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The atlantic salmon: Genetics, conservation and management

Atlantic Salmon is a cultural icon throughout its North Atlantic range; it is the focus of probably the World’s highest profile recreational fishery and is the basis for one of the World’s largest aquaculture industries. Despite this, many wild stocks of salmon are in decline and underpinning this is a dearth of information on the nature and extent of population structuring and adaptive population differentiation, and its implications for species conservation. This important new book will go a long way to rectify this situation by providing a thorough review of the genetics of Atlantic salmon. Sponsored by the European Union and the Atlantic Salmon Trust, this book comprises the work of an international team of scientists, carefully integrated and edited to provide a landmark book of vital interest to all those working with Atlantic salmon.

Book

Using carbon dioxide in fisheries and aquatic invasive species management

To restore native fish populations, fisheries programs often depend on active removal of aquatic invasive species. Chemical removal can be an effective method of eliminating aquatic invasive species, but chemicals can induce mortality in nontarget organisms and persist in the environment. Carbon dioxide (CO 2 ) is an emerging alternative to traditional chemical control agents because it has been demonstrated to be toxic to fish, but is naturally occurring and readily neutralized. In addition, CO 2 is a commercially available gas, is highly soluble, and has high absorption efficiency. When these characteristics are paired with advances in modern, large-scale gas delivery technologies, opportunities to use CO 2 in natural or artificial (e.g., canals) waters to manage fish become increasingly feasible. Our objective is to describe the history of CO 2 use in fisheries and outline potential future applications of CO 2 to suppress and manipulate aquatic species in field and aquaculture settings.

Fisheries

Stocking fish in inland waters: Opportunities and risks for sustainable food systems

Stocking is one of the foremost tools in the inland fisheries management toolbox, but it comes with both opportunities and risks. Stocking is often used as compensation for depleted wild populations, particularly where recruitment processes have been disrupted, but it can introduce disease, disrupt community structures, reduce genetic integrity, and cause conflicts between fishery stakeholders. Despite its widespread use, examples of effective stocking for food fisheries in inland waters are sparse in the peer-reviewed literature. Nevertheless, it is well established that stocking is frequently used to maintain fish yield, so there is a need to conduct the practice in a robust manner that minimises the potential risks. This paper serves as the front matter for a special section of Fisheries Management and Ecology focused on fresh waters feeding the world, which resulted from two panel sessions, one focused on aquaculture and one focused on stocking, hosted by the international InFish research network ( https://infish.org/ ). The paper highlights current practices of fish stock enhancement in inland waters for food, examines potential synergies and interactions of stock enhancement programmes with aquaculture, and provides an outline framework for responsible management of fish stock enhancement.

Fisheries Management and Ecology

Assessing habitat use and population dynamics of fisheries resources at Kaloko Fishpond

Throughout Hawai'i, fishponds are considered by their local communities as important cultural touchstones, a source of local, sustainably produced food, and an important component to the development of community-based management for nearshore fisheries. Within Kaloko-Honokōhau National Historical Park, the restoration of Kaloko Fishpond for traditional aquaculture management is a goal of both the National Park Service (NPS) and Hui Kaloko-Honokōhau, a community-based group of kia'i, i.e., caretakers and native Hawaiian cultural practitioners. However, existing data on the demographics and condition of the fish populations within the pond, and the fish-habitat quality are poor to non-existent. Therefore, the objectives of this study were to: catalog fish species composition and distribution in the pond; estimate the abundance of focal species/taxonomic groups; and evaluate the occupancy patterns of the invasive algae Acanthophora spicifera and Upside-down Jellyfish Cassiopea andromeda. As part of these objectives, a survey protocol and analysis framework were designed and evaluated to ensure that the NPS and community group would be able to refine and implement them to continue their monitoring efforts. We conducted dual-observer shore-based visual surveys multiple times per week during September-October 2020 and April-September 2022. A total of 41 species/taxonomic groups were recorded over the course of the surveys. The largest number of species/taxonomic groups were observed at survey stations located on or near the kuapā, or wall separating the fishpond from the ocean. N-mixture models fitted to the data estimated a total population of 353 – 392 mullets, 134 – 192 flagtails (āholehole), and 189 – 277 Milkfish (Awa) Chanos chanos occurring within the 1.2-ha portion of Kaloko Fishpond that could be surveyed visually from the shoreline. Multi-season occupancy models fitted to the surveyed presence of A. spicifera and Upside-down Jellyfish indicted sites throughout most of the pond exhibited moderate and consistent occupancy (ψ = 0.30 – 0.40) throughout much of the pond, except for the northeast corner of the pond (Kaloko Iki) where colonization rates were lower and extinction rates higher than other areas within Kaloko. The visual survey method developed for this study provides a low-cost and effective starting point for the development of methodology that can be used both by NPS personnel and volunteers from the community group. However, we were only able to estimate fish populations for approximately 24% of the area of Kaloko Fishpond with this method. Given that the deeper areas of Kaloko Fishpond are completely inaccessible to the visual survey method used, generating population estimates for the entire pond based on the parameters estimated in the current study is not recommended without further investigation into fish movement and habitat use. Various means to refine this protocol to better meet the needs and abilities of the NPS and community group are proposed.

Hawaii

Use of a subsurface plankton layer to benefit a cage-culture fishery in Lake Phewa, Nepal

The Nepalese government and some 225 families in the private sector are engaged in an expanding aquaculture program in lakes Phewa, Begnas and Rupa in the Pokhara Valley, Nepal (Swar & Pradhan 1992). Bighead carp ( Aristichthys nobilis ) and silver carp ( Hypopthalmichthys molitrix ) are propagated in hatchery ponds and are raised to market size in mesh enclosures (having sides, tops and bottoms) suspended to a depth of 2 m. Some 300 cages are presently in use, with annual production varying from 3.4 kg/m 3 Lake Phewa to about 5 kg/m 3 in lakes Begnas and Rupa (Swar & Pradhan 1992). These cage-reared fish are an important source of animal protein and revenue (Swar 1981). Tourism in the region provides growers a continuous market for their fish.

Lake Begnas, Lake Phewa, Lake Rupa

Coproduction and modeling spatial contact networks prevent bias about infectious hematopoietic necrosis virus transmission for Snake River Basin salmonids

Much remains unknown about variation in pathogen transmission across the geographic range of a free-ranging fish or animal species and about the influence of movement (associated with husbandry practices or animal behavior) on pathogen transmission. Salmonid hatcheries are an ideal system in which to study these processes. Salmonid hatcheries are managed for endangered species recovery, supplementation of threatened or at-risk fish stocks, support of fisheries, and ecosystem stability. Infectious hematopoietic necrosis virus (IHNV) is a rhabdovirus of significant concern to salmon aquaculture. Landscape IHNV transmission dynamics previously had been estimated only for salmonid hatcheries in the Lower Columbia River Basin (LCRB). The objectives of this study were to estimate IHNV transmission dynamics in a unique geographic region, the Snake River Basin (SRB), and to quantitatively estimate the effect of model coproduction on inference because previous assessments of coproduction have been qualitative. In contrast to the LCRB, the SRB has hatchery complexes consisting of a main hatchery and ≥1 satellite facility. Knowledge about hatchery complexes was held by a subset of project researchers but would not have been available to project modelers without coproduction. Project modelers generated and tested multiple versions of Bayesian susceptible-exposedinfected models to realistically represent the SRB and estimate the effect of coproduction. Models estimated the frequency of transmission routes, route-specific infection probabilities, and infection probabilities for combinations of salmonid hosts and IHNV lineages. Model results indicated that in the SRB, avoiding exposure to IHNV-positive adult salmonids is the most important action to prevent juvenile infections. Migrating adult salmonids exposed juvenile cohort-sites most frequently, and the infection probability was greatest following exposure to migrating adults. Without coproduction, the frequency of exposure by migrating adults would have been overestimated by 70 cohort-sites, and the infection probability following exposure to migrating adults would have been underestimated by∼0.09. The coproduced model had less uncertainty in the infection probability if no transmission route could be identified (Bayesian credible interval (BCI) width = 0.12) compared to the model without coproduction (BCI width = 0.34). Evidence for virus lineage MD specialization on steelhead and rainbow trout (both Oncorhynchus mykiss) was apparent without model coproduction. In the SRB, we found a greater probability of virus lineage UC infection in Chinook salmon (Oncorhynchus tshawytscha) compared to in O. mykiss, whereas in the LCRB, UC more clearly exhibited a generalist approach. Coproduction influenced estimates that depended on transmission routes, which operated differently at main hatcheries and satellite sites within hatchery complexes. Hatchery complexes are found outside of the SRB and are not specific to salmonid hatcheries alone. There is great potential for coproduction and modeling spatial contact networks to advance understanding about infectious disease transmission in complex production systems and surrounding free-ranging animal populations.

Idaho, Oregon, Washington

Vertical distribution of the chloromonad flagellate Heterosigma carterae in columns: Implications for bloom development

Blooms of the marine flagellate Heterosigma carterae have been associated with catastrophic fish kills at mariculture facilities around the world. The precise cause(s) of the sudden appearance and disappearance of Heterosigma surface blooms has not been completely described or understood. Environmental data from prior studies of blooms indicate the presence of vertical stratification of the water column that is often induced by freshwater runoff. We report the relatively rapid concentration of Heterosigma cells at the surface of tubes shortly after the addition of distilled water to the surface. This phenomenon of cell concentration in surface waters may partially explain the sudden appearance of Heterosigma cells near the surface and subsequent disappearance when vertical stratification is lost due to turbulence or mixing. The results may lead to bloom mitigation techniques for net pen aquaculture.

Canadian Journal of Fisheries and Aquatic Sciences

Use of prepositioned grid electrofishers for the collection of robust redhorse broodstock

We investigated the potential of prepositioned grid electrofishers as a means of collecting broodstock for the rare robust redhorse Moxostoma robustum. We found that combined with visual observation, this technique allowed for the efficient capture of fish in breeding condition. We were able to harvest eggs in the field and bring only fertilized eggs into the hatchery. There was no need to induce spawning hormonally. Although their use is limited by water depth and clarity, prepositioned grid electrofishers used in conjunction with visual observation warrants further consideration as an effective tool for the collection of reproductively active broodstock for conservation purposes. ?? Copyright by the American Fisheries Society 2005.

North American Journal of Aquaculture

Assessing consumption of bioactive micro-particles by filter-feeding Asian carp

Silver carp Hypophthalmichthys molitrix (SVC) and bighead carp H. nobilis (BHC) have impacted waters in the US since their escape. Current chemical controls for aquatic nuisance species are non-selective. Development of a bioactive micro-particle that exploits filter-feeding habits of SVC or BHC could result in a new control tool. It is not fully understood if SVC or BHC will consume bioactive micro-particles. Two discrete trials were performed to: 1) evaluate if SVC and BHC consume the candidate micro-particle formulation; 2) determine what size they consume; 3) establish methods to evaluate consumption of filter-feeders for future experiments. Both SVC and BHC were exposed to small (50-100 μm) and large (150-200 μm) micro-particles in two 24-h trials. Particles in water were counted electronically and manually (microscopy). Particles on gill rakers were counted manually and intestinal tracts inspected for the presence of micro-particles. In Trial 1, both manual and electronic count data confirmed reductions of both size particles; SVC appeared to remove more small particles than large; more BHC consumed particles; SVC had fewer overall particles in their gill rakers than BHC. In Trial 2, electronic counts confirmed reductions of both size particles; both SVC and BHC consumed particles, yet more SVC consumed micro-particles compared to BHC. Of the fish that ate micro-particles, SVC consumed more than BHC. It is recommended to use multiple metrics to assess consumption of candidate micro-particles by filter-feeders when attempting to distinguish differential particle consumption. This study has implications for developing micro-particles for species-specific delivery of bioactive controls to help fisheries, provides some methods for further experiments with bioactive micro-particles, and may also have applications in aquaculture.

Journal of Aquaculture Research & Development

Comparative hydraulics of two fishery research circular tanks and recommendations for control of experimental bias

Hydraulic characteristics inside two research circular tanks (1.5-m and 1.2-m diameter) with the same volume of water were studied to understand how they might affect experimental bias by influencing the behavior and development of juvenile fish. Water velocities inside each tank were documented extensively and flow behavior studied. Surface inflow to the 1.5-m tank created a highly turbulent and aerated surface, and produced unevenly distributed velocities within the tank. A low-flow velocity, or "dead" zone, persisted just upstream of the surface inflow. A single submerged nozzle in the 1.2-m tank created uniform flow and did not cause undue turbulence or introduce air. Flow behavior in the 1.5-m tank is believed to have negatively affected the feeding behavior and physiological development of a group of juvenile fall chinook salmon, Oncorhynchus tshawytscha. A new inflow nozzle design provided comparable flow behavior regardless of tank size and water depth. Maintaining similar hydraulic conditions inside tanks used for various biological purposes, including fish research, would minimize experimental bias caused by differences in flow behavior. Other sources of experimental bias are discussed and recommendations given for reporting and control of experimental conditions in fishery research tank experiments.

Journal of Applied Aquaculture

In memoriam - William Toshio (Tosh) Yasutake, 1922-2016

William Toshio (Tosh) Yasutake, 1922-2016 passed away peacefully at home on December 12, 2016, at the age of 94. He is survived by Fumi, his wife of 66 years, as well as four children and six grandchildren. With his death, the fish health community has lost an outstanding scientist as well as a kind, unassuming, and wonderful human being. Tosh was born on June 10, 1922, in Seattle, Washington, to Jack and Hide Yasutake. He was in his first year of studies at the University of Washington when Pearl Harbor was attacked by Imperial Japan on December 7, 1941. Following the attack, Tosh and his family (father, mother, sister, and two brothers) were among the 110,000–120,000 people of Japanese ancestry who were forced from their homes on the Pacific coast and incarcerated in internment camps in the interior. In June 1942, Tosh enlisted in the U.S. Army, serving as an unarmed combat medic in the famed 442nd Regimental Combat Team, the most decorated unit for its size and length of service in the history of American warfare. Wounded in October 1944 during the Vosges Mountains campaign near Bruyères, France, Tosh was evacuated and missed the ensuing battle to rescue the “Lost Battalion,” at which his replacement was killed. Tosh returned to action in Italy in February 1945 and served until the end of the war in Europe, earning both a Purple Heart and a Bronze Star for bravery. In October 2010, the Congressional Gold Medal was awarded to the 442nd Regimental Combat Team, and in 2012 the surviving members were made chevaliers of the French Légion d’Honneur for actions contributing to the liberation of France in World War II. After the war, Tosh returned to the University of Washington on the GI Bill and received a B.S. degree in zoology in 1951. In 1953 he began his research career at the U.S. Fish and Wildlife Service’s Western Fish Nutrition Laboratory at Cook, Washington, where he conducted pioneering research on nutritional fish diseases with John Halver. Tosh was one of the first to recognize hepatomas in hatchery-reared Rainbow Trout and helped to trace the disease to an aflatoxin produced by the mold Aspergillus flavis , which grew during the storage of ingredients for fish diets. In 1960, he transferred to the Western Fisheries Research Center (WFRC) in Seattle (then called the Western Fish Disease Laboratory) to start a fish pathology diagnostic laboratory. There he described the histopathology of diseases of economically important fishes, identified etiologic agents, and worked with hatchery biologists to improve the health, quality, and survival of salmonids released from federal and state hatcheries. Tosh was instrumental in recognizing that the viruses of Oregon sockeye disease and Chinook Salmon virus disease were one entity and in giving the disease its present name: infectious hematopoietic necrosis. In recognition of his pioneering research, Tosh was awarded a doctorate in fish pathology by the University of Tokyo in 1980, the first American to have been so honored. In 1983, he published his classic textbook The Microscopic Anatomy of Salmonids: An Atlas , which quickly became a standard reference work in fish pathology and is still in wide use today. For his outstanding career achievements, in 1987 Tosh received the S. F. Snieszko Distinguished Service Award, the highest honor bestowed by the American Fisheries Society’s Fish Health Section (AFS–FHS). Tosh retired in 1988 but continued his research at the WFRC as a senior scientist emeritus, providing technical assistance to federal and state agencies and to the aquaculture industry worldwide. His culminating project was to digitize his lifetime collection of photomicrographs and prepare an atlas, “Histopathology of Selected Parasitic Salmonid Diseases: A Color Atlas,” that is now posted on the Web sites of the WFRC and the AFS–FHS. Although his presence will be sorely missed, his research contributions have become part of the foundation of today’s knowledge of fisheries biology and have assured him a place in history.

Journal of Aquatic Animal Health

Drivers and synergies in the management of inland fisheries: Searching for sustainable solutions

Freshwater is a shared resource. Water challenges (i.e., too much, too little, too dirty) are recognized to have global implications. Many sectors rely upon water and, in some cases, the limited availability of water leads to tough decisions. Though inland fish and fisheries play important roles in providing food security, human well-being, and ecosystem productivity, this sector is often underappreciated in water resource planning because valuation is difficult and governance is complex, unclear, or non-existent. Additionally, inland fisheries are an economically small sector and, in most cases, the value of inland fisheries will never be the main driver of decision making. At the 2015 Global Conference on Inland Fisheries, we convened a Drivers and Synergies panel and working group to discuss competing sectors (e.g., hydropower, transportation, agriculture, mining and oil and gas extraction, forestry, tourism and recreation, and aquaculture) and large-scale drivers which exist predominately outside of the water sectors (e.g., economic growth, diversifying economies, population growth, urbanization, and climate change). Drivers will influence these sectors and tradeoffs will be made. Management of sustainable inland water systems requires making informed choices emphasizing those services that will provide sustainable benefits for humans while maintaining well-functioning ecological systems.

Conference Paper

Practical application of disease resistance: A brook trout fishery selected for resistance to furunculosis

Selection is unwittingly influenced by nuances of fish culturists and adaptation of fish to intensive culture within artificial environments. When pathogens are present, susceptible individuals may be selectively eliminated from a population, accounting for inter-specific and intra-specific differences in susceptibility to disease. Biologists often intensify such selection to enhance resistance. Particularly important to this discourse is the selective breeding program initiated by the New York State Department of Environmental Conservation (Rome, NY, USA) to produce brown trout ( Salmo salar ) and brook trout ( Salvelinus fontinalis ) that are resistant to Aeromonas salmonicida . This program, specifically as it relates to brook trout, is reviewed throughout the current manuscript. In addition, we present a comparison between the performance of the Rome strain of brook trout to that of the Owhi strain of brook trout during a 17-month production cycle at the Ed Weed Fish Culture Station (Grand Isle, VT, USA) and after stocking into Vermont waters. The Owhi strain is used in recreational fisheries because it has good post-stocking survival, but these fish are sensitive to furunculosis. Our data indicated that the Rome strain had a food conversion rate of 1.3 that was slightly less than the 1.1 conversion rate of the Owhi brook trout. The growth rate measured as Monthly Temperature Units per inch (MTU/in.) among Rome brook trout (24.9 MTU/in.) was better than the Owhi brook trout (29.5 MTU/in.). Both the average length (23.6 cm) and weight (159.7 g) of individual Rome brook trout were superior to those of the Owhi strain (20.4 cm and 78.2 g, respectively). Just prior to stocking, survival within the hatchery was 84% among the Rome trout, but only 51% among the Owhi brook trout and mortality was attributed to a persistent epizootic of furunculosis. Microbiological assays indicated that the prevalence of A. salmonicida in dermal mucus attained equivalent levels within both strains of fish at different phases of the production cycle. The level of systemic infection, however, was regulated to a much greater extent by the Rome strain of brook trout throughout production. Our results indicated that the Rome brook trout strain satisfies management objectives for establishing an effective recreational brook trout fishery. Use of this strain also reduces management issues that complicate production when A. salmonicida is enzootic.

Vermont

Chronobiologic approach to aquaculture

Diel and seasonal changes in the environment directly or indirectly control many biological functions. Chronobiology, the study of biological functions in relation to time of day, time of year, lunar phases, and other consistent cues, could have important applications in aquaculture. Physiological conditions that vary seasonally include feeding time, tolerance of fish to stress, the state of gonad development, lipid and water content of muscle tissue, and the dress‐out weight of food fish. The quality of cultured fish may vary with the time of day when fish are fed, seined, graded, treated with therapeutic chemicals, injected with hormones, or physically disturbed. Efficiency of production and quality of aquacultural products might be improved if the activities of fish husbandry were timed to coincide with the biological rhythms of fish.

Transactions of the American Fisheries Society

Shellfish aquaculture farms as foraging habitat for nearshore fishes and crabs

Objective Oyster reefs across North America have declined precipitously over the past 140 years. In Washington State, Olympia oyster Ostrea lurida reefs historically provided water filtration and nearshore structural habitat for fishes and invertebrates, but this species is now functionally extinct across its historical range. In place of these naturally occurring reefs, shellfish farms consisting mainly of nonnative Pacific oysters Magallana gigas now occupy patches of nearshore habitat across Washington. These farms modify intertidal substrate by adding structural habitat via suspended oyster grow bags, predator exclusion nets, loose oyster beds, and other shellfish grow-out gear. As interest and investment in shellfish aquaculture have expanded both locally and globally, so has interest in how these farms modify intertidal habitat and whether the complex structure created by the shellfish and shellfish growing gear provides ecosystem services that are comparable to those of unfarmed areas, such as mudflats and eelgrass meadows. Methods In this study, we sought to quantify how shellfish farms are used as foraging habitat for several common nearshore species of fish and crabs in Puget Sound, Washington. We used direct observations of species-specific behaviors from underwater video to model how habitat type affected observed foraging rates. Result We obtained a total of 393 crab observations, 431 demersal fish observations, and 1856 pelagic fish observations across all seven farm sites. Several common species of pelagic fish (e.g., surfperch [Embiotocidae]) used aquaculture-growing gear more frequently than unfarmed areas as foraging habitat, but Metacarcinus spp. crabs displayed higher foraging frequency in unfarmed mudflats. Species groups such as sculpins (Cottidae) and small flatfish (Pleuronectidae) clearly used specific aquaculture-growing gear and mudflats in roughly equal proportion. Conclusion Our results indicate that shellfish farms within a larger nearshore habitat mosaic of eelgrass meadows, mudflats, bivalve aquaculture gear, and edge habitat can provide foraging habitat for several species of nearshore fish.

Washington

Outbreeding depression in hybrids between odd-and even-broodyear pink salmon

Fewer F 2 hybrids between even- and odd-broodline pink salmon ( Oncorhynchus gorbuscha ), which are lines that are genetically isolated by their strict two-year life cycle, survived than did F 2 controls, indicating outbreeding depression. Cryopreserved sperm of 40 broodyear 1990 males and of 40 broodyear 1991 males fertilized equal subsamples of eggs from 40 broodyear 1992 females. Return rates of F 1 hybrids (1.73%) and controls (1.63%) in 1994 did not differ significantly ( P =0.30). F 2 hybrid and control crosses were made from 40 males and 40 females selected at random from each return group. Offspring were differentially marked and released. In 1996, returns differed significantly ( P =0.011) between hybrids ( n =34, 0.34%) and controls ( n =44, 0.42%). The low rate of return of the control fish was similar to the measured return of a much larger group of tagged Auke Creek pink salmon, and probably not an artifact of the experiment. Although no increase in fluctuating asymmetry of paired meristic counts was observed in either F 1 or F 2 hybrids, size and some meristic counts of hybrids exceed measurements of controls, suggesting heterosis for those traits. The observations of decreased survival in F 2 hybrids confirm previous work [Gharrett, A.J., Smoker, W.W., 1991. Two generations of hybrids between even- and odd-year pink salmon ( O. gorbuscha ). Canadian Journal of Fisheries and Aquatic Science 48(9) 1744–1749]. Although genetic divergence between pink salmon broodlines is large and outbreeding depression might be expected in such unlikely hybrids, the results document the occurrence of outbreeding depression in salmon and signal caution in making management and aquacultural decisions that may create the possibility of outbreeding depression in self-sustaining or cultured populations.

Aquaculture

Science and innovation for battling invasive carp

The U.S. Geological Survey (USGS) is the Federal Government’s independent research agency that conducts research to inform management of invasive species. Bighead, black, grass, and silver carp, which are native to China, were originally stocked in aquaculture facilities to control algae, snails, and vegetation. These species have invaded the Mississippi River and are now established throughout the lower and middle Mississippi River Basins and some of its large tributaries where they damage ecosystems and harm economies. A reproducing population of grass carp in Lake Erie is a risk to the $7 billion Great Lakes fishery. The USGS is leading research efforts on risk assessment and on early detection of new invasions. The USGS is also developing and evaluating harvest methods, barriers and deterrents, and baits/attractants to provide Federal and State management agencies the tools needed to manage and reduce populations of these species.

Alabama, Arkansas, Illinois, Indiana, Iowa, Kansas