Molecular genetics and the management and conservation of marine organisms

Biochemical and molecular species identification techniques have a broad range of applications in the management and conservation of marine organisms. While species boundaries are not always clearly defined, phylogeneticists utilise autapomorphic characters to distinguish phylogenetic species. Genetic markers discriminate between marine taxa when traditional morphological distinctions are unclear. The applications of these techniques can be divided into four general categories. Firstly, compliance enforcement, which often depends on genetic identification techniques to enable officials to identify the species to which regulations pertain. Secondly, quality control applications, to allow for the testing of marine products to guard against fraudulent substitution with less valuable species, which is particularly pertinent since processing often obliterates identifiable features. Thirdly, a variety of applications to ecological and life-history studies and conservation management are reported. Here, the genetic identification techniques of species from cryptic life-cycle stages or of morphologically indistinct species are an indispensable tool for marine scientists, conservators and managers. Lastly, the application of genetic techniques for sourcing population origin is briefly discussed. The biochemical and molecular techniques applied to species identification all exploit phenotypic or genotypic polymorphisms that are sampled using either tertiary level protein based methods or primary level DNA based methods. In this review, examples of the applications along with the total protein, allozyme, serological, PCR and other DNA based methodologies are briefly described and some generalities with regard to their use are presented.     

Fish, Fact and Fantasy: a Long View

This paper suggests ways forward from the widely perceived present failures of fishery assessment and management. A history of fishery yield modelling is presented from the carefree days of the 1950s to the depressing series of stock collapses and depletions of the 1980s. Underlying this gruesome story has been the failure of management by quotas to arrest overcapacity in fishing power, the lack of robust and informative reference points and the inadequacy of methods dealing with some multispecies fisheries. The paper refines the use of the concept of Fext, defined as the minimum value of F in a self-regenerating yield model that leads to eventual extinction in a family of yield curves generated with a range of stock recruitment curves. Model reconstructions for North Sea cod and Icelandic herring make evident calamitous losses in catches forgone as result of the failure of rational management. An optimistic agenda that may achieve more effective fishery management in the future is presented. In some ways, we may have been trying to be too clever. A simple management system based on careful monitoring of fishing effort, biological targets such as F95, and exploitation of a diversity of fish resources may suffice to avert further disaster and hedge against uncertainty.     

An unlikely partnership: fishers’ participation in a small-scale fishery data collection program in the Timor Sea

Traditional fisheries stock assessment methods and fishery independent surveys are costly and time consuming exercises. However fishers trained in data collection and utilising other skills can reduce costs and improve fishery assessments and management. A data collection program was conducted by Australian and Indonesian scientists with small-scale Indonesian sea cucumber fishers to evaluate the approach and then capture its benefits. The data fishers recorded allowed for the first stock assessment of this trans-boundary fishery during its centuries-long existence at Scott Reef in north-western Australia. The program also included interviews with fishers capturing the social, economic, and demographic aspects of the fishery. Economic inputs to fishing were complemented by fishery revenue data voluntarily submitted when fishers returned to port and sold their catch. Catch data recorded by fishers demonstrated much higher abundances than estimates obtained using standard visual transect methods and accurately reflected the true catch composition. However, they also showed extreme rates of exploitation. Interviews revealed social and economic factors that would be important considerations if management interventions were made. The program’s approach and the time scientists spent on the fishers’ vessels were key ingredients to fishers’ participation and the utility of the results. Despite the program’s achievements the information generated has not led to improved management or had any direct benefits for the participants. Sustaining the program in the longer term requires that its value is better captured.     

Informatic tools for proteome profiling

In recent years, the practice of proteomics research has experienced a dramatic shift within the pharmaceutical and biotechnology industry with the widespread implementation of novel applications. The areas of interest extend all the way from discovery of novel drug, vaccine, and diagnostic targets, characterization of protein-based products, toxicology, and identification of surrogate markers of activity in clinical research, to the ability to provide information on the mechanisms of drug action. The power of two-dimensional gel electrophoresis as well as advances in mass spectrometric techniques combined with sequence database correlation have enabled speed and accuracy in identification of proteins in complex mixtures. This article surveys currently available software and informatic tools related to these methods for proteome profiling. The broad acceptance of these technologies, however, has not been accompanied by significant advances in the informatics and software tools necessary to support the analysis and management of the massive amounts of data generated in the process. In this context, this article also discusses the importance of relational databases for protein identification data management.     

An analysis of genetic stock identification on a small geographical scale using microsatellite markers,and its application in the management of a mixed‐stock fishery for Atlantic salmon Salmo salar in Ireland

A genetic stock identification (GSI) study was undertaken in a fishery for Atlantic salmon Salmo salar to determine the effects of restrictive fishery management measures on the stock composition of the fishery, and if accurate and precise stock composition estimates could be achieved on the small geographical scale where this fishery operates, using a suite of only seven microsatellite loci. The stock composition of the Foyle fishery was shown to comprise almost exclusively of Foyle origin fish in the 3 years after restrictive measures were introduced in 2007, compared to 85% the year before. This showed that the restrictive measures resulted in the Foyle fishery being transformed from a mixed‐stock fishery to an almost exclusively single‐stock fishery, and showed how GSI studies can guide and evaluate management decisions to successfully manage these fisheries. Highly accurate and precise stock composition estimates were achieved in this study, using both cBAYES and ONCOR genetic software packages. This suggests accurate and precise stock composition is possible even on small geographical scales.     

Comparison of SNPs and microsatellites for fine-scale application of genetic stock identification of Chinook salmon in the Columbia River Basin

Genetic stock identification (GSI) is an important tool in fisheries management. Microsatellites (μSATs) have been the dominant genetic marker for GSI; however, increasing availability and numerous advantages of single-nucleotide polymorphism (SNP) markers make them an appealing alternative. We tested performance of 13 μSAT vs. 92 SNP loci in a fine-scale application of GSI, using a new baseline for Chinook salmon consisting of 49 collections (n = 4014) distributed across the Columbia River Basin. In GSI, baseline genotypes for both marker sets were used independently to analyse a real fishery mixture (n = 2731) representing the total run of Chinook salmon passing Bonneville Dam in the Columbia River. Marker sets were evaluated using three criteria: (i) ability to differentiate reporting groups, (ii) proportion of correct assignment in mixture simulation tests and baseline leave-one-out analyses and (iii) individual assignment and confidence intervals around estimated stock proportions of a real fishery mixture. The μSATs outperformed the SNPs in resolving fine-scale relationships, but all 105 markers combined provided greatest power for GSI. SNPs were ranked by relative information content based on both an iterative procedure that optimized correct assignment to the baseline and ranking by minor allele frequency. For both methods, we identified a subset of the top 50 ranked loci, which were similar in assignment accuracy, and both reached maximum available power of the total 92 SNP loci (correct assignment = 73%). Our estimates indicate that between 100 and 200 highly informative SNP loci are required to meet management standards (correct assignment > 90%) for resolving stocks in finer-scale GSI applications.     

Using a tier classification system to evaluate the quality of bycatch estimates from fisheries

Bycatch continues to be a challenge to sustainable fisheries management (The term “bycatch” in this paper covers discards and does not include retained incidental catch). Bycatch estimates can inform stock status determinations by improving understanding of fishing mortality, and help managers monitor the effectiveness of regulations. Assessments of the quality of bycatch estimation programs and procedures are necessary to evaluate the precision and limitations of their results over time. NOAA Fisheries experts used a “Tier Classification System” (TCS) to compare the quality of fish bycatch data and estimation methods for U.S. commercial fisheries in 2005 and 2015. The TCS included criteria related to data adequacy and analytical approaches. A comparison of U.S. fishery tier scores demonstrated that most fisheries were classified into higher tiers in 2015 compared to 2005 due to factors including improved sampling design. In addition, this comparison identified region-specific trends (e.g., mostly improvements occurred for Alaska fisheries with more mixed results for Greater Atlantic fisheries). The improvements in bycatch data quality and estimation methods in the United States are a result of financial investments in observer programs by NOAA Fisheries and industry partners, as well as effective conservation measures implemented by regional fishery management councils and NOAA Fisheries. The TCS was also used to assess bycatch data and estimation methods in all of Australia’s fishery jurisdictions for the decade 2010–19, illustrating the international applicability of the method. Overall, Australian state fisheries scored lower than federally managed fisheries in both the United States and Australia, reflecting the fact that the latter fisheries tend to be larger (and more valuable) than those in state jurisdictions, with a larger investment in observer programs. A comparison of tier scores and estimates of discards by fishery may provide a useful input for decision-making processes regarding allocation of resources to improve bycatch monitoring.

     

Recruitment prediction for Pacific herring (Clupea pallasi) on the west coast of Vancouver Island, Canada

The accurate prediction of recruitment to the fishery is a very important tool within the management structure of any fish stock being exploited. In the case of the Pacific herring, Clupea pallasi, fishery in Canada, a forecast of the abundance of each herring stock is particularly important for formulating an annual catch quota. The sustainable management of the fishery and the resource is based in part on accurate recruitment forecasting because Pacific herring are short-lived and so the recruitment contributes a significant part of the total spawning run targeted by the fishery each year. Several factors are believed be important in determining the success of recruitment besides spawners biomass. Since herrings are “r” strategists, conditions related to the egg, the planktonic, or even the juvenile stage might determine the future level of recruitment. Recently a formula that defines conditions for a semi-quantitative level of recruitment forecast was elaborated using genetic algorithms and current study attempts to improve on this model. Using salinity in two quarterly periods during the planktonic and pre-recruit stages, temperature and spawning biomass for the west coast of Vancouver Island stock, classification rules that define recruitment in 3 different levels (low, medium and high) were developed with a genetic algorithm, setting low and high boundaries for each condition. A 75% success in classifying recruitment was obtained. The model was shown to be particularly effective at predicting when the recruitment would be low, which could be important from the perspective of the Precautionary Approach and the sustainable management of this stock.     

Discovery and characterization of single nucleotide polymorphisms in coho salmon,Oncorhynchus kisutch

Molecular population genetic analyses have become an integral part of ecological investigation and population monitoring for conservation and management. Microsatellites have been the molecular marker of choice for such applications over the last several decades, but single nucleotide polymorphism (SNP) markers are rapidly expanding beyond model organisms. Coho salmon (Oncorhynchus kisutch) is native to the north Pacific Ocean and its tributaries, where it is the focus of intensive fishery and conservation activities. As it is an anadromous species, coho salmon typically migrate across multiple jurisdictional boundaries, complicating management and requiring shared data collection methods. Here, we describe the discovery and validation of a suite of novel SNPs and associated genotyping assays which can be used in the genetic analyses of this species. These assays include 91 that are polymorphic in the species and one that discriminates it from a sister species, Chinook salmon. We demonstrate the utility of these SNPs for population assignment and phylogeographic analyses, and map them against the draft trout genome. The markers constitute a large majority of all SNP markers described for coho salmon and will enable both population‐ and pedigree‐based analyses across the southern part of the species native range.     

DNA in Action: Rapid Application of DNA Variation to Sockeye Salmon Fisheries Management

Commitment to conservation-based management of exploited fish species imposes unprecedented requirements for adaptive, real-time management of biologically and socially complex mixed-stock fisheries such as those conducted for Pacific salmon. Stock identification is a key component of the management process, with population-specific timing and abundance information often incorporated into management decisions. By using both microsatellite and major histocompatibility complex genetic variation, we achieved highly accurate estimates of stock composition for Fraser River sockeye salmon. Over a 2-month period in 2002, we analyzed 9300 returning Fraser River sockeye salmon sampled in mixed-stock fisheries, and provided stock composition estimates to fishery managers within 9–30 h of sample delivery. Stock-specific exploitation targets governed by conservation concerns were achieved in this fishery.     

On the optimal path in the dynamic pool model for a fishery

Ecosystem-based fishery management (EBFM) is a new direction for fishery management, essentially reversing the order of management priorities to start with the ecosystem rather than the target species. This concept of management is a direct extension of the concept of a holistic approach incorporating interspecific interactions and physical environmental influences. However, because of the limited understanding of the complexity of marine ecosystems, few fisheries are actually managed on a multispecies basis. Even now, in order to specify a practical fishing policy we need a single-species model and utilize it by partially taking account of the effects of other factors mentioned above on the target species biomass. In fact, it is contended that in systems with moderate amounts of data, EBFM could be characterized by effective single-species management with the addition of precautionary set-asides for unknown ecosystem components. Hence, it is still necessary to examine a single-species model so as to clarify the extent of its applicability. The model investigated in this paper is what is called the dynamic pool model, which was proposed by C.W. Clark in the mid-1970s as a dynamic optimization of the classic Beverton and Holt static model for a fishery, in an attempt to make the process of growth and aging inherent in each of the creature resources reflect directly into the economic process. This dynamic model has been applied to a wide variety of commercial fish species. However, the applications have been largely confined to computer simulations using the discrete-time stand-by of the original Clark continuous-time model. This situation is caused mainly by the complexity of the mathematical structure of the Clark model. In this paper, we first specify the material related to the complexity. Subsequently, we provide a rigorous proof for the long-standing conjecture due to Clark concerning the optimal path or harvesting schedule. In addition, two derivative cases are examined: one is the case in which a year-class of fish leaves a given fishing sea area permanently before its natural biomass peaks, the other is the case in which the escapement of a year-class is required to be more than a given minimum level.     

The phylogeography of dusky dolphins (Lagenorhynchus obscurus): a critical examination of network methods and rooting procedures

We investigated the phylogeography and evolutionary history of dusky dolphins (Lagenorhynchus obscurus) using DNA sequences of the full mitochondrial cytochrome b gene in 124 individuals from the putative stocks off Peru, Argentina and Southwest Africa. While genetic differentiation within oceans is surprisingly low, there is no evidence for recent female gene flow between Atlantic and Pacific waters. Highest genetic variability in terms of sequence divergence and number of haplotypes is found in the Atlantic. Our analyses also indicate that the eastern South Pacific dusky dolphins stock should be considered a separate management unit. Given the high level of mortality experienced by the Peruvian dusky dolphin in local fishery activities, these findings have important implications for an objective management of the species. Furthermore, we analysed our mitochondrial sequence data with several widely used network estimation and rooting methods. The resulting intraspecific gene genealogies and rooting inferences exhibited substantial differences, underlying the limitations of some algorithms. Given that scientific hypotheses and management decisions depend strongly on inferred tree or network topologies, there is a clear need for a systematic comparative analysis of available methods. Finally, the present study indicates that (i) the dusky and the Pacific white-sided dolphins are sister species and (ii) not only the Westwind Drift hypothesis but also other models of dispersion are compatible with the current geographical distribution of dusky dolphins.     

Genetic diversity of upper Lake Constance whitefish Coregonus spp. under the influence of fisheries: a DNA study based on archived scale samples from 1932, 1975 and 2006

This investigation examined changes in the genetic diversity of pelagic upper Lake Constance (ULC) whitefish Coregonus wartmanni population before and after the alteration of fishery methods and management from 1932 to 2006. The study spans a period of pronounced changes in trophic status of the lake and transitions from traditional relatively unselective pelagic seine (Klusgarn) fishing to highly size‐selective nylon gillnet techniques. In addition, supportive breeding and stocking became most popular during the phase of eutrophication in the 1970s. The main hypothesis is that size‐selective fisheries and breeding lead to an overall decrease in genetic variability over time. A total of 215 archived C. wartmanni scale samples from 1932, 1975 and 2006 were analysed by genotyping 11 microsatellite loci. A comparison of population genetic parameters, including allelic richness, observed and expected heterozygosities, and estimates of effective population sizes, suggests that the genetic diversity of C. wartmanni population has not decreased. The appearance of new alleles in the gene pool in 1975 and 2006 may be indicative of admixture with other forms in the lake or with stocked allochthonous forms. Overall, the fisheries management practice in ULC, including the effects of size‐selective fisheries, supportive breeding and stocking, have not significantly altered the genetic diversity of Coregonus spp. over an 80 year period.     

Completely monodisperse, highly repetitive proteins for bioconjugate capillary electrophoresis: development and characterization

Protein-based polymers are increasingly being used in biomaterial applications because of their ease of customization and potential monodispersity. These advantages make protein polymers excellent candidates for bioanalytical applications. Here we describe improved methods for producing drag-tags for free-solution conjugate electrophoresis (FSCE). FSCE utilizes a pure, monodisperse recombinant protein, tethered end-on to a ssDNA molecule, to enable DNA size separation in aqueous buffer. FSCE also provides a highly sensitive method to evaluate the polydispersity of a protein drag-tag and thus its suitability for bioanalytical uses. This method is able to detect slight differences in drag-tag charge or mass. We have devised an improved cloning, expression, and purification strategy that enables us to generate, for the first time, a truly monodisperse 20 kDa protein polymer and a nearly monodisperse 38 kDa protein. These newly produced proteins can be used as drag-tags to enable longer read DNA sequencing by free-solution microchannel electrophoresis.     

三峡水库生态渔业发展策略与关键技术研究分析

针对三峡水库蓄水后水体资源丰富、水生态系统发育尚不完善、支流库湾藻类水华问题较严重、鱼类群落结构有待调控、水生生物资源未有效利用和转化的现状, 阐述了三峡水库生态渔业作为生态系统保护途径和绿色产业的必要性与重要性, 提出了三峡水库生态渔业发展的总体目标与基本原则, 认为三峡水库发展生态渔业应以生态安全保障和水质养护为首要任务, 严格控制外来物种的引种移植, 以土著鱼类自然繁殖保护和捕捞管理为主, 动态调控放流增殖的鱼类种类和数量为辅, 建立以鱼类群落合理配置和食物网结构优化为手段的水库生态系统调控技术体系, 促进高效的物质循环和能量流动, 实现环境保护和渔业增效的双赢。作者围绕渔业放流增殖、野生鱼类资源保护、捕捞管理、局部库区渔业调控、渔业生物控藻、社区渔业协调管理、生态渔业总体规划等方面, 分析了现阶段三峡水库生态渔业的重点研究任务与关键技术,同时建议加强相关生态学理论与方法研究、技术示范和成果应用, 为三峡水库以渔养水、渔-水和谐的综合管理提供决策依据。       

Genetic isolation between coastal and fishery‐impacted,offshore bottlenose dolphin (Tursiops spp.) populations

The identification of species and population boundaries is important in both evolutionary and conservation biology. In recent years, new population genetic and computational methods for estimating population parameters and testing hypotheses in a quantitative manner have emerged. Using a Bayesian framework and a quantitative model‐testing approach, we evaluated the species status and genetic connectedness of bottlenose dolphin (Tursiops spp.) populations off remote northwestern Australia, with a focus on pelagic ‘offshore’ dolphins subject to incidental capture in a trawl fishery. We analysed 71 dolphin samples from three sites beyond the 50 m depth contour (the inshore boundary of the fishery) and up to 170 km offshore, including incidentally caught and free‐ranging individuals associating with trawl vessels, and 273 dolphins sampled at 12 coastal sites inshore of the 50 m depth contour and within 10 km of the coast. Results from 19 nuclear microsatellite markers showed significant population structure between dolphins from within the fishery and coastal sites, but also among dolphins from coastal sites, identifying three coastal populations. Moreover, we found no current or historic gene flow into the offshore population in the region of the fishery, indicating a complete lack of recruitment from coastal sites. Mitochondrial DNA corroborated our findings of genetic isolation between dolphins from the offshore population and coastal sites. Most offshore individuals formed a monophyletic clade with common bottlenose dolphins (T. truncatus), while all 273 individuals sampled coastally formed a well‐supported clade of Indo‐Pacific bottlenose dolphins (T. aduncus). By including a quantitative modelling approach, our study explicitly took evolutionary processes into account for informing the conservation and management of protected species. As such, it may serve as a template for other, similarly inaccessible study populations.     

Contrasting patterns of population connectivity between regions in a commercially important mollusc Haliotis rubra: integrating population genetics,genomics and marine LiDAR data

Estimating contemporary genetic structure and population connectivity in marine species is challenging, often compromised by genetic markers that lack adequate sensitivity, and unstructured sampling regimes. We show how these limitations can be overcome via the integration of modern genotyping methods and sampling designs guided by LiDAR and SONAR data sets. Here we explore patterns of gene flow and local genetic structure in a commercially harvested abalone species (Haliotis rubra) from southeastern Australia, where the viability of fishing stocks is believed to be dictated by recruitment from local sources. Using a panel of microsatellite and genomewide SNP markers, we compare allele frequencies across a replicated hierarchical sampling area guided by bathymetric LiDAR imagery. Results indicate high levels of gene flow and no significant genetic structure within or between benthic reef habitats across 1400 km of coastline. These findings differ to those reported for other regions of the fishery indicating that larval supply is likely to be spatially variable, with implications for management and long‐term recovery from stock depletion. The study highlights the utility of suitably designed genetic markers and spatially informed sampling strategies for gaining insights into recruitment patterns in benthic marine species, assisting in conservation planning and sustainable management of fisheries.     

Quantitative proteomic analyses of crop seedlings subjected to stress conditions; a commentary

Quantitative proteomics is one of the analytical approaches used to clarify crop responses to stress conditions. Recent remarkable advances in proteomics technologies allow for the identification of a wider range of proteins than was previously possible. Current proteomic methods fall into roughly two categories: gel-based quantification methods, including conventional two-dimensional gel electrophoresis and two-dimensional fluorescence difference gel electrophoresis, and MS-based quantification methods consists of label-based and label-free protein quantification approaches. Although MS-based quantification methods have become mainstream in recent years, gel-based quantification methods are still useful for proteomic analyses. Previous studies examining crop responses to stress conditions reveal that each method has both advantages and disadvantages in regard to protein quantification in comparative proteomic analyses. Furthermore, one proteomics approach cannot be fully substituted by another technique. In this review, we discuss and highlight the basis and applications of quantitative proteomic analysis approaches in crop seedlings in response to flooding and osmotic stress as two environmental stresses.     

Fishery Induces Sperm Depletion and Reduction in Male Reproductive Potential for Crab Species under Male-Biased Harvest Strategy

Sperm depletion in males can occur when polygynous species are intensively exploited under a male-biased management strategy. In fisheries involving crabs species, the effects of this type of management on the reproductive potential is far from being understood. This study tests whether male-biased management of the principal Chilean crab fishery is able to affect the potential capacity of Metacarcinus edwardsii males to transfer sperm to females. Five localities in southern Chile, recording contrasting crab fishery landing, were selected to assess the potential of sperm depletion triggered by fishery. Seasonally, male crabs from each locality were obtained. Dry weight and histological condition of vasa deferentia and the Vaso-Somatic Index (VSI) were determined in order to use them as proxies for sperm depletion and male reproductive condition. A manipulative experiment was performed in the laboratory to estimate vasa deferentia weight and VSI from just-mated males in order to obtain a reference point for the potential effects of the fishery on sperm reserves. Sperm storage capacity is significantly affected by fisheries; during the mating season vasa deferentia from localities with low fishery intensity were heavier than those from high intensity fisheries, and these differences were even more evident in large males. Histological section showed that this disparity in vasa deferentia weight was explained principally by differences in the quantity of spermatophores rather than other seminal material. VSI was always higher in males from localities with low fishery intensity. Males from localities with high fishery intensity showed little capacity to recover sperm reserves and the VSI of these males remained below the values of the just-mated males. Detriment in the capacity of males to transfer sperm is the first step to sperm limitation in an exploited population, thus detection of sperm depletion can be an alert to introduce changes in the current management of crabs.     

Combining control measures for more effective management of fisheries under uncertainty: quotas, effort limitation and protected areas

We consider combinations of three types of control measures for the management of fisheries when the input information for policy decisions is uncertain. The methods considered include effort controls, catch quotas and area closures. We simulated a hypothetical fishery loosely based on the Icelandic cod fishery, using a simple spatially explicit dynamic model. We compared the performance with respect to conserving the resource and economic return for each type of control measure alone and in combination. In general, combining more than one type of primary direct control on fishing provides a greater buffer to uncertainty than any single form of fishery control alone. Combining catch quota control with a large closed area is a most effective system for reducing the risk of stock collapse and maintaining both short and long-term economic performance. Effort controls can also be improved by adding closed areas to the management scheme. We recommend that multiple control methods be used wherever possible and that closed areas should be used to buffer uncertainty. To be effective, these closed areas must be large and exclude all principal gears to provide real protection from fishing mortality.