmes and ensure the highest rate of genetic gain. The abundance of available genomic data and the development of high‐throughput genotyping platforms have facilitated the use of single nucleotide polymorphisms (SNPs) as the best DNA markers for genomic selection studies. Furthermore, the superior qualities of SNPs compared with those of microsatellite markers allow standardization between laboratories, which is crucial for developing an international set of markers for use in traceability studies. The objective of this study was to develop a high‐throughput SNP array to assign common carp pedigrees accurately. A 48‐SNP array was developed based on the Fluidigm genotyping platform, and a phylogenetic analysis was performed to distinguish different pedigrees. A likelihood‐based approach was used to infer parental pairs, and the pair with the highest LOD score (log of the ratio of the likelihood given parentage to likelihood given non‐parentage) was assigned. The SNP genotypes of the offspring and candidate parents tested were collected, and 94% of the offspring were assigned to the most‐likely parent pair, which was consistent with the actual pedigree records. Using this SNP assay will allow implementation of offspring testing at large commercial farms where improved accuracy of pedigree assignments and genetic evaluations will increase genetic gains in the common carp aquaculture industry.     

Selectivity metrics for fisheries management and advice

Fisheries management typically aims at controlling exploitation rate (e.g., Fbar) to ensure sustainable levels of stock size in accordance with established reference points (e.g., F_MSY, B_MSY). Population selectivity (“selectivity” hereafter), that is the distribution of fishing mortality over the different demographic components of an exploited fish stock, is also important because it affects both Maximum Sustainable Yield (MSY) and F_MSY, as well as stock resilience to overfishing. The development of an appropriate metric could make selectivity operational as an additional lever for fisheries managers to achieve desirable outcomes. Additionally, such a selectivity metric could inform managers on the uptake by fleets and effects on stocks of various technical measures. Here, we introduce three criteria for selectivity metrics: (a) sensitivity to selectivity changes, (b) robustness to recruitment variability and (c) robustness to changes in Fbar. Subsequently, we test a range of different selectivity metrics against these three criteria to identify the optimal metric. First, we simulate changes in selectivity, recruitment and Fbar on a virtual fish stock to study the metrics under controlled conditions. We then apply two shortlisted selectivity metrics to six European fish stocks with a known history of technical measures to explore the metrics’ response in real‐world situations. This process identified the ratio of F of the first recruited age–class to Fbar (Frec/Fbar) as an informative selectivity metric for fisheries management and advice.     

Fathead minnow reproduction: Implications for commercial culture

The fathead minnow, Pimephales promelas, is widely used as a bait, forage, and research fish in the United States. A hardy and fecund fish, this species has many attributes that are excellent for culture. Unfortunately, despite the widespread use of fathead minnows in toxicity testing and thousands of resulting publications, relatively little aquaculture‐related research has been conducted in support of commercial production. On the surface, current commercial fathead minnow production practices appear much the same as those of a decade ago. However, producers continue to refine culture methods, balancing broodfish stocking rates, spawning substrate quantity, and feeding rates in an attempt to meet both losses to predators and market demand. This review examines relevant reproduction‐related studies in the fields of ecology, behavior, toxicology, and aquaculture with the goal of advancing fathead minnow culture. In fathead minnow production, relative to the culture of food fish species, reproduction is vital, more so than rapid growth or a low feed conversion ratio. Fish numbers may exceed 1 million fish/ha, while feeding rates are relatively low and in feeder fish production, growth is deliberately restrained in order to maintain fish within market sizes year‐round. Underappreciated factors identified as affecting reproduction and with implications for commercial culture include: (a) poor egg adhesion to commonly used spawning substrates, (b) egg and fry cannibalism at high fish densities, and (c) the relatively short breeding period of individual males. Results highlight the importance of selecting an appropriate broodfish stocking rate based on fish size, anticipated pond fertility, and feeding program. New methods to improve reproductive performance will likely increase costs and will need to be accompanied by thorough economic analyses.     

Towards ecosystem-based fisheries management

Performance measures and reference points for the management of target species are now widely used in the fisheries of the developed world. To move us closer to an ecosystem‐based fisheries management framework, we look at the prospects for expanding current single‐species approaches for target species, by considering nontarget species. We also examine the development of performance measures and reference points for emergent ecosystem‐level properties. We conclude that the expansion of single‐species reference points to take account of the nontarget species of a fishery is tractable and desirable. In contrast, the use of performance measures for a single or a small selection of ecosystem metrics is not possible at present, owing to the absence of a clear understanding of their dynamics and a lack of underlying theory to explain their behaviour. However, recent methods that aggregate a wide range of metrics to provide an overall picture of the ecosystem status show promise and have a particular attraction because they have the potential to provide a framework for establishing a dialogue on management issues between all interested parties.     

Allelic segregation of sex‐linked microsatellite markers in Nile tilapia (Oreochromis niloticus) and validation of inheritance in YY population

Stocking of all‐male fingerling produced by direct administration of male hormone 17‐α‐methyltestosterone is the most preferred method for present‐day aquaculture of the Nile tilapia Oreochromis niloticus. However, due to the growing concern of negative impact of steroid hormone in food fish, production of ‘genetically male’ tilapia, which depends on the concrete and thorough understanding of sex determination, has long been a scientific curiosity. The objective of the present study was to identify reliable sex‐linked markers and to evaluate the applicability of those markers in terms of monosex production approach. ‘XY’ neofemales were produced by using synthetic oestrogen and identified through selective breeding and progeny testing. Three females with progeny not deviating from 3:1 sex ratio (male:female) were designated as ‘XY’ neofemales and were used subsequently to produce putative YY progeny. Among the fifteen microsatellite markers tested, marker ARO172 was most informative in differentiating male and female genotypes. Twenty‐seven F₂ fish from three families were identified as putative YY males based on marker genotyping, and four of them were crossed to produce F₃ to validate marker association by progeny testing. The YY males produced 86%–100% male progeny indicating ARO172 a unique sex‐linked marker applicable in marker‐assisted selection.     

Fish welfare: a challenge to the feelings-based approach, with implications for recreational fishing

Fish welfare issues are increasingly appearing on social and political agendas and have recently gained prominence in fisheries literature. By focusing on examples from recreational fishing, this paper challenges some of the previous accounts of fish welfare. Issues of concern encompass: (1) the feelings‐based approach to fish welfare; (2) the artificial divide between human beings and nature; and (3) ways in which stakeholders can address fish welfare issues. The different approaches to characterizing the interaction of humans with animals are animal welfare, animal liberation and animal rights. We show that the suffering‐centred approaches to fish welfare and the extension of the moral domain to fish – characteristic of the concepts of animal liberation and animal rights – are not the cornerstone of animal welfare. This, however, does not question the need of fisheries stakeholders to consider the well‐being of fish when interacting with them. There are many ways in which recreational fishing stakeholders can modify standard practices to improve the welfare of fish, without questioning fishing as an activity per se. Examples are choice of gear and handling techniques. Previous accounts have failed to include discussions of the many efforts – voluntary or mandated – pursued by fisheries stakeholders to reduce fish stress, injury and mortality. Progress towards addressing fish welfare issues will be enhanced by avoiding the viewing of humans as ‘non‐natural’ disturbance to fishes and keeping three types of crucial question in separate compartments. The three questions cover the symptoms of good and poor welfare, the conscious experience of suffering, and the ethical attitudes towards animals. Fish biologists should focus on the first question – objective measurement of biochemical, physiological and behavioural indicators – to evaluate whether human interactions with fish impair the latters’ health or prevent them from receiving what they need, if held in captivity.     

A synthetic control approach to estimate the effect of total allowable catches in the high seas

Total allowable catch restrictions (hereafter referred to as catch quotas) play an important role in maintaining healthy fish stocks. While studies have identified a positive relationship between catch quota implementation and improved stock status, these methods are subject to selection bias as catch quotas are typically applied to stocks that are depleted. We address this challenge using the synthetic control method, which estimates the causal effect of catch quotas on fishing mortality and biomass by predicting a synthetic counterfactual outcome. We focus on high seas stocks (tunas, billfishes, and sharks) managed by tuna Regional Fisheries Management Organizations (tRFMOs), first providing an overview of stock status and current management measures in place. We find that implementation of catch quotas by tRFMOs has more than doubled over the past decade. Second, we predict the hypothetical fishing mortality and biomass trajectory for seven high seas quota-managed stocks in absence of a catch quota. These “synthetic non-quota stocks” are predicted using a weighted selection of high seas non-quota stocks. Credibility of the synthetic non-quota stocks is evaluated through diagnostic checks, and robustness tests assess sensitivity to study design. Five credible fishing mortality synthetic controls are predicted: three add support to the hypothesis that catch quotas successfully reduce fishing mortality, while two find that catch quotas increase fishing mortality. While our analysis is limited in scope, given that all seven quota-managed stocks are managed under a single tRFMO, we highlight the potential for the synthetic control method in fisheries management evaluation.     

水产动物育种值估计方法及其应用的研究进展

育种值是选种和配种计划制定的基础,育种值估计是水产动物选择育种的重要内容之一,育种值估计的准确性直接影响着育种项目的遗传进展和选择效果。本文综述了3种育种值估计方法,选择指数、最佳线性无偏预测BLUP法和标记辅助BLUP方法的原理、优缺点及其在水产动物育种中的应用进展。众多研究表明,基于系谱结构和表型信息的BLUP方法将成为水产动物育种中一种快速有效的育种值估计方法。     

Testing of a pond‐side molecular diagnostic tool for the detection of white spot syndrome virus in shrimp aquaculture

White spot disease in penaeid shrimp is caused by the white spot syndrome virus (WSSV). It is the most economically important disease of farmed warm‐water shrimp, causing extensive economic losses estimated from $8 to $15 billion since its emergence in the 1990s. Early diagnosis of disease is critical in the management of outbreaks and to avoid crop losses. Diagnosis of white spot disease is generally carried out in centralized laboratory settings using molecular biology approaches. However, this mode of testing can be expensive and time consuming, requiring laboratory equipment, highly trained laboratory personnel, dedicated laboratory space, and long‐distance transportation of samples from field to lab. In‐field diagnostics are gaining credence as tools for rapid and early animal disease detection, allowing diagnosticians and farmers to potentially manage disease outbreaks from the pond side. In the present study, we describe the development and application of a new in‐field point‐of‐need diagnostic test and platform for the diagnosis of WSSV in remote settings (shrimp farms). We report its performance in laboratory and field settings and compare it with current gold‐standard diagnostic approaches. We discuss the potential benefits (and barriers to uptake) of applying such testing in the global shrimp farming sector.