Designing a global assessment of climate change on inland fishes and fisheries: knowns and needs

To date, there are few comprehensive assessments of how climate change affects inland finfish, fisheries, and aquaculture at a global scale, but one is necessary to identify research needs and commonalities across regions and to help guide decision making and funding priorities. Broadly, the consequences of climate change on inland fishes will impact global food security, the livelihoods of people who depend on inland capture and recreational fisheries. However, understanding how climate change will affect inland fishes and fisheries has lagged behind marine assessments. Building from a North American inland fisheries assessment, we convened an expert panel from seven countries to provide a first-step to a framework for determining how to approach an assessment of how climate change may affect inland fishes, capture fisheries, and aquaculture globally. Starting with the small group helped frame the key questions (e.g., who is the audience? What is the best approach and spatial scale?). Data gaps identified by the group include: the tolerances of inland fisheries to changes in temperature, stream flows, salinity, and other environmental factors linked to climate change, and the adaptive capacity of fishes and fisheries to adjust to these changes. These questions are difficult to address, but long-term and large-scale datasets are becoming more readily available as a means to test hypotheses related to climate change. We hope this perspective will help researchers and decision makers identify research priorities and provide a framework to help sustain inland fish populations and fisheries for the diversity of users around the globe.     

Population genomics of marine fishes: identifying adaptive variation in space and time

Studies of adaptive evolution have experienced a recent revival in population genetics of natural populations and there is currently much focus on identifying genomic signatures of selection in space and time. Insights into local adaptation, adaptive response to global change and evolutionary consequences of selective harvesting can be generated through population genomics studies, allowing the separation of the effects invoked by neutral processes (drift-migration) from those due to selection. Such knowledge is important not only for improving our basic understanding of natural as well as human-induced evolutionary processes, but also for predicting future trajectories of biodiversity and for setting conservation priorities. Marine fishes possess a number of features rendering them well suited for providing general insights into adaptive genomic evolution in natural populations. These include well-described population structures, substantial and rapidly developing genomic resources and abundant archived samples enabling temporal studies. Furthermore, superior possibilities for conducting large-scale experiments under controlled conditions, due to the economic resources provided by the large and growing aquaculture industry, hold great promise for utilizing recent technological developments. Here, we review achievements in marine fish genomics to date and highlight potential avenues for future research, which will provide both general insights into evolution in high gene flow species, as well as specific knowledge which can lead to improved management of marine organisms.     

Genomic and microarray approaches to coral reef conservation biology

New technologies based on DNA microarrays and comparative genomics hold great promise for providing the background biological information necessary for effective coral reef conservation and management. Microarray analysis has been used in a wide range of applications across the biological sciences, most frequently to examine simultaneous changes in the expression of large numbers of genes in response to experimental manipulation or environmental variation. Other applications of microarray methods include the assessment of divergence in gene sequences between species and the identification of fast-evolving genes. Arrays are presently available for only a limited range of species, but with appropriate controls they can be used for related species, thus avoiding the considerable costs associated with development of a system de novo. Arrays are in use or preparation to study stress responses, early development, and symbiosis in Acropora and Montastraea. Ongoing projects on several corals are making available large numbers of expressed gene sequences, enabling the identification of candidate genes for studies on gamete specificity, allorecognition and symbiont interactions. Over the next few years, microarray and comparative genomic approaches are likely to assume increasingly important and widespread use to study many aspects of the biology of coral reef organisms. Application of these genomic approaches to enhance our understanding of genetic and physiological correlates during stress, environmental disturbance and disease bears direct relevance to the conservation of coral reef ecosystems. S. Forêt and K.S. Kassahn contributed equally.     

Cultured fish: integrative biology and management of domestication and interactions with wild fish

Fish aquaculture for commodity production, fisheries enhancement and conservation is expanding rapidly, with many cultured species undergoing inadvertent or controlled domestication. Cultured fish are frequently released, accidentally and deliberately, into natural environments where they may survive well and impact on wild fish populations through ecological, genetic, and technical interactions. Impacts of fish released accidentally or for fisheries enhancement tend to be negative for the wild populations involved, particularly where wild populations are small, and/or highly adapted to local conditions, and/or declining. Captive breeding and supplementation can play a positive role in restoring threatened populations, but the biology of threatened populations and the potential of culture approaches for conserving them remain poorly understood. Approaches to the management of domestication and cultured‐wild fish interactions are often ad hoc, fragmented and poorly informed by current science. We develop an integrative biological framework for understanding and managing domestication and cultured‐wild fish interactions. The framework sets out how management practices in culture and for cultured fish in natural environments affect domestication processes, interactions between cultured and wild fish, and outcomes in terms of commodity production, fisheries yield, and conservation. We also develop a typology of management systems (specific combinations of management practices in culture and in natural environments) that are likely to provide positive outcomes for particular management objectives and situations. We close by setting out avenues for further research that will simultaneously improve fish domestication and management of cultured‐wild fish interactions and provide key insights into fundamental biology.     

功能基因组学的研究方法

基因组学的研究已从结构基因组学转向功能基因组学,功能基因组学时代对于基因功能的研究也由单一基因转向大规模,批量分析,本综述了功能基因组学的研究内容与方法,主要包括：差异显示反转录PCR,基因表达序列分析（SAGE）,微点阵,遗传足迹法,反求遗传学,蛋白质组学和生物信息学等新方法。     

Rapid,broad‐scale gene expression evolution in experimentally harvested fish populations

Gene expression changes potentially play an important role in adaptive evolution under human‐induced selection pressures, but this has been challenging to demonstrate in natural populations. Fishing exhibits strong selection pressure against large body size, thus potentially inducing evolutionary changes in life history and other traits that may be slowly reversible once fishing ceases. However, there is a lack of convincing examples regarding the speed and magnitude of fisheries‐induced evolution, and thus, the relevant underlying molecular‐level effects remain elusive. We use wild‐origin zebrafish (Danio rerio) as a model for harvest‐induced evolution. We experimentally demonstrate broad‐scale gene expression changes induced by just five generations of size‐selective harvesting, and limited genetic convergence following the cessation of harvesting. We also demonstrate significant allele frequency changes in genes that were differentially expressed after five generations of size‐selective harvesting. We further show that nine generations of captive breeding induced substantial gene expression changes in control stocks likely due to inadvertent selection in the captive environment. The large extent and rapid pace of the gene expression changes caused by both harvest‐induced selection and captive breeding emphasizes the need for evolutionary enlightened management towards sustainable fisheries.     

Domestication, comparative biology and interactions of wild and cultured fish: convenor's synthesis

Aquaculture is expanding rapidly and many fish species are brought into cultivation, entering a process of domestication with consequences for their morphology, physiology, ecology and evolution. In some species the abundance of cultured populations matches or exceeds that of wild stocks, and interactions between cultured and wild fish can pose significant conservation challenges. At the same time, captive breeding and re‐introduction play an important role in the conservation of some of the world's most endangered fishes. Drawing on contributions from the FSBI Symposium and the wider literature, we synthesize current knowledge of the process and extend of fish domestication, interactions between cultured and wild fish, and the use of cultured fish in fisheries enhancement and restoration. We provide a perspective on the role of biological issues within the wider context of aquaculture development and aquatic conservation biology, and conclude with a discussion of promising avenues for further research.     

Host-pathogen-environment interactions predict survival outcomes of adult sockeye salmon (Oncorhynchus nerka) released from fisheries

Incorporating host-pathogen(s)-environment axes into management and conservation planning is critical to preserving species in a warming climate. However, the role pathogens play in host stress resilience remains largely unexplored in wild animal populations. We experimentally characterized how independent and cumulative stressors (fisheries handling, high water temperature) and natural infections affected the health and longevity of released wild adult sockeye salmon (Oncorhynchus nerka) in British Columbia, Canada. Returning adults were collected before and after entering the Fraser River, yielding marine- and river-collected groups, respectively (N = 185). Fish were exposed to a mild (seine) or severe (gill net) fishery treatment at collection, and then held in flow-through freshwater tanks for up to four weeks at historical (14°C) or projected migration temperatures (18°C). Using weekly nonlethal gill biopsies and high-throughput qPCR, we quantified loads of up to 46 pathogens with host stress and immune gene expression. Marine-collected fish had less severe infections than river-collected fish, a short migration distance (100 km, 5–7 days) that produced profound infection differences. At 14°C, river-collected fish survived 1–2 weeks less than marine-collected fish. All fish held at 18°C died within 4 weeks unless they experienced minimal handling. Gene expression correlated with infections in river-collected fish, while marine-collected fish were more stressor-responsive. Cumulative stressors were detrimental regardless of infections or collection location, probably due to extreme physiological disturbance. Because river-derived infections correlated with single stressor responses, river entry probably decreases stressor resilience of adult salmon by altering both physiology and pathogen burdens, which redirect host responses toward disease resistance.     

Genomic resources for flatfish research and their applications

Flatfishes are a group of teleosts of high commercial and environmental interest, whose biology is still poorly understood. The recent rapid development of different 'omic' technologies is, however, enhancing the knowledge of the complex genetic control underlying different physiological processes of flatfishes. This review describes the different functional genomic approaches and resources currently available for flatfish research and summarizes different areas where microarray-based gene expression analysis has been applied. The increase in genome sequencing data has also allowed the construction of genetic linkage maps in different flatfish species; these maps are invaluable for investigating genome organization and identifying genetic traits of commercial interest. Despite the significant progress in this field, the genomic resources currently available for flatfish are still scarce. Further intensive research should be carried out to develop larger genomic sequence databases, high-density microarrays and, more detailed, complete linkage maps, using second-generation sequencing platforms. These tools will be crucial for further expanding the knowledge of flatfish physiology, and it is predicted that they will have important implications for wild fish population management, improved fish welfare and increased productivity in aquaculture.     

Vulnerability of individual fish to capture by trawling is influenced by capacity for anaerobic metabolism

The harvest of animals by humans may constitute one of the strongest evolutionary forces affecting wild populations. Vulnerability to harvest varies among individuals within species according to behavioural phenotypes, but we lack fundamental information regarding the physiological mechanisms underlying harvest-induced selection. It is unknown, for example, what physiological traits make some individual fish more susceptible to capture by commercial fisheries. Active fishing methods such as trawling pursue fish during harvest attempts, causing fish to use both aerobic steady-state swimming and anaerobic burst-type swimming to evade capture. Using simulated trawling procedures with schools of wild minnows Phoxinus phoxinus, we investigate two key questions to the study of fisheries-induced evolution that have been impossible to address using large-scale trawls: (i) are some individuals within a fish shoal consistently more susceptible to capture by trawling than others?; and (ii) if so, is this related to individual differences in swimming performance and metabolism? Results provide the first evidence of repeatable variation in susceptibility to trawling that is strongly related to anaerobic capacity and swimming ability. Maximum aerobic swim speed was also negatively correlated with vulnerability to trawling. Standard metabolic rate was highest among fish that were least vulnerable to trawling, but this relationship probably arose through correlations with anaerobic capacity. These results indicate that vulnerability to trawling is linked to anaerobic swimming performance and metabolic demand, drawing parallels with factors influencing susceptibility to natural predators. Selection on these traits by fisheries could induce shifts in the fundamental physiological makeup and function of descendent populations.     

Medaka as a model of transgenic fish.

The medaka (Oryzias latipes) is an egg-laying fresh-water fish. We describe the medaka as a model system of transgenic fish in germs of biological characteristics, manipulation of embryos, gene expression in development, and basic research in aquaculture. The fish are small (approximately 3 cm in length) and have a short generation time (approximately 3 months). The eggs are easy to manipulate. A foreign gene (e.g., the chicken delta crystallin gene) is transferred and expressed stage-dependently in development of medaka embryos. Growth hormone genes of vertebrates are transferred and expressed and, in some cases, accelerate growth of the fish. Thus, the medaka is one of the most promising models of transgenic fish for basic research of gene expression and aquaculture.     

Conservation physiology in practice: how physiological knowledge has improved our ability to sustainably manage Pacific salmon during up-river migration

Despite growing interest in conservation physiology, practical examples of how physiology has helped to understand or to solve conservation problems remain scarce. Over the past decade, an interdisciplinary research team has used a conservation physiology approach to address topical conservation concerns for Pacific salmon. Here, we review how novel applications of tools such as physiological telemetry, functional genomics and laboratory experiments on cardiorespiratory physiology have shed light on the effect of fisheries capture and release, disease and individual condition, and stock-specific consequences of warming river temperatures, respectively, and discuss how these findings have or have not benefited Pacific salmon management. Overall, physiological tools have provided remarkable insights into the effects of fisheries capture and have helped to enhance techniques for facilitating recovery from fisheries capture. Stock-specific cardiorespiratory thresholds for thermal tolerances have been identified for sockeye salmon and can be used by managers to better predict migration success, representing a rare example that links a physiological scope to fitness in the wild population. Functional genomics approaches have identified physiological signatures predictive of individual migration mortality. Although fisheries managers are primarily concerned with population-level processes, understanding the causes of en route mortality provides a mechanistic explanation and can be used to refine management models. We discuss the challenges that we have overcome, as well as those that we continue to face, in making conservation physiology relevant to managers of Pacific salmon.     

Aquaculture: a newly emergent food production sector—and perspectives of its impacts on biodiversity and conservation

The fisheries sector in the course of the last three decades have been transformed from a developed country to a developing country dominance. Aquaculture, the farming of waters, though a millennia old tradition during this period has become a significant contributor to food fish production, currently accounting for nearly 50?% of global food fish consumption; in effect transforming our dependence from a hunted to a farmed supply as for all our staple food types. Aquaculture and indeed the fisheries sector as a whole is predominated in the developing countries, and accordingly the development strategies adopted by the sector are influenced by this. Aquaculture also being a newly emerged food production sector has being subjected to an increased level of public scrutiny, and one of the most contentious aspects has been its impacts on biodiversity. In this synthesis an attempt is made to assess the impacts of aquaculture on biodiversity. Instances of major impacts on biodiversity conservation arising from aquaculture, such as land use, effluent discharge, effects on wild populations, alien species among others are highlighted and critically examined. The influence of paradigm changes in development strategies and modern day market forces have begun to impact on aquaculture developments. Consequently, improvements in practices and adoption of more environmentally friendly approaches that have a decreasing negative influence on biodiversity conservation are highlighted. An attempt is also made to demonstrate direct and or indirect benefits of aquaculture, such as through being a substitute to meet human needs for food, particularly over-exploited and vulnerable fish stocks, and for other purposes (e.g. medicinal ingredients), on biodiversity conservation, often a neglected entity.     

Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding

Atlantic salmon (Salmo salar L.) is among the most iconic and economically important fish species and was the first member of Salmonidae to have a high‐quality reference genome assembly published. Advances in genomics have become increasingly central to the genetic improvement of farmed Atlantic salmon as well as conservation of wild salmon stocks. The salmon genome has also been pivotal in shaping our understanding of the evolutionary and functional consequences arising from an ancestral whole‐genome duplication event characterising all Salmonidae members. Here, we provide a review of the current status of Atlantic salmon genetics and genomics, focussed on progress made from genome‐wide research aimed at improving aquaculture production and enhancing understanding of salmonid ecology, physiology and evolution. We present our views on the future direction of salmon genomics, including the role of emerging technologies (e.g. genome editing) in elucidating genetic features that underpin functional variation in traits of commercial and evolutionary importance.     

Searching for responsible and sustainable recreational fisheries in the Anthropocene

Recreational fisheries that use rod and reel (i.e., angling) operate around the globe in diverse freshwater and marine habitats, targeting many different gamefish species and engaging at least 220 million participants. The motivations for fishing vary extensively; whether anglers engage in catch-and-release or are harvest-oriented, there is strong potential for recreational fisheries to be conducted in a manner that is both responsible and sustainable. There are many examples of recreational fisheries that are well-managed where anglers, the angling industry and managers engage in responsible behaviours that both contribute to long-term sustainability of fish populations and the sector. Yet, recreational fisheries do not operate in a vacuum; fish populations face threats and stressors including harvest from other sectors as well as environmental change, a defining characteristic of the Anthropocene. We argue that the future of recreational fisheries and indeed many wild fish populations and aquatic ecosystems depends on having responsible and sustainable (R&S) recreational fisheries whilst, where possible, addressing, or at least lobbying for increased awareness about the threats to recreational fisheries emanating from outside the sector (e.g., climate change). Here, we first consider how the concepts of R&S intersect in the recreational fishing sector in an increasingly complex socio-cultural context. Next, we explore the role of the angler, angling industry and decision-makers in achieving R&S fisheries. We extend this idea further by considering the consequences of a future without recreational fisheries (either because of failures related to R&S) and explore a pertinent case study situated in Uttarakahand, India. Unlike other fisheries sectors where the number of participants is relatively small, recreational angling participants are numerous and widespread, such that if their actions are responsible, they have the potential to be a key voice for conservation and serve as a major force for good in the Anthropocene. What remains to be seen is whether this will be achieved, or if failure will occur to the point that recreational fisheries face increasing pressure to cease, as a result of external environmental threats, the environmental effects of recreational fishing and emerging ethical concerns about the welfare of angled fish.     

Understanding and managing enhancements: why fisheries scientists should care

Fisheries enhancements are a set of management approaches involving the use of aquaculture technologies to enhance or restore fisheries in natural ecosystems. Enhancements are widely used in inland and coastal fisheries, but have received limited attention from fisheries scientists. This paper sets out 10 reasons why fisheries scientists should care about understanding and managing enhancements. (1) Enhancements happen, driven mostly by resource users and managers rather than scientists. (2) Enhancements create complex fisheries systems that encompass and integrate everything fisheries stakeholders can practically manage. (3) Enhancements emerge in fisheries where the scope for technical and governance control is high, and they synergistically reinforce both. (4) Successful enhancements expand management options and achievable outcomes. (5) Many enhancements fail or do ecological harm but persist regardless. (6) Effective science engagement is crucial to developing beneficial enhancements and preventing harmful ones. (7) Good scientific guidance is available to aid development or reform of enhancements but is not widely applied. (8) Enhancement research advances, integrates and unifies the fisheries sciences. (9) Enhancements provide unique opportunities for learning about natural fish populations and fisheries. (10) Needs, opportunities and incentives for enhancements are bound to increase.