Coastal marine fisheries and the habitats that support them are under extensive and increasing pressures from numerous anthropogenic stressors that occur at multiple spatial and temporal scales and ...often intersect in unexpected ways. Frequently, the scales at which these fisheries are managed do not match the scales of the stressors, much less the geographic scale of species biology. In general, fishery management is ill prepared to address these stressors, as underscored by the continuing lack of integration of fisheries and habitat management. However, research of these fisheries is increasingly being conducted at spatial and temporal scales that incorporate biology and ecological connectivity of target species, with growing attention to the foundational role of habitat. These efforts are also increasingly engaging stakeholders and rights holders in research, education, and conservation. This multi-method approach is essential for addressing pressing conservation challenges that are common to flats ecosystems. Flats fisheries occur in the shallow, coastal habitat mosaic that supports fish species that are accessible to and desirable to target by recreational fishers. Because these species rely upon coastal habitats, the anthropogenic stressors can be especially intense—habitat alteration (loss and degradation) and water quality declines are being exacerbated by climate change and increasing direct human impacts (e.g., fishing effort, boat traffic, depredation, pollution). The connections necessary for effective flats conservation are of many modes and include ontogenetic habitat connectivity; connections between stressors and impacts to fishes; connections between research and management, such as research informing spawning area protections; and engagement of stakeholders and rights holders in research, education, and management. The articles included in this Special Issue build upon a growing literature that is filling knowledge gaps for flats fishes and their habitats and increasingly providing the evidence to inform resource management. Indeed, numerous articles in this issue propose or summarize direct application of research findings to management with a focus on current and future conservation challenges. As with many other fisheries, a revised approach to management and conservation is needed in the Anthropocene.
War is an ever-present force that has the potential to alter the biosphere. Here we review the potential consequences of modern war and military activities on ecosystem structure and function. We ...focus on the effects of direct conflict, nuclear weapons, military training, and military produced contaminants. Overall, the aforementioned activities were found to have overwhelmingly negative effects on ecosystem structure and function. Dramatic habitat alteration, environmental pollution, and disturbance contributed to population declines and biodiversity losses arising from both acute and chronic effects in both terrestrial and aquatic systems. In some instances, even in the face of massive alterations to ecosystem structure, recovery was possible. Interestingly, military activity was beneficial under specific conditions, such as when an exclusion zone was generated that generally resulted in population increases and (or) population recovery; an observation noted in both terrestrial and aquatic systems. Additionally, military technological advances (e.g., GPS technology, drone technology, biotelemetry) have provided conservation scientists with novel tools for research. Because of the challenges associated with conducting research in areas with military activities (e.g., restricted access, hazardous conditions), information pertaining to military impacts on the environment are relatively scarce and are often studied years after military activities have ceased and with no knowledge of baseline conditions. Additional research would help to elucidate the environmental consequences (positive and negative) and thus reveal opportunities for mitigating negative effects while informing the development of optimal strategies for rehabilitation and recovery.
Transcriptional reprogramming forms a major part of a plant's response to pathogen infection. Many individual components and pathways operating during plant defense have been identified, but our ...knowledge of how these different components interact is still rudimentary. We generated a high-resolution time series of gene expression profiles from a single Arabidopsis thaliana leaf during infection by the necrotrophic fungal pathogen Botrytis cinerea. Approximately one-third of the Arabidopsis genome is differentially expressed during the first 48 h after infection, with the majority of changes in gene expression occurring before significant lesion development. We used computational tools to obtain a detailed chronology of the defense response against B. cinerea, highlighting the times at which signaling and metabolic processes change, and identify transcription factor families operating at different times after infection. Motif enrichment and network inference predicted regulatory interactions, and testing of one such prediction identified a role for TGA3 in defense against necrotrophic pathogens. These data provide an unprecedented level of detail about transcriptional changes during a defense response and are suited to systems biology analyses to generate predictive models of the gene regulatory networks mediating the Arabidopsis response to B. cinerea.
Considerable time and money are expended in the pursuit of catching fish with hooks (e.g., handlining, angling, longlining, trolling, drumlining) across the recreational, commercial and subsistence ...fishing sectors. The fish and other aquatic organisms (e.g., squid) that are captured are not a random sample of the population because external (e.g., turbidity) and underlying internal variables (e.g., morphology) contribute to variation in vulnerability to hooks. Vulnerability is the probability of capture for any given fish in a given location at a given time and mechanistically explains the population‐level catchability coefficient, which is a fundamental and usually time‐varying (i.e., dynamic) variable in fisheries science and stock assessment. The mechanistic drivers of individual vulnerability to capture are thus of interest to fishers by affecting catch rates, but are also of considerable importance to fisheries managers whenever hook‐and‐line‐generated data contribute to stock assessments. In this paper, individual vulnerability to hooks is conceptualized as a dynamic state, in which individual fish switch between vulnerable and invulnerable states as a function of three interdependent key processes: an individual fish's internal state, its encounter with the gear, and the characteristics of the encountered gear. We develop a new conceptual framework of “vulnerability,” summarize the major drivers of fish vulnerability, and conclude that fish vulnerability involves complex processes. To understand vulnerability, a shift to interdisciplinary research and the integration of ecophysiology, fish ecology, fisheries ecology and human movement ecology, facilitated by new technological developments, is required.
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Of late there have been several syntheses that consider the biological effectiveness of fishways. These syntheses emphasize the importance of generating estimates of attraction and passage ...efficiency, using electronic tagging techniques, as the “gold standard” for determining if a fishway is indeed successful at passing target species upstream to meet ecological, management, and conservation goals. Such an emphasis on efficiency is potentially problematic if estimates of attraction and passage efficiency are biased or otherwise fail to reliably represent the true biological effectiveness of a fishway. Indeed, erroneous estimates could lead to management decisions (in terms of both design criteria and operational decisions) that are costly in terms of economic expenditures and failed conservation outcomes for populations, species and ecosystems. Here we review the factors that are necessary to consider when determining the reliability of efficiency estimates for fishways and provide suggestions for improving such estimates. Clearly there is need for greater attention to the effects of various capture (including gear and the timing and location of capture), handling, and tagging protocols on fish necessary to monitor individual passage success given the potential for procedures to influence organismal condition and behavior. In addition, there is need for more long-term tagging studies (monitoring individuals across multiple seasons), mechanistic studies to understand the biological basis for differences in efficiency estimates, greater use of control studies to account for natural levels of migration failure/behavioral heterogeneity, technical validation of electronic tagging equipment (to account for tag failure and detection efficiency), and the use of approaches that combine individual monitoring with population-level studies (including modeling exercises). Also relevant is the need to better understand the proportion of fish that need to pass a fishway to address ecological, management and conservation targets, as well as identify the proportion of a population that is actually motivated to attempt passage in a given season. Failure to think critically about the factors for a given study/site that have the potential to influence estimates of passage and attraction efficiency will impede the ability of science and monitoring activities to inform fishway design and operation and ultimately improve aquatic ecosystems.
Though reported capture fisheries are dominated by marine production, inland fish and fisheries make substantial contributions to meeting the challenges faced by individuals, society, and the ...environment in a changing global landscape. Inland capture fisheries and aquaculture contribute over 40% to the world's reported finfish production from less than 0.01% of the total volume of water on earth. These fisheries provide food for billions and livelihoods for millions of people worldwide. Herein, using supporting evidence from the literature, we review 10 reasons why inland fish and fisheries are important to the individual (food security, economic security, empowerment), to society (cultural services, recreational services, human health and well-being, knowledge transfer and capacity building), and to the environment (ecosystem function and biodiversity, as aquatic “canaries”, the “green food” movement). However, the current limitations to valuing the services provided by inland fish and fisheries make comparison with other water resource users extremely difficult. This list can serve to demonstrate the importance of inland fish and fisheries, a necessary first step to better incorporating them into agriculture, land-use, and water resource planning, where they are currently often underappreciated or ignored.
Aquatic animals are integral to ocean and freshwater ecosystems and their resilience, are depended upon globally for food sustainability, and support coastal communities and Indigenous peoples. ...However, global aquatic environments are changing profoundly due to anthropogenic actions and environmental change. These changes are altering distributions, movements, and survival of aquatic animals in ways that are not well understood. The Ocean Tracking Network (OTN) is a global partnership that is filling this knowledge gap. OTN Canada, a pan-Canadian (and beyond) research network, was launched in 2010 with visionary funding by the Canadian government. In our introduction to this special issue, we briefly overview how this interdisciplinary network has used state-of-the-art technologies, infrastructure, electronic tags and sensors, and associated cutting-edge research and training programs to better understand changing marine and freshwater dynamics and their impact on ecosystems, resources, and animal ecology. These studies have provided unprecedented insights into animal ecology and resource management at a range of spatial and temporal scales and by interfacing animal movements with novel measures of environment, physiology, disease, genetics–genomics, and anthropogenic stressors.
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