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Sample records for basin anadromous salmonid

  1. Integrated Hatchery Operations Team: Policies and Procedures for Columbia Basin Anadromous Salmonid Hatcheries, 1994 Annual Report.

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    Integrated Hatchery Operations Team (Northwest Power Planning Council, Portland, OR)

    1995-01-01

    This document outlines regional policies and procedures for hatchery operations in the Columbia River Basin. The purpose of these policies is to provide regional guidelines by which all anadromous fish hatcheries will be operated. These policies will be adopted by the fisheries co-managers, and will provide guidance to operate hatcheries in an efficient and biologically sound manner. The hatchery policies presented in this manual are not intended to establish production priorities. Rather, the intent is to guide hatchery operations once production numbers are established. Hatchery operations discussed in this report include broodstock collection, spawning, incubation of eggs, fish rearing and feeding, fish release, equipment maintenance and operations, and personnel training. Decisions regarding production priorities must be provided by fishery managers through a comprehensive plan that addresses both natural and hatchery fish production. The Integrated Hatchery Operations Team is a multi-agency group called for by the Northwest Power Planning Council. This team was directed to develop new basinwide policies for managing and operating all existing and future anadromous fish hatcheries in the Columbia River Basin. The parties pledge to confer with each other and to use their authorities and resources to accomplish these mutually acceptable hatchery practices.

  2. Survey of Artificial Production of Anadromous Salmonids in the Columbia River Basin, 1981-1985 Final Report.

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    Washington, Percy M.

    1985-11-25

    The overall objective of this project is to collect, organize, and summarize data concerning anadromous fish culture stations of the Columbia River system for 1981, 1982, and 1983 and to create a data archive system with a means of making this information available to the public.

  3. Outplanting Anadromous Salmonids, A Lilterature Study.

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    Smith, Eugene M.

    1985-10-01

    This paper presents a list of more than 200 references on topics associated with offstation releases of hatchery stocks of anadromous fish used to supplement or reestablish wild rearing. The narrative briefly reviews influences of genetics, rearing density of fish in the natural environment, survival rates observed from outplanted stocks, and estimation procedures for stocking rates and rearing densities. We have attempted to summarize guidelines and recommendations for fishery managers to consider. Based on tagging studies, a typical smolt release from a Willamette River hatchery would return 0.29% of the smolts to the stream of release as adults. Catch to escapement ratios for adult Willamette chinook vary widely between broods, but on average two fish are caught for each fish that escapes. The catch is about evenly divided between offshore and freshwater harvest. British Columbia is the primary location of offshore harvest, and the lower Willamette River is the primary location of freshwater harvest. Review of departmental policy indicates that only Willamette stock spring chinook are currently acceptable for use in a proposed outplant study within the Willamette basin. Further, most Oregon Department of Fish and Wildlife district management biologists would prefer not to transfer any stocks of spring chinook between drainage subbasins. State fishery managers identified 16 Willamette basin streams as being suitable for supplementation with spring chinook from hatcheries. We reviewed the potential for rearing salmon in reservoirs throughout the basin. Use of the Carmen-Smith spawning channel, which was constructed on the upper McKenzie River in 1960, has generally declined with the decline in populations of chinook salmon in this river. The Carmen-Smith channel still provides a spawning place for those relatively few adult chinook that still return each year, but more fishery benefits may result from other uses of this facility. 7 figs., 8 tabs.

  4. Latent Toxicity of Endothall to Anadromous Salmonids During Seawater Challenge.

    Science.gov (United States)

    Courter, Lauren A; Garrison, Thomas M; Courter, Ian I

    2016-05-01

    Limited evidence exists on the latent effects of toxicant exposure on the seawater adaptability of anadromous salmon and steelhead. It is unclear whether such an effect exists for the widely used and relatively non-toxic herbicide endothall. Coho salmon, Oncorhynchus kisutch (coho), Chinook salmon, O. tshawytscha (Chinook), and anadromous rainbow trout, O. mykiss (steelhead) were subjected to a 10-day seawater challenge following freshwater treatments [0-12 mg acid equivalent (a.e)./L at 96 h]. Mean survival resulted in 82 % (n = 225), 84 % (n = 133), 90 % (n = 73) and 59 % (n = 147) survival for 0, 3-5, 6-8, and 9-12 mg a.e./L, respectively. Our results indicate a lower toxicity threshold compared with previously reported acute toxicity results, but higher compared with previous seawater challenge studies. We demonstrate the utility of the seawater challenge assay to accurately define toxic effects of pesticides on salmonids with complex life-histories.

  5. Influence of forest and rangeland management on anadromous fish habitat in Western North America: habitat requirements of anadromous salmonids.

    Science.gov (United States)

    D.W. Reiser; T.C. Bjornn

    1979-01-01

    Habitat requirements of anadromous and some resident salmonid fishes have been described for various life stages, including upstream migration of adults, spawning, incubation, and juvenile rearing. Factors important in the migration of adults are water temperature, minimum water depth, maximum water velocity, turbidity, dissolved oxygen, and...

  6. Increased levels of harvest and habitat law enforcement and public awareness for anadromous salmonids and resident fish in the Columbia River Basin - Demonstration period, 1992-1994. Final report

    International Nuclear Information System (INIS)

    1995-06-01

    This report was funded by the Bonneville Power Administration (BPA), US Department of Energy, as part of BPA's program to protect, mitigate, and enhance fish and wildlife affected by the development and operation of hydroelectric facilities on the Columbia River and its tributaries. Illegal harvest and violation of habitat protection regulations are factors affecting the survival of many native species of anadromous and resident fish in the Columbia Basin

  7. Increased Levels of Harvest and Habitat Law Enforcement and Public Awareness for Anadromous Salmonids and Resident Fish in the Columbia River Basin -- Demonstration Period, 1992--1994, Final Report.

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    NeSmith, Frank (Idaho Department of Fish and Game, Boise, ID); Long, Mack (Montana Department of Fish, Wildlife and Paks, Kalispell, MT); Matthews, Dayne (Washington Department of Fish and Wildlife, Olympia, WA)

    1995-06-01

    This report was funded by the Bonneville Power Administration (BPA), US Department of Energy, as part of BPA`s program to protect, mitigate, and enhance fish and wildlife affected by the development and operation of hydroelectric facilities on the Columbia River and its tributaries. Illegal harvest and violation of habitat protection regulations are factors affecting the survival of many native species of anadromous and resident fish in the Columbia Basin.

  8. A synthesis of tagging studies examining the behaviour and survival of anadromous salmonids in marine environments.

    Directory of Open Access Journals (Sweden)

    S Matthew Drenner

    Full Text Available This paper synthesizes tagging studies to highlight the current state of knowledge concerning the behaviour and survival of anadromous salmonids in the marine environment. Scientific literature was reviewed to quantify the number and type of studies that have investigated behaviour and survival of anadromous forms of Pacific salmon (Oncorhynchus spp., Atlantic salmon (Salmo salar, brown trout (Salmo trutta, steelhead (Oncorhynchus mykiss, and cutthroat trout (Oncorhynchus clarkii. We examined three categories of tags including electronic (e.g. acoustic, radio, archival, passive (e.g. external marks, Carlin, coded wire, passive integrated transponder [PIT], and biological (e.g. otolith, genetic, scale, parasites. Based on 207 papers, survival rates and behaviour in marine environments were found to be extremely variable spatially and temporally, with some of the most influential factors being temperature, population, physiological state, and fish size. Salmonids at all life stages were consistently found to swim at an average speed of approximately one body length per second, which likely corresponds with the speed at which transport costs are minimal. We found that there is relatively little research conducted on open-ocean migrating salmonids, and some species (e.g. masu [O. masou] and amago [O. rhodurus] are underrepresented in the literature. The most common forms of tagging used across life stages were various forms of external tags, coded wire tags, and acoustic tags, however, the majority of studies did not measure tagging/handling effects on the fish, tag loss/failure, or tag detection probabilities when estimating survival. Through the interdisciplinary application of existing and novel technologies, future research examining the behaviour and survival of anadromous salmonids could incorporate important drivers such as oceanography, tagging/handling effects, predation, and physiology.

  9. Anadromous salmonids of the Hanford Reach, Columbia River: 1984 status

    Energy Technology Data Exchange (ETDEWEB)

    Becker, C.D.

    1985-09-01

    The Hanford Reach, a regulated but flowing section of the Columbia River, supports spawning populations of fall chinook salmon and steelhead. It also serves as a migration route for upriver runs of chinook, coho and sockeye salmon, and of steelhead. Environmental studies conducted in association with activities on the Hanford Site provide a basis for assessing present ecological conditions in the Hanford Reach. Spawning populations of fall chinook salmon at Hanford increased dramatically after 1960, when Priest Rapids Dam was completed, and have remained relatively stable since 1969. Generally, upriver runs of spring, summer, and fall chinook salmon have been depressed, but the fall run has been increasing since 1980. Habitat modification represents the greatest threat to sustained production of fall chinook salmon in the Hanford Reach. Operations on and near the Hanford Site releases of small amounts of radioactivity from onsite operations to river and groundwater, and operation of a steam electric plant, can have negligible effects on salmonids and other aquatic resources. Possible activities with potential future impacts include development of a multi-unit power plant complex at Hanford, construction of a low-head hydroelectric dam above Richland, flow fluctuations from peaking power generation at Priest Rapids Dam, irrigation and reductions of instream flows, and dredging and commercial navigation above Hanford. If reproducing populations of fall chinook salmon and steelhead are to survive in the mid-Columbia River, the Hanford Reach must remain flowing, undeveloped for navigation, and with unimpaired water quality. 156 refs., 16 figs., 7 tabs.

  10. Influence of Habitat Modifications on Habitat Composition and Anadromous Salmonid Populations in Fish Creek, Oregon, 1983-1988 Annual Report.

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    Reeves, Gordon H.; Everest, Fred H. (Oregon State University, Pacific Northwest Forest and Range Experiment Station, Corvallis, OR); Hohler, David B. (Mount Hood National Forest, Clackamas River Ranger District, Estacada, OR)

    1990-05-01

    Modification of degraded habitats to increase populations of anadromous salmonids is a major focus of management agencies throughout the Pacific Northwest. Millions of dollars are spent annually on such efforts. Inherent in implementing habitat improvements is the need for quantitative evaluation of the biological and physical effects of such work. Reeves et al. (in press), however, noted that such evaluations are rare, making it difficult to assess the true results of habitat work. While it is not economically possible to thoroughly evaluate every habitat project, it is essential that intensive evaluations be done on selected representative projects. One such evaluation program has been underway since 1982 on Fish Creek, a tributary of the Clackamas River near Estacada, OR. Habitat modification has been done by the USDA Forest Service, Estacada Ranger District, Mt. Hood National Forest with funding provided in part by the Bonneville Power Administration (BPA). The USDA Forest Service, Anadromous Fish Habitat Research Unit, Pacific Northwest Research Station (PNW), Corvallis, OR is charged with: (1) evaluating the biological and physical responses to habitat modifications on a basin scale; and (2) developing a cost-benefit analysis of the program. Preliminary results have been reported in a series of annual publications, Everest and Sedell 1983, 1984 and Everest et al. 1985, 1986, 1987, 1988. The objectives of this paper are to: (1) report 1988 observations of biological and physical changes in habitat, salmonid populations, and smolt production in Fish Creek, and (2) examine preliminary trends in fish habitat and populations related to habitat improvement over the period 1983-1988. We have prefaced the trends in the latter objective as preliminary because we believe it could take a minimum of 10 years before the full biological and physical responses to habitat work are realized. We therefore urge caution in interpreting these preliminary results.

  11. Intestinal fluid absorption in anadromous salmonids: importance of tight junctions and aquaporins

    Directory of Open Access Journals (Sweden)

    Kristina eSundell

    2012-09-01

    Full Text Available The anadromous salmonid life cycle includes both fresh water (FW and seawater (SW stages. The parr-smolt transformation (smoltification pre–adapt the fish to SW while still in FW. The osmoregulatory organs change their mode of action from a role of preventing water inflow in FW, to absorb ions to replace water lost by osmosis in SW. During smoltification, the drinking rate increases, in the intestine the ion and fluid transport increases and is further elevated after SW entry. In SW, the intestine absorbs ions to create an inwardly directed water flow which is accomplished by increased Na+,K+-ATPase (NKA activity in the basolateral membrane, driving ion absorption via ion channels and/or co-transporters. This review will aim at discussing the expression patterns of the ion transporting proteins involved in intestinal fluid absorption in the FW stage, during smoltification and after SW entry. Of equal importance for intestinal fluid absorption as the active absorption of ions, is the permeability of the epithelium to ions and water. During the smoltification the increase in NKA activity and water uptake in SW is accompanied by decreased paracellular permeability suggesting a redirection of the fluid movement from a paracellular route in FW, to a transcellular route in SW. Increased transcellular fluid absorption could be achieved by incorporation of aquaporins (AQPs into the enterocyte membranes and/or by a change in fatty acid profile of the enterocyte lipid bilayer. An increased incorporation of unsaturated fatty acids into the membrane phospholipids will increase water permeability by enhancing the fluidity of the membrane. A second aim of the present review is therefore to discuss the presence and regulation of expression of AQPs in the enterocyte membrane as well as to discuss the profile of fatty acids present in the membrane phospholipids during different stages of the salmonid lifecycle.

  12. Impact of beaver dams on abundance and distribution of anadromous salmonids in two lowland streams in Lithuania.

    Science.gov (United States)

    Virbickas, Tomas; Stakėnas, Saulius; Steponėnas, Andrius

    2015-01-01

    European beaver dams impeded movements of anadromous salmonids as it was established by fishing survey, fish tagging and redd counts in two lowland streams in Lithuania. Significant differences in abundancies of other litophilic fish species and evenness of representation by species in the community were detected upstream and downstream of the beaver dams. Sea trout parr marked with RFID tags passed through several successive beaver dams in upstream direction, but no tagged fish were detected above the uppermost dam. Increase in abundances of salmonid parr in the stream between the beaver dams and decrease below the dams were recorded in November, at the time of spawning of Atlantic salmon and sea trout, but no significant changes were detected in the sections upstream of the dams. After construction of several additional beaver dams in the downstream sections of the studied streams, abundance of Atlantic salmon parr downstream of the dams decreased considerably in comparison with that estimated before construction.

  13. Impact of beaver dams on abundance and distribution of anadromous salmonids in two lowland streams in Lithuania.

    Directory of Open Access Journals (Sweden)

    Tomas Virbickas

    Full Text Available European beaver dams impeded movements of anadromous salmonids as it was established by fishing survey, fish tagging and redd counts in two lowland streams in Lithuania. Significant differences in abundancies of other litophilic fish species and evenness of representation by species in the community were detected upstream and downstream of the beaver dams. Sea trout parr marked with RFID tags passed through several successive beaver dams in upstream direction, but no tagged fish were detected above the uppermost dam. Increase in abundances of salmonid parr in the stream between the beaver dams and decrease below the dams were recorded in November, at the time of spawning of Atlantic salmon and sea trout, but no significant changes were detected in the sections upstream of the dams. After construction of several additional beaver dams in the downstream sections of the studied streams, abundance of Atlantic salmon parr downstream of the dams decreased considerably in comparison with that estimated before construction.

  14. Stock Assessment of Columbia River Anadromous Salmonids : Final Report, Volume I, Chinook, Coho, Chum and Sockeye Salmon Summaries.

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    Howell, Philip J.

    1986-07-01

    The purpose was to identify and characterize the wild and hatchery stocks of salmon and steelhead in the Columbia River Basin on the basis of currently available information. This report provides a comprehensive compilation of data on the status and life histories of Columbia Basin salmonid stocks.

  15. Stock Summary Reports for Columbia River Anadromous Salmonids, Volume V; Idaho Subbasins, 1992 CIS Summary Report.

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    Keifer, Sharon (Idaho Department of Fish and Game, Boise, ID); Rowe, Mike (Shoshone-Bannock Tribes, Fort Hall, ID); Hatch, Keith (Columbia River Inter-Tribal Fish Commission, Portland, OR)

    1993-05-01

    An essential component of the effort to rebuild the Columbia Basin's anadromous fish resources is that available information and experience be organized and shared among numerous organizations and individuals. Past experience and knowledge must form the basis for actions into the future. Much of this knowledge exists only in unpublished form in agency and individual files. Even that information which is published in the form of technical and contract reports receives only limited distribution and is often out of print and unavailable after a few years. Only a small fraction of the basin's collective knowledge is captured in permanent and readily available databases (such as the Northwest Environmental Database) or in recognized journals. State, tribal, and federal fishery managers have recognized these information management problems and have committed to a program, the Coordinated Information System Project, to capture and share more easily the core data and other information upon which management decisions are based. That project has completed scoping and identification of key information needs and development of a project plan. Work performed under the CIS project will be coordinated with and extend information contained in the Northwest Environmental Database. Construction of prototype systems will begin in Phase 3. This report is one in a series of seven describing the results of the Coordinated Information System scoping and needs identification phase. A brief description of each of these reports is given.

  16. Risk assessment for the reintroduction of anadromous salmonids upstream of Chief Joseph and Grand Coulee Dams, Northeastern Washington

    Science.gov (United States)

    Hardiman, Jill M.; Breyta, Rachel B.; Haskell, Craig A.; Ostberg, Carl O.; Hatten, James R.; Connolly, Patrick J.

    2017-09-12

    The Upper Columbia United Tribes (UCUT; Spokane, Colville, Kootenai, Coeur d’Alene, and Kalispel Tribes) and Washington Department of Fish and Wildlife want to reintroduce anadromous salmonids to their historical range to restore ecosystem function and lost cultural and spiritual relationships in the upper Columbia River, northeastern Washington. The UCUT contracted with the U.S. Geological Survey to assess risks to resident taxa (existing fish populations in the reintroduction area upstream of Chief Joseph and Grand Coulee Dams) and reintroduced salmon associated with reintroduction. We developed a risk assessment framework for reintroduction of anadromous salmonids upstream of Chief Joseph and Grand Coulee Dams. To accomplish this goal, we applied strategies identified in previous risk assessment frameworks for reintroduction. The risk assessment is an initial step towards an anadromous reintroduction strategy. An initial list of potential donor sources for reintroduction species was developed from previous published sources for Chinook Salmon (Oncorhynchus tshawytscha) donors in the Transboundary Reach of the Columbia River, British Columbia; an ecological risk assessment of upper Columbia River hatchery programs on non-target taxa of concern; and a review of existing hatchery programsDuring two workshops, we further identified and ranked potential donor sources of anadromous Redband Trout (steelhead; O. mykiss), Chinook Salmon, Sockeye Salmon (O. nerka), and Coho Salmon (O. kisutch). We also identified resident fish populations of interest and their primary habitat, location, status, and pathogen concerns to determine the potential risks of reintroduction. Species were deemed of interest based on resource management and potential interactions (that is, genetics, competition, and predation) with introduced species. We developed tables of potential donors by species and characterized potential sources (hatchery and natural origins), populations (individual runs

  17. CTUIR Umatilla Anadromous Fisheries Habitat Project : A Columbia River Basin Fish Habitat Project 2008 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Hoverson, Eric D.; Amonette, Alexandra

    2009-02-09

    The Umatilla Anadromous Fisheries Habitat Project (UAFHP) is an ongoing effort to protect, enhance, and restore riparian and instream habitat for the natural production of anadromous salmonids in the Umatilla River Basin, Northeast Oregon. Flow quantity, water temperature, passage, and lack of in-stream channel complexity have been identified as the key limiting factors in the basin. During the 2008 Fiscal Year (FY) reporting period (February 1, 2008-January 31, 2009) primary project activities focused on improving instream and riparian habitat complexity, migrational passage, and restoring natural channel morphology and floodplain function. Eight primary fisheries habitat enhancement projects were implemented on Meacham Creek, Birch Creek, West Birch Creek, McKay Creek, West Fork Spring Hollow, and the Umatilla River. Specific restoration actions included: (1) rectifying one fish passage barrier on West Birch Creek; (2) participating in six projects planting 10,000 trees and seeding 3225 pounds of native grasses; (3) donating 1000 ft of fencing and 1208 fence posts and associated hardware for 3.6 miles of livestock exclusion fencing projects in riparian areas of West Birch and Meacham Creek, and for tree screens to protect against beaver damage on West Fork Spring Hollow Creek; (4) using biological control (insects) to reduce noxious weeds on three treatment areas covering five acres on Meacham Creek; (5) planning activities for a levee setback project on Meacham Creek. We participated in additional secondary projects as opportunities arose. Baseline and ongoing monitoring and evaluation activities were also completed on major project areas such as conducting photo point monitoring strategies activities at the Meacham Creek Large Wood Implementation Project site (FY2006) and at additional easements and planned project sites. Fish surveys and aquatic habitat inventories were conducted at project sites prior to implementation. Proper selection and implementation of

  18. Predation by Northern Pikeminnow and tiger muskellunge on juvenile salmonids in a high–head reservoir: Implications for anadromous fish reintroductions

    Science.gov (United States)

    Sorel, Mark H.; Hansen, Adam G.; Connelly, Kristin A.; Wilson, Andrew C.; Lowery, Erin D.; Beauchamp, David A.

    2016-01-01

    The feasibility of reintroducing anadromous salmonids into reservoirs above high-head dams is affected by the suitability of the reservoir habitat for rearing and the interactions of the resident fish with introduced fish. We evaluated the predation risk to anadromous salmonids considered for reintroduction in Merwin Reservoir on the North Fork Lewis River in Washington State for two reservoir use-scenarios: year-round rearing and smolt migration. We characterized the role of the primary predators, Northern Pikeminnow Ptychocheilus oregonensis and tiger muskellunge (Northern Pike Esox lucius × Muskellunge E. masquinongy), by using stable isotopes and stomach content analysis, quantified seasonal, per capita predation using bioenergetics modeling, and evaluated the size and age structures of the populations. We then combined these inputs to estimate predation rates of size-structured population units. Northern Pikeminnow of FL ≥ 300 mm were highly cannibalistic and exhibited modest, seasonal, per capita predation on salmonids, but they were disproportionately much less abundant than smaller, less piscivorous, conspecifics. The annual predation on kokanee Oncorhynchus nerka (in biomass) by a size-structured unit of 1,000 Northern Pikeminnow having a FL ≥ 300 mm was analogous to 16,000–40,000 age-0 spring Chinook Salmon O. tshawytscha rearing year-round, or 400–1,000 age-1 smolts migrating April–June. The per capita consumption of salmonids by Northern Pikeminnow having a FL ≥ 200 mm was relatively low, due in large part to spatial segregation during the summer and the skewed size distribution of the predator population. Tiger muskellunge fed heavily on Northern Pikeminnow, other nonsalmonids, and minimally on salmonids. In addition to cannibalism within the Northern Pikeminnow population, predation by tiger muskellunge likely contributed to the low recruitment of larger (more piscivorous) Northern Pikeminnow, thereby decreasing the risk of predation to

  19. Stock Summary Reports for Columbia River Anadromous Salmonids, Volume 1; Oregon Subbasins Below Bonneville Dam, 1992 CIS Summary Report.

    Energy Technology Data Exchange (ETDEWEB)

    Olsen, Eric; Pierce, Paige (Oregon Department of Fish and Wildlife, Clackamas, OR); Hatch, Keith (Columbia River Inter-Tribal Fish Commission, Portland, OR)

    1993-05-01

    An essential component of the effort to rebuild the Columbia Basin's anadromous fish resources is that available information and experience be organized and shared among numerous organizations and individuals. Past experience and knowledge must form the basis for actions into the future. Much of this knowledge exists only in unpublished form in agency and individual files. Even that information which is published in the form of technical and contract reports receives only limited distribution and is often out of print and unavailable after a few years. Only a small fraction of the basin's collective knowledge is captured in permanent and readily available databases (such as the Northwest Environmental Database) or in recognized journals. State, tribal, and federal fishery managers have recognized these information management problems and have committed to a program, the Coordinated Information System Project, to capture and share more easily the core data and other information upon which management decisions are based. That project has completed scoping and identification of key information needs and development of a project plan. Work performed under the CIS project will be coordinated with and extend information contained in the Northwest Environmental Database. Construction of prototype systems will begin in Phase 3. This report is one in a series of seven describing the results of the Coordinated Information System scoping and needs identification phase. A brief description of each of these reports follows. This report (Roger 1992) summarizes and integrates the results of the next five reports and relates them to deliverables identified in the Phase II cooperative agreement. Broader issues of organization and operation which are not appropriate for the more focused reports are also discussed. This report should be viewed as an executive summary for the CIS project to date. If one wants a quick overview of the CIS project, this report and the project

  20. Stock Summary Reports for Columbia River Anadromous Salmonids, Volume II; Oregon Subbasins Above Bonneville Dam, 1992 CIS Summary Report.

    Energy Technology Data Exchange (ETDEWEB)

    Olsen, Eric; Pierce, Paige (Oregon Department of Fish and Wildlife, Clackamas, OR); Hatch, Keith (Columbia River Inter-Tribal Fish Commission, Portland, OR)

    1993-05-01

    An essential component of the effort to rebuild the Columbia Basin's anadromous fish resources is that available information and experience be organized and shared among numerous organizations and individuals. Past experience and knowledge must form the basis for actions into the future. Much of this knowledge exists only in unpublished form in agency and individual files. Even that information which is published in the form of technical and contract reports receives only limited distribution and is often out of print and unavailable after a few years. Only a small fixtion of the basin's collective knowledge is captured in permanent and readily available databases (such as the Northwest Environmental Database) or in recognized journals. State, tribal, and fedend fishery managers have recognized these information management problems and have committed to a program, the Coordinated Information System Project, to capture and share more easily the core data and other information upon which management decisions am based. That project has completed scoping and identification of key information needs and development of a project plan. Work performed under the CM project will be coordinated with and extend information contained in the Northwest Environmental Database. Construction of prototype systems will begin in Phase 3. This report is one in a series of seven describing the results of the Coordinated Information System scoping and needs identification phase. A brief description of each of these reports follows. This report (Roger 1992) summarizes and integrates the results of the next five reports and relates them to deliverables identified in the Phase II cooperative agreement. Broader issues of organization and operation which are not appropriate for the more focused reports are also discussed. This report should be viewed as an executive summary for the CM project to date. If one wants a quick overview of the CIS project, this report and the project plan

  1. Trophic feasibility of reintroducing anadromous salmonids in three reservoirs on the north fork Lewis River, Washington: Prey supply and consumption demand of resident fishes

    Science.gov (United States)

    Sorel, Mark H.; Hansen, Adam G.; Connelly, Kristin A.; Beauchamp, David A.

    2016-01-01

    The reintroduction of anadromous salmonids in reservoirs is being proposed with increasing frequency, requiring baseline studies to evaluate feasibility and estimate the capacity of reservoir food webs to support reintroduced populations. Using three reservoirs on the north fork Lewis River as a case study, we demonstrate a method to determine juvenile salmonid smolt rearing capacities for lakes and reservoirs. To determine if the Lewis River reservoirs can support reintroduced populations of juvenile stream-type Chinook Salmon Oncorhynchus tshawytscha, we evaluated the monthly production of daphniaDaphnia spp. (the primary zooplankton consumed by resident salmonids in the system) and used bioenergetics to model the consumption demand of resident fishes in each reservoir. To estimate the surplus of Daphnia prey available for reintroduced salmonids, we assumed a maximum sustainable exploitation rate and accounted for the consumption demand of resident fishes. The number of smolts that could have been supported was estimated by dividing any surplus Daphnia production by the simulated consumption demand of an individual Chinook Salmon fry rearing in the reservoir to successful smolt size. In all three reservoirs, densities of Daphnia were highest in the epilimnion, but warm epilimnetic temperatures and the vertical distribution of planktivores suggested that access to abundant epilimnetic prey was limited. By comparing accessible prey supply and demand on a monthly basis, we were able to identify potential prey supply bottlenecks that could limit smolt production and growth. These results demonstrate that a bioenergetics approach can be a valuable method of examining constraints on lake and reservoir rearing capacity, such as thermal structure and temporal food supply. This method enables numerical estimation of rearing capacity, which is a useful metric for managers evaluating the feasibility of reintroducing Pacific salmon Oncorhynchus spp. in lentic systems.

  2. An epidemiological model of virus transmission in salmonid fishes of the Columbia River Basin

    Science.gov (United States)

    Ferguson, Paige F. B.; Breyta, Rachel; Brito, Ilana L.; Kurath, Gael; LaDeau, Shannon L.

    2018-01-01

    We have developed a dynamic epidemiological model informed by records of viral presence and genotypes to evaluate potential transmission routes maintaining a viral pathogen in economically and culturally important anadromous fish populations. In the Columbia River Basin, infectious hematopoietic necrosis virus (IHNV) causes severe disease, predominantly in juvenile steelhead trout (Oncorhynchus mykiss) and less frequently in Chinook salmon (O. tshawytscha). Mortality events following IHNV infection can be devastating for individual hatchery programs. Despite reports of high local mortality and extensive surveillance efforts, there are questions about how viral transmission is maintained. Modeling this system offers important insights into disease transmission in natural aquatic systems, as well as about the data requirements for generating accurate estimates about transmission routes and infection probabilities. We simulated six scenarios in which testing rates and the relative importance of different transmission routes varied. The simulations demonstrated that the model accurately identified routes of transmission and inferred infection probabilities accurately when there was testing of all cohort-sites. When testing records were incomplete, the model accurately inferred which transmission routes exposed particular cohort-sites but generated biased infection probabilities given exposure. After validating the model and generating guidelines for result interpretation, we applied the model to data from 14 annual cohorts (2000–2013) at 24 focal sites in a sub-region of the Columbia River Basin, the lower Columbia River (LCR), to quantify the relative importance of potential transmission routes in this focal sub-region. We demonstrate that exposure to IHNV via the return migration of adult fish is an important route for maintaining IHNV in the LCR sub-region, and the probability of infection following this exposure was relatively high at 0.16. Although only 1% of

  3. Confederated Tribes Umatilla Indian Reservation (CTUIR) Umatilla Anadromous Fisheries Habitat Project : A Columbia River Basin Fish Habitat Project : Annual Report Fiscal Year 2007.

    Energy Technology Data Exchange (ETDEWEB)

    Hoverson, Eric D.; Amonette, Alexandra

    2008-12-02

    The Umatilla Anadromous Fisheries Habitat Project (UAFHP) is an ongoing effort to protect, enhance, and restore riparian and instream habitat for the natural production of anadromous salmonids in the Umatilla River Basin, Northeast Oregon. Flow quantity, water temperature, passage, and lack of in-stream channel complexity have been identified as the key limiting factors in the basin. During the 2007 Fiscal Year (FY) reporting period (February 1, 2007-January 31, 2008) primary project activities focused on improving instream and riparian habitat complexity, migrational passage, and restoring natural channel morphology and floodplain function. Eight fisheries habitat enhancement projects were implemented on Meacham Creek, Camp Creek, Greasewood Creek, Birch Creek, West Birch Creek, and the Umatilla River. Specific restoration actions included: (1) rectifying five fish passage barriers on four creeks, (2) planting 1,275 saplings and seeding 130 pounds of native grasses, (3) constructing two miles of riparian fencing for livestock exclusion, (4) coordinating activities related to the installation of two off-channel, solar-powered watering areas for livestock, and (5) developing eight water gap access sites to reduce impacts from livestock. Baseline and ongoing monitoring and evaluation activities were also completed on major project areas such as conducting photo point monitoring strategies activities at the Meacham Creek Large Wood Implementation Project site (FY2006) and at all existing easements and planned project sites. Fish surveys and aquatic habitat inventories were conducted at project sites prior to implementation. Monitoring plans will continue throughout the life of each project to oversee progression and inspire timely managerial actions. Twenty-seven conservation easements were maintained with 23 landowners. Permitting applications for planned project activities and biological opinions were written and approved. Project activities were based on a variety

  4. Evaluation of juvenile salmonid outmigration and survival in the lower Umatilla River basin. Annual report, 1996

    International Nuclear Information System (INIS)

    Knapp, S.M.; Kern, J.C.; Cameron, W.A.; Snedaker, S.M.; Carmichael, R.W.

    1996-01-01

    This is the second year report of a multi-year project that monitors the outmigration and survival of hatchery and naturally-produced juvenile salmonids in the lower Umatilla River. This project supplements and complements ongoing or completed fisheries projects in the Umatilla River basin. Knowledge gained on outmigration and survival will assist researchers and managers in adapting hatchery practices, flow enhancement strategies, canal operations, and supplementation and enhancement efforts for natural and restored fish populations. The authors also report on tasks related to evaluating juvenile salmonid passage at Three Mile Falls Dam and West Extension Canal

  5. Climate-induced trends in predator–prey synchrony differ across life-history stages of an anadromous salmonid

    Science.gov (United States)

    Bell, Donovan A.; Kovach, Ryan; Vulstek, Scott C.; Joyce, John E.; Tallmon, David A.

    2017-01-01

    Differential climate-induced shifts in phenology can create mismatches between predators and prey, but few studies have examined predator–prey mismatch across multiple life-history stages. We used long-term data from a warming stream with shifting salmonid migration timings to quantify intra-annual migration synchrony between predatory Dolly Varden (Salvelinus malma) and Pacific salmon prey and examined how predator–prey synchrony has been influenced by climate change. We demonstrate that Dolly Varden have become increasingly mismatched with spring downstream migrations of abundant pink salmon (Oncorhynchus gorbuscha) juveniles. However, Dolly Varden have remained matched with fall upstream migrations of spawning Pacific salmon, including coho (Oncorhynchus kisutch), sockeye (Oncorhynchus nerka), and pink salmon. Downstream predator–prey migration synchrony decreased over time and with higher temperatures, particularly with pink salmon. In contrast, upstream migration synchrony was temporally stable and increased with rising temperatures. Differing trends in Dolly Varden predator–prey synchrony may be explained by the direct use of salmon to cue upstream migration, but not downstream migration. Overall, we show that climate change can have differing impacts on predator–prey synchrony across life-history stages.

  6. Stock Summary Reports for Columbia River Anadromous Salmonids, Volume III; Washington Subbasin Below McNary Dam, 1992 CIS Summary Report.

    Energy Technology Data Exchange (ETDEWEB)

    Hatch, Keith (Columbia River Inter-Tribal Fish Commission, Portland, OR); Hymer, Joe (Washington Department of Fisheries, Battleground, WA); Wastel, Mike (Washington Department of Wildlife, Olympia, WA)

    1993-05-01

    An essential component of the effort to rebuild the Columbia Basin's anadromous fish resources is that available information and experience be organized and shared among numerous organizations and individuals. Past experience and knowledge must form the basis for actions into the future. Much of this knowledge exists only in unpublished form in agency and individual files. Even that information which is published in the form of technical and contract reports receives only limited distribution and is often out of print and unavailable after a few years. Only a small fraction of the basin's collective knowledge is captured in permanent and readily available databases (such as the Northwest Environmental Database) or in recognized journals. State, tribal, and federal fishery managers have recognized these information management problems and have committed to a program, the Coordinated Information System Project, to capture and share more easily the core data and other information upon which management decisions are based. That project has completed scoping and identification of key information needs and development of a project plan. Work performed under the CIS project will be coordinated with and extend information contained in the Northwest Environmental Database. Construction of prototype systems will begin in Phase 3. This report is one in a series of seven describing the results of the Coordinated Information System scoping and needs identification phase. A brief description of each of these reports is given.

  7. Enumeration of Juvenile Salmonids in the Okanogan Basin Using Rotary Screw Traps, Performance Period: March 15, 2006 - July 15, 2006.

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Peter N.; Rayton, Michael D.

    2007-05-01

    The Colville Tribes identified the need for collecting baseline census data on the timing and abundance of juvenile salmonids in the Okanogan River basin for the purpose of documenting local fish populations, augmenting existing fishery data and assessing natural production trends of salmonids. This report documents and assesses the pilot year of rotary trap capture of salmonid smolts on the Okanogan River. The project is a component of the Colville Tribes Okanogan Basin Monitoring and Evaluation Program (OBMEP) which began in 2004. Trapping for outmigrating fish began on 14 March 2006 and continued through 11 July 2006. Anadromous forms of Oncorhynchus, including summer steelhead (O. mykiss), Chinook (O. tshawytscha), and sockeye (O. nerka), were targeted for this study; all have verified, natural production in the Okanogan basin. Both 8-ft and 5-ft rotary screw traps were deployed on the Okanogan River from the Highway 20 Bridge and typically fished during evening hours or 24 hours per day, depending upon trap position and discharge conditions. Juvenile Chinook salmon were the most abundant species trapped in 2006 (10,682 fry and 2,024 smolts), followed by sockeye (205 parr and 3,291 smolts) and steelhead (1 fry and 333 smolts). Of the trapped Chinook, all fry were wild origin and all but five of the smolts were hatchery-reared. All trapped sockeye were wild origin and 88% of the steelhead smolts were hatchery-reared. Mark-recapture experiments were conducted using Chinook fry and hatchery-reared steelhead smolts (sockeye were not used in 2006 because the peak of the juvenile migration occurred prior to the onset of the mark-recapture experiments). A total of 930 chinook fry were marked and released across eight separate release dates (numbers of marked Chinook fry released per day ranged from 34 to 290 fish). A total of 11 chinook fry were recaptured for an overall trap efficiency of 1.18%. A total of 710 hatchery-reared steelhead were marked and released across

  8. Umatilla River Basin Anadromous Fish Habitat Enhancement Project : 1995 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, R.Todd

    1996-05-01

    During the 1995 - 96 project period, four new habitat enhancement projects were implemented under the Umatilla River Basin Anadromous Fish Habitat Enhancement Project by the Confederated Tribes of the Umatilla Indian Reservation (CTUIR) in the upper Umatilla River Basin. A total of 38,644 feet of high tensile smooth wire fencing was constructed along 3.6 miles of riparian corridor in the Meacham Creek, Wildhorse Creek, Greasewood Creek, West Fork of Greasewood Creek and Mission Creek watersheds. Additional enhancements on Wildhorse Creek and the lower Greasewood Creek System included: (1) installation of 0.43 miles of smooth wire between river mile (RM) 10.25 and RM 10.5 Wildhorse Creek (fence posts and structures had been previously placed on this property during the 1994 - 95 project period), (2) construction of 46 sediment retention structures in stream channels and maintenance to 18 existing sediment retention structures between RM 9.5 and RM 10.25 Wildhorse Creek, and (3) revegetation of stream corridor areas and adjacent terraces with 500 pounds of native grass seed or close species equivalents and 5,000 native riparian shrub/tree species to assist in floodplain recovery, stream channel stability and filtering of sediments during high flow periods. U.S. Fish and Wildlife Service (USFWS), Bureau of Indian Affairs (BIA) and Environmental Protection Agency (EPA) funds were cost shared with Bonneville Power Administration (BPA) funds, provided under this project, to accomplish habitat enhancements. Water quality monitoring continued and was expanded for temperature and turbidity throughout the upper Umatilla River Watershed. Physical habitat surveys were conducted on the lower 13 river miles of Wildhorse Creek and within the Greasewood Creek Project Area to characterize habitat quality and to quantify various habitat types by area.

  9. Grande Ronde Basin Fish Habitat Enhancement Project : 1998 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    McGowan, Vance R.; Powell, Russ M.

    1999-05-01

    The primary goal of ''The Grande Ronde Basin Fish Habitat Improvement Project'' is to access, create, improve, protect, and restore reparian and instream habitat for anadromous salmonids, thereby maximizing opportunities for natural fish production within the basin.

  10. Umatilla River Basin Anadromous Fish Habitat Enhancement Project : 2001 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, R. Todd; Sexton, Amy D.

    2003-02-01

    The Umatilla River Basin Anadromous Fish Habitat Enhancement Project continued to identify impacted stream reaches throughout the Umatilla River Basin for habitat improvements during the 2001 project period. Public outreach efforts, biological and physical monitoring, and continued development of a Umatilla Subbasin Watershed Assessment assisted the project in fostering public cooperation, targeting habitat deficiencies and determining habitat recovery measures. Projects continued to be maintained on 49 private properties, one 25-year Non-Exclusive Bureau of Indian Affairs' Easement was secured, six new projects implemented and two existing project areas improved to enhance anadromous fish habitat. New project locations included sites on the mid Umatilla River, upper Umatilla River, Mission Creek, Cottonwood Creek and Buckaroo Creek. New enhancements included: (1) construction of 11,264 feet of fencing between River Mile 43.0 and 46.5 on the Umatilla River, (2) a stream bank stabilization project implemented at approximately River Mile 63.5 Umatilla River to stabilize 330 feet of eroding stream bank and improve instream habitat diversity, included construction of eight root wad revetments and three boulder J-vanes, (3) drilling a 358-foot well for off-stream livestock watering at approximately River Mile 46.0 Umatilla River, (4) installing a 50-foot bottomless arch replacement culvert at approximately River Mile 3.0 Mission Creek, (5) installing a Geoweb stream ford crossing on Mission Creek (6) installing a 22-foot bottomless arch culvert at approximately River Mile 0.5 Cottonwood Creek, and (7) providing fence materials for construction of 21,300 feet of livestock exclusion fencing in the Buckaroo Creek Drainage. An approximate total of 3,800 native willow cuttings and 350 pounds of native grass seed was planted at new upper Umatilla River, Mission Creek and Cottonwood Creek project sites. Habitat improvements implemented at existing project sites included

  11. Expert initial review of Columbia River Basin salmonid management models: Summary report

    International Nuclear Information System (INIS)

    Barnthouse, L.W.

    1993-10-01

    Over the past years, several fish passage models have been developed to examine the downstream survival of salmon during their annual migration through the Columbia River reservoir system to below Bonneville Dam. More recently, models have been created to simulate the survival of salmon throughout the entire life cycle. The models are used by various regional agencies and native American tribes to assess impacts of dam operation, harvesting, and predation on salmonid abundance. These models are now also being used to assess extinction probabilities and evaluate restoration alternatives for threatened and endangered salmonid stocks. Oak Ridge National Laboratory (ORNL) coordinated an initial evaluation of the principal models by a panel of outside, expert reviewers. None of the models were unequivocally endorsed by any reviewer. Significant strengths and weaknesses were noted for each with respect to reasonability of assumptions and equations, adequacy of documentation, adequacy of supporting data, and calibration procedures. Although the models reviewed differ in some important respects, all reflect a common conceptual basis in classical population dynamic theory and a common empirical basis consisting of the available time series of salmonid stock data, hydrographic records, experimental studies of dam passage parameters, and measurements of reservoir mortality. The results of this initial review are not to be construed as a comprehensive scientific peer review of existing Columbia River Basin (CRB) salmon population models and data. The peer review process can be enhanced further by a dynamic exchange regional modelers and scientific panel experts involving interaction and feedback

  12. Influence of forest and rangeland management on anadromous fish habitat in Western North America: planning forest roads to protect salmonid habitat.

    Science.gov (United States)

    Carlton S. Yee; Terry D. Roelofs

    1980-01-01

    The construction and existence of forest roads, landings, and decking areas may have significant effects on anadromous fish habitat . Major effects discussed in this paper are increased sedimentation from transportation networks, the hindrance to fish migration of drainage structures, and possible changes in water quality from road stabilization additives. Guidelines...

  13. Epidemiology and Control of Infectious Diseases of Salmonids in the Columbia River Basin, 1983 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Fryer, John L.

    1984-11-01

    The Department of Microbiology at Oregon State University with funding from the Bonneville Power Administration conducted a study relating to the epidemiology and control of three fish diseases of salmonids in the Columbia River Basin. These three diseases were ceratomyxosis which is caused by the myxosporidan parasite Ceratomyxa shasta, bacterial kidney disease, the etiological agent of which is Renibacterium salmoninarum, and infectious hematopoietic necrosis, which is caused by a rhabdovirus. Each of these diseases is highly destructive and difficult or impossible to treat with antimicrobial agents. The presence of ceratomyxosis in rainbow trout exposed at McNary and Little Goose Dams extends the range of this disease about 200 miles further up the Columbia River and into the Snake River drainage. Wallowa steelhead trout were less resistant to this disease than other upriver stocks tested. Juvenile salmonids entering the Columbia River estuary were collected periodically between May to September, 1983. Nine percent of the beach seined chinook salmon and 5, 11 and 12%, respectively, of the purse seined coho and chinook salmon and steelhead trout were infected with Ceratomyxa shasta. Experiments indicated ceratomyxosis progresses in salt water at the same rate as in fresh water once the fish have become infected. These data indicate a longer exposure to infective stages of C. shasta than previously identified and that approximately 10% of the migrating salmonids are infected and will probably die from this organism after entering salt water. Since sampling began in 1981 the bacterial kidney disease organism, Renibacterium salmoninarum, has been detected by the fluorescent antibody test in seven salmonid species caught in the open ocean off the coasts of Washington and Oregon. The bacterium has been found primarily in chinook salmon (11%) with lesions in 2.5% of these fish. This disease was also detected at levels ranging from 17% in coho salmon to 25% in chinook

  14. Basin-scale availability of salmonid spawning gravel as influenced by channel type and hydraulic roughness in mountain catchments.

    Science.gov (United States)

    John M. Buffington; David R. Montgomery; Harvey M. Greenberg

    2004-01-01

    A general framework is presented for examining the effects of channel type and associated hydraulic roughness on salmonid spawning-gravel availability in mountain catchments. Digital elevation models are coupled with grain-size predictions to provide basin-scale assessments of the potential extent and spatial pattern of spawning gravels. To demonstrate both the model...

  15. Potential effects of climate change on streambed scour and risks to salmonid survival in snow-dominated mountain basins

    Science.gov (United States)

    Jaime R. Goode; John M. Buffington; Daniele Tonina; Daniel J. Isaak; Russell F. Thurow; Seth Wenger; David Nagel; Charlie Luce; Doerthe Tetzlaff; Chris Soulsby

    2013-01-01

    Snowmelt-dominated basins in northern latitudes provide critical habitat for salmonids. As such, these systems may be especially vulnerable to climate change because of potential shifts in the frequency, magnitude, and timing of flows that can scour incubating embryos. A general framework is presented to examine this issue, using a series of physical models that link...

  16. Enumeration of Salmonids in the Okanogan Basin Using Underwater Video, Performance Period: October 2005 (Project Inception) - 31 December 2006.

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Peter N.; Rayton, Michael D.; Nass, Bryan L.; Arterburn, John E.

    2007-06-01

    The Confederated Tribes of the Colville Reservation (Colville Tribes) identified the need for collecting baseline census data on the timing and abundance of adult salmonids in the Okanogan River Basin in order to determine basin and tributary-specific spawner distributions, evaluate the status and trends of natural salmonid production in the basin, document local fish populations, and augment existing fishery data. This report documents the design, installation, operation and evaluation of mainstem and tributary video systems in the Okanogan River Basin. The species-specific data collected by these fish enumeration systems are presented along with an evaluation of the operation of a facility that provides a count of fish using an automated method. Information collected by the Colville Tribes Fish & Wildlife Department, specifically the Okanogan Basin Monitoring and Evaluation Program (OBMEP), is intended to provide a relative abundance indicator for anadromous fish runs migrating past Zosel Dam and is not intended as an absolute census count. Okanogan Basin Monitoring and Evaluation Program collected fish passage data between October 2005 and December 2006. Video counting stations were deployed and data were collected at two locations in the basin: on the mainstem Okanogan River at Zosel Dam near Oroville, Washington, and on Bonaparte Creek, a tributary to the Okanogan River, in the town of Tonasket, Washington. Counts at Zosel Dam between 10 October 2005 and 28 February 2006 are considered partial, pilot year data as they were obtained from the operation of a single video array on the west bank fishway, and covered only a portion of the steelhead migration. A complete description of the apparatus and methodology can be found in 'Fish Enumeration Using Underwater Video Imagery - Operational Protocol' (Nass 2007). At Zosel Dam, totals of 57 and 481 adult Chinook salmon were observed with the video monitoring system in 2005 and 2006, respectively. Run

  17. Epidemiology and Control of Infectious Diseases of Salmonids in the Columbia River Basin, 1987 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Fryer, John L.

    1989-01-01

    The Department of Microbiology at Oregon State University with funding from the Bonneville Power Administration has been conducting a study concerning the epidemiology and control of three fish pathogens which cause major disease problems in salmonids of the Columbia River basin. The pathogens studied include Cera to myxa Shasta, the myxosporean parasite which causes ceratomyxosis; Renibacterium salmoninarum, the bacterium which is the etiological agent of bacterial kidney disease; and the rhabdovirus which causes infectious hematopoietic necrosis (IHN). During this project, the host and geographic range of C. Shasta have been more precisely determined and the known geographic range has been significantly expanded. The effects of the parasite on fish migrating through the Columbia River and on their introduction into salt water have been examined. Similar studies have been conducted with R. salmoninarum and it has been shown that bacterial kidney disease occurs at all life stages of salmonids and is responsible for mortality in both fresh and salt water. It has also been demonstrated that different isolates of R. salmoninarum have different antigenic composition. Results of demonstration projects designed to control IHN by using UV treated water for early rearing of salmonid fry were equivocal. The scope of the project was considerably narrowed and focused during the past two years The project has concentrated on a study concerning the biology of C. Shasta and the identification of potential chemotherapeutants for control of bacterial kidney disease. The emphasis of work on C. Shasta has been its pathogenesis. This aspect of the parasite has been investigated using histopathologic and immunologic methodology. Mode of transmission, the nature of the infectious stage, and potential intermediate hosts of the parasite have also been areas of active research. Classes of chemotherapeutants with the highest potential for efficacy against R. salmoninarum have been

  18. Epidemiology and Control of Infectious Diseases of Salmonids in the Columbia River Basin, 1986 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Fryer, John L.

    1986-12-01

    The Department of Microbiology at Oregon State University with funding from the Bonneville Power Administration conducted a study relating to the epidemiology and control of three fish diseases of salmonids in the Columbia River Basin. These three diseases were ceratomyxosis caused by the myxosporidan parasite Ceratomyxa Shasta, bacterial kidney disease, the causative agent Renibacterium salmoninarum, and infectious hematopoietic necrosis, caused by a rhabdovirus. Each of these diseases is highly destructive and difficult or impossible to treat with antimicrobial agents. The geographic range of the infectious stage of C. Shasta has been extended to include the Snake River to the Oxbow and Hells Canyon Dams. These are the farthest upriver sites tested. Infections of ceratomyxosis were also initiated in the east fork of the Lewis River and in the Washougal River in Washington. Laboratory studies with this parasite failed to indicate that tubeficids are required in its life cycle. Bacterial kidney disease has been demonstrated in all life stages of salmonids: in the eggs, fry, smolts, juveniles and adults in the ocean, and in fish returning to fresh water. Monoclonal antibodies produced against R. salmoninarum demonstrated antigenic differences among isolates of the bacterium. Monoclonal antibodies also showed antigens of R. salmoninarum which are similar to those of a wide variety of gram positive and gram negative bacteria. A demonstration project at Round Butte Hatchery showed U V treatment to be an effective method for reducing the microbial population of the water supply and could reduce risks of IHNV. Tangential flow filtration was used successfully to concentrate IHNV from environmental water. At Round Butte Hatchery the carrier rate of IHNV in adults was very low and there was no subsequent mortality resulting from IHN in juveniles.

  19. Ecological aspects of nematode parasites of introduced salmonids from Valdivia river basin, Chile

    Directory of Open Access Journals (Sweden)

    Patricio Torres

    1991-03-01

    Full Text Available Between 1986 and 1987 fishes distributed among the following species introduced in Chile, and from different sectors of the Valdivia river basin (39º30' - 40º00', 73º30' - 71º45'W, were examined: 348 Salmo trutta, 242 Salmo gairdneri, 24 Cyprinus carpio and 52 Gambusia affinis holbrooki. The presence of Camallanus corderoi and Contracaecum sp. in S. gairdneri and of C. corderoi in S. trutta is recorded in Chile for the first time. Cyprinus carpio and G. a. holbrooki did not present infections by nematodes. The prevalence and mean intensity of the infections by nematodes presented significant differences among some sectors of the Valdivia river basin. In general, the prevalence and intensity of the infections by C. corderoi were greater than those by Contracaecum sp. The infections in S. gairdneri were higher than in S. trutta. The sex of the hosts had no influence on the prevalence and intensity of the infections by both nematodes. The length of the hosts did have an influence, except in the case of the infections by Contracaecum sp. in S, gairdneri. The infrapopulations of both nematode species showed over dispersion in most cases. The diet of the examined salmonids suggests that they would become infected principally throught the consuption of autochthonous fishes.

  20. Habitat Quality and Anadromous Fish Production on the Warm Springs Reservation. Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Fritsch, Mark A.

    1995-06-01

    The number of anadromous fish returning to the Columbia River and its tributaries has declined sharply in recent years. Changes in their freshwater, estuarine, and ocean environments and harvest have all contributed to declining runs of anadromous fish. Restoration of aquatic resources is of paramount importance to the Confederated Tribes of the Warm Springs (CTWS) Reservation of Oregon. Watersheds on the Warm Springs Reservation provide spawning and rearing habitat for several indigenous species of resident and anadromous fish. These streams are the only ones in the Deschutes River basin that still sustain runs of wild spring chinook salmon, Oncorhynchus, tshawytscha. Historically, reservation streams supplied over 169 km of anadromous fish habitat. Because of changes in flows, there are now only 128 km of habitat that can be used on the reservation. In 1981, the CTWS began a long-range, 3-phase study of existing and potential fish resources on the reservation. The project, consistent with the Northwest Power Planning Council`s Fish and Wildlife Program, was designed to increase the natural production of anadromous salmonids on the reservation.

  1. Habitat quality and anadromous fish production on the Warm Springs Reservation. Final report

    International Nuclear Information System (INIS)

    Fritsch, M.A.

    1995-06-01

    The number of anadromous fish returning to the Columbia River and its tributaries has declined sharply in recent years. Changes in their freshwater, estuarine, and ocean environments and harvest have all contributed to declining runs of anadromous fish. Restoration of aquatic resources is of paramount importance to the Confederated Tribes of the Warm Springs (CTWS) Reservation of Oregon. Watersheds on the Warm Springs Reservation provide spawning and rearing habitat for several indigenous species of resident and anadromous fish. These streams are the only ones in the Deschutes River basin that still sustain runs of wild spring chinook salmon, Oncorhynchus, tshawytscha. Historically, reservation streams supplied over 169 km of anadromous fish habitat. Because of changes in flows, there are now only 128 km of habitat that can be used on the reservation. In 1981, the CTWS began a long-range, 3-phase study of existing and potential fish resources on the reservation. The project, consistent with the Northwest Power Planning Council's Fish and Wildlife Program, was designed to increase the natural production of anadromous salmonids on the reservation

  2. Assessment of Salmonids and their Habitat Conditions in the Walla Walla River Basin within Washington, 2001 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Mendel, Glen Wesley; Trump, Jeremy; Karl, David

    2002-12-01

    Concerns about the decline of native salmon and trout populations have increased among natural resource managers and the public in recent years. As a result, a multitude of initiatives have been implemented at the local, state, and federal government levels. These initiatives include management plans and actions intended to protect and restore salmonid fishes and their habitats. In 1998 bull trout (Salvelinus confluentus) were listed under the Endangered Species Act (ESA), as ''Threatened'', for the Walla Walla River and its tributaries. Steelhead (Oncorhynchus mykiss) were listed as ''Threatened'' in 1999 for the mid-Columbia River and its tributaries. These ESA listings emphasize the need for information about these threatened salmonid populations and their habitats. The Washington Department of Fish and Wildlife (WDFW) is entrusted with ''the preservation, protection, and perpetuation of fish and wildlife....[and to] maximize public recreational or commercial opportunities without impairing the supply of fish and wildlife (WAC 77.12.010).'' In consideration of this mandate, the WDFW submitted a proposal in December 1997 to the Bonneville Power Administration (BPA) for a study to assess salmonid distribution, relative abundance, genetics, and the condition of salmonid habitats in the Walla Walla River basin. The primary purposes of this project are to collect baseline biological and habitat data, to identify major data gaps, and to draw conclusions whenever possible. The study reported herein details the findings of the 2001 field season (March to November, 2001).

  3. Developing a predation index and evaluating ways to reduce salmonid losses to predation in the Columbia River basin

    International Nuclear Information System (INIS)

    Nigro, A.A.

    1990-12-01

    We report our results of studies to develop a predation index and evaluate ways to reduce juvenile salmonid losses to predation in the Columbia River Basin. Study objectives of each were: develop an index to estimate predation losses of juvenile salmonids (Oncorhynchus spp) in reservoirs throughout the Columbia River Basin, describe the relationships among predator-caused mortality of juvenile salmonids and physical and biological variables, examine the feasibility of developing bounty, commercial or recreational fisheries on northern squawfish (Ptychocheilus oregonensis) and develop a plan to evaluate the efficacy of predator control fisheries; determine the economic feasibility of developing bounty and commercial fisheries for northern squawfish, assist ODFW with evaluating the economic feasibility of recreational fisheries for northern squawfish and assess the economic feasibility of utilizing northern squawfish, carp (Cyprinus carpio) and suckers (Castostomus spp) in multispecies fisheries; evaluate commercial technology of various fishing methods for harvesting northern squawfish in Columbia River reservoirs and field test the effectiveness of selected harvesting systems, holding facilities and transportation systems; and modify the existing Columbia River Ecosystem Model (CREM) to include processes necessary to evaluate effects of removing northern squawfish on their population size structure and abundance, document the ecological processes, mathematical equations and computer (FORTRAN) programming of the revised version of CREM and conduct systematic analyses of various predator removal scenarios, using revised CREM to generate the simulations. Individual reports are indexed separately

  4. Salmonid Gamete Preservation in the Snake River Basin, 2001 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, Robyn; Kucera, Paul

    2002-06-01

    Steelhead (Oncorhynchus mykiss) and chinook salmon (Oncorhynchus tshawytscha) populations in the Northwest are decreasing. Genetic diversity is being lost at an alarming rate. Along with reduced population and genetic variability, the loss of biodiversity means a diminished environmental adaptability. The Nez Perce Tribe (Tribe) strives to ensure availability of genetic samples of the existing male salmonid population by establishing and maintaining a germplasm repository. The sampling strategy, initiated in 1992, has been to collect and preserve male salmon and steelhead genetic diversity across the geographic landscape by sampling within the major river subbasins in the Snake River basin, assuming a metapopulation structure existed historically. Gamete cryopreservation conserves genetic diversity in a germplasm repository, but is not a recovery action for listed fish species. The Tribe was funded in 2001 by the Bonneville Power Administration (BPA) and the U.S. Fish and Wildlife Service Lower Snake River Compensation Plan (LSRCP) to coordinate gene banking of male gametes from Endangered Species Act (ESA) listed steelhead and spring and summer chinook salmon in the Snake River basin. In 2001, a total of 398 viable chinook salmon semen samples from the Lostine River, Catherine Creek, upper Grande Ronde River, Lookingglass Hatchery (Imnaha River stock), Lake Creek, the South Fork Salmon River weir, Johnson Creek, Big Creek, Capehorn Creek, Marsh Creek, Pahsimeroi Hatchery, and Sawtooth Hatchery (upper Salmon River stock) were cryopreserved. Also, 295 samples of male steelhead gametes from Dworshak Hatchery, Fish Creek, Grande Ronde River, Little Sheep Creek, Pahsimeroi Hatchery and Oxbow Hatchery were also cryopreserved. The Grande Ronde chinook salmon captive broodstock program stores 680 cryopreserved samples at the University of Idaho as a long-term archive, half of the total samples. A total of 3,206 cryopreserved samples from Snake River basin steelhead and

  5. Assessment of salmonids and their habitat conditions in the Walla Walla River Basin of Washington : 2000 annual report; ANNUAL

    International Nuclear Information System (INIS)

    Mendel, Glen Wesley; Karl, David; Coyle, Terrence

    2001-01-01

    Concerns about the decline of native salmon and trout populations have increased among natural resource managers and the public in recent years. As a result, a multitude of initiatives have been implemented at the local, state, and federal government levels. These initiatives include management plans and actions intended to protect and restore salmonid fishes and their habitats. In 1998 bull trout were listed under the Endangered Species Act (ESA), as ''Threatened'', for the Walla Walla River and its tributaries. Steelhead were listed as ''Threatened'' in 1999 for the mid-Columbia River and its tributaries. These ESA listings emphasize the need for information about the threatened salmonid populations and their habitats. The Washington Department of Fish and Wildlife (WDFW) is entrusted with ''the preservation, protection, and perpetuation of fish and wildlife....[and to] maximize public recreational or commercial opportunities without impairing the supply of fish and wildlife (WAC 77.12.010).'' In consideration of this mandate, the WDFW submitted a proposal in December 1997 to the Bonneville Power Administration (BPA) for a study to assess salmonid distribution, relative abundance, genetics, and the condition of their habitats in the Walla Walla River basin. The primary purposes of this project are to collect baseline biological and habitat data, to identify major data gaps, and to draw conclusions whenever possible. The study reported herein details the findings of the 2000 field season (March to November, 2000)

  6. Assessment of Salmonids and their Habitat Conditions in the Walla Walla River Basin of Washington : 2000 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Mendel, Glen Wesley; Karl, David; Coyle, Terrence

    2001-11-01

    Concerns about the decline of native salmon and trout populations have increased among natural resource managers and the public in recent years. As a result, a multitude of initiatives have been implemented at the local, state, and federal government levels. These initiatives include management plans and actions intended to protect and restore salmonid fishes and their habitats. In 1998 bull trout were listed under the Endangered Species Act (ESA), as ''Threatened'', for the Walla Walla River and its tributaries. Steelhead were listed as ''Threatened'' in 1999 for the mid-Columbia River and its tributaries. These ESA listings emphasize the need for information about the threatened salmonid populations and their habitats. The Washington Department of Fish and Wildlife (WDFW) is entrusted with ''the preservation, protection, and perpetuation of fish and wildlife....[and to] maximize public recreational or commercial opportunities without impairing the supply of fish and wildlife (WAC 77. 12.010).'' In consideration of this mandate, the WDFW submitted a proposal in December 1997 to the Bonneville Power Administration (BPA) for a study to assess salmonid distribution, relative abundance, genetics, and the condition of their habitats in the Walla Walla River basin. The primary purposes of this project are to collect baseline biological and habitat data, to identify major data gaps, and to draw conclusions whenever possible. The study reported herein details the findings of the 2000 field season (March to November, 2000).

  7. Salmonid Gamete Preservation in the Snake River Basin : 2000 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, Robyn; Kucera, Paul A. [Nez Perce Tribe. Dept. of Fisheries Resource Management, Lapwai, ID (US)

    2001-06-01

    Steelhead (Oncorhynchus mykiss) and chinook salmon (Oncorhynchus tshawytscha) populations in the Northwest are decreasing. Genetic diversity is being lost at an alarming rate. The Nez Perce Tribe (Tribe) strives to ensure availability of genetic samples of the existing male salmonid population by establishing and maintaining a germplasm repository. The sampling strategy, initiated in 1992, has been to collect and preserve male salmon and steelhead genetic diversity across the geographic landscape by sampling within the major river subbasins in the Snake River basin, assuming a metapopulation structure existed historically. Gamete cryopreservation conserves genetic diversity in a germplasm repository, but is not a recovery action for listed fish species. The Tribe was funded in 2000 by the Bonneville Power Administration (BPA) and the U.S. Fish and Wildlife Service Lower Snake River Compensation Plan (LSRCP) to coordinate gene banking of male gametes from Endangered Species Act listed steelhead and spring and summer chinook salmon in the Snake River basin. In 2000, a total of 349 viable chinook salmon semen samples from the Lostine River, Catherine Creek, upper Grande Ronde River, Lookingglass Hatchery (Imnaha River stock), Rapid River Hatchery, Lake Creek, the South Fork Salmon River weir, Johnson Creek, Big Creek, Capehorn Creek, Marsh Creek, Pahsimeroi Hatchery, and Sawtooth Hatchery (upper Salmon River stock) were cryopreserved. Also, 283 samples of male steelhead gametes from Dworshak Hatchery, Fish Creek, Grande Ronde River, Imnaha River, Little Sheep Creek, Pahsimeroi Hatchery and Oxbow Hatchery were also cryopreserved. The Tribe acquired 5 frozen steelhead samples from the Selway River collected in 1994 and 15 from Fish Creek sampled in 1993 from the U.S. Geological Survey, for addition into the germplasm repository. Also, 590 cryopreserved samples from the Grande Ronde chinook salmon captive broodstock program are being stored at the University of Idaho as

  8. Salmonid Gamete Preservation in the Snake River Basin, Annual Report 2002.

    Energy Technology Data Exchange (ETDEWEB)

    Young, William; Kucera, Paul

    2003-07-01

    In spite of an intensive management effort, chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) populations in the Northwest have not recovered and are currently listed as threatened species under the Endangered Species Act. In addition to the loss of diversity from stocks that have already gone extinct, decreased genetic diversity resulting from genetic drift and inbreeding is a major concern. Reduced population and genetic variability diminishes the environmental adaptability of individual species and entire ecological communities. The Nez Perce Tribe (NPT), in cooperation with Washington State University and the University of Idaho, established a germplasm repository in 1992 in order to preserve the remaining salmonid diversity in the region. The germplasm repository provides long-term storage for cryopreserved gametes. Although only male gametes can be cryopreserved, conserving the male component of genetic diversity will maintain future management options for species recovery. NPT efforts have focused on preserving salmon and steelhead gametes from the major river subbasins in the Snake River basin. However, the repository is available for all management agencies to contribute gamete samples from other regions and species. In 2002 a total of 570 viable semen samples were added to the germplasm repository. This included the gametes of 287 chinook salmon from the Lostine River, Catherine Creek, upper Grande Ronde River, Imnaha River (Lookingglass Hatchery), Lake Creek, South Fork Salmon River, Johnson Creek, Big Creek, Capehorn Creek, Marsh Creek, Pahsimeroi River (Pahsimeroi Hatchery), and upper Salmon River (Sawtooth Hatchery) and the gametes of 280 steelhead from the North Fork Clearwater River (Dworshak Hatchery), Fish Creek, Little Sheep Creek, Pahsimeroi River (Pahsimeroi Hatchery) and Snake River (Oxbow Hatchery). In addition, gametes from 60 Yakima River spring chinook and 34 Wenatchee River coho salmon were added to the

  9. Assessment of Salmonids and Their Habitat Conditions in the Walla Walla River Basin within Washington, Annual Report 2002-2003.

    Energy Technology Data Exchange (ETDEWEB)

    Mendel, Glen; Trump, Jeremy; Gembala, Mike

    2003-09-01

    This study began in 1998 to assess salmonid distribution, relative abundance, genetics, and the condition of salmonid habitats in the Walla Walla River basin. Stream flows in the Walla Walla Basin continue to show a general trend that begins with a sharp decline in discharge in late June, followed by low summer flows and then an increase in discharge in fall and winter. Manual stream flow measurements at Pepper bridge showed an increase in 2002 of 110-185% from July-September, over flows from 2001. This increase is apparently associated with a 2000 settlement agreement between the U.S. Fish and Wildlife Service (USFWS) and the irrigation districts to leave minimum flows in the river. Stream temperatures in the Walla Walla basin were similar to those in 2001. Upper montane tributaries maintained maximum summer temperatures below 65 F, while sites in mid and lower Touchet and Walla Walla rivers frequently had daily maximum temperatures well above 68 F (high enough to inhibit migration in adult and juvenile salmonids, and to sharply reduce survival of their embryos and fry). These high temperatures are possibly the most critical physiological barrier to salmonids in the Walla Walla basin, but other factors (available water, turbidity or sediment deposition, cover, lack of pools, etc.) also play a part in salmonid survival, migration, and breeding success. The increased flows in the Walla Walla, due to the 2000 settlement agreement, have not shown consistent improvements to stream temperatures. Rainbow/steelhead (Oncorhynchus mykiss) trout represent the most common salmonid in the basin. Densities of Rainbow/steelhead in the Walla Walla River from the Washington/Oregon stateline to Mojonnier Rd. dropped slightly from 2001, but are still considerably higher than before the 2000 settlement agreement. Other salmonids including; bull trout (Salvelinus confluentus), chinook salmon (Oncorhynchus tshawytscha), mountain whitefish (Prosopium williamsoni), and brown trout (Salmo

  10. Epidemiology and Control of Infectious Diseases of Salmonids in the Columbia River Basin, 1984 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Fryer, John L.

    1985-11-01

    The Department of Microbiology at Oregon State University with funding from the Bonneville Power Administration has conducted a study since 1983 relating to the epidemiology and control of three diseases of salmonids in the Columbia River Basin. These diseases are ceratomyxosis, caused by the protozoan parasite Ceratomyxa Shasta, bacterial kidney disease, the etiological agent of which is Renibacterium salmoninarum and infectious hematopoietic necrosis which is caused by a rhabdovirus. Each of these diseases is difficult or impossible to treat with antimicrobial agents. The presence of the infectious stage of C. shasta was again detected at Little Goose Dam on the Snake River. The prevalence of ceratomyxosis increased from 1.1% in 1984 to 10% in 1985. None of the susceptible rainbow trout exposed in the Yakima and Umatilla Rivers died of this disease. Ceratomyxosis in resistant chinook salmon smolts seined from the Columbia River just above the estuary seems dependent on whether or not they are held after capture in fresh or salt water. In fresh water the disease incidence ranged from 7--19%, whereas in salt water it ranged from 0--3%. These results which suggest that recovery from ceratomyxosis may occur after the smolts enter salt water are different from those obtained with susceptible Alsea steelhead trout where experimental groups in salt water have died at the same rate as those in fresh water. Comparing data from groups of Columbia River chinook smolts held after capture in either fresh or salt water, R. salmoninarum is a much more effective pathogen in the salt water environment. After four years of sampling smolts in the open ocean, numbers of this microorganism sufficient to cause death have been detected in chinook (7%) and, coho salmon (2%) and steelhead trout (1%). Results from three years of sampling have consistently indicated that additional fish infected with R. salmoninarum will be detected if egg washings are included in the procedures for

  11. Cle Elum Lake Anadromous Salmon Restoration Feasibility Study: Summary of Research, 1986-1999 Progress Report.

    Energy Technology Data Exchange (ETDEWEB)

    Dey, Douglas

    2000-04-01

    The focus of this research was to study the feasibility for anadromous salmonids to recolonize the habitat above reservoirs in the Yakima River without disruption to irrigation withdrawals. A primary concern was whether anadromous fish could successfully exit reservoirs and survive downstream passage through the Yakima and Columbia Rivers to the ocean.

  12. Confederated Tribes of the Umatilla Indian Reservation North Fork John Day River Basin Anadromous Fish Enhancement Project, Annual Report for FY 2001.

    Energy Technology Data Exchange (ETDEWEB)

    Macy, Tom L.; James, Gary A.

    2003-03-01

    The CTUIR North Fork John Day River Basin Anadromous Enhancement Project (NFJDAFEP) identified and prioritized stream reaches in The North Fork John day River basin for habitat improvements during the 2000 project period. Public outreach was emphasized during this first year of the project. During the past year we concentrated on satisfying landowner needs, providing cost share alternatives, providing joint projects and starting implementation. We presented multiple funding and enhancement options to landowners. We concentrated on natural recovery methods, riparian fencing and offstream livestock water developments. Under this BPA contract four riparian easements have been signed protecting almost 5 miles of tributary streams. There are nine offstream water developments associated with these easements. Some landowners chose to participate in other programs based on Tribal outreach efforts. Some landowners chose NRCS programs for enhancement and others chose OWEB as a funding source. The exact amount of stream protection due to other funding sources probably exceeds that by BPA, however most would not have entered any program without initial Tribal outreach. Cooperation between the NRCS/FSA/SWCDs and the Tribe to create joint projects and develop alternative funding scenarios for riparian enhancement was a major effort. The Tribe also worked with the North Fork John Day Watershed Council, USFS and ODFW to coordinate projects and support similar projects throughout the John Day Basin.

  13. Facultative anadromy in salmonids: linking habitat, individual life history decisions, and population-level consequences

    Science.gov (United States)

    Steven F. Railsback; Bret C. Harvey; Jason L. White

    2014-01-01

    Modeling and management of facultative anadromous salmonids is complicated by their ability to select anadromous or resident life histories. Conventional theory for this behavior assumes individuals select the strategy offering highest expected reproductive success but does not predict how population-level consequences such as a stream’s smolt production emerge from...

  14. The design and analysis of salmonid tagging studies in the Columbia Basin. Volume 2: Estimating salmonid survival with combined PIT-CWT tagging. Technical report

    International Nuclear Information System (INIS)

    Newman, K.

    1997-06-01

    Passive Integrated Transponder (PIT) tags and Coded Wire Tags (CWTs) in combination can provide information about salmonid survival that single tag releases may not. The release and recapture protocol affects which survival and recapture rates can be estimated and the precision of the estimates. For the particular case of Columbia river salmonids tagged with both PIT tags and CWTs, three different release and recapture protocols were evaluated. This report addresses the need to study the fate of salmon smolt in-river and their subsequent return as adults. Double-tagging procedures are investigated where PIT-tags would be used to provide in-river survival data during smolt outmigrations and coded-wire tags (CWT) used to provide adult return information. This report provides statistical models for the analysis of the joint data as well as recommendations on optimal tagging studies. Study costs and stress on smolt can be reduced by only PIT-tagging a subset of all the fish coded-wire-tagged, while retaining the information content and sampling precision

  15. Evaluation of Juvenile Salmonid Outmigration and Survival in the Lower Umatilla River Basin, Annual Report 2003-2006.

    Energy Technology Data Exchange (ETDEWEB)

    White, Tara

    2007-02-01

    This report summarizes activities conducted by the Oregon Department of Fish and Wildlife's Juvenile Outmigration and Survival M&E project in the Umatilla River subbasin between 2004-2006. Information is used to make informed decisions on hatchery effectiveness, natural production success, passage improvement and flow enhancement strategies. Data collected includes annual estimates of smolt abundance, migration timing, and survival, life history characteristics and productivity status and trends for spring and fall Chinook salmon, coho salmon and summer steelhead. Productivity data provided is the key subbasin scale measure of the effectiveness of salmon and steelhead restoration actions in the Umatilla River. Information is also used for regional planning and recovery efforts of Mid-Columbia River (MCR) ESA-listed summer steelhead. Monitoring is conducted via smolt trapping and PIT-tag interrogation at Three Mile Falls Dam. The Umatilla Juvenile Outmigration and Survival Project was established in 1994 to evaluate the success of management actions and fisheries restoration efforts in the Umatilla River Basin. Project objectives for the 2004-2006 period were to: (1) operate the PIT tag detection system at Three Mile Falls Dam (TMFD), (2) enhance provisional PIT-tag interrogation equipment at the east bank adult fish ladder, (3) monitor the migration timing, abundance and survival of naturally-produced juvenile salmonids and trends in natural production, (4) determine migration parameters and survival of hatchery-produced fish representing various rearing, acclimation and release strategies, (5) evaluate the relative survival between transported and non-transported fish, (6) monitor juvenile life history characteristics and evaluate trends over time, (7) investigate the effects of river, canal, fishway operations and environmental conditions on smolt migration and survival, (8) document the temporal distribution and diversity of resident fish species, and (9

  16. Salmonid Gamete Preservation in the Snake River Basin, 1998 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, Robyn; Kucera, Paul A. (Nez Perce Tribe, Lapwai, ID)

    1999-03-01

    Steelhead (Oncorhynchus mykiss) and salmon (Oncorhynchus tshawytscha)populations in the Northwest are decreasing. The Nez Perce Tribe (Tribe) was funded in 1998 by the Bonneville Power Administration to coordinate gene banking of male gametes from Endangered Species Act (ESA) listed steelhead and spring and summer chinook salmon in the Snake River basin.

  17. Factors Affecting the Survival of Upstream Migrant Adult Salmonids in the Columbia River Basin : Recovery Issues for Threatened and Endangered Snake River Salmon : Technical Report 9 of 11.

    Energy Technology Data Exchange (ETDEWEB)

    Dauble, Dennis D.; Mueller, Robert P.

    1993-06-01

    The Bonneville Power Administration (BPA) is developing conservation planning documentation to support the National Marine Fisheries Service`s (NMFS) recovery plan for Columbia Basin salmonid stocks that are currently listed under the Endangered Species Act (ESA). Information from the conservation planning documentation will be used as a partial scientific basis for identifying alternative conservation strategies and to make recommendations toward conserving, rebuilding, and ultimately removing these salmon stocks from the list of endangered species. This report describes the adult upstream survival study, a synthesis of biological analyses related to conditions affecting the survival of adult upstream migrant salmonids in the Columbia River system. The objective of the adult upstream survival study was to analyze existing data related to increasing the survival of adult migrant salmonids returning to the Snake River system. The fate and accountability of each stock during its upstream migration period and the uncertainties associated with measurements of escapement and survival were evaluated. Operational measures that affected the survival of adult salmon were evaluated including existing conditions, augmented flows from upstream storage release, and drawdown of mainstem reservoirs. The potential impacts and benefits of these measures to each ESA stock were, also described based on considerations of species behavior and run timing.

  18. Year-Round Monitoring of Contaminants in Neal and Rogers Creeks, Hood River Basin, Oregon, 2011-12, and Assessment of Risks to Salmonids.

    Directory of Open Access Journals (Sweden)

    Whitney B Hapke

    Full Text Available Pesticide presence in streams is a potential threat to Endangered Species Act listed salmonids in the Hood River basin, Oregon, a primarily forested and agricultural basin. Two types of passive samplers, polar organic chemical integrative samplers (POCIS and semipermeable membrane devices (SPMDs, were simultaneously deployed at four sites in the basin during Mar. 2011-Mar. 2012 to measure the presence of pesticides, polybrominated diphenyl ethers (PBDEs, and polychlorinated biphenyls (PCBs. The year-round use of passive samplers is a novel approach and offers several new insights. Currently used pesticides and legacy contaminants, including many chlorinated pesticides and PBDEs, were present throughout the year in the basin's streams. PCBs were not detected. Time-weighted average water concentrations for the 2-month deployment periods were estimated from concentrations of chemicals measured in the passive samplers. Currently used pesticide concentrations peaked during spring and were detected beyond their seasons of expected use. Summed concentrations of legacy contaminants in Neal Creek were highest during July-Sept., the period with the lowest streamflows. Endosulfan was the only pesticide detected in passive samplers at concentrations exceeding Oregon or U.S. Environmental Protection Agency water-quality thresholds. A Sensitive Pesticide Toxicity Index (SPTI was used to estimate the relative acute potential toxicity among sample mixtures. The acute potential toxicity of the detected mixtures was likely greater for invertebrates than for fish and for all samples in Neal Creek compared to Rogers Creek, but the indices appear to be low overall (<0.1. Endosulfans and pyrethroid insecticides were the largest contributors to the SPTIs for both sites. SPTIs of some discrete (grab samples from the basin that were used for comparison exceeded 0.1 when some insecticides (azinphos methyl, chlorpyrifos, malathion were detected at concentrations near or

  19. Year-round monitoring of contaminants in Neal and Rogers Creeks, Hood River Basin, Oregon, 2011-12, and assessment of risks to salmonids

    Science.gov (United States)

    Temple, Whitney B.; Morace, Jennifer L.; Nilsen, Elena B.; Alvarez, David; Masterson, Kevin

    2016-01-01

    Pesticide presence in streams is a potential threat to Endangered Species Act listed salmonids in the Hood River basin, Oregon, a primarily forested and agricultural basin. Two types of passive samplers, polar organic chemical integrative samplers (POCIS) and semipermeable membrane devices (SPMDs), were simultaneously deployed at four sites in the basin during Mar. 2011–Mar. 2012 to measure the presence of pesticides, polybrominated diphenyl ethers (PBDEs), and polychlorinated biphenyls (PCBs). The year-round use of passive samplers is a novel approach and offers several new insights. Currently used pesticides and legacy contaminants, including many chlorinated pesticides and PBDEs, were present throughout the year in the basin’s streams. PCBs were not detected. Time-weighted average water concentrations for the 2-month deployment periods were estimated from concentrations of chemicals measured in the passive samplers. Currently used pesticide concentrations peaked during spring and were detected beyond their seasons of expected use. Summed concentrations of legacy contaminants in Neal Creek were highest during July–Sept., the period with the lowest streamflows. Endosulfan was the only pesticide detected in passive samplers at concentrations exceeding Oregon or U.S. Environmental Protection Agency water-quality thresholds. A Sensitive Pesticide Toxicity Index (SPTI) was used to estimate the relative acute potential toxicity among sample mixtures. The acute potential toxicity of the detected mixtures was likely greater for invertebrates than for fish and for all samples in Neal Creek compared to Rogers Creek, but the indices appear to be low overall (grab) samples from the basin that were used for comparison exceeded 0.1 when some insecticides (azinphos methyl, chlorpyrifos, malathion) were detected at concentrations near or exceeding acute water-quality thresholds. Early life stages and adults of several sensitive fish species, including salmonids, are

  20. Global climate change and effects on Pacific Northwest salmonids: An exploratory case study

    Energy Technology Data Exchange (ETDEWEB)

    Shankle, S.A.

    1990-09-01

    Recently, a number of papers have addressed global warming and freshwater fisheries. The recent report to Congress by the US Environmental Protection Agency included an analysis of potential effects of global warming on fisheries of the Great Lakes, California, and the Southeast. In California, the report stated that salinity increases in the San Francisco Bay could enhance the abundance of marine fish species, while anadromous species could be adversely affected. This paper discusses global climate changes and the effects on Pacific Northwest Salmonids. The impacts of climate change or Spring Chinook production in the Yakima Sub-basin was simulated using a computer modeling system developed for the Northwest Power planning council. 35 refs., 1 fig., 1 tab.

  1. Parasites as biological tags of marine, freshwater and anadromous fishes in North America from the Tropics to the Arctic.

    Science.gov (United States)

    Marcogliese, David J; Jacobson, Kym C

    2015-01-01

    Parasites have been considered as natural biological tags of marine fish populations in North America for almost 75 years. In the Northwest Atlantic, the most studied species include Atlantic cod (Gadus morhua), Atlantic herring (Clupea harengus) and the redfishes (Sebastes spp.). In the North Pacific, research has centred primarily on salmonids (Oncorhynchus spp.). However, parasites have been applied as tags for numerous other pelagic and demersal species on both the Atlantic and Pacific coasts. Relatively few studies have been undertaken in the Arctic, and these were designed to discriminate anadromous and resident salmonids (Salvelinus spp.). Although rarely applied in fresh waters, parasites have been used to delineate certain fish stocks within the Great Lakes-St Lawrence River basin. Anisakid nematodes and the copepod Sphyrion lumpi frequently prove useful indicators in the Northwest Atlantic, while myxozoan parasites prove very effective on the coast and open seas of the Pacific Ocean. Relative differences in the ability of parasites to discriminate between fish stocks on the Pacific and Atlantic coasts may be due to oceanographic and bathymetric differences between regions. Molecular techniques used to differentiate populations and species of parasites show promise in future applications in the field.

  2. Influences of Stocking Salmon Carcass Analogs on Salmonids in Yakima River Tributaries, 2001-2002 Technical Report.

    Energy Technology Data Exchange (ETDEWEB)

    Pearsons, Todd N.; Johnson, Christopher L. (Washington Department of Fish and Wildlife, Olympia, WA)

    2003-04-01

    The benefits that marine derived nutrients from adult salmon carcasses provide to juvenile salmonids are increasingly being recognized. Current estimates suggest that only 6-7% of marine-derived nitrogen and phosphorus that were historically available to salmonids in the Pacific Northwest are currently available. Food limitation may be a major constraint limiting the restoration of salmonids. A variety of methods have been proposed to offset this nutrient deficit including: allowing greater salmon spawning escapement, stocking hatchery salmon carcasses, and stocking inorganic nutrients. Unfortunately, each of these methods has some ecological or socio-economic shortcoming. We intend to overcome many of these shortcomings by making and evaluating a pathogen free product that simulates a salmon carcass (analog). Abundant sources of marine derived nutrients are available such as fish offal from commercial fishing and salmon carcasses from hatcheries. However, a method for recycling these nutrients into a pathogen free analog that degrades at a similar rate as a natural salmon carcass has never been developed. We endeavored to (1) develop a salmon carcass analog that will increase the food available to salmonids, (2) determine the pathways that salmonids use to acquire food from analogs, and (3) determine the benefits to salmonids and the potential for application to salmonid restoration. We used a before-after-control-impact-paired design in six tributaries of the upper Yakima basin to determine the utility of stocking carcass analogs. Our preliminary results suggest that the introduction of carcass analogs into food-limited streams can be used to restore food pathways previously provided by anadromous salmon. The analogs probably reproduced both of the major food pathways that salmon carcasses produce: direct consumption and food chain enhancement. Trout and salmon fed directly on the carcass analogs during the late summer and presumably benefited from the increased

  3. Evaluation of the Life History of Native Salmonids in the Malheur River Basin; Cooperative Bull Trout/Redband Trout Research Project, 2002-2003 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Alan; Soupir, Jim (US Forest Service, Prairie City Ranger District, Prairie City, OR); Schwabe, Lawrence (Burns Paiute Tribe, Department of Fish and Wildlife, Burns, OR)

    2003-08-01

    The Malheur River is a 306-kilometer tributary to the Snake River, which drains 12,950 square kilometers. The Malheur River originates in the Blue Mountains and flows into the Snake River near Ontario, Oregon. The climate of the basin is characterized by hot dry summers, occasionally exceeding 38 C, and cold winters that may drop below -29 C. Average annual precipitation is 30 centimeters in the lower reaches. Wooded areas consist primarily of mixed fir and pine forest in the higher elevations. Sagebrush and grass communities dominate the flora in the lower elevations. Efforts to document salmonid life histories, water quality, and habitat conditions have continued in fiscal year 2002. Bull trout Salvelinus confluentus are considered to be cold water species and are temperature-dependant. Due to the interest of bull trout from various state and Federal agencies, a workgroup was formed to develop project objectives related to bull trout. Table 1 lists individuals that participated in the 2002 work group. This report will reflect work completed during the Bonneville Power Administration contract period starting April 1, 2002, and ending March 31, 2003. All tasks were conducted within this timeframe, and a more detailed timeframe may be referred to in each individual report.

  4. Anadromous salmonids in the Delta: New science 2006–2016

    Science.gov (United States)

    Perry, Russell W.; Buchanan, Rebecca A.; Brandes, Patricia L.; Burau, Jon R.; Israel, Joshua A

    2016-01-01

    As juvenile salmon enter the Sacramento–SanJoaquin River Delta (“the Delta”) they disperse among its complex channel network where they are subject to channel-specific processes that affect their rate of migration, vulnerability to predation, feeding success, growth rates, and ultimately, survival. In the decades before 2006, tools available to quantify growth, dispersal, and survival of juvenile salmon in this complex channel network were limited.Fortunately, thanks to technological advances such as acoustic telemetry and chemical and structural otolith analysis, much has been learned over the past decade about the role of the Delta in the life cycle of juvenile salmon. Here, we review new science between 2006and 2016 that sheds light on how different life stages and runs of juvenile salmon grow, move, and survive in the complex channel network of the Delta. One of the most important advances during the past decade has been the widespread adoption of acoustic telemetry techniques. Use of telemetry has shed light on how survival varies among alternative migration routes and the proportion of fish that use each migration route. Chemical and structural analysis of otoliths has provided insights about when juveniles left their natal river and provided evidence of extended rearing in the brackish or saltwater regions of the Delta. New advancements in genetics now allow individuals captured by trawls to be assigned to specific runs. Detailed information about movement and survival in the Delta has spurred development of agent-based models of juvenile salmon that are coupled to hydrodynamic models. Although much has been learned, knowledge gaps remain about how very small juvenile salmon (fry and parr) use the Delta. Understanding how all life stages of juvenile salmon grow, rear, and survive in the Delta is critical for devising management strategies that support a diversity of life history strategies.

  5. Evaluation of the Life History of Native Salmonids in the Malheur River Basin; Cooperative Bull Trout/Redband Trout Research Project, 2000-2001 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Gonzales, Dan; Schwabe, Lawrence; Wenick, Jess (Burns Paiute Tribe, Department of Fish and Wildlife, Burns, OR)

    2001-08-01

    The Malheur basin lies within southeastern Oregon. The Malheur River is a tributary to the Snake River, entering at about River Kilometer (RK) 595. The hydrological drainage area of the Malheur River is approximately 12,950 km{sup 2} and is roughly 306 km in length. The headwaters of the Malheur River originate in the Blue Mountains at elevations of 6,500 to 7,500 feet, and drops to an elevation of 2000 feet at the confluence with the Snake River near Ontario, Oregon. The climate of the Malheur basin is characterized by hot dry summers, occasionally exceeding 38 C and cold winters that may drop below -29 C. Average annual precipitation is 300 centimeters and ranges from 100 centimeters in the upper mountains to less than 25 centimeters in the lower reaches (Gonzalez 1999). Wooded areas consist primarily of mixed fir and pine forest in the higher elevations. Sagebrush and grass communities dominate the flora in the lower elevations. Efforts to document salmonid life histories, water quality, and habitat conditions have continued in fiscal year 2000. The Burns Paiute Tribe (BPT), United States Forest Service (USFS), and Oregon Department of Fish and Wildlife (ODFW), have been working cooperatively to achieve this common goal. Bull trout ''Salvenlinus confluentus'' have specific environmental requirements and complex life histories making them especially susceptible to human activities that alter their habitat (Howell and Buchanan 1992). Bull trout are considered to be a cold-water species and are temperature dependent. This presents a challenge for managers, biologists, and private landowners in the Malheur basin. Because of the listing of bull trout under the Endangered Species Act as threatened and the current health of the landscape, a workgroup was formed to develop project objectives related to bull trout. This report will reflect work completed during the Bonneville Power contract period starting 1 April 2000 and ending 31 March 2001. The

  6. Restoring Anadromous Fish Habitat in the Lapwai Creek Watershed, Technical Report 2003-2006.

    Energy Technology Data Exchange (ETDEWEB)

    Rasmussen, Lynn

    2007-02-01

    The Restoring Anadromous Fish Habitat in the Lapwai Creek Watershed is a multi-phase project to enhance steelhead trout in the Lapwai Creek watershed by improving salmonid spawning and rearing habitat. Habitat is limited by extreme high runoff events, low summer flows, high water temperatures, poor instream cover, spawning gravel siltation, and sediment, nutrient and bacteria loading. Funded by the Bonneville Power Administration (BPA) as part of the Northwest Power Planning Council's Fish and Wildlife Program, the project assists in mitigating damage to steelhead runs caused by the Columbia River hydroelectric dams. The project is sponsored by the Nez Perce Soil and Water Conservation District (District). Target fish species include steelhead trout (Oncorhynchus mykiss). Steelhead trout within the Snake River Basin were listed in 1997 as threatened under the Endangered Species Act. Accomplishments for the contract period December 1, 2003 through February 28, 2004 include; seven grade stabilization structures, 0.67 acres of wetland plantings, ten acres tree planting, 500 linear feet streambank erosion control, two acres grass seeding, and 120 acres weed control.

  7. Influences of Stocking Salmon Carcass Analogs on Salmonids in Klickitat River Tributaries, 2001-2005 Completion Report.

    Energy Technology Data Exchange (ETDEWEB)

    Zendt, Joe; Sharp, Bill (Yakama Nation Fisheries, Toppenish, WA)

    2006-09-01

    This report describes the work completed by the Yakama Nation Fisheries Program (YNFP) in the Klickitat subbasin in south-central Washington under BPA innovative project No.200105500--Influences of stocking salmon carcass analogs on salmonids in Columbia River Tributaries. Salmon carcasses historically provided a significant source of marine-derived nutrients to many stream systems in the Columbia basin, and decreased run sizes have led to a loss of this nutrient source in many streams. Partners in this project developed a pathogen-free carcass analog and stocked the analogs in streams with the following objectives: restoring food availability to streams with reduced anadromous salmon returns; mimicking the natural pathways and timing of food acquisition by salmonids; minimizing unintended negative ecological effects; and increasing the growth and survival of salmonids. In the Klickitat subbasin, carcass analogs were stocked in two streams in 2002 and 2003; a third stream was used as a control. Salmonid fish abundance, growth, and stomach contents were monitored in all three streams before and after carcass analog placement. Fish, invertebrate, and periphyton samples were also collected for stable isotope analysis (to determine if nutrients from carcass analogs were incorporated into the stream food web). Water quality samples were also collected to determine if nutrient overloading occurred in streams. Significant differences in growth were found between fish in treated and untreated stream reaches. Fish in treatment reaches exhibited higher instantaneous growth rates approximately one month after the first carcass analog stocking. Stomach contents sampling indicated that salmonid fish routinely consumed the carcass analog material directly, and that stomach fullness of fish in treatment reaches was higher than in untreated reaches in the first few weeks following carcass analog stockings. No significant differences were detected in fish abundance between

  8. Culture of salmonid fishes

    National Research Council Canada - National Science Library

    Stickney, Robert R

    1991-01-01

    .... In recognition of the growing concern that aquaculture development has the potential to negatively impact the natural environment, a chapter on controversies surrounding salmonid culture has been included...

  9. Comparison of the fatty acid profile of muscle neutral lipids and phospholipids of up-river anadromous sea lamprey (Petromyzon marinus L. from three Portuguese river basins

    Directory of Open Access Journals (Sweden)

    Sara Pinela

    2009-12-01

    Full Text Available Composition of fatty acid profile of muscle neutral lipids (NL and phospholipids (PL of sea lamprey that enter the Portuguese rivers Minho, Tagus and Guadiana during their non-trophic spawning migration was analysed. The fatty acid profile exhibited differences in the percentage among NL and PL and between river basins. Similarities were found in the fatty acid profile of NL. Monounsaturated fatty acids (MUFA were the most representative, followed by saturated fatty acids (SFA and finally by polyunsaturated fatty acids (PUFA. Monoenic 16:1 and 18:1ω9 formed a considerable percentage of total fatty acids, followed by SFA 14:0 and 16:0. EPA and DHA were the dominant PUFA fatty acids. In terms of NL, the fatty acid that contributed for the discrimination between the three river basins was 18:1ω7. Individuals from the Minho river basin exhibited a different fatty acid profile of PL characterised by a low PUFA percentage when compared with lampreys from the Tagus and Guadiana river basins. Muscle PL fraction showed that the two monoenes, 16:1 and 18:1ω9, occurred at high percentage, followed by 16:0 and 14:0 (SFA. Among PUFA, DHA was the most representative fatty acid. The fatty acids that contributed to the separation between the three river basins were 16:0, 18:4ω3 and 24:1ω9. Although the results point in the direction of a possible difference between the fatty acid composition of the NL and PL fractions in the muscle samples from the three river basins, further studies, especially in tissues where fatty acid composition will be less sensitive to diet and environmental factors, are necessary to confirm this hypothesis.

  10. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin : Evaluating Wetland Restoration Projects in the Columbia River Estuary using Hydroacoustic Telemetry Arrays to Estimate Movement, Survival, and Residence Times of Juvenile Salmonids, Volume XXII (22).

    Energy Technology Data Exchange (ETDEWEB)

    Perry, Russell W.; Skalski, John R.

    2008-08-01

    Wetlands in the Columbia River estuary are actively being restored by reconnecting these habitats to the estuary, making more wetland habitats available to rearing and migrating juvenile salmon. Concurrently, thousands of acoustically tagged juvenile salmonids are released into the Columbia River to estimate their survival as they migrate through the estuary. Here, we develop a release-recapture model that makes use of these tagged fish to measure the success of wetland restoration projects in terms of their contribution to populations of juvenile salmon. Specifically, our model estimates the fraction of the population that enter the wetland, survival within the wetland, and the mean residence time of fish within the wetland. Furthermore, survival in mainstem Columbia River downstream of the wetland can be compared between fish that remained the mainstem and entered the wetland. These conditional survival estimates provide a means of testing whether the wetland improves the subsequent survival of juvenile salmon by fostering growth or improving their condition. Implementing such a study requires little additional cost because it takes advantage of fish already released to estimate survival through the estuary. Thus, such a study extracts the maximum information at minimum cost from research projects that typically cost millions of dollars annually.

  11. Proceedings from a Workshop on Ecological Carrying Capacity of Salmonids in the Columbia River Basin : Measure 7.1A of the Northwest Power Planning Council`s 1994 Fish and Wildlife Program : Report 3 of 4, Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Gary E.; Neitzel, D.A.; Mavros, William V.

    1996-05-01

    This report contains the proceedings of a workshop held during 1995 in Portland, Oregon. The objective of the workshop was to assemble a group of experts that could help us define carrying capacity for Columbia River Basin salmonids. The workshop was one activity designed to answer the questions asked in Measure 7.1A of the Council`s Fish and Wildlife Program. Based, in part, on the information we learned during the workshop we concluded that the approach inherent in 7.1A will not increase understanding of ecology, carrying capacity, or limiting factors that influence salmon under current conditions. Measure 7.1A requires a definition of carrying capacity and a list of determinants (limiting factors) of capacity. The implication or inference then follows that by asking what we know and do not know about the determinants will lead to research that increases our understanding of what is limiting salmon survival. It is then assumed that research results will point to management actions that can remove or repair the limiting factors. Most ecologists and fisheries scientists that have studied carrying capacity clearly conclude that this approach is an oversimplification of complex ecological processes. To pursue the capacity parameter, that is, a single number or set of numbers that quantify how many salmon the basin or any part of the basin can support, is meaningless by itself and will not provide useful information.

  12. A simple model that identifies potential effects of sea-level rise on estuarine and estuary-ecotone habitat locations for salmonids in Oregon, USA

    Science.gov (United States)

    Rebecca Flitcroft; Kelly Burnett; Kelly. Christiansen

    2013-01-01

    Diadromous aquatic species that cross a diverse range of habitats (including marine, estuarine, and freshwater) face different effects of climate change in each environment. One such group of species is the anadromous Pacific salmon (Oncorhynchus spp.). Studies of the potential effects of climate change on salmonids have focused on both marine and...

  13. Assessment of Native Salmonids Above Hells Canyon Dam, Idaho; 1998 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, Kevin A. (Idaho Department of Fish and Game, Boise, ID)

    1999-03-01

    Native resident salmonids in the western United States are in decline throughout much of their range. The purpose of the multi-phased project is to restore native salmonids in the upper Snake River basin to self-sustaining, harvestable levels.

  14. 76 FR 21858 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2011-04-19

    ... steelhead, SR fall Chinook, and SR spr/sum Chinook. The purpose of the project is to continue developing a..., PS Chinook, and LCR coho salmon during the course of headwater stream surveys over wide parts of... anadromous fish response at habitat restoration projects throughout the John Day Basin. Currently, many...

  15. 78 FR 28805 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-05-16

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS..., NMFS received an application, including an HGMP, from the Idaho Department of Fish and Game, a section... the Snake River basin, rear juveniles, and release eggs, juveniles, and adult fish into upper Salmon...

  16. 78 FR 74116 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-12-10

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... plans and request for comment. SUMMARY: Notice is hereby given that the Oregon Department of Fish and... River and Columbia River basins by providing hatchery fish to support fishing opportunities while...

  17. 77 FR 63294 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2012-10-16

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... Klallam Tribe and the Washington Department of Fish and Wildlife have submitted five Hatchery and Genetic... programs are currently operating, and all five hatchery programs raise fish native to the Elwha River basin...

  18. 78 FR 25954 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-05-03

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... 15, 2012, NMFS received an application, including an HGMP, from the Idaho Department of Fish and Game... salmon returning to the Snake River basin, rear juveniles, and release eggs, juveniles, and adult fish...

  19. NIS occurrence - Non-native species impacts on threatened and endangered salmonids

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The objectives of this project: a) Identify the distribution of non-natives in the Columbia River Basin b) Highlight the impacts of non-natives on salmonids c)...

  20. Fish Individual-based Numerical Simulator (FINS): A particle-based model of juvenile salmonid movement and dissolved gas exposure history in the Columbia River Basin

    International Nuclear Information System (INIS)

    Scheibe, Timothy D.; Richmond, Marshall C.

    2002-01-01

    This paper describes a numerical model of juvenile salmonid migration in the Columbia and Snake Rivers. The model, called the Fish Individual-based Numerical Simulator or FINS, employs a discrete, particle-based approach to simulate the migration and history of exposure to dissolved gases of individual fish. FINS is linked to a two-dimensional (vertically-averaged) hydrodynamic simulator that quantifies local water velocity, temperature, and dissolved gas levels as a function of river flow rates and dam operations. Simulated gas exposure histories can be input to biological mortality models to predict the effects of various river configurations on fish injury and mortality due to dissolved gas supersaturation. Therefore, FINS serves as a critical linkage between hydrodynamic models of the river system and models of biological impacts. FINS was parameterized and validated based on observations of individual fish movements collected using radiotelemetry methods during 1997 and 1998 . A quasi-inverse approach was used to decouple fish swimming movements from advection with the local water velocity, allowing inference of time series of non-advective displacements of individual fish from the radiotelemetry data. Statistical analyses of these displacements are presented, and confirm that strong temporal correlation of fish swimming behavior persists in some cases over several hours. A correlated random-walk model was employed to simulate the observed migration behavior, and parameters of the model were estimated that lead to close correspondence between predictions and observations

  1. Evaluation of the Life History of Native Salmonids in the Malheur River Basin; Cooperative Bull Trout/Redband Trout Research Project, 1999-2000 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Schwabe, Lawrence; Tiley, Mark (Burns Paiute Tribe, Department of Fish and Wildlife, Burns, OR); Perkins, Raymond R. (Oregon Department of Fish and Wildlife, Ontario, OR)

    2000-11-01

    The purpose of this study is to document the seasonal distribution of adult/sub-adult bull trout (Salvelinus confluentus) in the Malheur River basin. Due to the decline of bull trout in the Columbia Basin, the United States Fish and Wildlife Service listed bull trout as a threatened species in June 1998. Past land management activities; construction of dams; and fish eradication projects in the North Fork and Middle Fork Malheur River by poisoning have worked in concert to cumulatively impact native species in the Malheur Basin (Bowers et. al. 1993). Survival of the remaining bull trout populations is severely threatened (Buchanan 1997). 1999 Research Objects are: (1) Document the migratory patterns of adult/sub-adult bull trout in the North Fork Malheur River; (2) Determine the seasonal bull trout use of Beulah Reservoir and bull trout entrainment; and (3) Timing and location of bull trout spawning in the North Fork Malheur River basin. The study area includes the Malheur basin from the mouth of the Malheur River located near Ontario, Oregon to the headwaters of the North Fork Malheur River (Map 1). All fish collected and most of the telemetry effort was done on the North Fork Malheur River subbasin (Map 2). Fish collection was conducted on the North Fork Malheur River at the tailwaters of Beulah Reservoir (RK 29), Beulah Reservoir (RK 29-RK 33), and in the North Fork Malheur River at Crane Crossing (RK 69) to the headwaters of the North Fork Malheur. Radio telemetry was done from the mouth of the Malheur River in Ontario, Oregon to the headwaters of the North Fork Malheur. This report will reflect all migration data collected from 3/1/99 to 12/31/99.

  2. Juvenile Salmonid Metrics - Ocean Survival of Salmonids

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A study to evaluate the role of changing ocean conditions on growth and survival of juvenile salmon from the Columbia River basin as they enter the Columbia River...

  3. The Reaches Project : Ecological and Geomorphic Dtudies Supporting Normative Flows in the Yakima River Basin, Washington, Final Report 2002.

    Energy Technology Data Exchange (ETDEWEB)

    Stanford, Jack A.; Lorang, Mark N.; Matson, Phillip L. (University of Montana, Flathead Lake Biological Station, Poison, MT)

    2002-10-01

    The Yakima River system historically produced robust annual runs of chinook, sockeye, chum and coho salmon and steelhead. Many different stocks or life history types existed because the physiography of the basin is diverse, ranging from very dry and hot in the high desert of the lower basin to cold and wet in the Cascade Mountains of the headwaters (Snyder and Stanford 2001). Habitat diversity and life history diversity of salmonids are closely correlated in the Yakima Basin. Moreover, habitat diversity for salmonids and many other fishes maximizes in floodplain reaches of river systems (Ward and Stanford 1995, Independent Scientific Group 2000). The flood plains of Yakima River likely were extremely important for spawning and rearing of anadromous salmonids (Snyder and Stanford 2001). However, Yakima River flood plains are substantially degraded. Primary problems are: revetments that disconnect main and side channel habitats; dewatering associated with irrigation that changes base flow conditions and degrades the shallow-water food web; chemical and thermal pollution that prevents proper maturation of eggs and juveniles; and extensive gravel mining within the floodplain reaches that has severed groundwater-channel connectivity, increased thermal loading and increased opportunities for invasions of nonnative species. The Yakima River is too altered from its natural state to allow anything close to the historical abundance and diversity of anadromous fishes. Habitat loss, overharvest and dam and reservoir passage problems in the mainstem Columbia River downstream of the Yakima, coupled with ocean productivity variation, also are implicated in the loss of Yakima fisheries. Nonetheless, in an earlier analysis, Snyder and Stanford (2001) concluded that a significant amount of physical habitat remains in the five floodplain reaches of the mainstem river because habitat-structuring floods do still occur on the remaining expanses of floodplain environment. Assuming main

  4. Umatilla Basin Natural Production Monitoring and Evaluation; 2003-2004 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, Jesse D.M.; Contor, Craig C.; Hoverson, Eric (Confederated Tribes of the Umatilla Indian Reservation, Department of Natural Resources, Pendleton, OR)

    2005-10-01

    Basin developed with the efforts to restore natural populations of spring and fall Chinook salmon, (Oncorhynchus tshawytsha) coho salmon and (O. kisutch) and enhance summer steelhead (O. mykiss). The need for restoration began with agricultural development in the early 1900's that extirpated salmon and reduced steelhead runs (BOR 1988). The most notable development was the construction and operation of Three-Mile Falls Dam (3MD) and other irrigation projects that dewatered the Umatilla River during salmon migrations. The Confederated Tribes of the Umatilla Indian Reservation (CTUIR) and the Oregon Department of Fish and Wildlife (ODFW) developed the Umatilla Hatchery Master Plan to restore the historical fisheries in the basin. The plan was completed in 1990 and included the following objectives: (1) Establish hatchery and natural runs of Chinook and coho salmon. (2) Enhance existing summer steelhead populations through a hatchery program. (3) Provide sustainable tribal and non-tribal harvest of salmon and steelhead. (4) Maintain the genetic characteristics of salmonids in the Umatilla River Basin. (5) Produce almost 48,000 adult returns to Three-Mile Falls Dam. The goals were reviewed in 1999 and were changed to 31,500 adult salmon and steelhead returns (Table 2). We conduct core long-term monitoring activities each year as well as two and three-year projects that address special needs for adaptive management. Examples of these projects include adult passage evaluations (Contor et al. 1995, Contor et al. 1996, Contor et al. 1997, Contor et al. 1998), genetic monitoring (Currens & Schreck 1995, Narum et al. 2004), and habitat assessment surveys (Contor et al. 1995, Contor et al. 1996, Contor et al. 1997, Contor et al. 1998). Our project goal is to provide quality information to managers and researchers working to restore anadromous salmonids to the Umatilla River Basin. This is the only project that monitors the restoration of naturally producing salmon and

  5. Protect Anadromous Salmonids in the Mainstem Corridor, Monitoring and Evaluation, Annual Report 200-2001.

    Energy Technology Data Exchange (ETDEWEB)

    Vigg, Steven; Johnson, John

    2002-02-01

    In this annual Monitoring & Evaluation (M&E) report to the Bonneville Power Administration (BPA), we summarize significant activities and performance measures resultant from enhanced protection by Columbia River Inter-Tribal Fisheries Enforcement (CRITFE) in the mainstem corridor (BPA Project 2000-056). This report covers the Fiscal Year (FY) 2000 performance period -- May 15, 2000 to May 14, 2001. Quarterly progress reports have previously been submitted to BPA and are posted on the M&E Web site (www.Eco-Law.net) -- for the time period April-December 2000 (Vigg 2000b,c,d) and for the period January-June 2001 (Vigg 2001a,b). We also present comprehensive data representing the first quarter of year 2000 in this report for a pre-project comparison. In addition, we have analyzed specific annual enforcement statistics to evaluate trends during the baseline period 1996-2000. Additional statistics and more years of comprehensive baseline data are now being summarized, and will be presented in future M&E annual reports--to provide a longer time series for evaluation of trends in input, output and outcome performance standards.

  6. marine survival ecosystem indicators - Estimating the ecosystem indicators of anadromous salmonids in the Puget Sound region

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The objective of this project is to develop a simple approach for estimating the marine survival and causes of trends in survival. Data is a summary of ecosystem...

  7. Grande Ronde Basin Fish Habitat Enhancement Project : 2000 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    McGowan, Vance R.; Powell, Russ M.; Stennfeld, Scott P.

    2001-04-01

    On July 1, 1984 the Bonneville Power Administration and the Oregon Department of Fish and Wildlife entered into an agreement to initiate fish habitat enhancement work in the Joseph Creek subbasin of the Grande Ronde River Basin in northeast Oregon. In July of 1985 the Upper and Middle Grande Ronde River, and Catherine Creek subbasins were included in the intergovernmental contract, and on March 1, 1996 the Wallowa River subbasin was added. The primary goal of ''The Grande Ronde Basin Fish Habitat Enhancement Project'' is to access, create, improve, protect, and restore riparian and instream habitat for anadromous salmonids, thereby maximizing opportunities for natural fish production within the basin. This project provided for implementation of Program Measure 703 (C)(1), Action Item 4.2 of the Northwest Power Planning Council's Columbia River Basin Fish and Wildlife Program (NPPC, 1987), and continues to be implemented as offsite mitigation for mainstem fishery losses caused by the Columbia River hydro-electric system. All work conducted by the Oregon Department of Fish and Wildlife is on private lands and therefore requires that considerable time be spent developing rapport with landowners to gain acceptance of, and continued cooperation with this program throughout 10-15 year lease periods. This project calls for passive regeneration of habitat, using riparian enclosure fencing as the primary method to restore degraded streams to a normative condition. Active remediation techniques using plantings, off-site water developments, site-specific instream structures, or whole channel alterations are also utilized where applicable. Individual projects contribute to and complement ecosystem and basin-wide watershed restoration efforts that are underway by state, federal, and tribal agencies, and local watershed councils. Work undertaken during 2000 included: (1) Implementing 2 new projects in the Grande Ronde drainage, and retrofitting one old

  8. Seasonal Juvenile Salmonid Presence and Migratory Behavior in the Lower Columbia River

    Energy Technology Data Exchange (ETDEWEB)

    Carter, Jessica A.; McMichael, Geoffrey A.; Welch, Ian D.; Harnish, Ryan A.; Bellgraph, Brian J.

    2009-04-30

    To facilitate preparing Biological Assessments of proposed channel maintenance projects, the Portland District of the U.S. Army Corps of Engineers contracted the Pacific Northwest National Laboratory to consolidate and synthesize available information about the use of the lower Columbia River and estuary by juvenile anadromous salmonids. The information to be synthesized included existing published documents as well as data from five years (2004-2008) of acoustic telemetry studies conducted in the Columbia River estuary using the Juvenile Salmon Acoustic Telemetry System. For this synthesis, the Columbia River estuary includes the section of the Columbia River from Bonneville Dam at river kilometer (Rkm) 235 downstream to the mouth where it enters the Pacific Ocean. In this report, we summarize the seasonal salmonid presence and migration patterns in the Columbia River estuary based on information from published studies as well as relevant data from acoustic telemetry studies conducted by NOAA Fisheries and the Pacific Northwest National Laboratory (PNNL) between 2004 and 2008. Recent acoustic telemetry studies, conducted using the Juvenile Salmon Acoustic Telemetry System (JSATS; developed by the Portland District of the U.S. Army Corps of Engineers), provided information on the migratory behavior of juvenile steelhead (O. mykiss) and Chinook salmon in the Columbia River from Bonneville Dam to the Pacific Ocean. In this report, Section 2 provides a summary of information from published literature on the seasonal presence and migratory behavior of juvenile salmonids in the Columbia River estuary and plume. Section 3 presents a detailed synthesis of juvenile Chinook salmon and steelhead migratory behavior based on use of the JSATS between 2004 and 2008. Section 4 provides a discussion of the information summarized in the report as well as information drawn from literature reviews on potential effects of channel maintenance activities to juvenile salmonids rearing in

  9. A resilience approach can improve anadromous fish restoration

    Science.gov (United States)

    Waldman, John R.; Wilson, Karen A.; Mather, Martha E.; Snyder, Noah P.

    2016-01-01

    Most anadromous fish populations remain at low levels or are in decline despite substantial investments in restoration. We explore whether a resilience perspective (i.e., a different paradigm for understanding populations, communities, and ecosystems) is a viable alternative framework for anadromous fish restoration. Many life history traits have allowed anadromous fish to thrive in unimpacted ecosystems but have become contemporary curses as anthropogenic effects increase. This contradiction creates a significant conservation challenge but also makes these fish excellent candidates for a resilience approach. A resilience approach recognizes the need to maintain life history, population, and habitat characteristics that increase the ability of a population to withstand and recover from multiple disturbances. To evaluate whether a resilience approach represents a viable strategy for anadromous fish restoration, we review four issues: (1) how resilience theory can inform anadromous fish restoration, (2) how a resilience-based approach is fundamentally different than extant anadromous fish restoration strategies, (3) ecological characteristics that historically benefited anadromous fish persistence, and (4) examples of how human impacts harm anadromous fish and how a resilience approach might produce more successful outcomes. We close by suggesting new research and restoration directions for implementation of a resilience-based approach.

  10. Migratory Behavior and Survival of Juvenile Salmonids in the Lower Columbia River and Estuary in 2009

    Energy Technology Data Exchange (ETDEWEB)

    McMichael, Geoffrey A.; Harnish, Ryan A.; Bellgraph, Brian J.; Carter, Jessica A.; Ham, Kenneth D.; Titzler, P. Scott; Hughes, Michael S.

    2010-08-01

    The study reported herein was funded as part of the Anadromous Fish Evaluation Program, which is managed by the U.S. Army Corps of Engineers (USACE). The Anadromous Fish Evaluation Program study code is EST P 02 01: A Study of Salmonid Survival and Behavior through the Columbia River Estuary Using Acoustic Tags. The study was conducted by the Pacific Northwest National Laboratory (PNNL) and National Oceanic and Atmospheric Administration (NOAA) Fisheries for the USACE Portland District. Estimated survival of acoustic-tagged juvenile Chinook salmon and steelhead through the lower Columbia River and estuary in 2009 was lowest in the final 50 km of the estuary. Probability of survival was relatively high (>0.90) for yearling and subyearling Chinook salmon from the Bonneville Dam forebay (rkm 236) to Three-tree Point (rkm 49.6). Survival of juvenile Chinook salmon declined sharply through the lower 50 km of the estuary. Acoustic-tagged steelhead smolts did not survive as well as juvenile Chinook salmon between Bonneville Dam and the mouth of the Columbia River. Steelhead survival began to decline farther upstream (at rkm 86) relative to that of the Chinook salmon stocks. Subyearling Chinook salmon survival decreased markedly as the season progressed. It remains to be determined whether later migrating subyearling Chinook salmon are suffering increasing mortality as the season progresses or whether some portion of the apparent loss is due to fish extending their freshwater residence. This study provided the first glimpse into what promises to be a very informative way to learn more about how juvenile salmonid passage experiences through the FCRPS may influence their subsequent survival after passing Bonneville Dam. New information regarding the influence of migration pathway through the lower 50 km of the Columbia River estuary on probability of survival of juvenile salmonids, combined with increased understanding regarding the foraging distances and time periods of

  11. A mathematical model of salmonid spawning habitat

    Science.gov (United States)

    Robert N. Havis; Carlos V. Alonzo; Keith E Woeste; Russell F. Thurow

    1993-01-01

    A simulation model [Salmonid Spawning Analysis Model (SSAM)I was developed as a management tool to evaluate the relative impacts of stream sediment load and water temperature on salmonid egg survival. The model is usefi.il for estimating acceptable sediment loads to spawning habitat that may result from upland development, such as logging and agriculture. Software in...

  12. The Umatilla Basin Natural Production Monitoring and Evaluation Project, 2008 Annual Progress Report.

    Energy Technology Data Exchange (ETDEWEB)

    Contor, Craig R.; Harris, Robin; King, Marty [Confederated Tribes of the Umatilla Indian Reservation

    2009-06-10

    salmon (O. kisutch), and enhance summer steelhead (O. mykiss). The need for restoration began with agricultural development in the early 1900's that extirpated salmon and reduced steelhead runs (Bureau of Reclamation, BOR 1988). The most notable development was the construction and operation of Three Mile Falls Dam (TMD) and other irrigation projects which dewatered the Umatilla River during salmon migrations. CTUIR and ODFW developed the Umatilla Hatchery Master Plan to restore fisheries to the basin. The plan was completed in 1990 and included the following objectives which were updated in 1999: (1) Establish hatchery and natural runs of Chinook and coho salmon. (2) Enhance existing summer steelhead populations through a hatchery program. (3) Provide sustainable tribal and non-tribal harvest of salmon and steelhead. (4) Maintain the genetic characteristics of salmonids in the Umatilla River Basin. (5) Increase annual returns to Three Mile Falls Dam to 31,500 adult salmon and steelhead. In the past the M&E project conducted long-term monitoring activities as well as two and three-year projects that address special needs for adaptive management. Examples of these projects include adult passage evaluations, habitat assessment surveys (Contor et al. 1995, Contor et al. 1996, Contor et al. 1997, Contor et al. 1998), and genetic monitoring (Currens & Schreck 1995, Narum et al. 2004). The project's goal is to provide quality information to managers and researchers working to restore anadromous salmonids to the Umatilla River Basin. The status of completion of each of BPA's standardized work element was reported in 'Pisces'(March 2008) and is summarized.

  13. Grande Ronde Basin Fish Habitat Enhancement Project, Annual Report 2002-2003.

    Energy Technology Data Exchange (ETDEWEB)

    McGowan, Vance

    2003-08-01

    On July 1, 1984 the Bonneville Power Administration and the Oregon Department of Fish and Wildlife entered into an agreement to initiate fish habitat enhancement work in the Joseph Creek subbasin of the Grande Ronde River Basin in northeast Oregon. In July of 1985 the Upper and Middle Grande Ronde River, and Catherine Creek subbasins were included in the intergovernmental contract, and on March 1, 1996 the Wallowa River subbasin was added. The primary goal of 'The Grande Ronde Basin Fish Habitat Enhancement Project' is to create, protect, and restore riparian and instream habitat for anadromous salmonids, thereby maximizing opportunities for natural fish production within the basin. This project provided for implementation of Program Measure 703 (C)(1), Action Item 4.2 of the Northwest Power Planning Council's Columbia River Basin Fish and Wildlife Program (NPPC, 1987), and continues to be implemented as offsite mitigation for mainstem fishery losses caused by the Columbia River hydro-electric system. All work conducted by the Oregon Department of Fish and Wildlife is on private lands and therefore requires that considerable time be spent developing rapport with landowners to gain acceptance of, and continued cooperation with this program throughout 10-15 year lease periods. This project calls for passive regeneration of habitat, using riparian exclosure fencing as the primary method to restore degraded streams to a normative condition. Active remediation techniques using plantings, off-site water developments, site-specific instream structures, or whole channel alterations are also utilized where applicable. Individual projects contribute to and complement ecosystem and basin-wide watershed restoration efforts that are underway by state, federal, and tribal agencies, and local watershed councils. Work undertaken during 2002 included: (1) Implementing 1 new fencing project in the Wallowa subbasin that will protect an additional 0.95 miles of stream

  14. Elwha genetics - Elwha river salmonid genetics

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Elwha Dam is in the process of being removed, with fish restoration to occur in areas previously inaccessible to salmonids. Fish recovery anticipates that...

  15. Model structure of the stream salmonid simulator (S3)—A dynamic model for simulating growth, movement, and survival of juvenile salmonids

    Science.gov (United States)

    Perry, Russell W.; Plumb, John M.; Jones, Edward C.; Som, Nicholas A.; Hetrick, Nicholas J.; Hardy, Thomas B.

    2018-04-06

    Fisheries and water managers often use population models to aid in understanding the effect of alternative water management or restoration actions on anadromous fish populations. We developed the Stream Salmonid Simulator (S3) to help resource managers evaluate the effect of management alternatives on juvenile salmonid populations. S3 is a deterministic stage-structured population model that tracks daily growth, movement, and survival of juvenile salmon. A key theme of the model is that river flow affects habitat availability and capacity, which in turn drives density dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily time series of discharge, water temperature, and usable habitat area or carrying capacity. The physical characteristics of each habitat unit and the number of fish occupying each unit, in turn, drive survival and growth within each habitat unit and movement of fish among habitat units.The purpose of this report is to outline the underlying general structure of the S3 model that is common among different applications of the model. We have developed applications of the S3 model for juvenile fall Chinook salmon (Oncorhynchus tshawytscha) in the lower Klamath River. Thus, this report is a companion to current application of the S3 model to the Trinity River (in review). The general S3 model structure provides a biological and physical framework for the salmonid freshwater life cycle. This framework captures important demographics of juvenile salmonids aimed at translating management alternatives into simulated population responses. Although the S3 model is built on this common framework, the model has been constructed to allow much flexibility in application of the model to specific river systems. The ability for practitioners to include system-specific information for the

  16. Food supplies of stream-dwelling salmonids

    Science.gov (United States)

    Wipfli, Mark S.

    2009-01-01

    Much is known about the importance of the physical characteristics of salmonid habitat in Alaska and the Pacific Northwest, with far less known about the food sources and trophic processes within these habitats, and the role they play in regulating salmonid productivity. Freshwater food webs supporting salmonids in Alaska rely heavily on nutrient, detritus and prey subsidies from both marine and terrestrial ecosystems. Adult salmon provide a massive input of marine biomass to riverine ecosystems each year when they spawn, die, and decompose, and are a critical food source for young salmon in late summer and fall; riparian forests provide terrestrial invertebrates to streams, which at times comprise over half of the food ingested by stream-resident salmonids; and up-slope, fishless headwater streams are a year-round source of invertebrates and detritus for fish downstream. The quantity of these food resources vary widely depending on source, season, and spatial position within a watershed. Terrestrial invertebrate inputs from riparian habitats are generally the most abundant food source in summer. Juvenile salmonids in streams consume roughly equal amounts of freshwater and terrestrially-derived invertebrates during most of the growing season, but ingest substantial amounts of marine resources (salmon eggs and decomposing salmon tissue) when these food items are present. Quantity, quality, and timing of food resources all appear to be important driving forces in aquatic food web dynamics, community nutrition, and salmonid growth and survival in riverine ecosystems.

  17. Okanogan Subbasin Water Quality and Quantity Report for Anadromous Fish in 2006.

    Energy Technology Data Exchange (ETDEWEB)

    Colville Tribes, Department of Fish & Wildlife

    2007-12-01

    Fish need water of sufficient quality and quantity in order to survive and reproduce. The list of primary water quality indicators appropriate for monitoring of anadromous fish, as identified by the Upper Columbia Monitoring Strategy, includes: discharge, temperature, dissolved oxygen, pH, turbidity, conductivity, nitrogen, phosphorus and ammonia. The Colville Tribes Fish and Wildlife Department began evaluating these water quality indicators in 2005 and this report represents data collected from October 1, 2005 through September 30, 2006. We collected empirical status and trend data from various sources to evaluate each water quality indicator along the main stem Okanogan and Similkameen Rivers along with several tributary streams. Each water quality indicator was evaluated based upon potential impacts to salmonid survival or productivity. Specific conductance levels and all nutrient indicators remained at levels acceptable for growth, survival, and reproduction of salmon and steelhead. These indicators were also considered of marginal value for monitoring environmental conditions related to salmonids within the Okanogan subbasin. However, discharge, temperature, turbidity, dissolved oxygen and pH in that order represent the water quality indicators that are most useful for monitoring watershed health and habitat changes and will help to evaluate threats or changes related to salmon and steelhead restoration and recovery. On the Okanogan River minimum flows have decreased over the last 12 years at a rate of -28.3CFS/year as measured near the town of Malott, WA. This trend is not beneficial for salmonid production and efforts to reverse this trend should be strongly encouraged. Turbidity levels in Bonaparte and Omak Creek were a concern because they had the highest monthly average readings. Major upland disturbance in the Bonaparte Creek watershed has occurred for decades and agricultural practices within the riparian areas along this creek have lead to major

  18. Juvenile Salmonid Trophic Data - Ocean Survival of Salmonids

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A study to evaluate the role of changing ocean conditions on growth and survival of juvenile salmon from the Columbia River basin as they enter the Columbia River...

  19. Juvenile Salmonid Necropsy Data - Ocean Survival of Salmonids

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A study to evaluate the role of changing ocean conditions on growth and survival of juvenile salmon from the Columbia River basin as they enter the Columbia River...

  20. Juvenile Salmonid Parasite Data - Ocean Survival of Salmonids

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A study to evaluate the role of changing ocean conditions on growth and survival of juvenile salmon from the Columbia River basin as they enter the Columbia River...

  1. Columbia River System Operation Review : Final Environmental Impact Statement, Appendix C: Anadromous Fish and Juvenile Fish Transportation.

    Energy Technology Data Exchange (ETDEWEB)

    Columbia River System Operation Review (U.S.)

    1995-11-01

    This Appendix C of the Final Environmental Impact Statement for the Columbia River System discusses impacts on andromous fish and juvenile fish transportation. The principal andromous fish in the Columbia basin include salmonid species (Chinook, coho, and sockeye salmon, and steelhead) and nonsalmoinid andromous species (sturgeon, lamprey, and shad). Major sections in this document include the following: background, scope and process; affected environment for salmon and steelhead, shaded, lamprey, sturgeon; study methods; description of alternatives: qualitative and quantitative findings.

  2. ON THE ORIGIN OF THE BALKAN PENINSULA SALMONIDS

    Directory of Open Access Journals (Sweden)

    Simo Georgiev

    2003-12-01

    Full Text Available This paper puts forward the knowledge of the immigration itineraries of the ancestors of five extant salmonid species on Balkan Peninsula which are the following: Acantholingua ohridana (Steindachner, 1892, Hucho hucho (Linnaeus, 1758, Salmo trutta Linnaeus, 1758, Salmothymus obtusirostris Heckel, 1851 and Thymallus thymallus (Linnaeus, 1758. The thesis for the migration itineraries is based on the anatomical, molecular and zoogeographical facts recently published. These latest facts complement or reject the previous thesis that considered the origin of separate species, which in this paper are analyzed together. A new position on the origin of some S. trutta populations inhabiting the Mediterranean Sea watershed is proposed. The new thesis is that they did not inhabit it from the west, through the Atlantic Ocean and Gibraltar, but from the North, through the branches of the former Sarmatian Sea, using the continental way. A. ohridana and S. obtusirostris, the only endemic Balkanean salmonids, have developed here from the mutual ancestor with the extant Siberian Brachymystax lenok (Pallas, 1773. This ancestor came first, together with the S. trutta lineage known as »marmorata«. Using the same migration way, the T. thymallus population of Soča River, the North.West boundary of Balkan Peninsula remained restricted at that corner of Adriatic Sea watershed. In the Black Sea watershed (the Danube River flow extension on Balkan Peninsula the distribution of T. thymallus coincides with the distribution of H. hucho. The thesis which has been proposed for this, largest contemporary Balkan Peninsula salmonid fish was that it came here last, after the connections between the Mediterranean Sea basin and once existent Sarmatian Sea disappeared. This occurred after the end of the last glaciations. This has been concluded on the basis of the exclusion of the areas of the »marmorata« lineage of S. trutta (Mediterranean Sea watershed and H. hucho (Black Sea

  3. Non-Salmonid Abundance - Line Features [ds186

    Data.gov (United States)

    California Natural Resource Agency — The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. The "Other Fish" category contains data collected...

  4. Application of otolith shape analysis in identifying different ecotypes of Coilia ectenes in the Yangtze Basin, China

    Digital Repository Service at National Institute of Oceanography (India)

    Radhakrishnan, K.V.; Li, Y.; Jayalakshmy, K.V.; Liu, M.; Murphy, B.R.; Xie, S.

    of the distributional range of the species in the Yangtze Basin, were digitized and analyzed. Canonical Discriminant Analysis (CDA) of the shape indices and Fourier descriptors pooled together showed three distinct clusters of individuals representing anadromous, land...

  5. An assessment of stream habitat and nutrients in the Elwha River basin: implications for restoration

    Science.gov (United States)

    Munn, Mark D.; Black, R.W.; Haggland, A.L.; Hummling, M.A.; Huffman, R.L.

    1999-01-01

    The Elwha River was once famous for its 10 runs of anadromous salmon which included chinook that reportedly exceeded 45 kilograms. These runs either ceased to exist or were significantly depleted after the construction of the Elwha (1912) and Glines Canyon (1927) Dams, which resulted in the blockage of more than 113 kilometers of mainstem river and tributary habitat. In 1992, in response to the loss of the salmon runs in the Elwha River Basin, President George Bush signed the Elwha River Ecosystem and Fisheries Restoration Act, which authorizes the Secretary of the Interior to remove both dams for ecosystem restoration. The objective of this U.S. Geological Survey (USGS) study was to begin describing baseline conditions for assessing changes that will result from restoration. The first step was to review available physical, chemical, and biological information on the Elwha River Basin. We found that most studies have focused on anadromous fish and habitat and that little information is available on water quality, habitat classification, geomorphic processes, and riparian and aquatic biological communities. There is also a lack of sufficient data on baseline conditions for assessing future changes if restoration occurs. The second component of this study was to collect water-quality and habitat data, filling information gaps. This information will permit a better understanding of the relation between physical habitat and nutrient conditions and changes that may result from salmon restoration. We collected data in the fall of 1997 and found that the concentrations of nitrogen and phosphorous were generally low, with most samples having concentrations below detection limits. Detectable concentrations of nitrogen were associated with sites in the lower reach of the Elwha River, whereas the few detections of phosphorus were at sites throughout the basin. Nutrient data indicate that the Elwha River and its tributaries are oligotrophic. Results of the stream

  6. A review of the likely effects of climate change on anadromous Atlantic salmon Salmo salar and brown trout Salmo trutta, with particular reference to water temperature and flow.

    Science.gov (United States)

    Jonsson, B; Jonsson, N

    2009-12-01

    The present paper reviews the effects of water temperature and flow on migrations, embryonic development, hatching, emergence, growth and life-history traits in light of the ongoing climate change with emphasis on anadromous Atlantic salmon Salmo salar and brown trout Salmo trutta. The expected climate change in the Atlantic is for milder and wetter winters, with more precipitation falling as rain and less as snow, decrease in ice-covered periods and frequent periods with extreme weather. Overall, thermal limits for salmonids are species specific. Scope for activity and growth and optimal temperature for growth increase with temperature to an optimal point before constrain by the oxygen content of the water. The optimal temperature for growth decreases with increasing fish size and varies little among populations within species, whereas the growth efficiency may be locally adapted to the temperature conditions of the home stream during the growth season. Indirectly, temperature influences age and size at smolting through its effect on growth. Time of spawning, egg hatching and emergence of the larvae vary with temperature and selective effects on time of first feeding. Traits such as age at first maturity, longevity and fecundity decrease with increasing temperature whilst egg size increases with temperature. Water flow influences the accessibility of rivers for returning adults and speed of both upstream and downstream migration. Extremes in water flow and temperature can decrease recruitment and survival. There is reason to expect a northward movement of the thermal niche of anadromous salmonids with decreased production and population extinction in the southern part of the distribution areas, migrations earlier in the season, later spawning, younger age at smolting and sexual maturity and increased disease susceptibility and mortality. Future research challenges are summarized at the end of the paper.

  7. Next-generation salmonid alphavirus vaccine development

    NARCIS (Netherlands)

    Hikke, M.C.

    2016-01-01

    ABSTRACT Aquaculture is essential to meet the current and future demands for seafood to feed the world population. Atlantic salmon and rainbow trout are two of the most cultured aquaculture species. A pathogen that threatens these species is salmonid alphavirus (SAV). A current inactivated virus

  8. Next-generation salmonid alphavirus vaccine development

    NARCIS (Netherlands)

    Hikke, M.C.

    2016-01-01

    ABSTRACT

    Aquaculture is essential to meet the current and future demands for seafood to feed the world population. Atlantic salmon and rainbow trout are two of the most cultured aquaculture species. A pathogen that threatens these species is salmonid alphavirus (SAV). A current inactivated

  9. Population structure in an anadromous fish Tenualosa ilisha using ...

    African Journals Online (AJOL)

    WATER INDIA

    2013-05-29

    May 29, 2013 ... there is little or no movement between rivers and little intermingling of three populations. Thus, aim of the study was to analyze population structure of commercially important tropical anadromous fish T. ilisha from Ganga and Hooghly using mitochondrial DNA cytochrome b gene sequence polymorphism.

  10. Grande Ronde Basin Fish Habitat Enhancement Project : 2007 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    McGowan, Vance R.; Morton, Winston H.

    2008-12-30

    On July 1, 1984 the Bonneville Power Administration and the Oregon Department of Fish and Wildlife entered into an intergovernmental contract to initiate fish habitat enhancement work in the Joseph Creek subbasin of the Grande Ronde River Basin in northeast Oregon. In 1985 the Upper and Middle Grande Ronde River, and Catherine Creek subbasins were included in the contract, and in 1996 the Wallowa River subbasin was added. The primary goal of 'The Grande Ronde Basin Fish Habitat Enhancement Project' is to create, protect, and restore riparian and instream habitat for anadromous salmonids, thereby maximizing opportunities for natural fish production within the basin. This project provided for implementation of Program Measure 703 (C)(1), Action Item 4.2 of the Northwest Power Planning Council's Columbia River Basin Fish and Wildlife Program (NPPC, 1987), and continues to be implemented as offsite mitigation for mainstem fishery losses caused by the Columbia River hydro-electric system. All work conducted by the Oregon Department of Fish and Wildlife and partners is on private lands and therefore requires that considerable time be spent developing rapport with landowners to gain acceptance of, and continued cooperation with this program throughout 10-15 year lease periods. Both passive and active restoration treatment techniques are used. Passive regeneration of habitat, using riparian exclosure fencing and alternate water sources are the primary method to restore degraded streams when restoration can be achieved primarily through changes in management. Active restoration techniques using plantings, bioengineering, site-specific instream structures, or whole stream channel alterations are utilized when streams are more severely degraded and not likely to recover in a reasonable timeframe. Individual projects contribute to and complement ecosystem and basin-wide watershed restoration efforts that are underway by state, federal, and tribal agencies, and

  11. A Two-Stage Information-Theoretic Approach to Modeling Landscape-Level Attributes and Maximum Recruitment of Chinook Salmon in the Columbia River Basin.

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, William L.; Lee, Danny C.

    2000-11-01

    Many anadromous salmonid stocks in the Pacific Northwest are at their lowest recorded levels, which has raised questions regarding their long-term persistence under current conditions. There are a number of factors, such as freshwater spawning and rearing habitat, that could potentially influence their numbers. Therefore, we used the latest advances in information-theoretic methods in a two-stage modeling process to investigate relationships between landscape-level habitat attributes and maximum recruitment of 25 index stocks of chinook salmon (Oncorhynchus tshawytscha) in the Columbia River basin. Our first-stage model selection results indicated that the Ricker-type, stock recruitment model with a constant Ricker a (i.e., recruits-per-spawner at low numbers of fish) across stocks was the only plausible one given these data, which contrasted with previous unpublished findings. Our second-stage results revealed that maximum recruitment of chinook salmon had a strongly negative relationship with percentage of surrounding subwatersheds categorized as predominantly containing U.S. Forest Service and private moderate-high impact managed forest. That is, our model predicted that average maximum recruitment of chinook salmon would decrease by at least 247 fish for every increase of 33% in surrounding subwatersheds categorized as predominantly containing U.S. Forest Service and privately managed forest. Conversely, mean annual air temperature had a positive relationship with salmon maximum recruitment, with an average increase of at least 179 fish for every increase in 2 C mean annual air temperature.

  12. Demonstration of the salmonid humoral response to Renibacterium salmoninarum using a monoclonal antibody against salmonid immunoglobulin

    Science.gov (United States)

    Bartholomew, J.L.; Arkoosh , M.R.; Rohovec, J.S.

    1991-01-01

    The specificity of the antibody response of salmonids to Renibacterium salmoninarum antigens was demonstrated by western blotting techniques that utilized a monoclonal antibody against salmonid immunoglobulin. In this study, the specificity of the response in immunized chinook salmon Oncorhynchus tshawytschawas compared with the response in naturally infected chinook salmon and coho salmon O. kisutch, and immunized rabbits. The antibody response in immunized salmon and rabbits and the naturally infected fish was primarily against the 57–58kilodalton protein complex. In addition to recognizing these proteins in the extracellular fraction and whole-cell preparations, antibody from the immunized salmon and rabbits detected four proteins with lower molecular masses. Western blotting techniques allow identification of the specific antigens recognized and are a useful tool for comparing the immunogenicity of different R. salmoninarumpreparations. Immunofluorescent techniques with whole bacteria were less sensitive than western blotting in detecting salmonid anti-R. salmoninarumantibody.

  13. Juvenile salmonid monitoring in the White Salmon River, Washington, post-Condit Dam removal, 2016

    Science.gov (United States)

    Jezorek, Ian G.; Hardiman, Jill M.

    2017-06-23

    Condit Dam, at river kilometer 5.3 on the White Salmon River, Washington, was breached in 2011 and removed completely in 2012, allowing anadromous salmonids access to habitat that had been blocked for nearly 100 years. A multi-agency workgroup concluded that the preferred salmonid restoration alternative was natural recolonization with monitoring to assess efficacy, followed by a management evaluation 5 years after dam removal. Limited monitoring of salmon and steelhead spawning has occurred since 2011, but no monitoring of juveniles occurred until 2016. During 2016, we operated a rotary screw trap at river kilometer 2.3 (3 kilometers downstream of the former dam site) from late March through May and used backpack electrofishing during summer to assess juvenile salmonid distribution and abundance. The screw trap captured primarily steelhead (Oncorhynchus mykiss; smolts, parr, and fry) and coho salmon (O. kisutch; smolts and fry). We estimated the number of steelhead smolts at 3,851 (standard error = 1,454) and coho smolts at 1,093 (standard error = 412). In this document, we refer to O. mykiss caught at the screw trap as steelhead because they were actively migrating, but because we did not know migratory status of O. mykiss caught in electrofishing surveys, we simply refer to them as O. mykiss or steelhead/rainbow trout. Steelhead and coho smolts tagged with passive integrated transponder tags were subsequently detected downstream at Bonneville Dam on the Columbia River. Few Chinook salmon (O. tshawytscha) fry were captured, possibly as a result of trap location or effects of a December 2015 flood. Sampling in Mill, Buck, and Rattlesnake Creeks (all upstream of the former dam site) showed that juvenile coho were present in Mill and Buck Creeks, suggesting spawning had occurred there. We compared O. mykiss abundance data in sites on Buck and Rattlesnake Creeks to pre-dam removal data. During 2016, age-0 O. mykiss were more abundant in Buck Creek than in 2009 or

  14. Influences of forest and rangeland management on salmonid fishes and their habitats

    National Research Council Canada - National Science Library

    Meehan, William R

    1991-01-01

    Contents : Stream ecosystems - Salmonid distributions and life histories - Habitat requirements of salmonids in streams - Natural processes - Timber harvesting, silvicultrue and watershed processes - Forest...

  15. An Ecosystem-Based Approach to Habitat Restoration Projects with Emphasis on Salmonids in the Columbia River Estuary, 2003 Technical Report.

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, G.; Thom, R.; Whiting, A. (Pacific Northwest National Laboratory)

    2003-11-01

    Habitat restoration in the Columbia River estuary (CRE) is an important off-site mitigation action in the 2000 Biological Opinion (BiOp), an operation of the Federal Columbia River Power System. The CRE, defined as the tidally influenced stretch of river from the mouth to Bonneville Dam 146 miles upstream, is part of the migration pathway for anadromous fish in the Columbia Basin, including salmon listed under the Endangered Species Act (ESA). Salmon in various stages of life, from fry to adults, use tidal channels and wetlands in the CRE to feed, find refuge from predators, and transition physiologically from freshwater to saltwater. Over the last 100 years, however, the area of some wetland habitats has decreased by as much as 70% because of dike and levee building, flow regulation, and other activities. In response to the decline in available habitat, the BiOp's Reasonable and Prudent Alternative (RPA) included mandates to 'develop a plan addressing the habitat needs of juvenile salmon and steelhead in the estuary' (RPA Action 159) and 'develop and implement an estuary restoration program with a goal of protecting and enhancing 10,000 acres of tidal wetlands and other key habitats' (RPA Action 160). To meet Action 159 and support Action 160, this document develops a science-based approach designed to improve ecosystem functions through habitat restoration activities in the CRE. The CRE habitat restoration program's goal and principles focus on habitat restoration projects in an ecosystem context. Since restoration of an entire ecosystem is not generally practical, individual habitat restoration projects have the greatest likelihood of success when they are implemented with an ecosystem perspective. The program's goal is: Implementation of well-coordinated, scientifically sound projects designed to enhance, protect, conserve, restore, and create 10,000 acres of tidal wetlands and other key habitats to aid rebuilding of ESA

  16. Yersinia ruckeri infections in salmonid fish.

    Science.gov (United States)

    Tobback, E; Decostere, A; Hermans, K; Haesebrouck, F; Chiers, K

    2007-05-01

    Yersinia ruckeri is the causative agent of yersiniosis or enteric redmouth disease leading to significant economic losses in salmonid aquaculture worldwide. Infection may result in a septicaemic condition with haemorrhages on the body surface and in the internal organs. Despite the significance of the disease, very little information is available on the pathogenesis, hampering the development of preventive measures to efficiently combat this bacterial agent. This review discusses the agent and the disease it causes. The possibility of the presence of similar virulence markers and/or pathogenic mechanisms between the Yersinia species which elicit disease in humans and Y. ruckeri is also examined.

  17. Introduced northern pike predation on salmonids in southcentral Alaska

    Science.gov (United States)

    Sepulveda, Adam J.; Rutz, David S.; Ivey, Sam S.; Dunker, Kristine J.; Gross, Jackson A.

    2013-01-01

    Northern pike (Esox lucius) are opportunistic predators that can switch to alternative prey species after preferred prey have declined. This trophic adaptability allows invasive pike to have negative effects on aquatic food webs. In Southcentral Alaska, invasive pike are a substantial concern because they have spread to important spawning and rearing habitat for salmonids and are hypothesised to be responsible for recent salmonid declines. We described the relative importance of salmonids and other prey species to pike diets in the Deshka River and Alexander Creek in Southcentral Alaska. Salmonids were once abundant in both rivers, but they are now rare in Alexander Creek. In the Deshka River, we found that juvenile Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (O. kisutch) dominated pike diets and that small pike consumed more of these salmonids than large pike. In Alexander Creek, pike diets reflected the distribution of spawning salmonids, which decrease with distance upstream. Although salmonids dominated pike diets in the lowest reach of the stream, Arctic lamprey (Lampetra camtschatica) and slimy sculpin (Cottus cognatus) dominated pike diets in the middle and upper reaches. In both rivers, pike density did not influence diet and pike consumed smaller prey items than predicted by their gape-width. Our data suggest that (1) juvenile salmonids are a dominant prey item for pike, (2) small pike are the primary consumers of juvenile salmonids and (3) pike consume other native fish species when juvenile salmonids are less abundant. Implications of this trophic adaptability are that invasive pike can continue to increase while driving multiple species to low abundance.

  18. Watershed processes, fish habitat, and salmonid distribution in the Tonsina River (Copper River watershed), Alaska

    Science.gov (United States)

    Booth, D. B.; Ligon, F. K.; Sloat, M. R.; Amerson, B.; Ralph, S. C.

    2007-12-01

    The Copper River watershed is a critical resource for northeastern Pacific salmon, with annual escapements in the millions. The Tonsina River basin, a diverse 2100-km2 tributary to the Copper River that supports important salmonid populations, offers an opportunity to integrate watershed-scale channel network data with field reconnaissance of physical processes and observed distribution of salmonid species. Our long-term goals are to characterize habitats critical to different salmonid life stages, describe the geologic context and current geologic processes that support those habitats in key channel reaches, and predict their watershed-wide distribution. The overarching motivation for these goals is resource conservation, particularly in the face of increased human activity and long-term climate change. Channel geomorphology within the Tonsina River basin reflects inherited glacial topography. Combinations of drainage areas, slopes, channel confinement, and sediment-delivery processes are unique to this environment, giving rise to channel "types" that are recognizable but that do not occur in the same positions in the channel network as in nonglaciated landscapes. We also recognize certain channel forms providing fish habitat without analog in a nonglacial landscape, notably relict floodplain potholes from once-stranded and long-melted ice blocks. Salmonid species dominated different channel types within the watershed network. Sockeye salmon juveniles were abundant in the low-gradient, turbid mainstem; Chinook juveniles were also captured in the lower mainstem, with abundant evidence of spawning farther downstream. Coho juveniles were abundant in upper, relatively large tributaries, even those channels with cobble-boulder substrates and minimal woody debris that provide habitats more commonly utilized by Chinook in low-latitude systems. More detailed field sampling also revealed that patterns of species composition and abundance appeared related to small

  19. Factors influencing the spawning migration of female anadromous brown trout

    DEFF Research Database (Denmark)

    Svendsen, Jon Christian; Koed, Anders; Aarestrup, Kim

    2004-01-01

    ' occurred under conditions of similar water temperature and stream discharge. Manual tracking indicated that in the pre-spawning state, the distance migrated over 3 days was positively correlated with stream discharge and water temperature, whereas in the post-spawning state, the total distance migrated......Radio telemetry was employed to study movements of adult female anadromous brown trout Salmo trutta (sea trout) during upstream spawning migration and following spawning in a stream with tributaries. Sea trout were monitored by manual tracking and by automatic listening stations. The latter...

  20. Functional analysis of all salmonid genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

    OpenAIRE

    Macqueen, Daniel J.; Primmer, Craig R.; Houston, Ross D.; Nowak, Barbara F.; Bernatchez, Louis; Bergseth, Steinar; Davidson, William S.; Gallardo-Escarate, Christian; Goldammer, Tom; Guiguen, Yann; Iturra, Patricia; Kijas, James W; Koop, Ben F.; Lien, Sigbjorn; Maass, Alejandro

    2017-01-01

    We describe an emerging initiative - the "Functional Analysis of All Salmonid Genomes" (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, through to improving the efficiency and sustainability of aqu...

  1. 77 FR 41168 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2012-07-12

    ... Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric... Washington Department of Fish and Wildlife (WDFW), Idaho Department of Fish and Game, and the Bureau of...

  2. 77 FR 31835 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2012-05-30

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XC049 Endangered and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric...

  3. 78 FR 60254 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-10-01

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... regulations governing listed fish and wildlife permits (50 CFR 222-226). NMFS issues permits based on findings... conduct water quality, [[Page 60255

  4. 78 FR 34653 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-06-10

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XC717 Endangered and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration, Commerce. ACTION: Notice of decision and availability of...

  5. 78 FR 43145 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-07-19

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XC767 Endangered and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration, Commerce. ACTION: Notice of availability. SUMMARY: This...

  6. Population Structure of Columbia River Basin Chinook Salmon and Steelhead Trout, Technical Report 2001.

    Energy Technology Data Exchange (ETDEWEB)

    Brannon, E.L.; National Science Foundation (U.S.)

    2002-08-01

    promoting the ability for anadromous salmonids to respond to change by assuring that the genetic diversity to facilitate such responses is present. The key in developing an effective recovery program for chinook salmon and steelhead is to recognize that multiple life history forms associated with temperature characterize the species in the Columbia Basin, and recovery measures taken must address the biological requirements of the population unit within the environmental template identified. Unless such measures are given first and highest priority, establishment of biologically self-sustaining populations will be restrained.

  7. Oceanographic Trawl Data - Ocean Survival of Salmonids

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A study to evaluate the role of changing ocean conditions on growth and survival of juvenile salmon from the Columbia River basin as they enter the Columbia River...

  8. Zooplankton Data - Ocean Survival of Salmonids

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A study to evaluate the role of changing ocean conditions on growth and survival of juvenile salmon from the Columbia River basin as they enter the Columbia River...

  9. CTD Oceanographic Data - Ocean Survival of Salmonids

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A study to evaluate the role of changing ocean conditions on growth and survival of juvenile salmon from the Columbia River basin as they enter the Columbia River...

  10. 76 FR 57717 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2011-09-16

    ... Environmental Services (DWR-ES), in West Sacramento, CA (16543). This document serves to notify the public of... request. The applications and related documents are available for review by appointment: Protected... salmonid migration timing and salmonid spawning and rearing habitats; and data collection on fry and...

  11. Divergence with gene flow between Ponto-Caspian refugia in an anadromous cyprinid Rutilus frisii revealed by multiple gene phylogeography.

    Science.gov (United States)

    Kotlík, Petr; Marková, Silvia; Choleva, Lukás; Bogutskaya, Nina G; Ekmekçi, F Guler; Ivanova, Petya P

    2008-02-01

    The Black and Caspian Seas have experienced alternating periods of isolation and interconnection over many Milankovitch climate oscillations and most recently became separated when the meltwater overflow from the Caspian Sea ceased at the end of the last glaciation. Climate-induced habitat changes have indisputably had profound impacts on distribution and demography of aquatic species, yet uncertainties remain about the relative roles of isolation and dispersal in the response of species shared between the Black and Caspian Sea basins. We examined these issues using phylogeographical analysis of an anadromous cyprinid fish Rutilus frisii. Bayesian coalescence analyses of sequence variation at two nuclear and one mitochondrial genes suggest that the Black and Caspian Seas supported separate populations of R. frisii during the last glaciation. Parameter estimates from the fitted isolation-with-migration model showed that their separation was not complete, however, and that the two populations continued to exchange genes in both directions. These analyses also suggested that majority of migrations occurred during the Pleistocene, showing that the variation shared between the Black and Caspian Seas is the result of ancient dispersal along the temporary natural connections between the basins, rather than of incomplete lineage sorting or recent human-mediated dispersal. Gene flow between the refugial populations was therefore an important source of genetic variation, and we suggest that it facilitated the evolutionary response of the populations to changing climate.

  12. Biological and Physical Inventory of Clear Creek, Orofino Creek, and the Potlatch River, Tributary Streams of the Clearwater River, Idaho, 1984 Technical Report.

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, David B.

    1985-05-01

    Clear Creek, Orofino Creek, and Potlatch Creek, three of the largest tributaries of the lower Clearwater River Basin, were inventoried during 1984. The purpose of the inventory was to identify where anadromous salmonid production occurs and to recommend enhancement alternatives to increase anadromous salmonid habitat in these streams. Anadromous and fluvial salmonids were found in all three drainages. The lower reach of Clear Creek supported a low population of rainbow-steelhead, while the middle reach supported a much greater population of rainbow-steelhead. Substantial populations of cutthroat trout were also found in the headwaters of Clear Creek. Rainbow-steelhead and brook trout were found throughout Orofino Creek. A predominant population of brook trout was found in the headwaters while a predominant population of rainbow-steelhead was found in the mainstem and lower tributaries of Orofino Creek. Rainbow-steelhead and brook trout were also found in the Potlatch River. Generally, the greatest anadromous salmonid populations in the Potlatch River were found within the middle reach of this system. Several problems were identified which would limit anadromous salmonid production within each drainage. Problems affecting Clear Creek were extreme flows, high summer water temperature, lack of riparian habitat, and high sediment load. Gradient barriers prevented anadromous salmonid passage into Orofino Creek and they are the main deterrent to salmonid production in this system. Potlatch River has extreme flows, high summer water temperature, a lack of riparian habitat and high sediment loads. Providing passage over Orofino Falls is recommended and should be considered a priority for improving salmonid production in the lower Clearwater River Basin. Augmenting flows in the Potlatch River is also recommended as an enhancement measure for increasing salmonid production in the lower Clearwater River Basin. 18 refs., 5 figs., 85 tabs.

  13. Turbulence investigation and reproduction for assisting downstream migrating juvenile salmonids, Part II of II: Effects of induced turbulence on behavior of juvenile salmon, 2001-2005 final report

    Science.gov (United States)

    Perry, R.; Farley , M.; Hansen, G.; Morse , J.; Rondorf, D.

    2005-01-01

    Passage through dams is a major source of mortality of anadromous juvenile salmonids because some populations must negotiate up to eight dams in Columbia and Snake rivers. Dams cause direct mortality when fish pass through turbines, but dams may also cause indirect mortality by altering migration conditions in rivers. Forebays immediately upstream of dams have decreased the water velocity of rivers and may contribute substantially to the total migration delay of juvenile salmonids. Recently, Coutant (2001a) suggested that in addition to low water velocities, lack of natural turbulence may contribute to migration delay by causing fish to lose directional cues. Coutant (2001a) further hypothesized that restoring turbulence in dam forebays may reduce migration delay by providing directional cues that allow fish to find passage routes more quickly (Coutant 2001a). Although field experiments have yielded proof of the concept of using induced turbulence to guide fish to safe passage routes, little is known about mechanisms actually causing behavioral changes. To test hypotheses about how turbulence influences movement and behavior of migrating juvenile salmonids, we conducted two types of controlled experiments at Cowlitz Falls Dam, Washington. A common measure of migration delay is the elapsed time between arrival at, and passage through, a dam. Therefore, for the first set of experiments, we tested the effect of induced turbulence on the elapsed time needed for fish to traverse through a raceway and pass over a weir at its downstream end (time trial experiment). If turbulence helps guide fish to passage routes, then fish should pass through the raceway quicker in the presence of appropriately scaled and directed turbulent cues. Second, little is known about how the physical properties of water movement provide directional cues to migrating juvenile salmonids. To examine the feasibility of guiding fish with turbulence, we tested whether directed turbulence could guide

  14. Turbulence Investigation and Reproduction for Assisting Downstream Migrating Juvenile Salmonids, Part II of II; Effects of Induced Turbulence on Behavior of Juvenile Salmon, 2001-2005 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Perry, Russell W.; Farley, M. Jared; Hansen, Gabriel S. (US Geological Survey, Western Fisheries Research Center, Columbia River Research Laboratory, Cook, WA)

    2005-07-01

    Passage through dams is a major source of mortality of anadromous juvenile salmonids because some populations must negotiate up to eight dams in Columbia and Snake rivers. Dams cause direct mortality when fish pass through turbines, but dams may also cause indirect mortality by altering migration conditions in rivers. Forebays immediately upstream of dams have decreased the water velocity of rivers and may contribute substantially to the total migration delay of juvenile salmonids. Recently, Coutant (2001a) suggested that in addition to low water velocities, lack of natural turbulence may contribute to migration delay by causing fish to lose directional cues. Coutant (2001a) further hypothesized that restoring turbulence in dam forebays may reduce migration delay by providing directional cues that allow fish to find passage routes more quickly (Coutant 2001a). Although field experiments have yielded proof of the concept of using induced turbulence to guide fish to safe passage routes, little is known about mechanisms actually causing behavioral changes. To test hypotheses about how turbulence influences movement and behavior of migrating juvenile salmonids, we conducted two types of controlled experiments at Cowlitz Falls Dam, Washington. A common measure of migration delay is the elapsed time between arrival at, and passage through, a dam. Therefore, for the first set of experiments, we tested the effect of induced turbulence on the elapsed time needed for fish to traverse through a raceway and pass over a weir at its downstream end (time trial experiment). If turbulence helps guide fish to passage routes, then fish should pass through the raceway quicker in the presence of appropriately scaled and directed turbulent cues. Second, little is known about how the physical properties of water movement provide directional cues to migrating juvenile salmonids. To examine the feasibility of guiding fish with turbulence, we tested whether directed turbulence could guide

  15. Sustaining salmonid populations: A caring understanding of naturalness of taxa

    Science.gov (United States)

    Nielsen, Jennifer L.; Regier, Henry A.; Knudsen, E. Eric

    2004-01-01

    Species of the family of Salmonidae occur naturally in Northern Hemisphere waters that remain clear and cool to cold in summer. For purposes of reproduction, salmonids generally behaviorally respond to the currents of streams and lakes in recently glaciated areas. For feeding and maturation, many larger species migrate into existing systems of large lakes, seas, and oceans. The subfamilies include Salmoninae, Coregoninae, and Thymallinae. In many locales and regions of the hemisphere, numerous species of these subfamilies evolved and self-organized into species flocks or taxocenes of bewildering complexity. For example, any individual species may play different or unique ecological roles in different taxocenes. The northern Pacific and Atlantic Ocean ecosystems, with their seas and tributaries, each contained a metacomplex of such taxocenes that, in their natural state some centuries ago, resembled each other but differed in many ways. Humans have valued all species of this family for subsistence, ceremonial, naturalist, gustatory, angling, and commercial reasons for centuries. Modern progressive humans (MPHs), whose industrial and commercial enterprises have gradually spread over this hemisphere in recent time, now affect aquatic ecosystems at all scales from local to global. These human effects mingle in complex ways that together induce uniquely natural salmonid taxocenes to disintegrate with the loss of species, including those groups least tolerant to human manipulations, but extending more recently to those taxa more adapted to anthropogenic change. As we leave the modern era, dominated by MPHs, will we find ways to live sustainably with salmonid taxocenes that still exhibit self-organizational integrity, or will only individual, isolated populations of salmonid species, derived from those most tolerant of MPHs, survive? To achieve future sustainability of salmonids, we suggest implementation of a search for intuitive knowledge based on faith in the wisdom of

  16. A salmonid EST genomic study: genes, duplications, phylogeny and microarrays

    Directory of Open Access Journals (Sweden)

    Brahmbhatt Sonal

    2008-11-01

    Full Text Available Abstract Background Salmonids are of interest because of their relatively recent genome duplication, and their extensive use in wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most widely studied groups of fish. Results 298,304 expressed sequence tags (ESTs from Atlantic salmon (69% of the total, 11,664 chinook, 10,813 sockeye, 10,051 brook trout, 10,975 grayling, 8,630 lake whitefish, and 3,624 northern pike ESTs were obtained in this study and have been deposited into the public databases. Contigs were built and putative full-length Atlantic salmon clones have been identified. A database containing ESTs, assemblies, consensus sequences, open reading frames, gene predictions and putative annotation is available. The overall similarity between Atlantic salmon ESTs and those of rainbow trout, chinook, sockeye, brook trout, grayling, lake whitefish, northern pike and rainbow smelt is 93.4, 94.2, 94.6, 94.4, 92.5, 91.7, 89.6, and 86.2% respectively. An analysis of 78 transcript sets show Salmo as a sister group to Oncorhynchus and Salvelinus within Salmoninae, and Thymallinae as a sister group to Salmoninae and Coregoninae within Salmonidae. Extensive gene duplication is consistent with a genome duplication in the common ancestor of salmonids. Using all of the available EST data, a new expanded salmonid cDNA microarray of 32,000 features was created. Cross-species hybridizations to this cDNA microarray indicate that this resource will be useful for studies of all 68 salmonid species. Conclusion An extensive collection and analysis of salmonid RNA putative transcripts indicate that Pacific salmon, Atlantic salmon and charr are 94–96% similar while the more distant whitefish, grayling, pike and smelt are 93, 92, 89 and 86% similar to salmon. The salmonid transcriptome reveals a complex history of gene duplication that is

  17. Determine the Influence of Time Held in “Knockdown” Anesthesia on Survival and Stress of Surgically Implanted Juvenile Salmonids

    Energy Technology Data Exchange (ETDEWEB)

    Woodley, Christa M.; Wagner, Katie A.; Knox, Kasey M.

    2012-01-31

    The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed for the U.S. Army Corp of Engineers Portland District (USACE) to address questions related to survival and performance measures of juvenile salmonids as they pass through the Federal Columbia River Power System (FCRPS). Researchers using JSATS acoustic transmitters (ATs) were tasked with standardizing the surgical implantation procedure to ensure that the stressors of handling and surgery on salmonids were consistent and less likely to cause effects of tagging in survival studies. Researchers questioned whether the exposure time in 'knockdown' anesthesia (or induction) to prepare fish for surgery could influence the survival of study fish (CBSPSC 2011). Currently, fish are held in knockdown anesthesia after they reach Stage 4 anesthesia until the completion of the surgical implantation of a transmitter, varies from 5 to 15 minutes for studies conducted in the Columbia Basin. The Columbia Basin Surgical Protocol Steering Committee (CBSPSC ) expressed concern that its currently recommended 10-minute maximum time limit during which fish are held in anesthetic - tricaine methanesulfonate (MS-222, 80 mg L-1 water) - could increase behavioral and physiological costs, and/or decrease survival of outmigrating juvenile salmonids. In addition, the variability in the time fish are held at Stage 4 could affect the data intended for direct comparison of fish within or among survival studies. Under the current recommended protocol, if fish exceed the 10-minute time limit, they are to be released without surgical implantation, thereby increasing the number of fish handled and endangered species 'take' at the bypass systems for FCRPS survival studies.

  18. Contribution of anadromous fish to the diet of European catfish in a large river system

    Science.gov (United States)

    Syväranta, Jari; Cucherousset, Julien; Kopp, Dorothée; Martino, Aurélia; Céréghino, Régis; Santoul, Frédéric

    2009-05-01

    Many anadromous fish species, when migrating from the sea to spawn in fresh waters, can potentially be a valuable prey for larger predatory fish, thereby efficiently linking these two ecosystems. Here, we assess the contribution of anadromous fish to the diet of European catfish ( Silurus glanis) in a large river system (Garonne, southwestern France) using stable isotope analysis and allis shad ( Alosa alosa) as an example of anadromous fish. Allis shad caught in the Garonne had a very distinct marine δ13C value, over 8‰ higher after lipid extraction compared to the mean δ13C value of all other potential freshwater prey fish. The δ13C values of European catfish varied considerably between these two extremes and some individuals were clearly specializing on freshwater prey, whereas others specialized on anadromous fish. The mean contribution of anadromous fish to the entire European catfish population was estimated to be between 53% and 65%, depending on the fractionation factor used for δ13C.

  19. Occurrence and significance of atypical Aeromonas salmonicida in non-salmonid and salmonid fish species : A review

    DEFF Research Database (Denmark)

    Wiklund, T.; Dalsgaard, Inger

    1998-01-01

    . Macroscopical and microscopical studies oi ulcerated fish indicate internal organs are infrequently invaded by atypical A. salmonicida. This view is supported by the fact that atypical strains are irregularly isolated from visceral organs of ulcerated fish. High mortality caused by atypical A. salmonicida has...... been observed in populations of wild non- salmonids and farmed salmonids, although the association between the mortality in the wild fish stocks and atypical A. salmonicida has not always been properly assessed. In injection experiments the pathogenicity of the atypical strains examined showed large...

  20. Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture.

    Science.gov (United States)

    Macqueen, Daniel J; Primmer, Craig R; Houston, Ross D; Nowak, Barbara F; Bernatchez, Louis; Bergseth, Steinar; Davidson, William S; Gallardo-Escárate, Cristian; Goldammer, Tom; Guiguen, Yann; Iturra, Patricia; Kijas, James W; Koop, Ben F; Lien, Sigbjørn; Maass, Alejandro; Martin, Samuel A M; McGinnity, Philip; Montecino, Martin; Naish, Kerry A; Nichols, Krista M; Ólafsson, Kristinn; Omholt, Stig W; Palti, Yniv; Plastow, Graham S; Rexroad, Caird E; Rise, Matthew L; Ritchie, Rachael J; Sandve, Simen R; Schulte, Patricia M; Tello, Alfredo; Vidal, Rodrigo; Vik, Jon Olav; Wargelius, Anna; Yáñez, José Manuel

    2017-06-27

    We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

  1. Variation in salmonid life histories: patterns and perspectives.

    Science.gov (United States)

    Mary F. Willson

    1997-01-01

    Salmonid fishes differ in degree of anadromy, age of maturation, frequency of reproduction, body size and fecundity, sexual dimorphism, breeding season, morphology, and, to a lesser degree, parental care. Patterns of variation and their possible significance for ecology and evolution and for resource management are the focus of this review.

  2. Modeling potential river management conflicts between frogs and salmonids

    Science.gov (United States)

    Steven F. Railsback; Bret C. Harvey; Sarah J. Kupferberg; Margaret M. Lang; Scott McBain; Hart H. Welsh

    2016-01-01

    Management of regulated rivers for yellow-legged frogs (Rana boylii) and salmonids exemplifies potential conflicts among species adapted to different parts of the natural flow and temperature regimes. Yellow-legged frogs oviposit in rivers in spring and depend on declining flows and warming temperatures for egg and tadpole survival and growth,...

  3. Physiological levels of testosterone kill salmonid leukocytes in vitro

    Science.gov (United States)

    Slater, C.H.; Schreck, C.B.

    1997-01-01

    Adult spring chinook salmon (Oncorhynchus tshawytscha) elaborate high plasma concentrations of testosterone during sexual maturation, and these levels of testosterone have been shown to reduce the salmonid immune response in vitro. Our search for the mechanism of testosterone's immunosuppressive action has led to the characterization of an androgen receptor in salmonid leukocytes. In the present study we examined the specific effects that testosterone had on salmonid leukocytes. Direct counts of viable leukocytes after incubation with and without physiological levels of testosterone demonstrate a significant loss of leukocytes in cultures exposed to testosterone. At least 5 days of contact with testosterone was required to produce significant immunosuppression and addition of a 'conditioned media' (supernatant from proliferating lymphocytes not exposed to testosterone) did not reverse the immunosuppressive effects of testosterone. These data lead us to conclude that testosterone may exert its immunosuppressive effects by direct action on salmonid leukocytes, through the androgen receptor described, and that this action leads to the death of a significant number of these leukocytes.

  4. Co-Speciation of the Ectoparasite Gyrodactylus teuchis (Monogenea, Platyhelminthes and Its Salmonid Hosts.

    Directory of Open Access Journals (Sweden)

    Christoph Hahn

    Full Text Available Co-speciation is a fundamental concept of evolutionary biology and intuitively appealing, yet in practice hard to demonstrate as it is often blurred by other evolutionary processes. We investigate the phylogeographic history of the monogenean ectoparasites Gyrodactylus teuchis and G. truttae on European salmonids of the genus Salmo. Mitochondrial cytochrome oxidase subunit 1 and the nuclear ribosomal internal transcribed spacer 2 were sequenced for 189 Gyrodactylus individuals collected from 50 localities, distributed across most major European river systems, from the Iberian- to the Balkan Peninsula. Despite both anthropogenic and naturally caused admixture of the principal host lineages among major river basins, co-phylogenetic analyses revealed significant global congruence for host and parasite phylogenies, providing firm support for co-speciation of G. teuchis and its salmonid hosts brown trout (S. trutta and Atlantic salmon (S. salar. The major split within G. teuchis, coinciding with the initial divergence of the hosts was dated to ~1.5 My BP, using a Bayesian framework based on an indirect calibration point obtained from the host phylogeny. The presence of G. teuchis in Europe thus predates some of the major Pleistocene glaciations. In contrast, G. truttae exhibited remarkably low intraspecific genetic diversity. Given the direct life cycle and potentially high transmission potential of gyrodactylids, this finding is interpreted as indication for a recent emergence (<60 ky BP of G. truttae via a host-switch. Our study thus suggests that instances of two fundamentally different mechanisms of speciation (co-speciation vs. host-switching may have occurred on the same hosts in Europe within a time span of less than 1.5 My in two gyrodactylid ectoparasite species.

  5. Yakima Basin Fish Passage Project, Phase 2

    International Nuclear Information System (INIS)

    1991-08-01

    Implementation of the Yakima Basin Fish Passage Project -- Phase 2 would significantly improve the production of anadromous fish in the Yakima River system. The project would provide offsite mitigation and help to compensate for lower Columbia River hydroelectric fishery losses. The Phase 2 screens would allow greater numbers of juvenile anadromous fish to survive. As a consequence, there would be higher returns of adult salmon and steelhead to the Yakima River. The proposed action would play an integral part in the overall Yakima River anadromous fish enhancement program (fish passage improvement, habitat enhancement, hatchery production increases, and harvest management). These would be environmental benefits associated with implementation of the Fish Passage and Protective Facilities Phase 2 Project. Based on the evaluation presented in this assessment, there would be no significant adverse environmental impacts if the proposed action was carried forward. No significant adverse environmental effects have been identified from construction and operation of the Yakima Phase 2 fish passage project. Proper design and implementation of the project will ensure no adverse effects will occur. Based on the information in this environmental analysis, BPA's and Reclamation's proposal to construct these facilities does not constitute a major Federal action that could significantly affect the quality of the human environment. 8 refs., 4 figs., 6 tabs

  6. Yakima Basin Fish Passage Project, Phase 2

    Energy Technology Data Exchange (ETDEWEB)

    1991-08-01

    Implementation of the Yakima Basin Fish Passage Project -- Phase 2 would significantly improve the production of anadromous fish in the Yakima River system. The project would provide offsite mitigation and help to compensate for lower Columbia River hydroelectric fishery losses. The Phase 2 screens would allow greater numbers of juvenile anadromous fish to survive. As a consequence, there would be higher returns of adult salmon and steelhead to the Yakima River. The proposed action would play an integral part in the overall Yakima River anadromous fish enhancement program (fish passage improvement, habitat enhancement, hatchery production increases, and harvest management). These would be environmental benefits associated with implementation of the Fish Passage and Protective Facilities Phase 2 Project. Based on the evaluation presented in this assessment, there would be no significant adverse environmental impacts if the proposed action was carried forward. No significant adverse environmental effects have been identified from construction and operation of the Yakima Phase 2 fish passage project. Proper design and implementation of the project will ensure no adverse effects will occur. Based on the information in this environmental analysis, BPA's and Reclamation's proposal to construct these facilities does not constitute a major Federal action that could significantly affect the quality of the human environment. 8 refs., 4 figs., 6 tabs.

  7. Polyphasic characterization of Aeromonas salmonicida isolates recovered from salmonid and non-salmonid fish

    Science.gov (United States)

    Diamanka, A.; Loch, T.P.; Cipriano, R.C.; Faisal, M.

    2013-01-01

    Michigan's fisheries rely primarily upon the hatchery propagation of salmonid fish for release in public waters. One limitation on the success of these efforts is the presence of bacterial pathogens, including Aeromonas salmonicida, the causative agent of furunculosis. This study was undertaken to determine the prevalence of A. salmonicida in Michigan fish, as well as to determine whether biochemical or gene sequence variability exists among Michigan isolates. A total of 2202 wild, feral and hatchery-propagated fish from Michigan were examined for the presence of A. salmonicida. The examined fish included Chinook salmon, Oncorhynchus tshawytscha (Walbaum), coho salmon, O. kisutcha (Walbaum), steelhead trout, O. mykiss (Walbaum), Atlantic salmon, Salmo salar L., brook trout, Salvelinus fontinalis (Mitchill), and yellow perch, Perca flavescens (Mitchill). Among these, 234 fish yielded a brown pigment-producing bacterium that was presumptively identified as A. salmonicida. Further phenotypic and phylogenetic analyses identified representative isolates as Aeromonas salmonicida subsp. salmonicida and revealed some genetic and biochemical variability. Logistic regression analyses showed that infection prevalence varied according to fish species/strain, year and gender, whereby Chinook salmon and females had the highest infection prevalence. Moreover, this pathogen was found in six fish species from eight sites, demonstrating its widespread nature within Michigan.

  8. Enloe Dam Passage Project, Volume I, 1984 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Fanning, M.L.

    1985-07-01

    This report discusses issues related to the provision of fish passage facilities at Enloe Dam and the introduction of anadromous salmonid fish to the upper Similkameen River basin. The species of fish being considered is a summer run of steelhead trout adapted to the upper Columbia basin. (ACR)

  9. Influence of forest and rangeland management on anadromous fish habitat in Western North America: economic considerations.

    Science.gov (United States)

    William R. tech. ed. Meehan

    1985-01-01

    Although many effects of forest and rangeland management on anadromous fisheries are difficult to measure, economic methods for the evaluation of costs and benefits can be helpful. Such methods can be used to address questions of equity as well as efficiency. Evaluations of equity can show who bears the costs and who captures the benefits of management actions, but...

  10. 77 FR 41167 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2012-07-12

    ... Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric... CFR parts 222-226) governing listed fish and wildlife permits. Species Covered in This Notice This...), and release of fish. Permit 15730 authorizes SPAWN non-lethal and low levels of unintentional lethal...

  11. 77 FR 63295 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2012-10-16

    ... Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric... to the ESA and NMFS regulations governing listed fish and wildlife permits (50 CFR parts 222-226... necessarily reflect the views of NMFS. Application Received Permit 17428 The U.S. Fish and Wildlife Service...

  12. 77 FR 51520 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2012-08-24

    ... Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric... fish and wildlife permits (50 CFR parts 222-226). NMFS issues permits based on findings that such... described below, researchers do not expect to kill any listed fish but a small number, up to 20 percent...

  13. 77 FR 27186 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2012-05-09

    ... Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric... accordance with section 10(a)(1)(A) of the ESA (16 U.S.C. 1531 et. seq) and regulations governing listed fish...), anesthetized, sampled for biological data (length, weight, disease status) and tissues/scales. The fish would...

  14. 75 FR 56986 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2010-09-17

    ... designed to determine the fishes' freshwater movements and how those movements are affected by the area's... Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric..., OR (ph.: 503-231-2005, Fax: 503-230-5441, e-mail: [email protected] ). Permit application...

  15. Influence of forest and rangeland management on anadromous fish habitat in Western North America: forest chemicals.

    Science.gov (United States)

    L.A. Norris; H.W. Lorz; S.V. Gregory

    1983-01-01

    Herbicides, insecticides, fertilizers, and fire retardants are chemicals used to protect or enhance certain forest resources. Their use may directly affect anadromous fish by exposing them to toxic amounts of the chemical. Indirect effects are also possible through chemically induced alteration of habitat, including direct effects on fish-food organisms.Data...

  16. 76 FR 5339 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2011-01-31

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XA182 Endangered and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... are issued in accordance with and are subject to the ESA and NMFS regulations governing listed fish...

  17. 78 FR 59005 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-09-25

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... with Section 10(a)(1)(A) of the ESA of 1973 (16 U.S.C. 1531-1543) and regulations governing listed fish.... Applications Received Permit 1415 The U.S. Fish and Wildlife Services' (USFWS) Red Bluff Fish and Wildlife...

  18. 77 FR 67796 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2012-11-14

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XC342 Endangered and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... NMFS regulations governing listed fish and wildlife permits (50 CFR parts 222-226). Those individuals...

  19. 78 FR 32378 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-05-30

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... application was provided by the Washington Department of Fish and Wildlife (WDFW) and the Public Utility... Department of Fish and Wildlife submitted an application for an ESA permit to operate the Nason Creek spring...

  20. 77 FR 67794 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2012-11-14

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS.... 1531 et. seq) and regulations governing listed fish and wildlife permits (50 CFR 222-226). NMFS issues... implemented as part of the Whatcom Creek Long-term Restoration Plan by documenting fish population trends...

  1. 77 FR 2037 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2012-01-13

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XA928 Endangered and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... advises the public that a direct take permit has been issued to the Washington Department of Fish and...

  2. 77 FR 76001 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2012-12-26

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... regulations governing listed fish and wildlife permits(50 CFR parts 222-226). NMFS issues permits based on... described below, researchers do not expect to kill any listed fish but a small number may die as an...

  3. 78 FR 69374 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-11-19

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS...)(1)(A) of the ESA (16 U.S.C. 1531 et. seq) and regulations governing listed fish and wildlife permits... proposes to capture the fish (using backpack electrofishing), identify, and release them. The WDNR does not...

  4. 75 FR 2106 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2010-01-14

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... NMFS regulations (50 CFR parts 222-226) governing listed fish and wildlife permits. Species Covered in... steelhead not to exceed 2 percent of the total number of fish captured for each life stage and species...

  5. 78 FR 18963 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-03-28

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... governing listed fish and wildlife permits (50 CFR parts 222-226). NMFS issues permits based on findings... Administrator for Fisheries, NMFS. Applications Received Permit 17551 The California Department of Fish and...

  6. 76 FR 6400 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2011-02-04

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS...)(1)(A) of the ESA (16 U.S.C. 1531 et seq.) and regulations governing listed fish and wildlife permits..., the U.S. Fish and Wildlife Service (USFWS) submitted an application and supporting documents to NMFS...

  7. 78 FR 77659 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-12-24

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XD040 Endangered and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... NMFS regulations (50 CFR parts 222-226) governing listed fish and wildlife permits. [[Page 77660...

  8. 76 FR 2664 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2011-01-14

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS...) and 14092 (applicant: California Department of Fish and Game). In that notice, the permit application... American green sturgeon associated with conducting surveys measuring fish response to initial and...

  9. 78 FR 31518 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-05-24

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XC690 Endangered and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... Department of Fish and Wildlife (ODFW), Washington Department of Fish and Wildlife (WDFW), and U.S. Bureau of...

  10. 77 FR 3743 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2012-01-25

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... with section 10(a)(1)(A) of the ESA of 1973 (16 U.S.C. 1531-1543) and regulations governing listed fish... listed fish but a small number may die as an unintended result of the research activities. The objectives...

  11. 78 FR 79674 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-12-31

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... the ESA (16 U.S.C. 1531 et seq.) and regulations governing listed fish and wildlife permits (50 CFR.... Fish and Wildlife Service (USFWS) submitted an application and supporting documents to NMFS for a...

  12. 76 FR 5338 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2011-01-31

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XA183 Endangered and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... regulations (50 CFR parts 222-226) governing listed fish and wildlife permits. [[Page 5339

  13. 76 FR 6401 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2011-02-04

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XA110 Endangered and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... and the Washington Department of Fish and Wildlife submitted to NMFS, pursuant to the protective...

  14. 76 FR 8713 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2011-02-15

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... (16 U.S.C. 1531-1543) and regulations governing listed fish and wildlife permits (50 CFR parts 222-226... handling of fish is already covered under the Incidental Take Statement associated with the Biological...

  15. 76 FR 2663 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2011-01-14

    ... and Threatened Species; Take of Anadromous Fish AGENCY: National Marine Fisheries Service (NMFS... and steelhead, and natural juvenile green sturgeon while carrying out a study measuring fish response... species, taking of length measurements), tissue sampling, release of moribund fish or fish carcasses back...

  16. Endocrine systems in juvenile anadromous and landlocked Atlantic salmon (Salmo salar): Seasonal development and seawater acclimation

    DEFF Research Database (Denmark)

    Nilsen, Tom O; Ebbesson, Lars O E; Kiilerich, Pia

    2008-01-01

    -smolt transformation (smoltification) period and following four days and one month seawater (SW) acclimation. Plasma GH and gill GH receptor (GHR) mRNA levels increased continuously during the spring smoltification period in the anadromous, but not in landlocked salmon. There were no differences in plasma IGF-I levels...

  17. Relationship between growth and standard metabolic rate: measurement artefacts and implications for habitat use and life-history adaptation in salmonids.

    Science.gov (United States)

    Rosenfeld, Jordan; Van Leeuwen, Travis; Richards, Jeffrey; Allen, David

    2015-01-01

    Mass-specific standard metabolic rate (SMR, or maintenance metabolism) varies greatly among individuals. Metabolism is particularly sensitive to variation in food consumption and growth creating the potential for significant bias in measured SMR for animals that are growing (e.g. juveniles) or of uncertain nutritional status. Consequently, interpreting individual variation in metabolism requires a sound understanding of the potentially confounding role of growth and the relative importance of fixed (genetic) vs. environmental drivers of SMR variation. We review the role of growth in measured SMR variation in juvenile salmonids, with the goals of (i) understanding the contribution of growth (and food consumption) to SMR variation through ontogeny, (ii) understanding the relative contributions of tissue maintenance and biosynthesis (overhead costs of growth) to apparent SMR variation, and (iii) using intrinsic growth effects on SMR to model how alternate life-history strategies may influence growth and measured SMR in juvenile salmonids. SMR measures on juveniles, even when post-absorptive, may be inflated by delayed growth-associated overhead costs, unless juveniles are on a maintenance ration (i.e. not growing). Empirical measurements of apparent SMR in food restricted vs. satiated 2-5 g juvenile salmon demonstrate that estimates may be inflated by as much as 67% due to delayed overhead costs of growth, even when SMR measurements are taken 35 h post-feeding. These results indicate that a substantial component of variation in apparent SMR among juvenile salmonids may be associated with (i) environmentally driven variation in ration (where elevated SMR measurements are an artefact of delayed growth overhead costs), (ii) intrinsic (genetic) or plastic organ-system trade-offs related to increasing investment in metabolically expensive digestive tissue responsible for processing food and (iii) intrinsic (genetic) variation in maximum body size and growth among

  18. Genetics and genomics of disease resistance in salmonid species

    Directory of Open Access Journals (Sweden)

    José Manuel Yáñez

    2014-11-01

    Full Text Available Infectious and parasitic diseases generate large economic losses in salmon farming. A feasible and sustainable alternative to prevent disease outbreaks may be represented by genetic improvement for disease resistance. To include disease resistance into the breeding goal, prior knowledge of the levels of genetic variation for these traits is required. Furthermore, the information from the genetic architecture and molecular factors involved in resistance against diseases may be used to accelerate the genetic progress for these traits. In this regard, marker assisted selection and genomic selection are approaches which incorporate molecular information to increase the accuracy when predicting the genetic merit of selection candidates. In this article we review and discuss key aspects related to disease resistance in salmonid species, from both a genetic and genomic perspective, with emphasis in the applicability of disease resistance traits into breeding programs in salmonids.

  19. Cle Elum Lake Restoration Feasibility Study: Fish Husbandry Research, 1988-1991 Progress Report.

    Energy Technology Data Exchange (ETDEWEB)

    Flagg, Thomas A.

    1991-09-01

    The National Marine Fisheries Service (NMFS) and the Bonneville Power Administration (BPA) are involved in a project to evaluate the feasibility of re-establishing anadromous salmon runs to Cle Elum Lake in the Yakima River Basin of Washington state. Historically, the Yakima River system supported large runs of anadromous salmonids that contributed significantly to the Columbia River harvest. Habitat destruction and overfishing drastically reduced run abundance prior to the early 1900s. Salmon runs were eliminated from upper reaches of the Yakima River Basin with development of irrigation storage reservoirs without fishways in the early 1900s. The goal of the NMFS/BPA project is to determine if it is feasible for anadromous salmonids to recolonize the habitat above Cle Elum Dam under the present format of irrigation water withdrawal from the reservoir. The primary concern is whether anadromous fish can successfully exit Cle Elum Lake and survive downstream passage through the Yakima and Columbia Rivers to the ocean.

  20. Endocrine systems in juvenile anadromous and landlocked Atlantic salmon (Salmo salar): Seasonal development and seawater acclimation

    Science.gov (United States)

    Nilsen, Tom O.; Ebbesson, Lars O.E.; Kiilerich, P.; Bjornsson, B. Th; Madsen, Steffen S.; McCormick, S.D.; Stefansson, S.O.

    2008-01-01

    The present study compares developmental changes in plasma levels of growth hormone (GH), insulin-like growth factor I (IGF-I) and cortisol, and mRNA levels of their receptors and the prolactin receptor (PRLR) in the gill of anadromous and landlocked Atlantic salmon during the spring parr-smolt transformation (smoltification) period and following four days and one month seawater (SW) acclimation. Plasma GH and gill GH receptor (GHR) mRNA levels increased continuously during the spring smoltification period in the anadromous, but not in landlocked salmon. There were no differences in plasma IGF-I levels between strains, or any increase during smoltification. Gill IGF-I and IGF-I receptor (IGF-IR) mRNA levels increased in anadromous salmon during smoltification, with no changes observed in landlocked fish. Gill PRLR mRNA levels remained stable in both strains during spring. Plasma cortisol levels in anadromous salmon increased 5-fold in May and June, but not in landlocked salmon. Gill glucocorticoid receptor (GR) mRNA levels were elevated in both strains at the time of peak smoltification in anadromous salmon, while mineralocorticoid receptor (MR) mRNA levels remained stable. Only anadromous salmon showed an increase of gill 11??-hydroxysteroid dehydrogenase type-2 (11??-HSD2) mRNA levels in May. GH and gill GHR mRNA levels increased in both strains following four days of SW exposure in mid-May, whereas only the anadromous salmon displayed elevated plasma GH and GHR mRNA after one month in SW. Plasma IGF-I increased after four days in SW in both strains, decreasing in both strains after one month in SW. Gill IGF-I mRNA levels were only increased in landlocked salmon after 4 days in SW. Gill IGF-IR mRNA levels in SW did not differ from FW levels in either strain. Gill PRLR mRNA did not change after four days of SW exposure, and decreased in both strains after one month in SW. Plasma cortisol levels did not change following SW exposure in either strain. Gill GR, 11

  1. System-wide significance of predation on juvenile salmonids in Columbia and Snake River reservoirs and evaluation of predation control measures. Annual report 1993

    International Nuclear Information System (INIS)

    Gadomski, D.M.; Poe, T.P.

    1994-01-01

    This project had three major goals. The first was to assist the Oregon Department of Fish and Wildlife with predation indexing as part of an effort to estimate the relative magnitude of juvenile salmonid losses to northern squawfish Ptychocheilus oregonensis in reservoirs throughout the Columbia River Basin. The second goal was to evaluate the northern squawfish control program and test critical assumptions about mid-reservoir predation processes. The final goal was to determine mechanisms underlying northern squawfish recruitment and factors affecting year-class strength

  2. Diversity of Flavobacterium psychrophilum and the potential use of its phages for protection against bacterial cold water disease in salmonids

    DEFF Research Database (Denmark)

    Castillo, D.; Higuera, G.; Villa, M.

    2012-01-01

    Flavobacterium psychrophilum causes rainbow trout fry syndrome (RTFS) and cold water disease (CWD) in salmonid aquaculture. We report characterization of F. psychrophilum strains and their bacteriophages isolated in Chilean salmonid aquaculture. Results suggest that under laboratory conditions ph...

  3. Vertebrae classification models - Validating classification models that use morphometrics to identify ancient salmonid (Oncorhynchus spp.) vertebrae to species

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Using morphometric characteristics of modern salmonid (Oncorhynchus spp.) vertebrae, we have developed classification models to identify salmonid vertebrae to the...

  4. Feeding modes in stream salmonid population models: Is drift feeding the whole story?

    Science.gov (United States)

    Bret Harvey; Steve Railsback

    2014-01-01

    Drift-feeding models are essential components of broader models that link stream habitat to salmonid populations and community dynamics. But is an additional feeding mode needed for understanding and predicting salmonid population responses to streamflow and other environmental factors? We addressed this question by applying two versions of the individual-based model...

  5. Gas bubble disease monitoring and research of juvenile salmonids

    International Nuclear Information System (INIS)

    Maule, A.G.; Beeman, J.; Hans, K.M.; Mesa, M.G.; Haner, P.; Warren, J.J.

    1997-10-01

    This document describes the project activities 1996--1997 contract year. This report is composed of three chapters which contain data and analyses of the three main elements of the project: field research to determine the vertical distribution of migrating juvenile salmonids, monitoring of juvenile migrants at dams on the Snake and Columbia rivers, and laboratory experiments to describe the progression of gas bubble disease signs leading to mortality. The major findings described in this report are: A miniature pressure-sensitive radio transmitter was found to be accurate and precise and, after compensation for water temperature, can be used to determine the depth of tagged-fish to within 0.32 m of the true depth (Chapter 1). Preliminary data from very few fish suggest that depth protects migrating juvenile steelhead from total dissolved gas supersaturation (Chapter 1). As in 1995, few fish had any signs of gas bubble disease, but it appeared that prevalence and severity increased as fish migrated downstream and in response to changing gas supersaturation (Chapter 2). It appeared to gas bubble disease was not a threat to migrating juvenile salmonids when total dissolved gas supersaturation was < 120% (Chapter 2). Laboratory studies suggest that external examinations are appropriate for determining the severity of gas bubble disease in juvenile salmonids (Chapter 3). The authors developed a new method for examining gill arches for intravascular bubbles by clamping the ventral aorta to reduce bleeding when arches were removed (Chapter 3). Despite an outbreak of bacterial kidney disease in the experimental fish, the data indicate that gas bubble disease is a progressive trauma that can be monitored (Chapter 3)

  6. Review of the negative influences of non-native salmonids on native fish species

    Science.gov (United States)

    Turek, Kelly C.; Pegg, Mark A.; Pope, Kevin L.

    2013-01-01

    Non-native salmonids are often introduced into areas containing species of concern, yet a comprehensive overview of the short- and long-term consequences of these introductions is lacking in the Great Plains. Several authors have suggested that non-native salmonids negatively inflfluence species of concern. The objective of this paper is to review known interactions between non-native salmonids and native fifishes, with a focus on native species of concern. After an extensive search of the literature, it appears that in many cases non-native salmonids do negatively inflfl uence species of concern (e.g., reduce abundance and alter behavior) via different mechanisms (e.g., predation and competition). However, there are some instances in which introduced salmonids have had no perceived negative inflfl uence on native fifi shes. Unfortunately, the majority of the literature is circumstantial, and there is a need to experimentally manipulate these interactions.

  7. State of Idaho Augmented Anadromous Fish Health Monitoring, 1987 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Foott, J. Scott; Hauck, A. Kent

    1988-05-01

    The anadromous fish health monitoring program began in full operation in January 1988 after the hiring of the lead pathologist. This short operating period limits the amount of information available at the time of this writing. Pre-release sampling of smolts revealed the presence of several sub-clinical pathogens. Organosomatic analysis results demonstrated no major abnormalities in the examined stocks. The results of the 1988 steelhead broodstock sampling are still pending.

  8. What is "fallback"?: metrics needed to assess telemetry tag effects on anadromous fish behavior

    Science.gov (United States)

    Frank, Holly J.; Mather, Martha E.; Smith, Joseph M.; Muth, Robert M.; Finn, John T.; McCormick, Stephen D.

    2009-01-01

    Telemetry has allowed researchers to document the upstream migrations of anadromous fish in freshwater. In many anadromous alosine telemetry studies, researchers use downstream movements (“fallback”) as a behavioral field bioassay for adverse tag effects. However, these downstream movements have not been uniformly reported or interpreted. We quantified movement trajectories of radio-tagged anadromous alewives (Alosa pseudoharengus) in the Ipswich River, Massachusetts (USA) and tested blood chemistry of tagged and untagged fish held 24 h. A diverse repertoire of movements was observed, which could be quantified using (a) direction of initial movements, (b) timing, and (c) characteristics of bouts of coupled upstream and downstream movements (e.g., direction, distance, duration, and speed). Because downstream movements of individual fish were almost always made in combination with upstream movements, these should be examined together. Several of the movement patterns described here could fall under the traditional definition of “fallback” but were not necessarily aberrant. Because superficially similar movements could have quite different interpretations, post-tagging trajectories need more precise definitions. The set of metrics we propose here will help quantify tag effects in the field, and provide the basis for a conceptual framework that helps define the complicated behaviors seen in telemetry studies on alewives and other fish in the field.

  9. Inter-Tributary Movements by Resident Salmonids across a Boreal Riverscape.

    Directory of Open Access Journals (Sweden)

    Kale T Bentley

    Full Text Available Stream-dwelling fishes inhabit river networks where resources are distributed heterogeneously across space and time. Current theory emphasizes that fishes often perform large-scale movements among habitat patches for reproduction and seeking refugia, but assumes that fish are relatively sedentary during growth phases of their life cycle. Using stationary passive integrated transponder (PIT-tag antennas and snorkel surveys, we assessed the individual and population level movement patterns of two species of fish across a network of tributaries within the Wood River basin in southwestern Alaska where summer foraging opportunities vary substantially among streams, seasons, and years. Across two years, Arctic grayling (Thymallus arcticus and rainbow trout (Oncorhynchus mykiss exhibited kilometer-scale movements among streams during the summer growing season. Although we monitored movements at a small fraction of all tributaries used by grayling and rainbow trout, approximately 50% of individuals moved among two or more streams separated by at least 7 km within a single summer. Movements were concentrated in June and July, and subsided by early August. The decline in movements coincided with spawning by anadromous sockeye salmon, which offer a high-quality resource pulse of food to resident species. Inter-stream movements may represent prospecting behavior as individuals seek out the most profitable foraging opportunities that are patchily distributed across space and time. Our results highlight that large-scale movements may not only be necessary for individuals to fulfill their life-cycle, but also to exploit heterogeneously spaced trophic resources. Therefore, habitat fragmentation and homogenization may have strong, but currently undescribed, ecological effects on the access to critical food resources in stream-dwelling fish populations.

  10. Inter-Tributary Movements by Resident Salmonids across a Boreal Riverscape

    Science.gov (United States)

    Bentley, Kale T.; Schindler, Daniel E.; Armstrong, Jonathan B.; Cline, Timothy J.; Brooks, Gabriel T.

    2015-01-01

    Stream-dwelling fishes inhabit river networks where resources are distributed heterogeneously across space and time. Current theory emphasizes that fishes often perform large-scale movements among habitat patches for reproduction and seeking refugia, but assumes that fish are relatively sedentary during growth phases of their life cycle. Using stationary passive integrated transponder (PIT)-tag antennas and snorkel surveys, we assessed the individual and population level movement patterns of two species of fish across a network of tributaries within the Wood River basin in southwestern Alaska where summer foraging opportunities vary substantially among streams, seasons, and years. Across two years, Arctic grayling (Thymallus arcticus) and rainbow trout (Oncorhynchus mykiss) exhibited kilometer-scale movements among streams during the summer growing season. Although we monitored movements at a small fraction of all tributaries used by grayling and rainbow trout, approximately 50% of individuals moved among two or more streams separated by at least 7 km within a single summer. Movements were concentrated in June and July, and subsided by early August. The decline in movements coincided with spawning by anadromous sockeye salmon, which offer a high-quality resource pulse of food to resident species. Inter-stream movements may represent prospecting behavior as individuals seek out the most profitable foraging opportunities that are patchily distributed across space and time. Our results highlight that large-scale movements may not only be necessary for individuals to fulfill their life-cycle, but also to exploit heterogeneously spaced trophic resources. Therefore, habitat fragmentation and homogenization may have strong, but currently undescribed, ecological effects on the access to critical food resources in stream-dwelling fish populations. PMID:26379237

  11. Assessment of Native Salmonids Above Hells Canyon Dam, Idaho, 2002-2003 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, Kevin A.; Lamansky, Jr., James A. (Idaho Department of Fish and Game, Boise, ID)

    2004-03-01

    We assessed the relationships between specific stream attributes and Yellowstone cutthroat trout Oncorhynchus clarki bouvieri distribution and biomass at 773 stream reaches (averaging 100 m in length) throughout the Upper Snake River Basin in Idaho, in an effort to identify possible limiting factors. Because limiting factors were expected to vary across the range of cutthroat trout distribution in Idaho, separate logistic and multiple regression models were developed for each of the nine major river drainages to relate stream conditions to occurrence and biomass of cutthroat trout. Adequate stream flow to measure fish and habitat existed at 566 sites, and of those, Yellowstone cutthroat trout were present at 322 sites, while rainbow trout O. mykiss (or rainbow x cutthroat hybrids) and brook trout Salvelinus fontinalis occurred at 108 and 181 sites, respectively. In general, cutthroat trout presence at a specific site within a drainage was associated with a higher percentage of public property, higher elevation, more gravel and less fine substrate, and more upright riparian vegetation. However, there was much variation between drainages in the direction and magnitude of the relationships between stream characteristics and Yellowstone cutthroat trout occurrence and biomass, and in model strength. This was especially true for biomass models, in which we were able to develop models for only five drainages that explained more than 50% of the variation in cutthroat trout biomass. Sample size appeared to affect the strength of the biomass models, with a higher explanation of biomass variation in drainages with lower sample sizes. The occurrence of nonnative salmonids was not strongly related to cutthroat trout occurrence, but their widespread distribution and apparent ability to displace native cutthroat trout suggest they may nevertheless pose the largest threat to long-term cutthroat trout persistence in the Upper Snake River Basin.

  12. 78 FR 17355 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-03-21

    ... [email protected] . FOR FURTHER INFORMATION CONTACT: Jeffrey Jahn, Santa Rosa, CA (ph.: 707-575-6097, email.: Jeffrey[email protected] ). SUPPLEMENTARY INFORMATION: Species Covered in This Notice This notice... through June 15 on a four days a week schedule. Adult and smolt salmonids will be captured (fyke net...

  13. 76 FR 57717 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2011-09-16

    ... relevant to Federally endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha), threatened Central Valley spring-run Chinook salmon (O. tshawytscha), threatened California Central Valley... Fish and Game Central Valley Salmonid Tissue Archive to UC Davis, for purposes of genetic investigation...

  14. 78 FR 24382 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2013-04-25

    ... two vessels, (2) conducting research on acoustic differentiation between hake and Humboldt squid... history strategies among local salmonids (Chinook, chum, sea-run cutthroat, steelhead, and bull trout) and... be ``spot- shocking'' for presence and absence and would not typically cover broad, continuous areas...

  15. 77 FR 15719 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2012-03-16

    ..., from Friant Dam to the confluence of the Merced River, in Central Valley, California. CCV steelhead... the Merced River. Permit 16608 will expire on March 31, 2014. Permit 16531 was issued to FISHBIO... scientific research studies linking salmonid habitat and spatial variability in the Merced River, a tributary...

  16. How do land-based salmonid farms affect stream ecology?

    Energy Technology Data Exchange (ETDEWEB)

    Tello, A., E-mail: ag32@stir.ac.u [Institute of Aquaculture, University of Stirling, FK9 4LA (United Kingdom); Corner, R.A., E-mail: rac1@stir.ac.u [Institute of Aquaculture, University of Stirling, FK9 4LA (United Kingdom); Telfer, T.C., E-mail: tct1@stir.ac.u [Institute of Aquaculture, University of Stirling, FK9 4LA (United Kingdom)

    2010-05-15

    Increasing research is highlighting the fact that streams provide crucial ecosystem services through the biogeochemical and ecological processes they sustain. Freshwater land-based salmonid farms commonly discharge their effluents into low order, headwater streams, partly due to the fact that adequate freshwater resources for production are commonly found in undisturbed areas. We review the effects of salmonid farm effluents on different biological components of stream ecosystems. Relevant considerations related to the temporal and spatial scales of effluent discharge and ecological effects are discussed. These highlight the need to characterize the patterns of stressor discharge when assessing environmental impacts and designing ecological effects studies. The potential role of multiple stressors in disrupting ecosystem structure and function is discussed with an emphasis on aquaculture veterinary medicines. Further research on the effects of veterinary medicines using relevant exposure scenarios would significantly contribute to our understanding of their impact in relation to other effluent stressors. - This article reviews the effects of aquaculture effluents on stream ecosystems with an emphasis on veterinary medicines and the temporal patterns of effluent discharge.

  17. A global assessment of salmon aquaculture impacts on wild salmonids.

    Directory of Open Access Journals (Sweden)

    Jennifer S Ford

    2008-02-01

    Full Text Available Since the late 1980s, wild salmon catch and abundance have declined dramatically in the North Atlantic and in much of the northeastern Pacific south of Alaska. In these areas, there has been a concomitant increase in the production of farmed salmon. Previous studies have shown negative impacts on wild salmonids, but these results have been difficult to translate into predictions of change in wild population survival and abundance. We compared marine survival of salmonids in areas with salmon farming to adjacent areas without farms in Scotland, Ireland, Atlantic Canada, and Pacific Canada to estimate changes in marine survival concurrent with the growth of salmon aquaculture. Through a meta-analysis of existing data, we show a reduction in survival or abundance of Atlantic salmon; sea trout; and pink, chum, and coho salmon in association with increased production of farmed salmon. In many cases, these reductions in survival or abundance are greater than 50%. Meta-analytic estimates of the mean effect are significant and negative, suggesting that salmon farming has reduced survival of wild salmon and trout in many populations and countries.

  18. Old wine in new bottles: reaction norms in salmonid fishes.

    Science.gov (United States)

    Hutchings, J A

    2011-03-01

    Genetic variability in reaction norms reflects differences in the ability of individuals, populations and ultimately species to respond to environmental change. By increasing our understanding of how genotype × environment interactions influence evolution, studies of genetic variation in phenotypic plasticity serve to refine our capacity to predict how populations will respond to natural and anthropogenic environmental variability, including climate change. Given the extraordinary variability in morphology, behaviour and life history in salmonids, one might anticipate the research milieu on reaction norms in these fishes to be empirically rich and intellectually engaging. Here, I undertake a review of genetic variability in continuous and discontinuous (threshold) norms of reaction in salmonid fishes, as determined primarily (but not exclusively) by common-garden experiments. Although in its infancy from a numerical publication perspective, there is taxonomically broad evidence of genetic differentiation in continuous, threshold and bivariate reaction norms among individuals, families and populations (including inter-population hybrids and backcrosses) for traits as divergent as embryonic development, age and size at maturity, and gene expression. There is compelling inferential evidence that plasticity is heritable and that population differences in reaction norms can reflect adaptive responses, by natural selection, to local environments. As a stimulus for future work, a series of 20 research questions are identified that focus on reaction-norm variability, selection, costs and constraints, demographic and conservation consequences, and genetic markers and correlates of phenotypic plasticity.

  19. Salmon lice – impact on wild salmonids and salmon aquaculture

    Science.gov (United States)

    Torrissen, O; Jones, S; Asche, F; Guttormsen, A; Skilbrei, O T; Nilsen, F; Horsberg, T E; Jackson, D

    2013-01-01

    Salmon lice, Lepeophtheirus salmonis, are naturally occurring parasites of salmon in sea water. Intensive salmon farming provides better conditions for parasite growth and transmission compared with natural conditions, creating problems for both the salmon farming industry and, under certain conditions, wild salmonids. Salmon lice originating from farms negatively impact wild stocks of salmonids, although the extent of the impact is a matter of debate. Estimates from Ireland and Norway indicate an odds ratio of 1.1:1-1.2:1 for sea lice treated Atlantic salmon smolt to survive sea migration compared to untreated smolts. This is considered to have a moderate population regulatory effect. The development of resistance against drugs most commonly used to treat salmon lice is a serious concern for both wild and farmed fish. Several large initiatives have been taken to encourage the development of new strategies, such as vaccines and novel drugs, for the treatment or removal of salmon lice from farmed fish. The newly sequenced salmon louse genome will be an important tool in this work. The use of cleaner fish has emerged as a robust method for controlling salmon lice, and aquaculture production of wrasse is important towards this aim. Salmon lice have large economic consequences for the salmon industry, both as direct costs for the prevention and treatment, but also indirectly through negative public opinion. PMID:23311858

  20. How do land-based salmonid farms affect stream ecology?

    International Nuclear Information System (INIS)

    Tello, A.; Corner, R.A.; Telfer, T.C.

    2010-01-01

    Increasing research is highlighting the fact that streams provide crucial ecosystem services through the biogeochemical and ecological processes they sustain. Freshwater land-based salmonid farms commonly discharge their effluents into low order, headwater streams, partly due to the fact that adequate freshwater resources for production are commonly found in undisturbed areas. We review the effects of salmonid farm effluents on different biological components of stream ecosystems. Relevant considerations related to the temporal and spatial scales of effluent discharge and ecological effects are discussed. These highlight the need to characterize the patterns of stressor discharge when assessing environmental impacts and designing ecological effects studies. The potential role of multiple stressors in disrupting ecosystem structure and function is discussed with an emphasis on aquaculture veterinary medicines. Further research on the effects of veterinary medicines using relevant exposure scenarios would significantly contribute to our understanding of their impact in relation to other effluent stressors. - This article reviews the effects of aquaculture effluents on stream ecosystems with an emphasis on veterinary medicines and the temporal patterns of effluent discharge.

  1. Molecular epidemiology of salmonid alphavirus (SAV subtype 3 in Norway

    Directory of Open Access Journals (Sweden)

    Jansen Mona D

    2010-08-01

    Full Text Available Abstract Background Pancreas disease (PD is a viral fish disease which in recent years has significantly affected Norwegian salmonid aquaculture. In Norway, the aetiological agent salmonid alphavirus (SAV has been found to be represented by the subtype 3 only. SAV subtype 3 has in previous analyses been found to show a lower genetic divergence than the subtypes found to cause PD in Ireland and Scotland. The aim of this study was to evaluate the nucleotide (nt and amino acid divergence and the phylogenetic relationship of 33 recent SAV subtype 3 sequences. The samples from which the sequences were obtained originated from both PD endemic and non-endemic regions in an attempt to investigate agent origin/spread. Multiple samples throughout the seawater production phase from several salmonid populations were included to investigate genetic variation during an outbreak. The analyses were mainly based on partial sequences from the E2 gene. For some samples, additional partial 6 K and nsP3 gene sequences were available. Results The nucleotide divergence for all gene fragments ranged from total identity (0.0% divergence to 0.45% (1103 nt fragment of E2, 1.11% (451 nt fragment of E2, 0.94% (6 K and 0.28% (nsP3. This low nucleotide divergence corresponded well to previous reports on SAV 3 sequences; however the observed divergence for the short E2 fragment was higher than that previously reported. When compared to SAVH20/03 (AY604235, amino acid substitutions were detected in all assessed gene fragments however the in vivo significance of these on for example disease outbreak mortality could not be concluded on. The phylogenetic tree based on the 451 nt E2 fragment showed that the sequences divided into two clusters with low genetic divergence, representing only a single SAV subtype. Conclusions The analysed sequences represented two clusters of a single SAV subtype; however some of the observed sequence divergence was higher than that previously reported

  2. Genetic basis for body size variation between an anadromous and two derived lacustrine populations of threespine stickleback Gasterosteus aculeatus in southwest Alaska

    Science.gov (United States)

    Bowles, Ella; Johnston, Rebecca A.; Vanderzwan, Stevi L.; Rogers, Sean M.

    2016-01-01

    Abstract Body size is a highly variable trait among geographically separated populations. Size-assortative reproductive isolation has been linked to recent adaptive radiations of threespine stickleback (Gasterosteus aculeatus) into freshwater, but the genetic basis of the commonly found size difference between anadromous and derived lacustrine sticklebacks has not been tested. We studied the genetic basis of size differences between recently diverging stickleback lineages in southwest Alaska using a common environment experiment. We crossed stickleback within one anadromous (Naknek River) and one lake (Pringle Lake) population and between the anadromous and two lake populations (Pringle and JoJo Lakes), and raised them in a salinity of 4–6 ppt. The F1 anadromous and freshwater forms differed significantly in size, whereas hybrids were intermediate or exhibited dominance toward the anadromous form. Additionally, the size of freshwater F1s differed from their wild counterparts, with within-population F1s from Pringle Lake growing larger than their wild counterparts, while there was no size difference between lab-raised and wild anadromous fish. Sexual dimorphism was always present in anadromous fish, but not in freshwater, and not always in the hybrid crosses. These results, along with parallel changes among anadromous and freshwater forms in other regions, suggest that this heritable trait is both plastic and may be under divergent and/or sexual selection. PMID:29491893

  3. Survival and progression rates of anadromous brown trout kelts Salmo trutta during downstream migration in freshwater and at sea

    DEFF Research Database (Denmark)

    Aarestrup, Kim; Baktoft, Henrik; Thorstad, EB

    2015-01-01

    and returned to the fjord. The duration of the entire marine migration, from leaving to entering the river, was on average 163 d. The fish returned from the Kattegat Sea to the fjord between 22 July and 21 October. Upon return, the fish spent 1−90 d passing through Randers Fjord, with most individuals...... completing the reach within 4 d, suggesting that the kelts spent limited time foraging after returning to the fjord. The total survival during the entire marine migration, including the fjord, was a minimum of 29%. Our study provides data that are important for management of anadromous brown trout......The marine migration of post-spawning anadromous fish remains poorly understood. The present study examined survival and progression rates of anadromous brown trout Salmo trutta L. after spawning (kelts) during downriver, fjord, and sea migration. Kelts (n = 49) were captured in the Danish River...

  4. Basin Scale Evaluation of Stream Invertebrate Community Functional Organization

    Science.gov (United States)

    Cummins, K. W.; Matousek, J.; Shackelford, A. J.

    2005-05-01

    Invertebrate community functional organization was studied at the basin scale in the Freshwater Creek catchment in northern California in August and September, 2004. Timed, D-frame net samples were taken in six tributaries (study reaches 0.5 - 2.7 km) and two sections of the mainstem (3.4 and 4.5 km) of Freshwater Creek. The 317 samples from 106 sites were collected by habitat (cobble, 167; riparian litter, 82; fine sediments, 36; large woody debris, 32). The sample sites matched randomly selected locations within a sample frame of a concomitant juvenile salmonid survey. Juvenile salmonid stomach samples were also taken at each invertebrate survey site. Shredders and total collectors each dominated one tributary and one mainstem reach and scrapers dominated four tributaries. Using the invertebrate ecosystem surrogate method developed by Cummins and Merritt, half of the tributaries/mainstem reaches were characterized as heterotrophic, the other half as autotrophic. The invertebrate functional group community organization was strongly correlated with habitat type but, in general, the relationship with salmonid abundance was indirect. Initial analysis of juvenile salmonid stomachs from one stream (Cloney Gulch) indicated that food availability was good for drift-feeding fish.

  5. The Long-Term Effects of Large Wood Placement on Salmonid Habitat in East Fork Mill Creek, Redwood National and State Park, California

    Science.gov (United States)

    Rodriguez, D. L.; Stubblefield, A. P.

    2017-12-01

    The conservation and recovery of anadromous salmonids (Oncorhynchus sp.) depend on stream restoration and protection of freshwater habitats. Instream large wood dictates channel morphology, increase retention of terrestrial inputs such as organic matter, nutrients and sediment, and enhances the quality of fish habitat. Historic land use/land cover changes have resulted in aquatic systems devoid of this component. Restoration by placement of large wood jams is intended to restore physical and biological processes. An important question for scientists and managers, in addition to the initial effectiveness of restoration, is the persistence and fate of this type of project. In this study we compare channel change and large wood attributes on the East Fork of Mill Creek, a tributary of the Smith River in northern California, eight years after a major instream wood placement effort took place. Our results are compared with previously published data from before and one year after the restoration. Preliminary results suggest the dramatic increase in spawning gravel abundance and large wood accumulation observed in the earlier study have persisted. From 2008 to 2016 a reduction in median sediment size, ranging from 103-136 percent, has been observed in a majority of the sites. The sites have continued to grow in size and influence by racking floating wood from upstream and destabilizing proximate banks of riparian alder, increasing both instream large wood volume (5-196 %) and floodplain connectivity. Preliminary results also show a decrease in residual pool depth and an increase in pool length which may be attributed to floodplain connectivity. Changes to the following attributes are evaluated: 1) wood loading (total site wood volume, total wood volume in active channel, and wood piece count); 2) percent pool cover by large wood; 3) residual pool depth; 4) upstream sediment aggradation; 5) floodplain connectivity; and 6) mean sediment size directly above and below large

  6. Research, Monitoring, and Evaluation of Avian Predation on Salmonid Smolts in the Lower and Mid-Columbia River, 2006 Final Season Summary.

    Energy Technology Data Exchange (ETDEWEB)

    Roby, Daniel D. [USGS - Oregon Cooperative Fish and Wildlife Research Unit, Oregon State University; Collis, Ken [Real Time Research, Inc.; Lyons, Donald E. [USGS - Oregon Cooperative Fish and Wildlife Research Unit, Oregon State University

    2009-06-18

    This study investigates predation by piscivorous waterbirds on juvenile salmonids (Oncorhynchus spp.) from throughout the Columbia River Basin. During 2006, study objectives in the Columbia River estuary, work funded by the Bonneville Power Administration, were to (1) monitor and evaluate previous management initiatives to reduce Caspian tern (Hydroprogne caspia) predation on juvenile salmonids (smolts); (2) measure the impact of double-crested cormorant (Phalacrocorax auritus) predation on smolt survival, and assess potential management options to reduce cormorant predation; and (3) monitor large colonies of other piscivorous waterbirds in the estuary (i.e., glaucous-winged/western gulls [Larus glaucescens/occidentalis]) to determine the potential impacts on smolt survival. Study objectives on the mid-Columbia River, work funded by the Walla Walla District of the U.S. Army Corps of Engineers, were to (1) measure the impact of predation by Caspian terns and double-crested cormorants on smolt survival; and (2) monitor large nesting colonies of other piscivorous waterbirds (i.e., California gulls [L. californicus], ring-billed gulls [L. delawarensis], American white pelicans [Pelecanus erythrorhynchos]) on the mid-Columbia River to determine the potential for significant impacts on smolt survival. Our efforts to evaluate system-wide losses of juvenile salmonids to avian predation indicated that Caspian terns and double-crested cormorants were responsible for the vast majority of smolt losses to avian predators in the Columbia Basin, with most losses occurring in the Columbia River estuary. In 2006, East Sand Island in the Columbia River estuary supported the largest known breeding colonies of Caspian terns and double-crested cormorants in the world. The Caspian tern colony on East Sand Island consisted of about 9,200 breeding pairs in 2006, up slightly (but not significantly so) from the estimate of colony size in 2005 (8,820 pairs). There has not been a

  7. The phylogeography of salmonid proliferative kidney disease in Europe and North America.

    OpenAIRE

    Henderson, Matthew; Okamura, Beth

    2004-01-01

    Salmonid proliferative kidney disease (PKD) is caused by the myxozoan Tetracapsuloides bryosalmonae. Given the serious and apparently growing impact of PKD on farmed and wild salmonids, we undertook a phylogeographic study to gain insights into the history of genealogical lineages of T. bryosalmonae in Europe and North America, and to determine if the global expansion of rainbow trout farming has spread the disease. Phylogenetic analyses of internal transcribed spacer 1 sequences revealed a c...

  8. EFFECT OF NON-ESSENTIAL ELEMENTS (MERCURY. ARSENIC ON SALMONIDS (SALMONIDAE (REVIEW

    Directory of Open Access Journals (Sweden)

    І. Hrytsyniak

    2015-09-01

    Full Text Available Purpose. The problem of water ecosystem pollution with heavy metals achieved great actuality during recent years, both because of their significant distribution in environment, and wide spectrum of their toxic effects on fish organism. Much attention in modern scientific literature is given to the problem of the effects of heavy metals, including mercury and arsenic, on fish organism. However, investigations in this field are conducted mainly on cyprinids, while physiological and biochemical mechanisms of the effects of heavy metals on salmonids are less studied. According to this, the studies of the sources of heavy metals in water ecosystems, peculiarities of their action in salmonid organism on subcellular, cellular, tissue and organ levels, species and age-related peculiarities of the effects of heavy metals are of great scientific and practical importance. The purpose of this work is to review the mentioned problems. Findings. The work characterizes the effects of mercury and arsenic on salmonids on subcellular, cellular, tissue and organ levels. The article contains characteristic of conditions, under which toxic or lethal action of the mentioned xenobiotics on different species of salmonids was observed. Originality. The paper summarizes literature data concerning the effect of mercury and arsenic on salmonids. Attention is accented on the sources of the mentioned pollutants in surface waters, physiological and biochemical mechanisms of their effects on salmonids, and on factors, which determine the level of their toxicity. Lethal concentrations of mercury and arsenic to salmonids, depending on experiment duration, species and age-related peculiarities are presented. Practical value. Data presented in the review can be used for the explanation of physiological and biochemical mechanisms of the adaptation of salmonids to surface water pollution with heavy metals, diagnostics of fish pathologies caused by toxic effects of mercury and

  9. Research, Monitoring, and Evaluation of Avian Predation on Salmonid Smolts in the Lower and Mid-Columbia River, 2008 Draft Season Summary.

    Energy Technology Data Exchange (ETDEWEB)

    Roby, Daniel D. [USGS - Oregon Cooperative Fish and Wildlife Research Unit, Department of Fisheries and Wildlife, Oregon State University; Collis, Ken [Real Time Research, Inc.; Lyons, Donald E. [USGS - Oregon Cooperative Fish and Wildlife Research Unit, Oregon State University

    2009-07-08

    This report describes investigations into predation by piscivorous colonial waterbirds on juvenile salmonids (Oncorhynchus spp.) from throughout the Columbia River basin during 2008. East Sand Island in the Columbia River estuary again supported the largest known breeding colony of Caspian terns (Hydroprogne caspia) in the world (approximately 10,700 breeding pairs) and the largest breeding colony of double-crested cormorants (Phalacrocorax auritus) in western North America (approximately 10,950 breeding pairs). The Caspian tern colony increased from 2007, but not significantly so, while the double-crested cormorant colony experienced a significant decline (20%) from 2007. Average cormorant nesting success in 2008, however, was down only slightly from 2007, suggesting that food supply during the 2008 nesting season was not the principal cause of the decline in cormorant colony size. Total consumption of juvenile salmonids by East Sand Island Caspian terns in 2008 was approximately 6.7 million smolts (95% c.i. = 5.8-7.5 million). Caspian terns nesting on East Sand Island continued to rely primarily on marine forage fishes as a food supply. Based on smolt PIT tag recoveries on the East Sand Island Caspian tern colony, predation rates were highest on steelhead in 2008; minimum predation rates on steelhead smolts detected passing Bonneville Dam averaged 8.3% for wild smolts and 10.7% for hatchery-raised smolts. In 2007, total smolt consumption by East Sand Island double-crested cormorants was about 9.2 million juvenile salmonids (95% c.i. = 4.4-14.0 million), similar to or greater than that of East Sand Island Caspian terns during that year (5.5 million juvenile salmonids; 95% c.i. = 4.8-6.2 million). The numbers of smolt PIT tags recovered on the cormorant colony in 2008 were roughly proportional to the relative availability of PIT-tagged salmonids released in the Basin, suggesting that cormorant predation on salmonid smolts in the estuary was less selective than tern

  10. Umatilla Basin natural production monitoring and evaluation. Annual report 1995-1996

    International Nuclear Information System (INIS)

    Contor, C.R.; Hoverson, E.; Kissner, P.; Volkman, J.

    1997-08-01

    This report summarizes the activities of the Umatilla Basin Natural Production Monitoring and Evaluation Project (UBNPME) from September 30, 1995 to September 29, 1996. This program was funded by Bonneville Power Administration and was managed under the Fisheries Program, Department of Natural Resources, Confederated Tribes of the Umatilla Indian Reservation. The goal was to evaluate the implementation of the Umatilla River Basin fisheries restoration plan with respect to natural production, adult passage, and tribal harvest. An estimated 56.1 river miles (RM) of habitat was inventoried on the lower Umatilla River (RM 0--56.1) from June 4, to August 1, 1996. The majority of the lower River was found to be too polluted and physically altered to provide suitable rearing or migration habitat for salmonids during the summer. High water temperatures, irrigation withdrawals, altered channels, and urban and agricultural pollution all contributed to degrade the lower Umatilla River. Small springs provided cooler waters and created small areas that were suitable for salmonid rearing. The river below the mouth of Mckay Creek (RM 27.2 to 50.6) was also cooler and more suitable to salmonid rearing when water was released from Mckay Dam. Two hundred sixty-three of 1,832 (14.4%) habitat units were electrofished from June 19 to August 29, 1996. The number of natural juvenile salmonids captured between RM 1.5--52.4 follow: (1) 141 juvenile steelhead (including resident rainbow trout; Oncoryhnchus mykiss), (2) 13 mountain whitefish (Prosopium williamsoni, including adults), (3) four chinook salmon (O. tshawytscha), and (4) two coho salmon (O. kisutch). The expanded population estimate for the areas surveyed was 2,445 salmonids. Mean density was 0.147 salmonids/100 square meter. Mean density of fast water habitat types was 4.5 times higher than slow water types (0.358 and 0.079 s/100 m 2 )

  11. Umatilla Basin Natural Production Monitoring and Evaluation; 1995-1996 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Contor, Craig R.; Kissner, Paul; Volkman, Jed [Confederated Tribes of the Umatilla Indian Reservation, Pendleton, OR (United States). Dept. of Natural Resources

    1997-08-01

    This report summarizes the activities of the Umatilla Basin Natural Production Monitoring and Evaluation Project (UBNPME) from September 30, 1995 to September 29, 1996. This program was funded by Bonneville Power Administration and was managed under the Fisheries Program, Department of Natural Resources, Confederated Tribes of the Umatilla Indian Reservation. The goal was to evaluate the implementation of the Umatilla River Basin fisheries restoration plan with respect to natural production, adult passage, and tribal harvest. An estimated 56.1 river miles (RM) of habitat was inventoried on the lower Umatilla River (RM 0--56.1) from June 4, to August 1, 1996. The majority of the lower River was found to be too polluted and physically altered to provide suitable rearing or migration habitat for salmonids during the summer. High water temperatures, irrigation withdrawals, altered channels, and urban and agricultural pollution all contributed to degrade the lower Umatilla River. Small springs provided cooler waters and created small areas that were suitable for salmonid rearing. The river below the mouth of Mckay Creek (RM 27.2 to 50.6) was also cooler and more suitable to salmonid rearing when water was released from Mckay Dam. Two hundred sixty-three of 1,832 (14.4%) habitat units were electrofished from June 19 to August 29, 1996. The number of natural juvenile salmonids captured between RM 1.5--52.4 follow: (1) 141 juvenile steelhead (including resident rainbow trout; Oncoryhnchus mykiss), (2) 13 mountain whitefish (Prosopium williamsoni, including adults), (3) four chinook salmon (O. tshawytscha), and (4) two coho salmon (O. kisutch). The expanded population estimate for the areas surveyed was 2,445 salmonids. Mean density was 0.147 salmonids/100 square meter. Mean density of fast water habitat types was 4.5 times higher than slow water types (0.358 and 0.079 s/100 m{sup 2}).

  12. Evaluation and Monitoring of Idaho Habitat Enhancement and Anadromous Fish Natural Production : Annual Report 1986.

    Energy Technology Data Exchange (ETDEWEB)

    Petrosky, Charles E.; Holubetz, Terry B.

    1987-11-01

    The Idaho Department of Fish and Game (IDFG) has been conducting an evaluation of existing and proposed habitat improvement projects for anadromous fish in the Clearwater River and Salmon River drainages over the last 3 years. Projects included in the evaluation are funded by or proposed for funding by the Bonneville Power Administration (BPA) under the Northwest Power Planning Act as off-site mitigation for downstream hydropower development on the Snake and Columbia rivers. This evaluation project is also funded under the same authority. A mitigation record is being developed to use increased smolt production (i.e., yield) at full-seeding as the best measure of benefit from a habitat enhancement project. Determination of full benefit from a project depends on completion or maturation of the project and presence of adequate numbers of fish to document actual increases in fish production. The depressed nature of upriver anadromous stocks have precluded measuring full benefits of any habitat enhancement project in Idaho. Partial benefit will be credited to the mitigation record in the interim period of run restoration.

  13. Divergence in physiological factors affecting swimming performance between anadromous and resident populations of brook charr Salvelinus fontinalis.

    Science.gov (United States)

    Crespel, A; Dupont-Prinet, A; Bernatchez, L; Claireaux, G; Tremblay, R; Audet, C

    2017-05-01

    In this study, an anadromous strain (L) and a freshwater-resident (R) strain of brook charr Salvelinus fontinalis as well as their reciprocal hybrids, were reared in a common environment and submitted to swimming tests combined with salinity challenges. The critical swimming speeds (U crit ) of the different crosses were measured in both fresh (FW) and salt water (SW) and the variations in several physiological traits (osmotic, energetic and metabolic capacities) that are predicted to influence swimming performance were documented. Anadromous and resident fish reached the same U crit in both FW and SW, with U crit being 14% lower in SW compared with FW. The strains, however, seemed to use different underlying strategies: the anadromous strain relied on its streamlined body shape and higher osmoregulatory capacity, while the resident strain had greater citrate synthase (FW) and lactate dehydrogenase (FW, SW) capacity and either greater initial stores or more efficient use of liver (FW, SW) and muscle (FW) glycogen during exercise. Compared with R ♀ L ♂ hybrids, L ♀ R ♂ hybrids had a 20% lower swimming speed, which was associated with a 24% smaller cardio-somatic index and higher physiological costs. Thus swimming performance depends on cross direction (i.e. which parental line was used as dam or sire). The study thus suggests that divergent physiological factors between anadromous and resident S. fontinalis may result in similar swimming capacities that are adapted to their respective lifestyles. © 2017 The Fisheries Society of the British Isles.

  14. A review of the past and present status of anadromous fish species in the Netherlands: is restocking the Rhine feasible?

    NARCIS (Netherlands)

    Groot, de S.J.

    2002-01-01

    The paper reviews the past, present and future of eight anadromous fish species inhabiting the Lower Rhine (The Netherlands), viz. -sturgeon (Acipenser sturio), whitefish and houting (Coregonus lavaretus, C. oxyrinchus), smelt (Osmerus eperlanus), allis and twaite shad (Alosa alosa, A. fallax), sea

  15. Influences of recreation influence of forest and rangeland management on anadromous fish habitat in Western North America: influences of recreation.

    Science.gov (United States)

    Roger N. Clark; Dave R. Gibbons; Gilbert B. Pauley

    1985-01-01

    Public and private lands in the United States are used by millions of people for recreational activities. Many of these activities occur in or near streams and coastal areas that produce various species of anadromous fish. A major concern of fishery managers is the possible adverse effect of recreational uses on fish habitat. Conversely, the management of fish habitats...

  16. Spawning migration and larval drift of anadromous North Sea houting (Coregonus oxyrinchus) in the River IJssel, the Netherlands

    NARCIS (Netherlands)

    Borcherding, J.; Breukelaar, A.W.; Winter, H.V.; Koenig, U.

    2014-01-01

    Anadromous North Sea houting (NSH, Coregonus oxyrinchus) was historically distributed in the Wadden Sea extending from Jutland (Denmark) to the Schelde delta (Netherlands). The species has been considered extinct in the Rhine since the 1940s; however, a successful re-introduction programme

  17. 76 FR 20558 - Endangered and Threatened Wildlife and Plants; 44 Marine and Anadromous Taxa: Adding 10 Taxa...

    Science.gov (United States)

    2011-04-13

    ... anadromous O. mykisssteelhead populations below natural and manmade impassable barriers in the Sacramento and... (steelhead) populations below natural and manmade impassable barriers in California streams from the Russian...) populations below natural and manmade impassable barriers in streams and tributaries to the Columbia River...

  18. Influence of forest and rangeland management on anadromous fish habitat in Western North America: impacts of natural events.

    Science.gov (United States)

    Douglas N. Swanston

    1980-01-01

    Natural events affecting vegetative cover and the hydrology and stability of a stream and its parent watershed are key factors influencing the quality of anadromous fish habitat. High intensity storms, drought, soil mass movement, and fire have the greatest impacts. Wind, stream icing, and the influence of insects and disease are important locally...

  19. The evolutionary ecology of alternative migratory tactics in salmonid fishes.

    Science.gov (United States)

    Dodson, Julian J; Aubin-Horth, Nadia; Thériault, Véronique; Páez, David J

    2013-08-01

    Extensive individual variation in spatial behaviour is a common feature among species that exhibit migratory life cycles. Nowhere is this more evident than in salmonid fishes; individual fish may complete their entire life cycle in freshwater streams, others may migrate variable distances at sea and yet others limit their migrations to larger rivers or lakes before returning to freshwater streams to spawn. This review presents evidence that individual variation in migratory behaviour and physiology in salmonid fishes is controlled by developmental thresholds and that part of the variation in proximal traits activating the development of alternative migratory tactics is genetically based. We summarize evidence that alternative migratory tactics co-exist within populations and that all individuals may potentially adopt any of the alternative phenotypes. Even though intra-specific genetic divergence of migratory tactics is uncommon, it may occur if female competition for oviposition sites results in spawning segregation of alternative phenotypes. Because of their polygenic nature, alternative migratory tactics are considered as threshold traits. Threshold traits have two characteristics: an underlying 'liability' trait that varies in a continuous fashion, and a threshold value which is responsible for the discreetness observed in phenotypic distribution. We review evidence demonstrating that body size is an adequate proxy for the liability trait controlling the decision to migrate, but that the same phenotypic outcome (anadromy or residency) may be reached by different developmental pathways. The evidence suggesting a significant heritable component in the development of alternative migratory tactics is subsequently reviewed, leading us to conclude that alternative migratory tactics have considerable potential to respond to selection and evolve. We review what is known about the proximal physiological mechanisms mediating the translation of the continuous value of the

  20. Using Songbird Monitoring to Guide and Evaluate Riparian Restoration in Salmonid-Focused Stream Rehabilitation Projects

    Science.gov (United States)

    Ryan D. Burnett; Thomas Gardali; Geoffrey R. Geupel

    2005-01-01

    A restoration effort, primarily focused on reducing stranding and improving passage of anadromous fish, has been undertaken along sections of lower Clear Creek, Shasta County, California. Similar projects are occurring throughout California and, indeed, all of North America. To monitor the effects of these efforts at Clear Creek we implemented a multi-faceted songbird...

  1. Occurrence and distribution of pesticides in surface waters of the Hood River basin, Oregon, 1999-2009

    Science.gov (United States)

    Temple, Whitney B.; Johnson, Henry M.

    2011-01-01

    The U.S. Geological Survey analyzed pesticide and trace-element concentration data from the Hood River basin collected by the Oregon Department of Environmental Quality (ODEQ) from 1999 through 2009 to determine the distribution and concentrations of pesticides in the basin's surface waters. Instream concentrations were compared to (1) national and State water-quality standards established to protect aquatic organisms and (2) concentrations that cause sublethal or lethal effects in order to assess their potential to adversely affect the health of salmonids and their prey organisms. Three salmonid species native to the basin are listed as "threatened" under the U.S. Endangered Species Act: bull trout, steelhead, and Chinook salmon. A subset of 16 sites was sampled every year by the ODEQ for pesticides, with sample collection targeted to months of peak pesticide use in orchards (March-June and September). Ten pesticides and four pesticide degradation products were analyzed from 1999 through 2008; 100 were analyzed in 2009. Nineteen pesticides were detected: 11 insecticides, 6 herbicides, and 2 fungicides. Two of four insecticide degradation products were detected. All five detected organophosphate insecticides and the one detected organochlorine insecticide were present at concentrations exceeding water-quality standards, sublethal effects thresholds, or acute toxicity values in one or more samples. The frequency of organophosphate detection in the basin decreased during the period of record; however, changes in sampling schedule and laboratory reporting limits hindered clear analysis of detection frequency trends. Detected herbicide and fungicide concentrations were less than water-quality standards, sublethal effects thresholds, or acute toxicity values. Simazine, the most frequently detected pesticide, was the only herbicide detected at concentrations within an order of magnitude (factor of 10) of concentrations that impact salmonid olfaction. Some detected

  2. Development of a systemwide predator control program: Stepwise implementation of a predator index, predator control fisheries, and evaluation plan in the Columbia River basin (Northern Squawfish Management Program). Section 1: Implementation; Annual report 1995

    International Nuclear Information System (INIS)

    Young, F.R.

    1997-04-01

    The authors report their results from the fifth year of a basinwide program to harvest northern squawfish (Ptychocheilus oregonensis) in an effort to reduce mortality due to northern squawfish predation on juvenile salmonids during their emigration from natal streams to the ocean. Earlier work in the Columbia River Basin suggested predation by northern squawfish on juvenile salmonids may account for most of the 10--20% mortality juvenile salmonids experience in each of eight Columbia and Snake River reservoirs. Modeling simulations based on work in John Day Reservoir from 1982 through 1988 indicated that if predator-sized northern squawfish were exploited at a 10--20% rate, the resulting restructuring of their population could reduce their predation on juvenile salmonids by 50%

  3. Bird Distribution and Abundance - Ocean Survival of Salmonids

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A study to evaluate the role of changing ocean conditions on growth and survival of juvenile salmon from the Columbia River basin as they enter the Columbia River...

  4. A standard operating procedure for the surgical implantation of transmitters in juvenile salmonids

    Science.gov (United States)

    Liedtke, T.L.; Beeman, J.W.; Gee, L.P.

    2012-01-01

    Biotelemetry is a useful tool to monitor the movements of animals and is widely applied in fisheries research. Radio or acoustic technology can be used, depending on the study design and the environmental conditions in the study area. A broad definition of telemetry also includes the use of Passive Integrated Transponder (PIT) tags, either separately or with a radio or acoustic transmitter. To use telemetry, fish must be equipped with a transmitter. Although there are several attachment procedures available, surgical implantation of transmitters in the abdominal cavity is recognized as the best technique for long-term telemetry studies in general (Stasko and Pincock, 1977; Winter, 1996; Jepsen, 2003), and specifically for juvenile salmonids, Oncorhynchus spp. (Adams and others, 1998a, 1998b; Martinelli and others, 1998; Hall and others, 2009). Studies that use telemetry assume that the processes by which the animals are captured, handled, and tagged, as well as the act of carrying the transmitter, will have minimal effect on their behavior and performance. This assumption, commonly stated as a lack of transmitter effects, must be valid if telemetry studies are to describe accurately the movements and behavior of an entire population of interest, rather than the subset of that population that carries transmitters. This document describes a standard operating procedure (SOP) for surgical implantation of radio or acoustic transmitters in juvenile salmonids. The procedures were developed from a broad base of published information, laboratory experiments, and practical experience in tagging thousands of fish for numerous studies of juvenile salmon movements near Columbia River and Snake River hydroelectric dams. Staff from the Western Fisheries Research Center's Columbia River Research Laboratory (CRRL) frequently have used telemetry studies to evaluate new structures or operations at hydroelectric dams in the Columbia River Basin, and these evaluations typically

  5. Comparative Analysis of the Shared Sex-Determination Region (SDR) among Salmonid Fishes.

    Science.gov (United States)

    Faber-Hammond, Joshua J; Phillips, Ruth B; Brown, Kim H

    2015-06-25

    Salmonids present an excellent model for studying evolution of young sex-chromosomes. Within the genus, Oncorhynchus, at least six independent sex-chromosome pairs have evolved, many unique to individual species. This variation results from the movement of the sex-determining gene, sdY, throughout the salmonid genome. While sdY is known to define sexual differentiation in salmonids, the mechanism of its movement throughout the genome has remained elusive due to high frequencies of repetitive elements, rDNA sequences, and transposons surrounding the sex-determining regions (SDR). Despite these difficulties, bacterial artificial chromosome (BAC) library clones from both rainbow trout and Atlantic salmon containing the sdY region have been reported. Here, we report the sequences for these BACs as well as the extended sequence for the known SDR in Chinook gained through genome walking methods. Comparative analysis allowed us to study the overlapping SDRs from three unique salmonid Y chromosomes to define the specific content, size, and variation present between the species. We found approximately 4.1 kb of orthologous sequence common to all three species, which contains the genetic content necessary for masculinization. The regions contain transposable elements that may be responsible for the translocations of the SDR throughout salmonid genomes and we examine potential mechanistic roles of each one. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Ecology of Juvenile Salmonids in Shallow Tidal Freshwater Habitats in the Vicinity of the Sandy River Delta, Lower Columbia River, 2007

    Energy Technology Data Exchange (ETDEWEB)

    Sobocinski, Kathryn L.; Johnson, Gary E.; Sather, Nichole K.; Storch, Adam; Jones, Tucker A.; Mallette, Christine; Dawley, Earl M.; Skalski, John R.; Teel, David; Moran, Paul

    2008-03-18

    This document is the first annual report for the study titled “Ecology of Juvenile Salmonids in Shallow Tidal Freshwater Habitats in the Vicinity of the Sandy River Delta in the Lower Columbia River.” Hereafter, we refer to this research as the Tidal Freshwater Monitoring (TFM) Study. The study is part of the research, monitoring, and evaluation effort developed by the Action Agencies (Bonneville Power Administration, U.S. Army Corps of Engineers, U.S. Bureau of Reclamation) in response to obligations arising from the Endangered Species Act as a result of operation of the Federal Columbia River Power System (FCRPS). The project is performed under the auspices of the Northwest Power and Conservation Council’s Columbia Basin Fish and Wildlife Program.

  7. An experimental field evaluation of winter carryover effects in semi-anadromous Brown trout (Salmo trutta)

    DEFF Research Database (Denmark)

    Midwood, Jonathan D.; Larsen, Martin Hage; Boel, Mikkel

    2015-01-01

    For semi-anadromous brown trout, the decision whether or not to smoltify and migrate to the sea is believed to be made at the end of the preceding summer in response to both local environmental conditions and individual physiological status. Stressors experienced during the fall may therefore...... influence their propensity to migrate as well as carry over into the winter resulting in mortality when fish face challenging environmental conditions. To evaluate this possibility, we artificially elevated cortisol levels in juvenile trout (via intracoelomic injection of cortisol in the fall) and used...... passive integrated transponder tags to compare their overwinter and spring survival, growth, and migration success relative to a control group. Results suggest that overwinter mortality is high for individuals in this population regardless of treatment. However, survival rates were 2.5 times lower...

  8. Decline of the North Sea houting: protective measures for an endangered anadromous fish

    DEFF Research Database (Denmark)

    Jepsen, Niels; Deacon, Michael; Koed, Anders

    2012-01-01

    Once an abundant fish species in the rivers of the Wadden Sea in northwest Europe, the North Sea houting Coregonus oxyrinchus (NSH) was at the brink of extinction 25 yr ago. The very last stronghold for this species was in the small Danish River Vidaa. In an attempt to preserve this anadromous...... whitefish species, juveniles were hatchery-reared and stocked in 6 Danish rivers flowing into the Wadden Sea. These stocking efforts were fairly successful, and the houting established populations in at least 2 of the rivers, but the underlying problem of habitat degradation and migration obstacles...... they were initially PIT-tagged, indicating some exchange/straying between adjacent rivers. Overall there is a good chance that this unique species was saved in the 11th hour by intervention from managers and the EU...

  9. Genomic population structure of freshwater-resident and anadromous ide (Leuciscus idus) in north-western Europe

    DEFF Research Database (Denmark)

    Skovrind, Mikkel; Olsen, Morten Tange; Garrett Vieira, Filipe Jorge

    2016-01-01

    Climate change experts largely agree that future climate change and associated rises in oceanic water levels over the upcoming decades, will affect marine salinity levels. The subsequent effects on fish communities in estuarine ecosystems however, are less clear. One species that is likely...... to become increasingly affected by changes in salinity is the ide (Leuciscus idus). The ide is a stenohaline freshwater fish that primarily inhabits rivers, with frequent anadromous behavior when sea salinity does not exceed 15%. Unlike most other anadromous Baltic Sea fish species, the ide has yet...... resident and anadromous ide populations in the western Baltic Sea region, and relate the results to the current salinity gradient and the demographic history of ide in the region. The sample sites separate into four clusters, with all anadromous populations in one cluster and the freshwater resident...

  10. Fasting augments PCB impact on liver metabolism in anadromous Arctic Char

    Science.gov (United States)

    Vijayan, M.M.; Aluru, N.; Maule, A.G.; Jorgensen, E.H.

    2006-01-01

    Anadromous arctic char (Salvelinus alpinus) undertake short feeding migrations to seawater every summer and accumulate lipids, while the rest of the year is spent in fresh water where the accumulated lipid reserves are mobilized. We tested the hypothesis that winter fasting and the associated polychlorinated biphenyls' (PCBs) redistribution from lipid depots to critical tissues impair the liver metabolic capacity in these animals. Char were administered Aroclor 1254 (0, 1, 10, and 100 mg/ kg body mass) orally and maintained for 4 months without feeding to mimic seasonal winter fasting, while fed groups (0 and 100 mg Aroclor 1254/kg) were maintained for comparison. A clear dose-related increase in PCB accumulation and cytochrome P4501A (CYP1A) protein content was observed in the livers of fasted fish. This PCB concentration and CYP1A response with the high dose of Aroclor were 1.5-fold and 3-fold greater in the fasted than in the fed fish, respectively. In fed fish, PCB exposure lowered liver glycogen content, whereas none of the other metabolic indicators were significantly affected. In fasted fish, PCB exposure depressed liver glycogen content and activities of glucose-6-phosphate dehydrogenase, alanine aminotransferase, lactate dehydrogenase, and phosphoenolpyruvate carboxykinase and elevated 3-hydroxyacylcoA dehydrogenase activity and glucocorticoid receptor protein expression. There were no significant impacts of PCB on heat shock protein 70 (hsp70) and hsp90 contents in either fed or fasted fish. Collectively, our study demonstrates that winter emaciation associated with the anadromous lifestyle predisposes arctic char to PCB impact on hepatic metabolism including disruption of the adaptive metabolic responses to extended fasting. ?? 2006 Oxford University Press.

  11. Comparison of the movement and recapture of salmonid fishes tagged at two power plants

    International Nuclear Information System (INIS)

    Romberg, G.P.; Thommes, M.M.

    1974-01-01

    Fish tagging studies were conducted in the vicinity of Point Beach Nuclear Plant and Waukegan Power Plant to determine whether there were any seasonal or site specific differences in the residence behavior of salmonids at thermal discharges. Results showed that there were differences in the abundance and time of peak abundance of trout and salmon at the two power plant discharges. Certain species reacted differently to the two discharges probably as a result of maturity and water temperature. Salmonids did not appear to remain at either discharge for long periods. Direction of migration was affected by stocking location and water temperature

  12. Umatilla Basin Natural Production Monitoring and Evaluation; 1992-1993 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Confederated Tribes of the Umatilla Indian Reservation, (Confederated Tribes of the Umatilla Indian Reservation, Pendleton, OR)

    1994-09-01

    This report summarizes the activities of the Umatilla Basin Natural Production Monitoring and Evaluation Project from September 30, 1992 to September 29, 1993. Examinations of historical flow and water temperature records and current physical habitat, indicate that the streams in the Umatilla River Basin vary in condition from extremely poor to good. Reduced flows and high water temperatures prevented salmonid production in the lower Umatilla River below river mile 75 during the summer and early fall. This was also true in the lower reaches of many tributaries. Isolated springs provided limited refuges in the mid Umatilla River and lower Meacham Creek. Suitable habitat for salmonids was found in the upper reaches of the mainstem and tributaries.

  13. Umatilla Basin natural production monitoring and evaluation. Annual progress report, 1994--1995

    International Nuclear Information System (INIS)

    Contor, C.R.; Hoverson, E.; Kissner, P.; Volkman, J.

    1996-04-01

    This report summarizes the activities of the Umatilla Basin Natural Production Monitoring and Evaluation Project (UBNPME) from September 30, 1994 to September 29, 1995. This program was funded by Bonneville Power Administration and was managed under the Fisheries Program, Department of Natural Resources, Confederated Tribes of the Umatilla Indian Reservation. An estimated 36.7 km (22.6 miles) of stream habitat were inventoried on the Umatilla River, Moonshine, Mission, Cottonwood and Coonskin Creeks. A total of 384 of 3,652 (10.5%) habitat units were electrofished. The number of juvenile fish captured follows: 2,953 natural summer steelhead (including resident rainbow trout; Oncorhynchus mykiss), one hatchery steelhead, 341 natural chinook salmon (O. tshawytscha), 163 natural coho salmon (O. kisutch), five bull trout (Salvelinus confluentus), 185 mountain whitefish (Prosopium williamsoni), and six northern squawfish (Ptychoicheilus oregonensis). The expanded population estimate for the areas surveyed was 73,716 salmonids with a mean density of 0.38 fish/m 2 . Relative salmonid abundance, seasonal distribution and habitat utilization were monitored at index sites throughout the basin. During index site monitoring, the following species were collected in addition to those listed above: american shad (Alosa sapidissima), smallmouth bass (Micropterus dolomieu), carp (Cyprinus carpio) and chiselmouth (Acrocheilus alutaceus). Thirty-nine sites were electrofished during the spring and summer seasons, while 36 sites were sampled in the fall season. A study of the migration movements and homing requirements of adult salmonids in the Umatilla River was conducted during the 1994-95 return years. Radio telemetry was used to evaluate the movements of adult salmonids past diversion dams in the lower Umatilla River and to determine migrational movements of salmonids following upstream transport

  14. A social–ecological perspective for riverscape management in the Columbia River Basin

    OpenAIRE

    Hand, Brian K.; Flint, Courtney G.; Frissell, Chris A.; Muhlfeld, Clint C.; Devlin, Shawn P.; Kennedy, Brian P.; Crabtree, Robert L.; McKee, W. Arthur; Luikart, Gordon; Stanford, Jack A.

    2018-01-01

    Riverscapes are complex, landscape-scale mosaics of connected river and stream habitats embedded in diverse ecological and socioeconomic settings. Social–ecological interactions among stakeholders often complicate natural-resource conservation and management of riverscapes. The management challenges posed by the conservation and restoration of wild salmonid populations in the Columbia River Basin (CRB) of western North America are one such example. Because of their ecological, cultural, and s...

  15. PCB disruption of the hypothalamus-pituitary-interrenal axis involves brain glucocorticoid receptor downregulation in anadromous Arctic charr

    Science.gov (United States)

    Aluru, N.; Jorgensen, E.H.; Maule, A.G.; Vijayan, M.M.

    2004-01-01

    We examined whether brain glucocorticoid receptor (GR) modulation by polychlorinated biphenyls (PCBs) was involved in the abnormal cortisol response to stress seen in anadromous Arctic charr (Salvelinus alpinus). Fish treated with Aroclor 1254 (0, 1, 10, and 100 mg/kg body mass) were maintained for 5 mo without feeding in the winter to mimic their seasonal fasting cycle, whereas a fed group with 0 and 100 mg/kg Aroclor was maintained for comparison. Fasting elevated plasma cortisol levels and brain GR content but depressed heat shock protein 90 (hsp90) and interrenal cortisol production capacity. Exposure of fasted fish to Aroclor 1254 resulted in a dose-dependent increase in brain total PCB content. This accumulation in fish with high PCB dose was threefold higher in fasted fish compared with fed fish. PCBs depressed plasma cortisol levels but did not affect in vitro interrenal cortisol production capacity in fasted charr. At high PCB dose, the brain GR content was significantly lower in the fasted fish and this corresponded with a lower brain hsp70 and hsp90 content. The elevation of plasma cortisol levels and upregulation of brain GR content may be an important adaptation to extended fasting in anadromous Arctic charr, and this response was disrupted by PCBs. Taken together, the hypothalamus-pituitary- interrenal axis is a target for PCB impact during winter emaciation in anadromous Arctic charr.

  16. Operation Plans for Anadromous Fish Production Facilities in the Columbia River Basin : Annual Report 1995, Volume I - Idaho.

    Energy Technology Data Exchange (ETDEWEB)

    Idaho Department of Fish and Game; US Fish and Wildlife Service; Nez Perce Tribe

    1996-06-01

    Clearwater Hatchery is located on the north bank of the North Fork of the Clearwater River, downstream from Dworshak Dam. It is approximately 72 miles from Lower Granite Dam, and 504 miles from the mouth of the Columbia River. Site elevation is approximately 994 feet above sea level. The hatchery is staffed with 8 FTE`s. Clearwater Hatchery has two pipelines from Dworshak Reservoir. One is attached to a floating platform and is capable of providing various temperatures at varying depths. The other is a stationary intake about 245 feet below the top of the dam. All water is gravity fed to the hatchery. An 18-inch intake pipe provides an estimated 10 cfs with temperature remaining constant at approximately 40T. The primary 42-inch intake pipe can draw water from 5 to 45 feet in depth with temperatures ranging from 55{degrees} to 60{degrees}F and 70 cfs of flow. This report describes the operations of the hatchery.

  17. Low Temperature-Dependent Salmonid Alphavirus Glycoprotein Processing and Recombinant Virus-Like Particle Formation

    NARCIS (Netherlands)

    Metz, S.W.H.; Feenstra, F.; Villoing, S.; Hulten, van M.C.; Lent, van J.W.M.; Koumans, J.; Vlak, J.M.; Pijlman, G.P.

    2011-01-01

    Pancreas disease (PD) and sleeping disease (SD) are important viral scourges in aquaculture of Atlantic salmon and rainbow trout. The etiological agent of PD and SD is salmonid alphavirus (SAV), an unusual member of the Togaviridae (genus Alphavirus). SAV replicates at lower temperatures in fish.

  18. Avian predation on juvenile salmonids in the Lower Columbia River; 1998 annual report

    International Nuclear Information System (INIS)

    Collis, Ken; Adamany, Stephanie; Roby, Daniel D.; Craig, David P.; Lyons, Donald E.

    2000-01-01

    The authors initiated a field study in 1997 to assess the impacts of fish-eating colonial waterbirds (i.e., terns, cormorants, and gulls) on the survival of juvenile salmonids in the lower Columbia River. Here the authors present results from the 1998 breeding season, the second field season of work on this project. The research objectives in 1998 were to: (1) determine the location, size, nesting chronology, nesting success, and population trajectories of breeding colonies of fish-eating birds in the lower Columbia River; (2) determine diet composition of fish-eating birds, including taxonomic composition and energy content of various prey types; (3) estimate forage fish consumption rates, with special emphasis on juvenile salmonids, by breeding adults and their young; (4) determine the relative vulnerability of different groups of juvenile salmonids to bird predation; (5) identify foraging range, foraging strategies, and habitat utilization by piscivorous waterbirds; and (6) test the feasibility of various alternative methods for managing avian predation on juvenile salmonids and develop recommendations to reduce avian predation, if warranted by the results

  19. Invasion versus isolation: Trade-offs in managing native salmonids with barriers to upstream movement

    Science.gov (United States)

    Kurt D. Fausch; Bruce E. Rieman; Jason B. Dunham; Michael K. Young; Douglas P. Peterson

    2009-01-01

    Conservation biologists often face the trade-off that increasing connectivity in fragmented landscapes to reduce extinction risk of native species can foster invasion by non-native species that enter via the corridors created, which can then increase extinction risk. This dilemma is acute for stream fishes, especially native salmonids, because their populations are...

  20. Avian Predation on Juvenile Salmonids in the Lower Columbia River: 1998 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Collis, Ken; Adamany, Stephanie; Roby, Daniel D.; Craig, David P.; Lyons, Donald E.

    2000-04-01

    The authors initiated a field study in 1997 to assess the impacts of fish-eating colonial waterbirds (i.e., terns, cormorants, and gulls) on the survival of juvenile salmonids in the lower Columbia River. Here the authors present results from the 1998 breeding season, the second field season of work on this project. The research objectives in 1998 were to: (1) determine the location, size, nesting chronology, nesting success, and population trajectories of breeding colonies of fish-eating birds in the lower Columbia River; (2) determine diet composition of fish-eating birds, including taxonomic composition and energy content of various prey types; (3) estimate forage fish consumption rates, with special emphasis on juvenile salmonids, by breeding adults and their young; (4) determine the relative vulnerability of different groups of juvenile salmonids to bird predation; (5) identify foraging range, foraging strategies, and habitat utilization by piscivorous waterbirds; and (6) test the feasibility of various alternative methods for managing avian predation on juvenile salmonids and develop recommendations to reduce avian predation, if warranted by the results.

  1. A Multiple Watershed Approach to Assessing the Effects of Habitat Restoration Actions on Anadromous and Resident Fish Populations, Technical Report 2003-2004.

    Energy Technology Data Exchange (ETDEWEB)

    Marmorek, David

    2004-03-01

    Habitat protection and restoration is a cornerstone of current strategies to restore ecosystems, recover endangered fish species, and rebuild fish stocks within the Columbia River Basin. Strategies featuring habitat restoration include the 2000 Biological Opinion on operation of the Federal Columbia River Power System (FCRPS BiOp) developed by the National Marine Fisheries Service (NMFS), the 2000 Biological Opinion on Bull Trout developed by the US Fish and Wildlife Service (USFWS), and Sub-Basin Plans developed under the Fish and Wildlife Program of the Northwest Power and Conservation Council (NWPCC). There is however little quantitative information about the effectiveness of different habitat restoration techniques. Such information is crucial for helping scientists and program managers allocate limited funds towards the greatest benefits for fish populations. Therefore, it is critical to systematically test the hypotheses underlying habitat restoration actions for both anadromous and resident fish populations. This pilot project was developed through a proposal to the Innovative Projects fund of the NWPCC (ESSA 2002). It was funded by the Bonneville Power Administration (BPA) following reviews by the Independent Scientific Review Panel (ISRP 2002), the Columbia Basin Fish and Wildlife Authority (CBFWA 2002), the NWPCC and BPA. The study was designed to respond directly to the above described needs for information on the effectiveness of habitat restoration actions, including legal measures specified in the 2000 FCRPS BiOp (RPA 183, pg. 9-133, NMFS 2000). Due to the urgency of addressing these measures, the timeline of the project was accelerated from a duration of 18 months to 14 months. The purpose of this pilot project was to explore methods for evaluating past habitat restoration actions and their effects on fish populations. By doing so, the project will provide a foundation of retrospective analyses, on which to build prospective, multi-watershed designs

  2. APPLICATION OF SALMONIDS (SALMONIDAE N THE BIOMONITORING OF AQUATIC ENVIRONMENT (REVIEW

    Directory of Open Access Journals (Sweden)

    D. Yanovych

    2016-03-01

    Full Text Available Purpose. Due to the pollution of fisheries water bodies by industrial and agricultural waste waters, as well as by xenobiotics coming from other sources, taking into account a pridictable increase in the amounts of such effluents in the short and long terms, the problems related to the study of the effects of the pollutants of different nature and origin on aquatic organisms, especially fish, as well as a prediction of possible adverse consequences on aquatic ecosystems, becomes particularly important. The aim of our work was an analysis and synthesis of existing literature data concerning the indication in the biomonitoring of aquatic environments based on biological markers of salmonids as highly sensitive objects of fish fauna to external factors. Findings. The review summarizes and systematizes the data concerning the use of salmonids in biomonitoring studies. Furthermore, we highlighted and characterized the specificity of bioindication parameters of the aquatic environment state, such as the biochemical, genetic, physiological, morphological, histopathological, behavioral and population markers and noted the effects of hydroecosystem ecotoxication on different levels of biological organization (cell, individual, population, fish community. We also described the possibility of biological monitoring based on saprobic indexes identified for indicator species belonging to salmonids. Originality. In the article describes the structure, pros and cons of the use of specific biomarkers of individual salmonid fish and their populations for assessing the ecological status of aquatic environments. Practical value. The data given in the article can be used to improve the system of the ecological monitoring of aquatic environments by extending the range of indicator indices with organism and population biomarkers of highly sensitive salmonid species.

  3. Monitoring anadromous fish populations in a context of habitat fragmentation and commercial exploitation

    Directory of Open Access Journals (Sweden)

    Gabriela Ribeiro Cardoso

    2015-12-01

    A video recording system was used to monitor fishway effectiveness. Simultaneously, eight abiotic parameters were continuously recorded. Boosted Regression Trees (BRTs were applied to relate fishway’s use by sea lamprey and Alosa spp. with abiotic predictors. A passive integrated transponder (PIT antenna system was also used to quantify passage efficiency for sea lampreys. A sample of the professional fisherman population was surveyed, and respective daily catches registered. Data counts, fishway efficiency and professional fishermen surveys allowed the estimation of the number of sea lampreys entering River Mondego to spawn. Video counts revealed that 8333 and 21979 sea lampreys, in 2013 and 2014, respectively, used the fishway, and 7503 and 3404 Alosa spp. passed during the same periods. BRTs identified flow as the most important variable explaining fishway use, suggesting that anadromous species prefer to use the fishway at relatively low flow conditions. About 30% of PIT-tagged lampreys transposed the fishway in the migratory season of 2014. Data surveys indicate a total catch of 11114 and 31746 sea lampreys, during 2013 and 2014, respectively, and 3053 and 6637 allis shads in the same seasons. Hence, we estimated that 38891 and 105006 sea lampreys entered River Mondego to reproduce in 2013 and 2014, respectively.

  4. Landslide-dammed paleolake perturbs marine sedimentation and drives genetic change in anadromous fish.

    Science.gov (United States)

    Mackey, Benjamin H; Roering, Joshua J; Lamb, Michael P

    2011-11-22

    Large bedrock landslides have been shown to modulate rates and processes of river activity by forming dams, forcing upstream aggradation of water and sediment, and generating catastrophic outburst floods. Less apparent is the effect of large landslide dams on river ecosystems and marine sedimentation. Combining analyses of 1-m resolution topographic data (acquired via airborne laser mapping) and field investigation, we present evidence for a large, landslide-dammed paleolake along the Eel River, CA. The landslide mass initiated from a high-relief, resistant outcrop which failed catastrophically, blocking the Eel River with an approximately 130-m-tall dam. Support for the resulting 55-km-long, 1.3-km(3) lake includes subtle shorelines cut into bounding terrain, deltas, and lacustrine sediments radiocarbon dated to 22.5 ka. The landslide provides an explanation for the recent genetic divergence of local anadromous (ocean-run) steelhead trout (Oncorhynchus mykiss) by blocking their migration route and causing gene flow between summer run and winter run reproductive ecotypes. Further, the dam arrested the prodigious flux of sediment down the Eel River; this cessation is recorded in marine sedimentary deposits as a 10-fold reduction in deposition rates of Eel-derived sediment and constitutes a rare example of a terrestrial event transmitted through the dispersal system and recorded offshore.

  5. Leptin and ghrelin in anadromous Arctic charr: cloning and change in expressions during a seasonal feeding cycle.

    Science.gov (United States)

    Frøiland, Eirik; Murashita, Koji; Jørgensen, Even Hjalmar; Kurokawa, Tadahide

    2010-01-01

    Anadromous (sea-migrating) Arctic charr (Salvelinus alpinus) display pronounced seasonal variations in food intake and growth and is an interesting model for studying mechanisms of appetite regulation. In this study cDNAs encoding for ghrelin (GHRL) and leptin (LEP) in Arctic charr were cloned, after which stomach GHRL and liver LEP mRNA expressions were examined by qPCR during a seasonal feeding cycle of semi-wild anadromous Arctic charr. The fish were captured as they returned from summer feeding in seawater and transferred to an indoor tank where they were fed in excess until October the year after. Growth rate was low in late winter, increased in late spring and reached a peak during summer, and then declined during autumn, when the fish became sexually mature. The changes in growth rate were associated with corresponding changes in the proportion of fish that had been eating at each sampling date, and whole body lipid status. Stomach GHRL mRNA expression was high in late winter, decreased to a nadir in mid-summer and increased again to a high level in early autumn. Liver LEP mRNA remained low during winter, spring and early summer, after which there was a gradual, 7-fold increase until October. The seasonal changes in ghrelin and leptin support a role of these hormones in the long-term regulation of energy homeostasis in the anadromous Arctic charr. It cannot be excluded, however, that the increase in liver leptin expression during autumn is related to sexual maturation.

  6. Intestinal coccidiosis of anadromous and landlocked alewives, Alosa pseudoharengus, caused by Goussia ameliae n. sp. and G. alosii n. sp. (Apicomplexa: Eimeriidae

    Directory of Open Access Journals (Sweden)

    Jan Lovy

    2015-08-01

    Full Text Available Anadromous alewives, Alosa pseudoharengus, have experienced significant population level declines caused by factors including habitat destruction. Alewives occur in two different life histories, anadromous and landlocked forms. The landlocked alewife evolved from ancestral anadromous populations, resulting in an exclusively freshwater and phenotypically unique form. The occurrence of parasites in a host is linked to the environment, making alewives an ideal model to compare parasitology within a single species with contrasting life histories. Currently, little information exists on the presence and impacts of parasites in these fish populations; the present study sets out to better understand coccidiosis in the threatened anadromous populations and to understand how coccidian parasites compare in both life history forms. The intestinal coccidian, Goussia ameliae n. sp., was described infecting the pyloric cecum of 76% and 86% of young-of-the-year and adult anadromous alewives, respectively, from the Maurice River, New Jersey, USA. The coccidian was found in landlocked alewife populations with a prevalence of 92% and 34% in YOY and adult fish, respectively. An analysis of the small subunit 18S ribosomal RNA gene of G. ameliae from both life history forms demonstrated that the coccidian had 100% sequence identity, confirming the same parasite species in both forms. Though genetic analysis demonstrated G. ameliae to be identical, some differences were observed in sporulation and morphology of the parasite within the two populations. The sporocysts in anadromous populations were shorter and wider, and sporulation timing differed from that of landlocked fish. These differences may either be attributed to differences in the host type or to the sporulation environment. Lastly, alewives from landlocked populations were frequently co-infected with a second coccidian species in the posterior intestine, which occurred at a lower prevalence. This species, G

  7. Physiological Assessment of Wild and Hatchery Juvenile Salmonids : Final Report, 2003.

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, Donald A.; Beckman, Brian R.; Dickhoff, Walton W.

    2003-08-01

    It is generally held that hatchery-reared salmonids are of inferior quality and have lower smolt-to-adult survival compared to naturally-reared salmon. The overall objectives of the work performed under this contract were the following: (1) Characterize the physiology and development of naturally rearing juvenile salmonids to: (2) Allow for the design of effective rearing programs for producing wild-like smolts in supplementation and production hatchery programs. (3) Examine the relationship between growth rate and size on the physiology and migratory performance of fish reared in hatchery programs. (4) Examine the interaction of rearing temperature and feed rate on the growth and smoltification of salmon for use in producing a more wild-like smolt in hatchery programs.

  8. Stream network geomorphology mediates predicted vulnerability of anadromous fish habitat to hydrologic change in southeast Alaska.

    Science.gov (United States)

    Sloat, Matthew R; Reeves, Gordon H; Christiansen, Kelly R

    2017-02-01

    networks will hamper efforts to understand and mitigate the vulnerability of anadromous fish habitat to climate-induced hydrologic change. © 2016 John Wiley & Sons Ltd.

  9. PCB impairs smoltification and seawater performance in anadromous Arctic charr (Salvelinus alpinus)

    Science.gov (United States)

    Jorgensen, E.H.; Aas-Hansen, O.; Maule, A.G.; Strand, J.E.T.; Vijayan, M.M.

    2004-01-01

    The impacts of polychlorinated biphenyl (PCB) exposure on smoltification and subsequent seawater performance were investigated in hatchery-reared, anadromous Arctic charr (Salvelinus alpinus). The fish were subjected to a 2-month summer seawater residence, after which they were orally dosed with 0 (Control, C), 1 (Low Dose, LD) or 100 mg Aroclor 1254 kg−1 body mass (High Dose, HD) in November. They were then held in fresh water, without being fed (to mimic their natural overwintering in freshwater), until they had smolted in June the next year. The smolts were then transferred to seawater and fed to mimic their summer feeding residence in seawater, followed by a period without food in freshwater from August until maturation in October. Compared with C and LD charr, the HD charr had either a transient or a permanent reduction in plasma growth hormone, insulin-like growth factor-1, and thyroxin and triiodothyronine titers during the period of smoltification. These hormonal alterations in the HD charr corresponded with impaired hyposmoregulatory ability in May and June, as well as reduced growth rate and survival after transference to seawater. Consequently, fewer fish in the HD group matured in October compared to the other two treatments. The HD fish had a liver PCB concentration ranging between 14 and 42 mg kg−1 wet mass, whereas there were similar, and very low, liver PCB concentrations in LD and C fish throughout the smolting period. Our findings suggest that PCB might compromise mechanisms important for fitness in a fish species living in an extreme environment.

  10. Phenotypic and genetic characterization of Piscirickettsia salmonis from Chilean and Canadian salmonids

    OpenAIRE

    Otterlei, Alexander; Brevik, Øyvind J; Jensen, Daniel; Duesund, Henrik; Sommerset, Ingunn; Frost, Petter; Mendoza, Julio; McKenzie, Peter; Nylund, Are; Apablaza, Patricia

    2016-01-01

    Background The study presents the phenotypic and genetic characterization of selected P. salmonis isolates from Atlantic salmon and rainbow trout suffering from SRS (salmonid rickettsial septicemia) in Chile and in Canada. The phenotypic characterization of the P. salmonis isolates were based on growth on different agar media (including a newly developed medium), different growth temperatures, antibiotics susceptibility and biochemical tests. Results This is the first study differentiating Ch...

  11. Gas bubble trauma monitoring and research of juvenile salmonids. 1995 Annual report

    International Nuclear Information System (INIS)

    Maule, A.G.; Mesa, M.G.; Hans, K.M.

    1997-07-01

    This report describes laboratory and field monitoring studies of gas bubble trauma (GBT) in migrating juvenile salmonids in the Snake and Columbia rivers. The first chapter describes laboratory studies of the progression of GBT signs leading to mortality and the use of the signs for GBT assessment. The progression and severity of GBT signs in juvenile salmonids exposed to different levels of total dissolved gas (TDG) and temperatures was assessed and quantified. Next, the prevalence, severity, and individual variation of GBT signs was evaluated to attempt to relate them to mortality. Finally, methods for gill examination in fish exposed to high TDG were developed and evaluated. Primary findings were: (1) no single sign of GBT was clearly correlated with mortality, but many GBT signs progressively worsened; (2) both prevalence and severity of GBT signs in several tissues is necessary; (3) bubbles in the lateral line were the earliest sign of GBT, showed progressive worsening, and had low individual variation but may develop poorly during chronic exposures; (4) fin bubbles had high prevalence, progressively worsened, and may be a persistent sign of GBT; and (5) gill bubbles appear to be the proximate cause of death but may only be relevant at high TDG levels and are difficult to examine. Chapter Two describes monitoring results of juvenile salmonids for signs of GBT. Emigrating fish were collected and examined for bubbles in fins and lateral lines. Preliminary findings were: (1) few fish had signs of GBT, but prevalence and severity appeared to increase as fish migrated downstream; (2) there was no apparent correlation between GBT signs in the fins, lateral line, or gills; (3) prevalence and severity of GBT was suggestive of long-term, non-lethal exposure to relatively low level gas supersaturated water; and (4) it appeared that GBT was not a threat to migrating juvenile salmonids. 24 refs., 26 figs., 3 tabs

  12. Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps

    Science.gov (United States)

    Gosselin, Thierry; Normandeau, Eric; Lamothe, Manuel; Isabel, Nathalie; Audet, Céline; Bernatchez, Louis

    2016-01-01

    Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, ∼65 Ma, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for nonmodel species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Here, we generate a high-density linkage map (3,826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify corresponding chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo, Coregonus, and the nonduplicated sister group for the salmonids, Northern Pike Esox lucius for identifying post-duplicated homeologs. To facilitate this process, we developed MapComp to identify identical and proximate (i.e. nearby) markers between linkage maps using a reference genome of a related species as an intermediate, increasing the number of comparable markers between linkage maps by 5-fold. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/ PMID:28173098

  13. Comparing stream-specific to generalized temperature models to guide salmonid management in a changing climate

    Science.gov (United States)

    Andrew K. Carlson,; William W. Taylor,; Hartikainen, Kelsey M.; Dana M. Infante,; Beard, Douglas; Lynch, Abigail

    2017-01-01

    Global climate change is predicted to increase air and stream temperatures and alter thermal habitat suitability for growth and survival of coldwater fishes, including brook charr (Salvelinus fontinalis), brown trout (Salmo trutta), and rainbow trout (Oncorhynchus mykiss). In a changing climate, accurate stream temperature modeling is increasingly important for sustainable salmonid management throughout the world. However, finite resource availability (e.g. funding, personnel) drives a tradeoff between thermal model accuracy and efficiency (i.e. cost-effective applicability at management-relevant spatial extents). Using different projected climate change scenarios, we compared the accuracy and efficiency of stream-specific and generalized (i.e. region-specific) temperature models for coldwater salmonids within and outside the State of Michigan, USA, a region with long-term stream temperature data and productive coldwater fisheries. Projected stream temperature warming between 2016 and 2056 ranged from 0.1 to 3.8 °C in groundwater-dominated streams and 0.2–6.8 °C in surface-runoff dominated systems in the State of Michigan. Despite their generally lower accuracy in predicting exact stream temperatures, generalized models accurately projected salmonid thermal habitat suitability in 82% of groundwater-dominated streams, including those with brook charr (80% accuracy), brown trout (89% accuracy), and rainbow trout (75% accuracy). In contrast, generalized models predicted thermal habitat suitability in runoff-dominated streams with much lower accuracy (54%). These results suggest that, amidst climate change and constraints in resource availability, generalized models are appropriate to forecast thermal conditions in groundwater-dominated streams within and outside Michigan and inform regional-level salmonid management strategies that are practical for coldwater fisheries managers, policy makers, and the public. We recommend fisheries professionals reserve resource

  14. Acoustic Telemetry Evaluation of Juvenile Salmonid Passage and Survival at John Day Dam with Emphasis on the Prototype Surface Flow Outlet, 2008

    Energy Technology Data Exchange (ETDEWEB)

    Weiland, Mark A.; Ploskey, Gene R.; Hughes, James S.; Deng, Zhiqun; Fu, Tao; Monter, Tyrell J.; Johnson, Gary E.; Khan, Fenton; Wilberding, Matthew C.; Cushing, Aaron W.; Zimmerman, Shon A.; Faber, Derrek M.; Durham, Robin E.; Townsend, Richard L.; Skalski, John R.; Kim, Jina; Fischer, Eric S.; Meyer, Matthew M.

    2009-12-01

    The main purpose of the study was to evaluate the performance of Top Spill Weirs installed at two spillbays at John Day Dam and evaluate the effectiveness of these surface flow outlets at attracting juvenile salmon away from the powerhouse and reducing turbine passage. The Juvenile Salmonid Acoustic Telemetry System (JSATS) was used to estimate survival of juvenile salmonids passing the dam and also for calculating performance metrics used to evaluate the efficiency and effectiveness of the dam at passing juvenile salmonids.

  15. Migratory salmonid redd habitat characteristics in the Salmon River, New York

    Science.gov (United States)

    Johnson, James H.; Nack, Christopher C.; McKenna, James E.

    2010-01-01

    Non-native migratory salmonids ascend tributaries to spawn in all the Great Lakes. In Lake Ontario, these species include Chinook salmon (Oncorhynchus tshawytscha), coho salmon (O. kisutch), steelhead (O. mykiss), and brown trout (Salmo trutta). Although successful natural reproduction has been documented for many of these species, little research has been conducted on their spawning habitat. We examined the spawning habitat of these four species in the Salmon River, New York. Differences in fish size among the species were significantly correlated with spawning site selection. In the Salmon River, the larger species spawned in deeper areas with larger size substrate and made the largest redds. Discriminant function analysis correctly classified redds by species 64–100% of the time. The size of substrate materials below Lighthouse Hill Dam is within the preferred ranges for spawning for these four species indicating that river armoring has not negatively impacted salmonid production. Intra-specific and inter-specific competition for spawning sites may influence redd site selection for smaller salmonids and could be an impediment for Atlantic salmon (S. salar) restoration.

  16. Ecology of Juvenile Salmonids in Shallow Tidal Freshwater Habitats in the Vicinity of the Sandy River Delta, Lower Columbia River, 2007 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Sobocinski, Kathryn; Johnson, Gary; Sather, Nichole [Pacific Northwest National Laboratory

    2008-03-17

    This document is the first annual report for the study titled 'Ecology of Juvenile Salmonids in Shallow Tidal Freshwater Habitats in the Vicinity of the Sandy River Delta in the Lower Columbia River'. Hereafter, we refer to this research as the Tidal Freshwater Monitoring (TFM) Study. The study is part of the research, monitoring, and evaluation effort developed by the Action Agencies (Bonneville Power Administration, U.S. Army Corps of Engineers, U.S. Bureau of Reclamation) in response to obligations arising from the Endangered Species Act as a result of operation of the Federal Columbia River Power System (FCRPS). The project is performed under the auspices of the Northwest Power and Conservation Council's Columbia Basin Fish and Wildlife Program. The goal of the 2007-2009 Tidal Freshwater Monitoring Study is to answer the following questions: In what types of habitats within the tidal freshwater area of the lower Columbia River and estuary (LCRE; Figure 1) are yearling and subyearling salmonids found, when are they present, and under what environmental conditions?1 And, what is the ecological importance2 of shallow (0-5 m) tidal freshwater habitats to the recovery of Upper Columbia River spring Chinook salmon and steelhead and Snake River fall Chinook salmon? Research in 2007 focused mainly on the first question, with fish stock identification data providing some indication of Chinook salmon presence at the variety of habitat types sampled. The objectives and sub-objectives for the 2007 study were as follows: (1) Habitat and Fish Community Characteristics-Provide basic data on habitat and fish community characteristics for yearling and subyearling salmonids at selected sites in the tidal freshwater reach in the vicinity of the Sandy River delta. (1a) Characterize vegetation assemblage percent cover, conventional water quality, substrate composition, and beach slope at each of six sampling sites in various tidal freshwater habitat types. (1b

  17. (Dahomey) Basin

    African Journals Online (AJOL)

    Timothy Ademakinwa

    13 km maximum width in the onshore at the basin axis along Nigerian and Republic of Benin boundary. This narrows westwards and eastwards to about 5 km (Coker and Ejedawe, 1987; Coker,. 2002). Detailed geology, evolution, stratigraphy and hydrocarbon occurrence of the basin have been described by Jones and ...

  18. Evaluation of stream flow effects on smolt survival in the Yakima River Basin, Washington, 2012-2014

    Science.gov (United States)

    Courter, Ian; Garrison, Tommy; Kock, Tobias J.; Perry, Russell W.

    2015-01-01

    The influence of stream flow on survival of emigrating juvenile (smolts) Pacific salmon Oncorhynchus spp. and steelhead trout O. mykiss is of key management interest. However, few studies have quantified flow effects on smolt migration survival, and available information does not indicate a consistent flow-survival relationship within the typical range of flows under management control. It is hypothesized that smolt migration and dam passage survival are positively correlated with stream flow because higher flows increase migration rates, potentially reducing exposure to predation, and reduce delays in reservoirs. However, available empirical data are somewhat equivocal concerning the influence of flow on smolt survival and the underlying mechanisms driving this relationship. Stream flow effects on survival of emigrating anadromous salmonids in the Yakima Basin have concerned water users and fisheries managers for over 20 years, and previous studies do not provide sufficient information at the resolution necessary to inform water operations, which typically occur on a small spatiotemporal scale. Using a series of controlled flow releases from 2012-2014, combined with radio telemetry, we quantified the relationship between flow and smolt survival from Roza Dam 208 km downstream to the Yakima River mouth, as well as for specific routes of passage at Roza Dam. A novel multistate mark-recapture model accounted for weekly variation in flow conditions experienced by radio-tagged fish. Groups of fish were captured and radio-tagged at Roza Dam and released at two locations, upstream at the Big Pines Campground (river kilometer [rkm] 211) and downstream in the Roza Dam tailrace (rkm 208). A total of 904 hatchery-origin yearling Chinook salmon O. tshawytscha were captured in the Roza Dam fish bypass, radio-tagged and released upstream of Roza Dam. Two hundred thirty seven fish were released in the tailrace of Roza Dam. Fish released in the tailrace of Roza Dam were tagged

  19. Development of an Index to Bird Predation of Juvenile Salmonids within the Yakima River, 1999 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Gassley, James M.; Grue, Christian E. (University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA)

    2001-10-01

    Avian predation of fish is suspected to contribute to the loss of juvenile spring chinook salmon in the Yakima Basin, potentially constraining natural production. In 1997 and 1998, the Yakama/Klickitat Fisheries Project (YKFP) and the Washington Department of Fish and Wildlife (WDFW)--whose goal is to increase natural production historically present within the Yakima River--initiated investigations to assess the feasibility of developing an index to avian predation of juvenile salmon within the river. This research--conducted by Dr. Steve Mathews and David Phinney of the University of Washington--confirmed that Ring-billed Gulls and Common Mergansers were the primary avian predators of juvenile salmon, and that under certain conditions could significantly impact migrating smolt populations. Beginning in 1999, the Washington Cooperative Fish and Wildlife Research Unit was asked by the YKFP and the WDFW to continue development of avian consumption indices. Monitoring methods developed by Mathews and Phinney were adopted (with modifications) and monitoring of impacts to juvenile salmon along river reaches and at areas of high predator/prey concentrations (colloquially referred to as ''hotspots'') continued. New efforts initiated in 1999 included piscivorous bird surveys at smolt acclimation sites operated by the Yakama Nation, monitoring of the North Fork Teanaway River for changes in avian piscivore abundance associated with the installation of the Jack Creek acclimation facility, and aerial surveys seeking to identify avian piscivores along the length of the Yakima River. In 1999, piscivorous birds were counted from river banks at hotspots and from a raft or drift boat along river reaches. Consumption by gulls was based on direct observations of foraging success and modeled abundance; consumption by Common Mergansers (which forage underwater) was estimated using published dietary requirements and modeled abundance. A second-order polynomial

  20. Anadromous char as an alternate food choice to marine animals: A synthesis of Hg concentrations, population features and other influencing factors

    Energy Technology Data Exchange (ETDEWEB)

    Evans, Marlene S., E-mail: marlene.evans@ec.gc.ca [Environment Canada, Water Science and Technology Directorate, 11 Innovation Blvd., Saskatoon SK S7N 3H5 (Canada); Muir, Derek C.G. [Environment Canada, Water Science and Technology Directorate, 867 Lakeshore Rd., Burlington, ON L7R 4A6 (Canada); Keating, Jonathan [Environment Canada, Water Science and Technology Directorate, 11 Innovation Blvd., Saskatoon SK S7N 3H5 (Canada); Wang, Xiaowa [Environment Canada, Water Science and Technology Directorate, 867 Lakeshore Rd., Burlington, ON L7R 4A6 (Canada)

    2015-03-15

    This study was conducted to confirm sporadic measurements made over the late 1970s to the early 1990s which determined that mercury (Hg) concentrations were low in anadromous char across Arctic and subarctic Canada including northern Québec and Labrador. Over 2004–2013, anadromous char populations across northern Canada were investigated at 20 sites for Hg concentrations and life history characteristics. Hg concentrations were extremely low in anadromous char muscle, typically < 0.05 μg/g (wet weight) and, at each location, generally increased with fish length, age and nitrogen isotope (δ{sup 15}N) ratio and decreased with condition factor and %lipid; correlations with carbon isotope (δ{sup 13}C) ratio were inconsistent. Location and year were significant variables influencing Hg concentrations over the study area; longitude and latitude also were significant influencing variables. Char length, weight, age, condition factor and lipid content explained additional variance. A tendency towards higher Hg concentrations with increasing latitude may be partially related to decreasing growth of char towards the north. However, Hg concentrations in char were positively correlated with growth rates suggesting that Hg concentrations in char also were higher in the more productive study areas, including to the west where mainland riverine inputs of terrestrial carbon, nutrients, and Hg were greater. The data base for assessing time trends in char was limited by the small number of years investigated at most locations, variable fish size across years, small sample size, etc. Where temporal trends were detected, they were of increase on the long term (1970s, 1980s or early 1990s to the present) but of decrease on the short term (early 2000s to present) with Nain (Labrador) showing the converse pattern. Higher Hg concentrations were also related to lower condition factor and cooler springs. Hg concentrations in anadromous char are compared with other terrestrial, aquatic

  1. Anadromous char as an alternate food choice to marine animals: A synthesis of Hg concentrations, population features and other influencing factors

    International Nuclear Information System (INIS)

    Evans, Marlene S.; Muir, Derek C.G.; Keating, Jonathan; Wang, Xiaowa

    2015-01-01

    This study was conducted to confirm sporadic measurements made over the late 1970s to the early 1990s which determined that mercury (Hg) concentrations were low in anadromous char across Arctic and subarctic Canada including northern Québec and Labrador. Over 2004–2013, anadromous char populations across northern Canada were investigated at 20 sites for Hg concentrations and life history characteristics. Hg concentrations were extremely low in anadromous char muscle, typically < 0.05 μg/g (wet weight) and, at each location, generally increased with fish length, age and nitrogen isotope (δ 15 N) ratio and decreased with condition factor and %lipid; correlations with carbon isotope (δ 13 C) ratio were inconsistent. Location and year were significant variables influencing Hg concentrations over the study area; longitude and latitude also were significant influencing variables. Char length, weight, age, condition factor and lipid content explained additional variance. A tendency towards higher Hg concentrations with increasing latitude may be partially related to decreasing growth of char towards the north. However, Hg concentrations in char were positively correlated with growth rates suggesting that Hg concentrations in char also were higher in the more productive study areas, including to the west where mainland riverine inputs of terrestrial carbon, nutrients, and Hg were greater. The data base for assessing time trends in char was limited by the small number of years investigated at most locations, variable fish size across years, small sample size, etc. Where temporal trends were detected, they were of increase on the long term (1970s, 1980s or early 1990s to the present) but of decrease on the short term (early 2000s to present) with Nain (Labrador) showing the converse pattern. Higher Hg concentrations were also related to lower condition factor and cooler springs. Hg concentrations in anadromous char are compared with other terrestrial, aquatic and

  2. Development of a systemwide predator control program: Stepwise implementation of a predation index, predator control fisheries, and evaluation plan in the Columbia River Basin. Section 1: Implementation. Annual report 1994

    International Nuclear Information System (INIS)

    Willis, C.F.; Young, F.R.

    1995-09-01

    The authors report the results from the forth year of a basinwide program to harvest northern squawfish (Ptychocheilus oregonensis) in an effort to reduce mortality due to northern squawfish predation on juvenile salmonids during their emigration from natal streams to the ocean. Earlier work in the Columbia River Basin suggested predation by northern squawfish on juvenile salmonids may account for most of the 10--20% mortality juvenile salmonids experience in each of eight Columbia and Snake River reservoirs. Modeling simulations based on work in John Day Reservoir from 1982 through 1988 indicated it is not necessary to eradicate northern squawfish to substantially reduce predation-caused mortality of juvenile salmonids. Instead, if northern squawfish were exploited at a 10--20% rate, reductions in numbers of larger, older fish resulting in restructuring of their population could reduce their predation on juvenile salmonids by 50% or more. Consequently, the authors designed and tested a sport-reward angling fishery and a commercial longline fishery in the John Day pool in 1990. They also conducted an angling fishery in areas inaccessible to the public at four dams on the mainstem Columbia River and at Ice Harbor Dam on the Snake River. Based on the success of these limited efforts, they implemented three test fisheries on a multi-pool, or systemwide, scale in 1991--a tribal longline fishery above Bonneville Dam, a sport-reward fishery, and a dam-angling fishery

  3. Anadromous char as an alternate food choice to marine animals: a synthesis of Hg concentrations, population features and other influencing factors.

    Science.gov (United States)

    Evans, Marlene S; Muir, Derek C G; Keating, Jonathan; Wang, Xiaowa

    2015-03-15

    This study was conducted to confirm sporadic measurements made over the late 1970s to the early 1990 s which determined that mercury (Hg) concentrations were low in anadromous char across Arctic and subarctic Canada including northern Québec and Labrador. Over 2004-2013, anadromous char populations across northern Canada were investigated at 20 sites for Hg concentrations and life history characteristics. Hg concentrations were extremely low in anadromous char muscle, typically Hg concentrations over the study area; longitude and latitude also were significant influencing variables. Char length, weight, age, condition factor and lipid content explained additional variance. A tendency towards higher Hg concentrations with increasing latitude may be partially related to decreasing growth of char towards the north. However, Hg concentrations in char were positively correlated with growth rates suggesting that Hg concentrations in char also were higher in the more productive study areas, including to the west where mainland riverine inputs of terrestrial carbon, nutrients, and Hg were greater. The data base for assessing time trends in char was limited by the small number of years investigated at most locations, variable fish size across years, small sample size, etc. Where temporal trends were detected, they were of increase on the long term (1970s, 1980s or early 1990 s to the present) but of decrease on the short term (early 2000s to present) with Nain (Labrador) showing the converse pattern. Higher Hg concentrations were also related to lower condition factor and cooler springs. Hg concentrations in anadromous char are compared with other terrestrial, aquatic and marine vertebrates in traditional diets. The known information on anadromous char is reviewed including population features, habitat, and harvests. Future Hg trend monitoring should focus on specific locations and harvest areas within these areas to better assess trends and influencing factors. Crown

  4. Summary report for Bureau of Fisheries stream habitat surveys: Cowlitz River basin. Final report 1934--1942

    International Nuclear Information System (INIS)

    McIntosh, B.A.; Clark, S.E.; Sedell, J.R.

    1995-07-01

    This document contains summary reports of stream habitat surveys, conducted in the Cowlitz River basin, by the Bureau of Fisheries (BOF, now National Marine Fisheries Service) from 1938--1942. These surveys were part of a larger project to survey streams in the Columbia River basin that provided, or had provided, spawning and rearing habitat for salmon and steelhead. The purpose of the survey was to determine the present condition of the various tributaries with respect to their availability and usefulness for the migration, breeding, and rearing of migratory fishes. Current estimates of the loss of anadromous fish habitat in the Columbia River Basin are based on a series of reports published from 1949--1952 by the US Fish and Wildlife Service

  5. Novel RAD sequence data reveal a lack of genomic divergence between dietary ecotypes in a landlocked salmonid population

    Science.gov (United States)

    Limborg, Morten T.; Larson, Wesley; Shedd, Kyle; Seeb, Lisa W.; Seeb, James E.

    2017-01-01

    Preservation of heritable ecological diversity within species and populations is a key challenge for managing natural resources and wild populations. Salmonid fish are iconic and socio-economically important species for commercial, aquaculture, and recreational fisheries across the globe. Many salmonids are known to exhibit ecological divergence within species, including distinct feeding ecotypes within the same lakes. Here we used 5559 SNPs, derived from RAD sequencing, to perform population genetic comparisons between two dietary ecotypes of sockeye salmon (Oncorhynchus nerka) in Jo-Jo Lake, Alaska (USA). We tested the standing hypothesis that these two ecotypes are currently diverging as a result of adaptation to distinct dietary niches; results support earlier conclusions of a single panmictic population. The RAD sequence data revealed 40 new SNPs not previously detected in the species, and our sequence data can be used in future studies of ecotypic diversity in salmonid species.

  6. Assess Current and Potential Salmonid Production in Rattlesnake Creek Associated with Restoration Efforts; Underwood Conservation District, Annual Report 2002-2003.

    Energy Technology Data Exchange (ETDEWEB)

    White, Jim

    2004-02-01

    This project addresses existing habitat conditions, fish population status, and restoration priority sites within the Rattlesnake Creek watershed, a sub-basin of the White Salmon River. Our partners in this project are the United States Geological Service (USGS), and the Yakama Indian Nation (YIN). Underwood Conservation District (UCD) is involved in the project via accomplishment of water quality monitoring, sampling for stable isotopes, and characterization of the watershed geomorphology. These work items are part of an effort to characterize the stream and riparian habitat conditions in Rattlesnake Creek, to help guide habitat and fish restoration work. Water chemistry and temperature information is being collected both on Rattlesnake Creek, and on other tributaries and the main stem of the White Salmon River. Information on the entire system enables us to compare results obtained from Rattlesnake Creek with the rest of the White Salmon system. Water chemistry and temperature data have been collected in a manner that is comparable with data gathered in previous years. The results from data gathered in the 2001-2002 performance period are reported in appendix A at the end of this 2002-2003 report. Additional work being conducted as part of this study includes; an estimate of salmonid population abundance (YIN and USGS); a determination of fish species composition, distribution, and life history (YIN and USGS), and a determination of existing kinds, distribution, and severity of fish diseases (YIN and USGS). The overall objective is to utilize the above information to prioritize restoration efforts in Rattlesnake Creek.

  7. Migrational Characteristics, Biological Observations, and Relative Survival of Juvenile Salmonids Entering the Columbia River Estuary, 1966-1983, 1985 Final Report of Research.

    Energy Technology Data Exchange (ETDEWEB)

    Dawley, Earl M.

    1986-04-01

    Natural runs of salmonids in the Columbia River basin have decreased as a result of hydroelectric-dam development, poor land- and forest-management, and over-fishing. This has necessitated increased salmon culture to assure adequate numbers of returning adults. Hatchery procedures and facilities are continually being modified to improve both the efficiency of production and the quality of juveniles produced. Initial efforts to evaluate changes in hatchery procedures were dependent upon adult contributions to the fishery and returns to the hatchery. Procedures were developed for sampling juvenile salmon and steelhead entering the Columbia River estuary and ocean plume. The sampling of hatchery fish at the terminus of their freshwater migration assisted in evaluating hatchery production techniques and identifying migrational or behavioral characteristics that influence survival to and through the estuary. The sampling program attempted to estimate survival of different stocks and define various aspects of migratory behavior in a large river, with flows during the spring freshet from 4 to 17 thousand cubic meters per second (m/sup 3//second).

  8. Can biosecurity and local network properties predict pathogen species richness in the salmonid industry?

    Science.gov (United States)

    Yatabe, Tadaishi; More, Simon J; Geoghegan, Fiona; McManus, Catherine; Hill, Ashley E; Martínez-López, Beatriz

    2018-01-01

    Salmonid farming in Ireland is mostly organic, which implies limited disease treatment options. This highlights the importance of biosecurity for preventing the introduction and spread of infectious agents. Similarly, the effect of local network properties on infection spread processes has rarely been evaluated. In this paper, we characterized the biosecurity of salmonid farms in Ireland using a survey, and then developed a score for benchmarking the disease risk of salmonid farms. The usefulness and validity of this score, together with farm indegree (dichotomized as ≤ 1 or > 1), were assessed through generalized Poisson regression models, in which the modeled outcome was pathogen richness, defined here as the number of different diseases affecting a farm during a year. Seawater salmon (SW salmon) farms had the highest biosecurity scores with a median (interquartile range) of 82.3 (5.4), followed by freshwater salmon (FW salmon) with 75.2 (8.2), and freshwater trout (FW trout) farms with 74.8 (4.5). For FW salmon and trout farms, the top ranked model (in terms of leave-one-out information criteria, looic) was the null model (looic = 46.1). For SW salmon farms, the best ranking model was the full model with both predictors and their interaction (looic = 33.3). Farms with a higher biosecurity score were associated with lower pathogen richness, and farms with indegree > 1 (i.e. more than one fish supplier) were associated with increased pathogen richness. The effect of the interaction between these variables was also important, showing an antagonistic effect. This would indicate that biosecurity effectiveness is achieved through a broader perspective on the subject, which includes a minimization in the number of suppliers and hence in the possibilities for infection to enter a farm. The work presented here could be used to elaborate indicators of a farm's disease risk based on its biosecurity score and indegree, to inform risk-based disease surveillance and control

  9. Predation on Chinook Salmon parr by hatchery salmonids and Fallfish in the Salmon River, New York

    Science.gov (United States)

    Johnson, James H.; Nack, Christopher C.; Chalupnicki, Marc; Abbett, Ross; McKenna, James E.

    2016-01-01

    Naturally reproduced Chinook Salmon Oncorhynchus tshawytscha contribute substantially to the fishery in Lake Ontario. The Salmon River, a Lake Ontario tributary in New York, produces the largest numbers of naturally spawned Chinook Salmon, with parr abundance in the river often exceeding 10 million. In the spring of each year, large numbers of hatchery salmonid yearlings—potential predators of Chinook Salmon parr—are released into the Salmon River by the New York State Department of Environmental Conservation. We sought to examine predation on Chinook Salmon parr in the Salmon River during May and June prior to out-migration. Over the 4 years examined (2009–2012), annual consumption of Chinook Salmon parr by hatchery-released yearling steelhead O. mykiss and Coho Salmon O. kisutch ranged from 1.5 to 3.3 million and from 0.4 to 2.1 million, respectively. In 2009, Fallfish Semotilus corporalis were estimated to consume 2.9 million Chinook Salmon parr. Predation was higher in May, when the average TL of Chinook Salmon parr was 44.5 mm, than in June. Fallfish were also important predators of naturally reproduced steelhead subyearlings, consuming an estimated 800,000 steelhead in 2009. Hatchery-released yearling salmonids consumed 13.8–15.3% of the Chinook Salmon parr that were estimated to be present in the Salmon River during 2010–2012. Earlier releases of hatchery salmonid yearlings could reduce the riverine consumption of Chinook Salmon parr by facilitating the out-migration of yearlings prior to Chinook Salmon emergence.

  10. Gas Bubble Disease Monitoring and Research of Juvenile Salmonids : Annual Report 1996.

    Energy Technology Data Exchange (ETDEWEB)

    Maule, Alec G.; Beeman, John W.; Hans, Karen M.; Mesa, M.G.; Haner, P.; Warren, J.J. [Geological Survey, Cook, WA (United States). Columbia River Research Lab.

    1997-10-01

    This document describes the project activities 1996--1997 contract year. This report is composed of three chapters which contain data and analyses of the three main elements of the project: field research to determine the vertical distribution of migrating juvenile salmonids, monitoring of juvenile migrants at dams on the Snake and Columbia rivers, and laboratory experiments to describe the progression of gas bubble disease signs leading to mortality. The major findings described in this report are: A miniature pressure-sensitive radio transmitter was found to be accurate and precise and, after compensation for water temperature, can be used to determine the depth of tagged-fish to within 0.32 m of the true depth (Chapter 1). Preliminary data from very few fish suggest that depth protects migrating juvenile steelhead from total dissolved gas supersaturation (Chapter 1). As in 1995, few fish had any signs of gas bubble disease, but it appeared that prevalence and severity increased as fish migrated downstream and in response to changing gas supersaturation (Chapter 2). It appeared to gas bubble disease was not a threat to migrating juvenile salmonids when total dissolved gas supersaturation was < 120% (Chapter 2). Laboratory studies suggest that external examinations are appropriate for determining the severity of gas bubble disease in juvenile salmonids (Chapter 3). The authors developed a new method for examining gill arches for intravascular bubbles by clamping the ventral aorta to reduce bleeding when arches were removed (Chapter 3). Despite an outbreak of bacterial kidney disease in the experimental fish, the data indicate that gas bubble disease is a progressive trauma that can be monitored (Chapter 3).

  11. Microhabitat preference of Anisakis simplex in three salmonid species

    DEFF Research Database (Denmark)

    Bahlool, Qusay Zuhair Mohammad; Skovgaard, Alf; Kania, Per Walter

    2012-01-01

    . simplex larvae were attached to the digestive tract (stomach, pyloric caeca, intestine), while the majority of larvae found in rainbow trout were located between the pyloric caeca. In Baltic salmon, nematodes were dispersed in and on spleen, head kidney, liver, swim bladder and musculature. Encapsulation...... and inflammatory cellular reactions differed accordingly. Histopathological and immunohistochemical studies using monoclonal antibodies raised against salmonid IgM, CD8 and MHCII were performed to detect the presence of immune cells around the infecting nematodes. None of the three fish species showed positive...

  12. Columbia River Basin Fish and Wildlife Program Work Plan for Fiscal Year 1988.

    Energy Technology Data Exchange (ETDEWEB)

    United States. Bonneville Power Administration; Northwest Power Planning Council (U.S.); Columbia Basin Fish and Wildlife Authority

    1987-10-01

    The FY 1988 Columbia River Basin Fish and Wildlife Program Work Plan (Work Plan) presents Bonneville Power Administration's plans for implementing the Columbia River Basin Fish and Wildlife Program (Program) in FY 1988. The Work Plan focuses on individual Action Items found in the amended Program for which Bonneville Power Administration (BPA) has determined it has authority and responsibility to implement. The FY 1988 Work Plan emphasizes continuation of 95 ongoing projects, most of which involve protection, mitigation, or enhancement of anadromous fishery resources. These continuing activities are summarized briefly by Program area: (1) mainstem passage; (2) artificial propagation; (3) natural propagation; (4) resident fish and wildlife; and (5) planning activities.

  13. Grande Ronde Basin Supplementation Program; Lostine River, 2000 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Onjukka, Sam T. (Oregon Department of Fish and Wildlife, Portland, OR); Harbeck, Jim (Nez Perce Tribe, Department of Fisheries Resource Management, Enterprise, OR)

    2003-03-01

    The Northwest Power Planning Council (NPPC) identified supplementation as a high priority to achieve its goal of increasing runs of anadromous fish in the Columbia Basin. Supplementation activities in the Lostine River and associated monitoring and evaluation conducted by the Nez Perce Tribe relate directly to the needs addressed in the Columbia River Basin Fish and Wildlife Program (NPPC 1994). Measure 7.4L.1 of the Program mandates that appropriate research accompany any proposed supplementation. In addition, measure 7.3B.2 of the Program stresses the need for evaluating supplementation projects to assess their ability to increase production. Finally, Section 7.4D.3 encourages the study of hatchery rearing and release strategies to improve survival and adaptation of cultured fish. In 1997, Oregon Department of Fisheries and Wildlife (ODFW) requested a modification of Permit 1011 to allow the take of adult spring chinook salmon. In 1998, the Nez Perce Tribe also requested a permit specific to activities on Lostine River. The permit was issued in 2000. A special condition in the permits required the development of a long term management plan for the spring chinook salmon of the Grande Ronde Basin. The Nez Perce Tribe, ODFW, and the Confederated Tribes of the Umatilla Indian Reservation (CTUIR) completed a formal long range plan entitled ''Grande Ronde Basin Endemic Spring Chinook Salmon Supplementation Program''. The program proposes to increase the survival of spring chinook salmon in the Grand Ronde Basin through hatchery intervention. Adult salmon from the Lostine River, Catherine Creek, and the Upper Grande Ronde River are used for a conventional supplementation program in the basin. The Nez Perce program currently operates under the ESA Section 10 Permit 1149.

  14. Grande Ronde Basin Supplementation Program; Lostine River, 2001 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Onjukka, Sam T. (Oregon Department of Fish and Wildlife, Portland, OR); Harbeck, Jim (Nez Perce Tribe, Department of Fisheries Resource Management, Enterprise, OR)

    2003-03-01

    The Northwest Power Planning Council (NPPC) identified supplementation as a high priority to achieve its goal of increasing runs of anadromous fish in the Columbia Basin. Supplementation activities in the Lostine River and associated monitoring and evaluation conducted by the Nez Perce Tribe relate directly to the needs addressed in the Columbia River Basin Fish and Wildlife Program (NPPC 1994). Measure 7.4L.1 of the Program mandates that appropriate research accompany any proposed supplementation. In addition, measure 7.3B.2 of the Program stresses the need for evaluating supplementation projects to assess their ability to increase production. Finally, Section 7.4D.3 encourages the study of hatchery rearing and release strategies to improve survival and adaptation of cultured fish. In 1997, Oregon Department of Fisheries and Wildlife (ODFW) requested a modification of Permit 1011 to allow the take of adult spring chinook salmon. In 1998, the Nez Perce Tribe also requested a permit specific to activities on Lostine River. The permit was issued in 2000. A special condition in the permits required the development of a long term management plan for the spring chinook salmon of the Grande Ronde Basin. The Nez Perce Tribe, ODFW, and the Confederated Tribes of the Umatilla Indian Reservation (CTUIR) completed a formal long range plan entitled ''Grande Ronde Basin Endemic Spring Chinook Salmon Supplementation Program''. The program proposes to increase the survival of spring chinook salmon in the Grand Ronde Basin through hatchery intervention. Adult salmon from the Lostine River, Catherine Creek, and the Upper Grande Ronde River are used for a conventional supplementation program in the basin. The Nez Perce program currently operates under the ESA Section 10 Permit 1149.

  15. Mature male parr contribution to the effective size of an anadromous Atlantic salmon (Salmo salar) population over 30 years.

    Science.gov (United States)

    Johnstone, Devon L; O'Connell, Michael F; Palstra, Friso P; Ruzzante, Daniel E

    2013-05-01

    We describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered threatened (COSEWIC 2010). We examined the genetic variability (13 microsatellite loci) in 869 out-migrating smolt and post-spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. We estimated the annual effective number of breeders (Nb) and the generational effective population size (Ne) through genetic methods and demographically using the adult sex ratio. Comparisons between genetic and demographic estimates show that the adult spawners inadequately explain the observed Ne estimates, suggesting that mature male parr are significantly increasing Nb and Ne over the study period. Spawning as parr appears to be a viable and important strategy in the near absence of adult males. © 2013 Blackwell Publishing Ltd.

  16. A social–ecological perspective for riverscape management in the Columbia River Basin

    Science.gov (United States)

    Hand, Brian K.; Flint, Courtney G.; Frissell, Chris A.; Muhlfeld, Clint C.; Devlin, Shawn P.; Kennedy, Brian P.; Crabtree, Robert L.; McKee, W. Arthur; Luikart, Gordon; Stanford, Jack A.

    2018-01-01

    Riverscapes are complex, landscape-scale mosaics of connected river and stream habitats embedded in diverse ecological and socioeconomic settings. Social–ecological interactions among stakeholders often complicate natural-resource conservation and management of riverscapes. The management challenges posed by the conservation and restoration of wild salmonid populations in the Columbia River Basin (CRB) of western North America are one such example. Because of their ecological, cultural, and socioeconomic importance, salmonids present a complex management landscape due to interacting environmental factors (eg climate change, invasive species) as well as socioeconomic and political factors (eg dams, hatcheries, land-use change, transboundary agreements). Many of the problems in the CRB can be linked to social–ecological interactions occurring within integrated ecological, human–social, and regional–climatic spheres. Future management and conservation of salmonid populations therefore depends on how well the issues are understood and whether they can be resolved through effective communication and collaboration among ecologists, social scientists, stakeholders, and policy makers.

  17. The phylogeography of salmonid proliferative kidney disease in Europe and North America.

    Science.gov (United States)

    Henderson, Matthew; Okamura, Beth

    2004-08-22

    Salmonid proliferative kidney disease (PKD) is caused by the myxozoan Tetracapsuloides bryosalmonae. Given the serious and apparently growing impact of PKD on farmed and wild salmonids, we undertook a phylogeographic study to gain insights into the history of genealogical lineages of T. bryosalmonae in Europe and North America, and to determine if the global expansion of rainbow trout farming has spread the disease. Phylogenetic analyses of internal transcribed spacer 1 sequences revealed a clade composed of all North American sequences plus a subset of Italian and French sequences. High genetic diversity in North America and the absence of genotypes diagnostic of the North American clade in the rest of Europe imply that southern Europe was colonized by immigration from North America; however, sequence divergence suggests that this colonization substantially pre-dated fisheries activities. Furthermore, the lack of southern European lineages in the rest of Europe, despite widespread rainbow trout farming, indicates that T. bryosalmonae is not transported through fisheries activities. This result strikingly contrasts with the commonness of fisheries-related introductions of other pathogens and parasites and indicates that fishes may be dead-end hosts. Our results also demonstrate that European strains of T. bryosalmonae infect and induce PKD in rainbow trout introduced to Europe.

  18. The waterfall paradox: How knickpoints disconnect hillslope and channel processes, isolating salmonid populations in ideal habitats

    Science.gov (United States)

    May, Christine; Roering, Joshua J.; Snow, Kyle; Griswold, Kitty; Gresswell, Robert E.

    2017-01-01

    Waterfalls create barriers to fish migration, yet hundreds of isolated salmonid populations exist above barriers and have persisted for thousands of years in steep mountainous terrain. Ecological theory indicates that small isolated populations in disturbance-prone landscapes are at greatest risk of extirpation because immigration and recolonization are not possible. On the contrary, many above-barrier populations are currently thriving while their downstream counterparts are dwindling. This quandary led us to explore geomorphic knickpoints as a mechanism for disconnecting hillslope and channel processes by limiting channel incision and decreasing the pace of base-level lowering. Using LiDAR from the Oregon Coast Range, we found gentler channel gradients, wider valleys, lower gradient hillslopes, and less shallow landslide potential in an above-barrier catchment compared to a neighboring catchment devoid of persistent knickpoints. Based on this unique geomorphic template, above-barrier channel networks are less prone to debris flows and other episodic sediment fluxes. These above-barrier catchments also have greater resiliency to flooding, owing to wider valleys with greater floodplain connectivity. Habitat preference models further indicate that salmonid habitat is present in greater quantity and quality in these above-barrier networks. Therefore the paradox of the persistence of small isolated fish populations may be facilitated by a geomorphic mechanism that both limits their connectivity to larger fish populations yet dampens the effect of disturbance by decreasing connections between hillslope and channel processes above geomorphic knickpoints.

  19. Functional characterization of water transport and cellular localization of three aquaporin paralogs in the salmonid intestine

    DEFF Research Database (Denmark)

    Madsen, Steffen S; Olesen, Jesper H; Bedal, Konstanze

    2011-01-01

    Intestinal water absorption is greatly enhanced in salmonids upon acclimation from freshwater (FW) to seawater (SW); however, the molecular mechanism for water transport is unknown. We conducted a pharmacological characterization of water absorption in the rainbow trout intestine along with an in......Intestinal water absorption is greatly enhanced in salmonids upon acclimation from freshwater (FW) to seawater (SW); however, the molecular mechanism for water transport is unknown. We conducted a pharmacological characterization of water absorption in the rainbow trout intestine along...... with an investigation of the distribution and cellular localization of three aquaporins (Aqp1aa, -1ab, and -8ab) in pyloric caeca, middle (M), and posterior (P) intestine of the Atlantic salmon. In vitro iso-osmotic water absorption (J(v)) was higher in SW than FW-trout and was inhibited by (mmol L(-1)): 0.1 KCN (41......%), 0.1 ouabain (72%), and 0.1 bumetanide (82%) suggesting that active transport, Na(+), K(+)-ATPase and Na(+), K(+), 2Cl(-)-co-transport are involved in establishing the driving gradient for water transport. J(v) was also inhibited by 1 mmol L(-1) HgCl(2), serosally (23% in M and 44% in P), mucosally...

  20. Spatial and temporal heterogeneity of infectious hematopoietic necrosis virus in Pacific Northwest salmonids

    Science.gov (United States)

    Breyta, Rachel; Black, Allison; Kaufman, John; Kurath, Gael

    2016-01-01

    The aquatic rhaboviral pathogen infectious hematopoietic necrosis virus (IHNV) causes acute disease in juvenile fish of a number of populations of Pacific salmonid species. Heavily managed in both marine and freshwater environments, these fish species are cultured during the juvenile stage in freshwater conservation hatcheries, where IHNV is one of the top three infectious diseases that cause serious morbidity and mortality. Therefore, a comprehensive study of viral genetic surveillance data representing 2590 field isolates collected between 1958 and 2014 was conducted to determine the spatial and temporal patterns of IHNV in the Pacific Northwest of the contiguous United States. Prevalence of infection varied over time, fluctuating over a rough 5–7 year cycle. The genetic analysis revealed numerous subgroups of IHNV, each of which exhibited spatial heterogeneity. Within all subgroups, dominant genetic types were apparent, though the temporal patterns of emergence of these types varied among subgroups. Finally, the affinity or fidelity of subgroups to specific host species also varied, where UC subgroup viruses exhibited a more generalist profile and all other subgroups exhibited a specialist profile. These complex patterns are likely synergistically driven by numerous ecological, pathobiological, and anthropogenic factors. Since only a few anthropogenic factors are candidates for managed intervention aimed at improving the health of threatened or endangered salmonid fish populations, determining the relative impact of these factors is a high priority for future studies.

  1. Relationship of otolith strontium-to-calcium ratios and salinity: Experimental validation for juvenile salmonids

    Science.gov (United States)

    Zimmerman, C.E.

    2005-01-01

    Analysis of otolith strontium (Sr) or strontium-to-calcium (Sr:Ca) ratios provides a powerful tool to reconstruct the chronology of migration among salinity environments for diadromous salmonids. Although use of this method has been validated by examination of known individuals and translocation experiments, it has never been validated under controlled experimental conditions. In this study, incorporation of otolith Sr was tested across a range of salinities and resulting levels of ambient Sr and Ca concentrations in juvenile chinook salmon (Oncorhynchus tshawytscha), coho salmon (Oncorhynchus kisutch), sockeye salmon (Oncorhynchus nerka), rainbow trout (Oncorhynchus rnykiss), and Arctic char (Salvelinus alpinus). Experimental water was mixed, using stream water and seawater as end members, to create experimental salinities of 0.1, 6.3, 12.7, 18.6, 25.5, and 33.0 psu. Otolith Sr and Sr:Ca ratios were significantly related to salinity for all species (r2 range: 0.80-0.91) but provide only enough predictive resolution to discriminate among fresh water, brackish water, and saltwater residency. These results validate the use of otolith Sr:Ca ratios to broadly discriminate salinity histories encountered by salmonids but highlight the need for further research concerning the influence of osmoregulation and physiological changes associated with smoking on otolith microchemistry.

  2. PCR-RFLP Method to Identify Salmonid Species of Economic Importance

    Directory of Open Access Journals (Sweden)

    Andreea Dudu

    2011-05-01

    Full Text Available The identification of different fish species by molecular methods has become necessary to avoid both the incorrect labelling of individuals involved in repopulation programmes and the commercial frauds on the fish market. Different fish species of great economical importance, like the salmonids, which are very much requested for their meat, can be identified using molecular techniques such as PCR-RFLP. The method is based on the amplification of a target region from the genome by PCR reaction followed by endonucleases digestion to detect the polymorphism of restriction fragments. In our study we analysed the following salmonid species from Romania: Salmo trutta fario, Salmo labrax, Salvelinus fontinalis, Onchorhynchus mykiss, Thymallus thymallus and Hucho hucho. In order to discriminate between the analysed species we amplified a fragment of mitochondrial genome comprising tRNAGlu/ cytochrome b/ tRNAThr/ tRNAPro/ D-loop/ tRNAPhe, followed by digestion with a specific restriction enzyme. The direct digestion of unpurified PCR products generated species-specific restriction patterns and proved to be a simple, reliable, inexpensive and fast method. Thus, it may be successfully utilized in specialized laboratories for the correct identification of the fish species for multiple purposes, including the traceability of fish food products.

  3. Functional morphology and biomechanics of the tongue-bite apparatus in salmonid and osteoglossomorph fishes

    Science.gov (United States)

    Camp, Ariel L; Konow, Nicolai; Sanford, Christopher P J

    2009-01-01

    The tongue-bite apparatus and its associated musculoskeletal elements of the pectoral girdle and neurocranium form the structural basis of raking, a unique prey-processing behaviour in salmonid and osteoglossomorph fishes. Using a quantitative approach, the functional osteology and myology of this system were compared between representatives of each lineage, i.e. the salmonid Salvelinus fontinalis (N =10) and the osteoglossomorph Chitala ornata(N = 8). Divergence was found in the morphology of the novel cleithrobranchial ligament, which potentially relates to kinematic differences between the raking lineage representatives. Salvelinus had greater anatomical cross-sectional areas of the epaxial, hypaxial and protractor hyoideus muscles, whereas Chitala had greater sternohyoideus and adductor mandibulae mass. Two osteology-based biomechanical models (a third-order lever for neurocranial elevation and a modified four-bar linkage for hyoid retraction) showed divergent force/velocity priorities in the study taxa. Salvelinus maximizes both force (via powerful cranial muscles) and velocity (through mechanical amplification) during raking. In contrast, Chitala has relatively low muscle force but more efficient force transmission through both mechanisms compared with Salvelinus. It remains unclear if and how behavioural modulation and specializations in the post-cranial anatomy may affect the force/velocity trade-offs in Chitala. Further studies of tongue-bite apparatus morphology and biomechanics in a broader species range may help to clarify the role that osteology and myology play in the evolution of behavioural diversity. PMID:19438765

  4. Biological and Physical Inventory of the Streams within the Nez Perce Reservation; Synopsis, 1982-1984 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Fuller, Ross K.; Kucera, P.A.; Johnson, D.B. (Nez Perce Tribe, Lapwai, ID)

    1985-08-01

    This report provides a synopsis for three years of inventory work on the streams in the Lower Clearwater Basin, Idaho. The main emphasis of the study was to document which streams presently support anadromous salmonids, the extent of production in those streams and the identification of those streams which may best respond to enhancement restoration activities. Rainbow-steelhead trout (Salmo gairdneri) were the most abundant anadromous salmonid found. Chinook salmon (Oncorhynchus tshawytscha) were found rarely except in the Lolo Creek Drainage. The main environmental problem affecting these streams was the extreme flow variations which commonly occur. This is due primarily to poor land management practices. Enhancement recommendations are suggested for these streams which include passage around barriers, barrier removal, riparian enhancement, instream habitat improvement, and better land use practices.

  5. Temporal and spatial variation in relative abundance and length structure of salmonids in reservoirs: Implications for monitoring

    Science.gov (United States)

    Rhea, D.T.; Hubert, W.A.; Gangl, R.S.; Whaley, R.A.

    2005-01-01

    Spatial and temporal variations in salmonid catch per unit effort (C/f) may affect monitoring efforts in lakes and reservoirs. This study evaluated the spatial and temporal variation in gill-net C/f and length structure of captured salmonids in nearshore (???7.6-m bottom depth) and offshore (>7.6-m bottom depth) areas of two Wyoming reservoirs. Floating experimental gill nets were set as nearshore and offshore pairs at 24 locations in both reservoirs during each of four sampling periods (spring, early summer, late summer, and fall). Salmonid C/f was significantly higher in nearshore areas than in offshore areas during all periods in one reservoir and during all periods except spring in the other reservoir. Mean C/f of rainbow trout Oncorhynchus mykiss was not significantly different between nearshore and offshore areas when water temperatures were 10-13??C in both reservoirs. Length structure of salmonids differed significantly between nearshore and offshore locations and among periods in both reservoirs. These patterns should be considered in both the design and analysis phases of monitoring efforts that use floating experimental gill nets and other sampling gears. ?? Copyright by the American Fisheries Society 2005.

  6. Influence of riparian canopy on macroinvertebrate composition and food habits of juvenile salmonids in several Oregon streams.

    Science.gov (United States)

    William R. Meehan

    1996-01-01

    The community composition of macroinvertebrates and the feeding habits of juvenile salmonids were studied in eight Oregon streams. Benthic, drift, sticky trap, and water trap samples were taken over a 3-year period, along with stomach samples of the fish. Samples were taken in stream reaches with and without riparian canopy. Both main effects—fish diet versus...

  7. Many Species, Many Threats: A Composite Risk Assessment of Climate Impacts for Salmonids in the Pacific Northwest

    Science.gov (United States)

    Graham, M. C.; Greene, C.; Beechie, T. J.; Raymond, C.

    2016-02-01

    The life cycles of salmonid species span freshwater, estuarine, and marine environments, exposing these economically, ecologically, and culturally important species to a wide variety of climate change threats. The diverse life histories of salmonids make them differentially vulnerable to climate change based on their use of different habitat types and the variability in climate change threats across these habitat types. Previous studies have focused mainly on assessing the vulnerability of particular life stages for a few species. Hence, we lack a broad perspective on how multiple climate threats are expected to impact the entire salmonid community, which spend much of their lives in marine waters. This lack of knowledge hampers our ability to prioritize various adaptation strategies for salmonid conservation. In order to conduct a more extensive vulnerability study of salmonids, we performed a life cycle-based risk assessment of climate change threats for nine species of salmonids (species within Oncorhynchus, Salvelinus, and Prosopium genera) inhabiting the Skagit River watershed, which is subject to an array of climate impacts. Our risk assessment integrated projections of impacts from various climate threats in freshwater, estuarine, and marine ecosystems with expert-based assessments of species-specific sensitivity and exposure. We found that projections (multiple global climate models under moderate emission scenarios) of both changes in magnitude and frequency of three flow-related freshwater impacts (flooding, low flows, and suspended sediment pulses) were more severe than threats in estuarine and marine habitats for which we could obtain projections. Combining projections with expert-based sensitivity and exposure scores revealed that these three threats exhibited the highest risk across all species. Of the nine species, the four most vulnerable were Chinook and coho salmon, steelhead, and bull trout. Even though these salmonids spend much of their lives

  8. Relationship between gill Na+,K+-ATPase activity and downstream movement in domesticated and first-generation offspring of wild anadromous brown trout ( Salmo trutta )

    DEFF Research Database (Denmark)

    Aarestrup, Kim; Nielsen, C.; Madsen, S.S.

    2000-01-01

    The relationship between smolt status and downstream movement following release was investigated in two stocks of hatchery- reared anadromous brown trout (Salmo trutta). Yearlings from a domesticated stock (DS) and first-generation offspring (F1) of wild anadromous trout were held under identical...... occasions into the River Salten. Using both dye-marked and radiotagged fish, downstream movement was monitored by either trapping 3 km downstream (dye-marked fish) or radiotracking on a daily basis. The experiments showed a positive correlation between smolt status (gill Na+,K+-ATPase activity......) and downstream movement. Gill Na+,K+-ATPase activity may therefore be used as an indicator of migratory readiness in brown trout. F1 and DS trout had the highest migration frequency when released as presmolts and smolts, respectively. Despite smaller size, F1 trout had similar or better survival than DS trout...

  9. Effects of river morphology, hydraulic gradients, and sediment deposition on water exchange and oxygen dynamics in salmonid redds.

    Science.gov (United States)

    Schindler Wildhaber, Y; Michel, C; Epting, J; Wildhaber, R A; Huber, E; Huggenberger, P; Burkhardt-Holm, P; Alewell, C

    2014-02-01

    Fine sediment decreasing gravel permeability and oxygen supply to incubating salmonid embryos, is often considered the main contributing factor for the observed decline of salmonid populations. However, oxygen supply to salmonid embryos also depends on hydraulic conditions driving water flow through the redd. A more generalized perspective is needed to better understand the constraints on successful salmonid incubation in the many heavily modified fluvial ecosystems of the Northern Hemisphere. The effects of hydraulic gradients, riverbed and redd morphology as well as fine sediment deposition on dissolved oxygen (DO) and water exchange was studied in 18 artificial redds at three sites along a modified river. Fifty percent of the redds in the two downstream sites were lost during high flow events, while redd loss at the upstream site was substantially lower (8%). This pattern was likely related to increasing flood heights from up- to downstream. Specific water infiltration rates (q) and DO were highly dynamic and driven on multiple temporal and spatial scales. Temporally, the high permeability of the redd gravel and the typical pit-tail structure of the new built redds, leading to high DO, disappeared within a month, when fine sediment had infiltrated and the redd structure was leveled. On the scale of hours to days, DO concentrations and q increased during high flows, but decreased during the falling limb of the water level, most likely related to exfiltration of oxygen depleted groundwater or hyporheic water. DO concentrations also decreased under prolonged base flow conditions, when increased infiltration of silt and clay particles clogged the riverbed and reduced q. Spatially, artificial log steps affected fine sediment infiltration, q and interstitial DO in the redds. The results demonstrate that multiple factors have to be considered for successful river management in salmonid streams, including riverbed structure and local and regional hydrogeological

  10. Can biosecurity and local network properties predict pathogen species richness in the salmonid industry?

    Science.gov (United States)

    More, Simon J.; Geoghegan, Fiona; McManus, Catherine; Hill, Ashley E.; Martínez-López, Beatriz

    2018-01-01

    Salmonid farming in Ireland is mostly organic, which implies limited disease treatment options. This highlights the importance of biosecurity for preventing the introduction and spread of infectious agents. Similarly, the effect of local network properties on infection spread processes has rarely been evaluated. In this paper, we characterized the biosecurity of salmonid farms in Ireland using a survey, and then developed a score for benchmarking the disease risk of salmonid farms. The usefulness and validity of this score, together with farm indegree (dichotomized as ≤ 1 or > 1), were assessed through generalized Poisson regression models, in which the modeled outcome was pathogen richness, defined here as the number of different diseases affecting a farm during a year. Seawater salmon (SW salmon) farms had the highest biosecurity scores with a median (interquartile range) of 82.3 (5.4), followed by freshwater salmon (FW salmon) with 75.2 (8.2), and freshwater trout (FW trout) farms with 74.8 (4.5). For FW salmon and trout farms, the top ranked model (in terms of leave-one-out information criteria, looic) was the null model (looic = 46.1). For SW salmon farms, the best ranking model was the full model with both predictors and their interaction (looic = 33.3). Farms with a higher biosecurity score were associated with lower pathogen richness, and farms with indegree > 1 (i.e. more than one fish supplier) were associated with increased pathogen richness. The effect of the interaction between these variables was also important, showing an antagonistic effect. This would indicate that biosecurity effectiveness is achieved through a broader perspective on the subject, which includes a minimization in the number of suppliers and hence in the possibilities for infection to enter a farm. The work presented here could be used to elaborate indicators of a farm’s disease risk based on its biosecurity score and indegree, to inform risk-based disease surveillance and

  11. Residual basins

    International Nuclear Information System (INIS)

    D'Elboux, C.V.; Paiva, I.B.

    1980-01-01

    Exploration for uranium carried out over a major portion of the Rio Grande do Sul Shield has revealed a number of small residual basins developed along glacially eroded channels of pre-Permian age. Mineralization of uranium occurs in two distinct sedimentary units. The lower unit consists of rhythmites overlain by a sequence of black shales, siltstones and coal seams, while the upper one is dominated by sandstones of probable fluvial origin. (Author) [pt

  12. Microhabitat preference of Anisakis simplex in 3 salmonid species: Immunological Implications

    DEFF Research Database (Denmark)

    Bahlool, Qusay Zuhair Mohammad; Buchmann, Kurt

    different salmonid species to investigate the in vivo behavioural difference of experimentally inoculated Anisakis parasite inside these fishes. Rainbow trout (Oncorhynchus mykiss), Baltic salmon (Salmo salar) and brown trout (Salmo trutta) were used in this experiment. Infection success differed between...... already at day 21 post infection. Immunohistochemical studies using monoclonal antibodies raised against IgT, IgM, CD8 and MHCII were used to detect the presence of immune cells around the infecting nematodes. None of the three fish species showed positive reactions for IgT and IgM bearing cells...... in inflammatory tissue in connection with the worms. CD8+ cells were detected in all three species but MHC II bearing cells were only found associated with encapsulated Anisakis in rainbow trout and brown trout, but not in Baltic salmon. In this study we have shown that Anisakis nematodes show a site predilection...

  13. The physiology and toxicology of salmonid eggs and larvae in relation to water quality criteria

    Energy Technology Data Exchange (ETDEWEB)

    Finn, Roderick Nigel [Department of Biology, University of Bergen, Allegaten 41, N-5020 Bergen (Norway)]. E-mail: nigel.finn@bio.uib.no

    2007-03-30

    The purpose of this review is to collate physiological knowledge on salmonid eggs and larvae in relation to water quality criteria. Salmonid genera reviewed include Coregonus, Thymallus, Salvelinus, Salmo, and Oncorhynchus spp. When physiological data for salmonids are lacking, the zebrafish and medaka models are included. The primary focus is on the underlying mechanisms involved in the hydro-mineral, thermal, and respiratory biology with an extended section on the xenobiotic toxicology of the early stages. Past and present data reveal that the eggs of salmonids are among the largest shed by any broadcast spawning teleost. Once ovulated, the physicochemical properties of the ovarian fluid provide temporary protection from external perturbations and maintain the eggs in good physiological condition until spawning. Following fertilisation and during early development the major structures protecting the embryo from poor water quality are the vitelline membrane, the enveloping layer and the chorion. The vitelline membrane is one of the least permeable membranes known, while the semi-permeable chorion provides both physical and chemical defense against metals, pathogens, and xenobiotic chemicals. In part these structures explain the lower sensitivity of the eggs to chemical imbalance compared to the larvae, however the lower metabolic rate and the chronology of gene expression and translational control suggest that developmental competence also plays a decisive role. In addition, maternal effect genes provide a defense potential until the mid-blastula transition. The transition between maternal effect genes and zygotic genes is a critical period for the embryo. The perivitelline fluids are an important trap for cations, but are also the major barrier to diffusion of gases and solutes. Acidic environmental pH interferes with acid-base and hydromineral balance but also increases the risk of aluminium and heavy metal intoxication. These risks are ameliorated somewhat by

  14. The physiology and toxicology of salmonid eggs and larvae in relation to water quality criteria

    International Nuclear Information System (INIS)

    Finn, Roderick Nigel

    2007-01-01

    The purpose of this review is to collate physiological knowledge on salmonid eggs and larvae in relation to water quality criteria. Salmonid genera reviewed include Coregonus, Thymallus, Salvelinus, Salmo, and Oncorhynchus spp. When physiological data for salmonids are lacking, the zebrafish and medaka models are included. The primary focus is on the underlying mechanisms involved in the hydro-mineral, thermal, and respiratory biology with an extended section on the xenobiotic toxicology of the early stages. Past and present data reveal that the eggs of salmonids are among the largest shed by any broadcast spawning teleost. Once ovulated, the physicochemical properties of the ovarian fluid provide temporary protection from external perturbations and maintain the eggs in good physiological condition until spawning. Following fertilisation and during early development the major structures protecting the embryo from poor water quality are the vitelline membrane, the enveloping layer and the chorion. The vitelline membrane is one of the least permeable membranes known, while the semi-permeable chorion provides both physical and chemical defense against metals, pathogens, and xenobiotic chemicals. In part these structures explain the lower sensitivity of the eggs to chemical imbalance compared to the larvae, however the lower metabolic rate and the chronology of gene expression and translational control suggest that developmental competence also plays a decisive role. In addition, maternal effect genes provide a defense potential until the mid-blastula transition. The transition between maternal effect genes and zygotic genes is a critical period for the embryo. The perivitelline fluids are an important trap for cations, but are also the major barrier to diffusion of gases and solutes. Acidic environmental pH interferes with acid-base and hydromineral balance but also increases the risk of aluminium and heavy metal intoxication. These risks are ameliorated somewhat by

  15. Comparative Study of Genome Divergence in Salmonids with Various Rates of Genetic Isolation

    Directory of Open Access Journals (Sweden)

    Elena A. Shubina

    2013-01-01

    Full Text Available The aim of the study is a comparative investigation of changes that certain genome parts undergo during speciation. The research was focused on divergence of coding and noncoding sequences in different groups of salmonid fishes of the Salmonidae (Salmo, Parasalmo, Oncorhynchus, and Salvelinus genera and the Coregonidae families under different levels of reproductive isolation. Two basic approaches were used: (1 PCR-RAPD with a 20–22 nt primer design with subsequent cloning and sequencing of the products and (2 a modified endonuclease restriction analysis. The restriction fragments were shown with sequencing to represent satellite DNA. Effects of speciation are found in repetitive sequences. The revelation of expressed sequences in the majority of the employed anonymous loci allows for assuming the adaptive selection during allopatric speciation in isolated char forms.

  16. THE RAPID DIAGNOSTICS OF SEX OF SALMONIDS USING DNA-MARKERS

    Directory of Open Access Journals (Sweden)

    Yu. P. Rud

    2014-12-01

    Full Text Available Based on nucleotide sequences of sex-specific DNA-markers of salmonid fishes the oligonucleotide primers for polymerase chain reaction were selected with purpose on rapid diagnostic of sex in rainbow trout Onchorhynchus mykiss, brown trout Salmo trutta, huchen Hucho hucho and grayling Thymallus thymallus. The specify of amplification was determined by nucleotide sequence analysis of PCR-products. All amplified fragments were referred to sex-specific locuses of Y chromosomes in males of investigated fish species. The PCR-products were in size of 880, 607, 521 and 558 for rainbow trout, brown trout, grayling and huchen respectively. Thus the sex determination in above mentioned fish species and identification of genotypic males under process of hormonal sex reversion can be provided using conventional PCR. Present method relates to rapid diagnostics because the data analysis and return of results back to fish farm take one single day.

  17. Bigger is not better: cortisol-induced cardiac growth and dysfunction in salmonids

    DEFF Research Database (Denmark)

    Johansen, Ida B.; Sandblom, Erik; Skov, Peter Vilhelm

    2017-01-01

    Stress and elevated cortisol levels are associated with pathological heart growth and cardiovascular disease in humans and other mammals. We recently established a link between heritable variation in post-stress cortisol production and cardiac growth in salmonid fish too. A conserved stimulatory...... effect of the otherwise catabolic steroid hormone cortisol is probably implied, but has to date not been established experimentally. Furthermore, whereas cardiac growth is associated with failure of the mammalian heart, pathological cardiac hypertrophy has not previously been described in fish. Here, we...... show that rainbow trout (Oncorhynchus mykiss) treated with cortisol in the diet for 45 days have enlarged hearts with lower maximum stroke volume and cardiac output. In accordance with impaired cardiac performance, overall circulatory oxygen-transporting capacity was diminished as indicated by reduced...

  18. Development of infectious cDNA clones of Salmonid alphavirus subtype 3

    Directory of Open Access Journals (Sweden)

    Karlsen Marius

    2010-09-01

    Full Text Available Abstract Background Salmonid alphavirus (SAV is a widespread pathogen in European aquaculture of salmonid fish. Distinct viral subtypes have been suggested based on sequence comparisons and some of these have different geographical distributions. In Norway, only SAV subtype 3 have so far been identified. Little is known about viral mechanisms important for pathogenesis and transmission. Tools for detailed exploration of SAV genomes are therefore needed. Results Infectious cDNA clones in which a genome of subtype 3 SAV is under the control of a CMV promoter were constructed. The clones were designed to express proteins that are putatively identical to those previously reported for the SAVH20/03 strain. A polyclonal antiserum was raised against a part of the E2 glycoprotein in order to detect expression of the subgenomic open reading frame (ORF encoding structural viral proteins. Transfection of the cDNA clone revealed the expression of the E2 protein by IFAT, and in serial passages of the supernatant the presence of infectious recombinant virus was confirmed through RT-PCR, IFAT and the development of a cytopathic effect similar to that seen during infection with wild type SAV. Confirmation that the recovered virus originated from the infectious plasmid was done by sequence identification of an introduced genetic tag. The recombinant virus was infectious also when an additional ORF encoding an EGFP reporter gene under the control of a second subgenomic alphavirus promoter was added. Finally, we used the system to study the effect of selected point mutations on infectivity in Chinook salmon embryo cells. While introduced mutations in nsP2197, nsP3263 and nsP3323 severely reduced infectivity, a serine to proline mutation in E2206 appeared to enhance the virus titer production. Conclusion We have constructed infectious clones for SAV based on a subtype 3 genome. The clones may serve as a platform for further functional studies.

  19. Infection experiments with novel Piscine orthoreovirus from rainbow trout (Oncorhynchus mykiss) in salmonids

    Science.gov (United States)

    Taksdal, Torunn; Olsen, Anne Berit; Wessel, Øystein; Mikkelsen, Susie Sommer; Alencar, Anna Luiza Farias; Olesen, Niels Jørgen

    2017-01-01

    A new disease in farmed rainbow trout (Onchorhyncus mykiss) was described in Norway in 2013. The disease mainly affected the heart and resembled heart and skeletal muscle inflammation (HSMI) in Atlantic salmon (Salmo salar L.). HSMI is associated with Piscine orthoreovirus (PRV), and a search for a similar virus in the diseased rainbow trout led to detection of a sequence with 85% similarity to PRV. This finding called for a targeted effort to assess the risk the new PRV-variant pose on farmed rainbow trout and Atlantic salmon by studying infection and disease pathogenesis, aiming to provide more diagnostic knowledge. Based on the genetic relationship to PRV, the novel virus is referred to as PRV-Oncorhynchus mykiss (PRV-Om) in contrast to PRV-Salmo salar (PRV-Ss). In experimental trials, intraperitoneally injected PRV-Om was shown to replicate in blood in both salmonid species, but more effectively in rainbow trout. In rainbow trout, the virus levels peaked in blood and heart of cohabitants 6 weeks post challenge, along with increased expression of antiviral genes (Mx and viperin) in the spleen, with 80–100% of the cohabitants infected. Heart inflammation was diagnosed in all cohabitants examined 8 weeks post challenge. In contrast, less than 50% of the Atlantic salmon cohabitants were infected between 8 and 16 weeks post challenge and the antiviral response in these fish was very low. From 12 weeks post challenge and onwards, mild focal myocarditis was demonstrated in a few virus-positive salmon. In conclusion, PRV-Om infects both salmonid species, but faster transmission, more notable antiviral response and more prominent heart pathology were observed in rainbow trout. PMID:28678799

  20. Rapid and sensitive detection of salmonid alphavirus using TaqMan real-time PCR.

    Science.gov (United States)

    Shi, Wen; Song, Aochen; Gao, Shuai; Wang, Yuting; Tang, Lijie; Xu, Yigang; Ren, Tong; Li, Yijing; Liu, Min

    2017-08-01

    Salmonid alphavirus (SAV) infection has led to the spread of salmon pancreas disease (PD) and sleeping disease (SD) to salmonids in several countries in Europe, resulting in tremendous economic losses to the fish farming industry. Recently, with increases in the fish import trade, many countries in which SAV has been unreported, such as China, may be seriously threatened by these diseases. It is therefore necessary to develop efficient detection methods for the prevention and diagnosis of SAV infection. In this study, a rapid and sensitive TaqMan real-time PCR method was established and assessed for this purpose. A specificity assay showed no cross-reactions with other common RNA viruses. Regression analysis and standard curves calculated from the Ct values of 10-fold serial dilutions of the standard plasmid showed that the assay was highly reproducible over a wide range of RNA input concentrations. The real-time PCR assay was able to detect SAV at a concentration as low as 1.5 × 10 1 copies, indicating that it is 10 7 times more sensitive than the approved conventional RT-PCR method (detection limit, 1.5 × 10 7 copies) after use on the same samples. Assessment of infected fish samples showed that this assay has a higher sensitivity than the previously reported Q_nsP1 assay. Thus, this TaqMan real-time PCR assay provides a rapid, sensitive, and specific detection method for SAV, offering improved technical support for the clinical diagnosis and epidemiology of SAV. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Relationship between channel morphology and foraging habitat for stream salmonids: Effects of body size

    Science.gov (United States)

    Cienciala, P.; Hassan, M. A.

    2014-12-01

    Channel morphology and dynamics strongly influence fish populations in running waters by defining habitat template for movement, spawning, incubation, and foraging. In this research we adopted a modeling approach to investigate how body size controls the relationship between salmonid fish and their foraging habitat in streams. Body size is a fundamental ecological parameter which affects resource acquisition, locomotory costs, metabolic rates, and competitive abilities. We focus on two specific questions. First, we examined how distinct types of channel morphology and associated flow fields shape specific growth potential for different body size classes of trout. Second, we modeled these fish-habitat relationships in a size-structured population in the presence of intraspecific competition. In the latter scenario, fish may not be able to occupy energetically optimal foraging habitat and the predicted specific growth potential may differ from the intrinsic habitat quality. To address the research questions, we linked a 2D hydrodynamic model with a bioenergetic foraging model for drift-feeding trout. Net energy intake, simulated for four study reaches with different channel morphology, was converted into maps of specific growth rate potential. We extended this model by including a component that enabled us to estimate territory size for fish of a given body size and account for the effects of competition on spatial distribution of fish. The predictions that emerge from our simulations highlight that fish body size is an important factor that determines the relationship between channel morphology and the quality of foraging habitat. The results also indicate that distinct types of channel morphology may give rise to different energetic conditions for different body size classes of drift-feeding salmonids.

  2. Impacts of Columbia River discharge on salmonid habitat: 2. Changes in shallow-water habitat

    Science.gov (United States)

    Kukulka, Tobias; Jay, David A.

    2003-09-01

    This is the second part of an investigation that analyzes human alteration of shallow-water habitat (SWH) available to juvenile salmonids in the tidal Lower Columbia River. Part 2 develops a one-dimensional, subtidal river stage model that explains ˜90% of the stage variance in the tidal river. This model and the tidal model developed in part 1 [, 2003] uncouple the nonlinear interaction of river tides and river stage by referring both to external forcing by river discharge, ocean tides, and atmospheric pressure. Applying the two models, daily high-water levels were predicted for a reach from rkm-50 to rkm-90 during 1974 to 1998, the period of contemporary management. Predicted water levels were related to the bathymetry and topography to determine the changes in shallow-water habitat area (SWHA) caused by flood control dikes and altered flow management. Model results suggest that diking and a >40% reduction of peak flows have reduced SWHA by ˜62% during the crucial spring freshet period during which juvenile salmon use of SWHA is maximal. Taken individually, diking and flow cycle alteration reduced spring freshet SWHA by 52% and 29%, respectively. SWHA has been both displaced to lower elevations and modified in its character because tidal range has increased. Our models of these processes are economical for the very long simulations (seasons to centuries) needed to understand historic changes and climate impacts on SWH. Through analysis of the nonlinear processes controlling surface elevation in a tidal river, we have identified some of the mechanisms that link freshwater discharge to SWH and salmonid survival.

  3. Infection experiments with novel Piscine orthoreovirus from rainbow trout (Oncorhynchus mykiss in salmonids.

    Directory of Open Access Journals (Sweden)

    Helena Hauge

    Full Text Available A new disease in farmed rainbow trout (Onchorhyncus mykiss was described in Norway in 2013. The disease mainly affected the heart and resembled heart and skeletal muscle inflammation (HSMI in Atlantic salmon (Salmo salar L.. HSMI is associated with Piscine orthoreovirus (PRV, and a search for a similar virus in the diseased rainbow trout led to detection of a sequence with 85% similarity to PRV. This finding called for a targeted effort to assess the risk the new PRV-variant pose on farmed rainbow trout and Atlantic salmon by studying infection and disease pathogenesis, aiming to provide more diagnostic knowledge. Based on the genetic relationship to PRV, the novel virus is referred to as PRV-Oncorhynchus mykiss (PRV-Om in contrast to PRV-Salmo salar (PRV-Ss. In experimental trials, intraperitoneally injected PRV-Om was shown to replicate in blood in both salmonid species, but more effectively in rainbow trout. In rainbow trout, the virus levels peaked in blood and heart of cohabitants 6 weeks post challenge, along with increased expression of antiviral genes (Mx and viperin in the spleen, with 80-100% of the cohabitants infected. Heart inflammation was diagnosed in all cohabitants examined 8 weeks post challenge. In contrast, less than 50% of the Atlantic salmon cohabitants were infected between 8 and 16 weeks post challenge and the antiviral response in these fish was very low. From 12 weeks post challenge and onwards, mild focal myocarditis was demonstrated in a few virus-positive salmon. In conclusion, PRV-Om infects both salmonid species, but faster transmission, more notable antiviral response and more prominent heart pathology were observed in rainbow trout.

  4. Migratory Behavior and Survival of Juvenile Salmonids in the Lower Columbia River, Estuary, and Plume in 2010

    Energy Technology Data Exchange (ETDEWEB)

    McMichael, Geoffrey A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Harnish, Ryan A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Skalski, John R. [Univ. of Washington, Seattle, WA (United States); Deters, Katherine A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Ham, Kenneth D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Townsend, Richard L. [Univ. of Washington, Seattle, WA (United States); Titzler, P. Scott [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hughes, Michael S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kim, Jin A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Trott, Donna M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2011-09-01

    Uncertainty regarding the migratory behavior and survival of juvenile salmonids passing through the lower Columbia River and estuary after negotiating dams on the Federal Columbia River Power System (FCRPS) prompted the development and application of the Juvenile Salmon Acoustic Telemetry System (JSATS). The JSATS has been used to investigate the survival of juvenile salmonid smolts between Bonneville Dam (river kilometer (rkm) 236) and the mouth of the Columbia River annually since 2004. In 2010, a total of 12,214 juvenile salmonids were implanted with both a passive integrated transponder (PIT) and a JSATS acoustic transmitter. Using detection information from JSATS receiver arrays deployed on dams and in the river, estuary, and plume, the survival probability of yearling Chinook salmon and steelhead smolts tagged at John Day Dam was estimated form multiple reaches between rkm 153 and 8.3 during the spring. During summer, the survival probability of subyearling Chinook salmon was estimated for the same reaches. In addition, the influence of routes of passage (e.g., surface spill, deep spill, turbine, juvenile bypass system) through the lower three dams on the Columbia River (John Day, The Dalles, and Bonneville) on juvenile salmonid smolt survival probability from the dams to rkm 153 and then between rkm 153 and 8.3 was examined to increase understanding of the immediate and latent effects of dam passage on juvenile salmon survival. Similar to previous findings, survival probability was relatively high (>0.95) for most groups of juvenile salmonids from the Bonneville Dam tailrace to about rkm 50. Downstream of rkm 50 the survival probability of all species and run types we examined decreased markedly. Steelhead smolts suffered the highest mortality in this lower portion of the Columbia River estuary, with only an estimated 60% of the tagged fish surviving to the mouth of the river. In contrast, yearling and subyearling Chinook salmon smolts survived to the mouth

  5. Summary Report for Bureau of Fisheries Stream Habitat Surveys : Yakima River Basin, 1934-1942, Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    McIntosh, Bruce A.; Clark, Sharon E.; Sedell, James R.

    1996-01-01

    This document contains summary reports of stream habitat surveys, conducted in the Yakima River basin, by the Bureau of Fisheries (BOF, now National Marine Fisheries Service) from 1934-1942. These surveys were part of a larger project to survey streams in the Columbia River basin that provided, or had provided, spawning and rearing habitat for salmon and steelhead (Rich, 1948). The purpose of the survey was, as described by Rich, 'to determine the present condition of the various tributaries with respect to their availability and usefulness for the migration, breeding, and rearing of migratory fishes'. Current estimates of the loss of anadromous fish habitat in the Columbia River Basin are based on a series of reports published from 1949-1952 by the U.S. Fish and Wildlife Service. The reports were brief, qualitative accounts of over 5000 miles of stream surveys conducted by the BOF from 1934-1946 (Bryant, 1949; Bryant and Parkhurst, 1950; Parkhurst, 1950a-c; Parkhurst et al., 1950). Despite their brevity, these BOF reports have formed the basis for estimating fish habitat losses and conditions in the Columbia River Basin (Fulton, 1968, 1970; Thompson, 1976; NPPC, 1986). Recently, the field notebooks from the BOF surveys were discovered. The data is now archived and stored in the Forest Science DataBank at Oregon State University (Stafford et al., 1984; 1988). These records are the earliest and most comprehensive documentation available of the condition and extent of anadromous fish habitat before hydropower development in the Columbia River Basin. They provide the baseline data for quantifying changes and setting a benchmark for future restoration of anadromous fish habitat throughout the Basin. The summaries in this book are exact replicates of the originals. Due to discrepancies between the field data and the summaries, the database should be used to assess pool and substrate conditions. This data is available from the Bonneville Power Administration

  6. Summary Report for Bureau of Fisheries Stream Habitat Surveys : Willamette River Basin, 1934-1942, Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    McIntosh, Bruce A.; Clark, Sharon E.; Sedell, James R.

    1995-01-01

    This document contains summary reports of stream habitat-surveys, conducted in the Willamette River basin, by the Bureau of Fisheries (BOF, now National Marine Fisheries Service) from 1934-1942. These surveys were part of a larger project to survey streams in the Columbia River basin that provided, or had provided, spawning and rearing habitat for salmon and steelhead (Rich, 1948). The purpose of the survey was, as described by Rich, 'to determine the present condition of the various tributaries with respect to their availability and usefulness for the migration, breeding, and rearing of migratory fishes'. Current estimates of the loss of anadromous fish habitat in the Columbia River Basin are based on a series of reports published from 1949-1952 by the U.S. Fish and Wildlife Service. The reports were brief, qualitative accounts of over 5000 miles of stream surveys conducted by the BOF from 1934-1946 (Bryant, 1949; Bryant and Parkhurst, 1950; Parkhurst, 1950a-c; Parkhurst et al., 1950). Despite their brevity, these BOF reports have formed the basis for estimating fish habitat losses and conditions in the Columbia River Basin (Fulton, 1968, 1970; Thompson, 1976; NPPC, 1986). Recently, the field notebooks from the BOF surveys were discovered. The data is now archived and stored in the Forest Science DataBank at Oregon State University (Stafford et al., 1984; 1988). These records are the earliest and most comprehensive documentation available of the condition and extent of anadromous fish habitat before hydropower development in the Columbia River Basin. They provide the baseline data for quantifying changes and setting a benchmark for future restoration of anadromous fish habitat throughout the Basin. The summaries contained in this book are exact replicates of the originals. Due to discrepancies between the field data and the summaries, the database should be used to assess pool and substrate conditions. This data is available from the Bonneville Power

  7. San Mateo Creek Basin

    Science.gov (United States)

    The San Mateo Creek Basin comprises approximately 321 square miles within the Rio San Jose drainage basin in McKinley and Cibola counties, New Mexico. This basin is located within the Grants Mining District (GMD).

  8. Evaluation of Behavioral Guidance Structure on Juvenile Salmonid Passage and Survival at Bonneville Dam in 2009

    Energy Technology Data Exchange (ETDEWEB)

    Faber, Derrek M.; Ploskey, Gene R.; Weiland, Mark A.; Deng, Zhiqun; Hughes, James S.; Kim, Jin A.; Fu, Tao; Fischer, Eric S.; Monter, Tyrell J.; Skalski, J. R.

    2011-03-01

    Pacific Northwest National Laboratory (PNNL) conducted an acoustic-telemetry study at Bonneville Dam in 2009 to evaluate the effects of a behavioral guidance structure (BGS) in the Bonneville Dam second powerhouse forebay on fish passage and survival through the second powerhouse (B2), the dam as a whole, and through the first powerhouse and spillway combined. The BGS was deployed to increase the survival of fish passing through B2 by increasing the percentage of outmigrating smolts entering the B2 Corner Collector (B2CC)—a surface flow outlet known to be a relatively benign route for downstream passage at this dam. The study relied on releases of live Juvenile Salmon Acoustic Telemetry System tagged smolts in the Columbia River and used acoustic telemetry to evaluate the approach, passage, and survival of passing juvenile salmon. Study results indicated that having turbine 11 in service is important for providing flow conditions that are comparable to those observed in pre-BGS years (2004 and 2005) and in 2008. This study supports the U.S. Army Corps of Engineers continual effort to improve conditions for juvenile anadromous fish passing through Columbia River dams.

  9. The potential influence of changing climate on the persistence of salmonids of the inland west

    Science.gov (United States)

    Haak, A.L.; Williams, J.E.; Isaak, D.; Todd, A.; Muhlfeld, C.C.; Kershner, J.L.; Gresswell, R.E.; Hostetler, S.W.; Neville, H.M.

    2010-01-01

    The Earth's climate warmed steadily during the 20th century, and mean annual air temperatures are estimated to have increased by 0.6°C (Intergovernmental Panel on Climate Change, 2007). Although many cycles of warming and cooling have occurred in the past, the most recent warming period is unique in its rate and magnitude of change (Siegenthaler and others, 2005) and in its association with anthropogenic emissions of greenhouse gases (Intergovernmental Panel on Climate Change , 2007). The climate in the western United States warmed in concert with the global trend but at an accelerated rate (+0.8°C during the 20th century; Saunders and others, 2008). The region could also prove especially sensitive to future changes because the relatively small human population is growing rapidly, as are demands on limited water supplies. Regional hydrological patterns are dominated by seasonal snow accumulation at upper elevations. Most of the region is relatively dry, and both terrestrial and aquatic ecosystems are strongly constrained b y water availability (Barnett and others, 2008; Brown and others, 2008). Stream environments are dynamic and climatically extreme, and salmonid fishes are the dominant elements of the native biodiversity (McPhail and Lindsey, 1986; Waples and others, 2008). Salmonids have broad economic and ecologic importance, but a century of intensive water resource development, nonnative fish stocking, and land use has significantly reduced many populations and several taxa are now protected under the Endangered Species Act (Thurow and others, 1997; Trotter, 2008). Because salmonids require relatively pristine, cold water environments and are often isolated in headwater habitats, members of this group may be especially vulnerable to the effects of a warming climate (Keleher and Rahel, 1996; Rieman and others, 2007; Williams and others, 2009). Warming during the 20th century drove a series of environmental trends that have profound implications for many

  10. Walla Walla River Basin Fish Habitat Enhancement Project, 2001-2002 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Volkman, Jed; Sexton, Amy D. (Confederated Tribes of the Umatilla Indian Reservation, Pendleton, OR)

    2003-04-01

    In 2001, the Confederated Tribes of the Umatilla Indian Reservation (CTUIR) Fisheries Habitat Program implemented stream habitat restoration and protection efforts in the Walla Walla River Basin with funding from Bonneville Power Administration (BPA). The objective of these efforts is to protect and restore habitat critical to the recovery of weak or reintroduced populations of salmonid fish. The CTUIR has currently enrolled six properties into this program: two on Couse Creek, two adjacent properties on Blue Creek, one on Patit Creek, and one property on the mainstem Walla Walla River. Since 1997, approximately 7 miles of critical salmonid habitat has been secured for restoration and protection under this project. Major accomplishments to date include the following: Secured approximately $250,000 in cost share; Secured 7 easements; Planted 30,000+ native plants; Installed 50,000+ cuttings; and Seeded 18 acres to native grass. Pre and post-project monitoring efforts were included for all projects, incorporating methodologies from CTUIR's Draft Monitoring Plan. Basin-wide monitoring also included the deployment of 6 thermographs to collect summer stream temperatures.

  11. Development of an Index to Bird Predation of Juvenile Salmonids within the Yakima River, 2001 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Major, III, Walter; Grue, Christian E.; Ryding, Kristen E. (University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA)

    2002-08-01

    Avian predation of fish is suspected to contribute to the loss of out-migrating juvenile salmonids in the Yakima Basin, potentially constraining natural and artificial production. In 1997 and 1998, the Yakima/ Klickitat Fisheries Project (YKFP)--whose goal is increasing natural production within the Yakima River--initiated investigations to assess the feasibility of developing an index to avian predation of juvenile salmon within the river. This research confirmed that Ring-billed Gulls and Common Mergansers were the primary avian predators of juvenile salmon (Phinney et al. 1998), and that under certain conditions could significantly impact migrating smolt populations. Beginning in 1999, the Washington Cooperative Fish and Wildlife Research Unit (WACFWRU) was asked by the YKFP to continue development of avian consumption indices. Monitoring methods developed by Phinney et al. (1998) were adopted (with modifications) and monitoring of impacts to juvenile salmon along river reaches and at areas of high predator/prey concentrations (colloquially referred to as ''hotspots'') has continued each year through 2001. In 2001, piscivorous birds were counted from river banks at hotspots and from a raft or drift boat along river reaches. Consumption by gulls at hotspots was based on direct observations of foraging success and modeled abundance; consumption by all other piscivorous birds was estimated using published dietary requirements and modeled abundance. Seasonal patterns of avian piscivore abundance were identified, diurnal patterns of gull abundance at hotspots were identified, and predation indices were calculated for hotspots and river reaches (for both spring and summer). Changes in survey methods in 2001 included the addition of surveys in the ''Canyon'' reach during spring and altering the method of directly measuring gull feeding rates at hotspots. Primary avian predators in 2001 were &apos

  12. Turbulence Investigation and Reproduction for Assisting Downstream Migrating Juvenile Salmonids, Part I of II, 2001-2002 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Hotchkiss, Rollin H. (Washington State University, Department of Civil and Environmental Engineers, Albrook Hydraulics Laboratory)

    2002-12-01

    Turbulence in gravel bed rivers plays a critical role in most stream processes including contaminant and nutrient transport, aquatic habitat selection, and natural channel design. While most hydraulic designs and fluid models are based on bulk velocity, migrating juvenile salmon experience and react to the temporally varied turbulent fluctuations. Without properly understanding and accounting for the continuous turbulent motions proper fishway design and guidance are impossible. Matching temporally varied flow to fish reactions is the key to guiding juvenile salmonids to safe passageways. While the ideal solution to fish guidance design would be to use specific fluid action-fish reaction mechanisms, such concrete cause and effect relations have not been established. One way to approach the problem of guidance is to hypothesize that in an environment lacking obvious bulk flow cues (like the reservoir environment), turbulent flow conditions similar to those experienced by juvenile salmonids in natural migration corridors will be attractive to juvenile salmonids. Proof of this hypothesis requires three steps: (1) gathering data on turbulence characteristics in natural migration corridors, (2) reproduction of the turbulence parameters in a controlled environment, and (3) testing the reproduced turbulence on actively migrating juvenile salmonids for increased passage efficiencies. The results from the third step have not been finalized, therefore this report will focus on understanding turbulent processes in gravel bed rivers and reproduction of turbulence in controlled environments for use in fish passage technologies. The purposes of this report are to (1) present data collected in natural gravel bed rivers, (2) present a simple method for reproduction of appropriate turbulence levels in a controlled environment, (3) compare these results to those from one prototype surface collector (PSC), and (4) discuss the implications on fish passage design.

  13. Adaptive landscapes and density-dependent selection in declining salmonid populations: going beyond numerical responses to human disturbance

    OpenAIRE

    Einum, Sigurd; Robertsen, Grethe; Fleming, Ian A

    2008-01-01

    Theory suggests an important role for population density in shaping adaptive landscapes through density-dependent selection. Here, we identify five methodological approaches for studying such selection, review the existing empirical evidence for it, and ask whether current declines in abundance can be expected to trigger evolutionary responses in salmonid fishes. Across taxa we find substantial amounts of evidence for population density influencing the location of adaptive peaks for a range o...

  14. Control strategy for viral diseases of salmonid fish, flounders and shrimp at hatchery and seed production facility in Japan

    OpenAIRE

    Yoshimizu, Mamoru

    2009-01-01

    Salmonid fish are important species for hatchery reared and released fish. Flounders and shrimp are also important species for seed production and sea-farming in Japan. Viral disease is one of the limitations of successful propagation of these species. Methods currently used to control viral diseases are 1) hygiene and sanitation in facilities, 2) disinfection of rearing and waste water using U. V. irradiation, ozonization and electrolyzation, 3) selection of pathogen-free brood stock by cell...

  15. Development of a system wide predator control program: Stepwise implementation of a predation index, predator control fisheries, and evaluation plan in the Columbia River Basin. Volume 2 - Evaluation: 1993 Annual report; ANNUAL

    International Nuclear Information System (INIS)

    Willis, C.F.; Ward, D.L.

    1995-01-01

    An attempt was made to determine the extent to which northern squawfish predation on juvenile salmonids is a problem in the Columbia River Basin, and to evaluate how effectively fisheries can be used to control northern squawfish populations and reduce juvenile salmonid losses to predation. These studies were initiated as part of a basinwide program to control northern squawfish predation and reduce mortality of juvenile salmonids on their migration to the ocean. Modeling simulations based on work in the John Day Reservoir from 1982 through 1988 indicated that if northern squawfish larger than 250 mm fork length were exploited, at a rate of 10-20%, reductions in their numbers and restructuring of their populations could reduce their predation on juvenile salmonids by 50% or more. The authors evaluated the success of three test fisheries conducted in 1993-a sport-reward fishery, a dam-angling fishery, and a trap-net fishery, to achieve a 10-20% exploitation rate on northern squawfish . The authors also began evaluating the response of northern squawfish populations to sustained fisheries. In addition, the authors gathered information regarding the economic, social, and legal feasibility of sustaining each fishery, and report on the structure and function of the fish collection and distribution system

  16. Development of a systemwide predator control program: Stepwise implementation of a predation index, predator control fisheries, and evaluation plan in the Columbia River Basin. Volume 2 -- Evaluation: 1993 Annual report

    International Nuclear Information System (INIS)

    Willis, C.F.; Ward, D.L.

    1995-06-01

    An attempt was made to determine the extent to which northern squawfish predation on juvenile salmonids is a problem in the Columbia River Basin, and to evaluate how effectively fisheries can be used to control northern squawfish populations and reduce juvenile salmonid losses to predation. These studies were initiated as part of a basinwide program to control northern squawfish predation and reduce mortality of juvenile salmonids on their migration to the ocean. Modeling simulations based on work in the John Day Reservoir from 1982 through 1988 indicated that if northern squawfish larger than 250 mm fork length were exploited, at a rate of 10--20%, reductions in their numbers and restructuring of their populations could reduce their predation on juvenile salmonids by 50% or more. The authors evaluated the success of three test fisheries conducted in 1993--a sport-reward fishery, a dam-angling fishery, and a trap-net fishery, to achieve a 10--20% exploitation rate on northern squawfish. The authors also began evaluating the response of northern squawfish populations to sustained fisheries. In addition, the authors gathered information regarding the economic, social, and legal feasibility of sustaining each fishery, and report on the structure and function of the fish collection and distribution system

  17. Adaptive landscapes and density-dependent selection in declining salmonid populations: going beyond numerical responses to human disturbance.

    Science.gov (United States)

    Einum, Sigurd; Robertsen, Grethe; Fleming, Ian A

    2008-05-01

    Theory suggests an important role for population density in shaping adaptive landscapes through density-dependent selection. Here, we identify five methodological approaches for studying such selection, review the existing empirical evidence for it, and ask whether current declines in abundance can be expected to trigger evolutionary responses in salmonid fishes. Across taxa we find substantial amounts of evidence for population density influencing the location of adaptive peaks for a range of traits, and, in the presence of frequency dependence, changing the shape of selection (stabilizing versus disruptive). For salmonids, biological and theoretical considerations suggest that the optimal value of a number of traits associated with juvenile competitive ability (e.g. egg size, timing of emergence from nests, dominance ability), may depend on population density. For adults, more direct experimental and comparative evidence suggest that secondary sexual traits can be subject to density-dependent selection. There is also evidence that density affects the frequency-dependent selection likely responsible for the expression of alternative male reproductive phenotypes in salmon. Less is known however about the role of density in maintaining genetic variation among juveniles. Further efforts are required to elucidate the indirect evolutionary effects of declining population abundances, both in salmonids and in other anthropogenically challenged organisms.

  18. Hydroacoustic Evaluation of Juvenile Salmonid Passage and Distribution at Lookout Point Dam, 2010

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Fenton; Johnson, Gary E.; Royer, Ida M.; Hughes, James S.; Fischer, Eric S.; Trott, Donna M.; Ploskey, Gene R.

    2011-07-01

    This report presents the results of an evaluation of juvenile salmonid passage and distribution at Lookout Point Dam (LOP) on the Middle Fork Willamette River. The study was conducted by the Pacific Northwest National Laboratory for the U.S. Army Corps of Engineers, Portland District (USACE). The goal of the study was to provide fish passage and distribution data to support decisions on long-term measures to enhance downstream passage at LOP and others dams in USACE’s Willamette Valley Project in response to the listing of Upper Willamette River Spring Chinook salmon (Oncorhynchus tshawytscha) and Upper Willamette River steelhead (O. mykiss) as threatened under the Endangered Species Act. During the year-long study period - February 1, 2010 to January 31, 2011the objectives of the hydroacoustic evaluation of fish passage and distribution at LOP were to: 1. Estimate passage rates, run timing, horizontal distribution, and diel distribution at turbine penstock intakes for smolt-size fish. 2. Estimate passage rates, run timing and diel distribution at turbine penstock intakes for small-size fish. 3. Estimate passage rates and run timing at the regulating outlets for smolt-size fish. 4. Estimate vertical distribution of smolt-size fish in the forebay near the upstream face of the dam. The fixed-location hydroacoustic technique was used to accomplish the objectives of this study. Transducers (420 kHz) were deployed in each penstock intake, above each RO entrance, and on the dam face; a total of nine transducers (2 single-beam and 7 split-beam) were used. We summarize the findings from the hydroacoustic evaluation of juvenile salmonid passage and distribution at LOP during February 2010 through January 2011 as follows. • Fish passage rates for smolt-size fish (> ~90 mm) were highest during December-January and lowest in mid-summer through early fall. • During the entire study period, an estimated total of 142,463 fish ± 4,444 (95% confidence interval) smolt

  19. Hydroacoustic Evaluation of Juvenile Salmonid Passage at The Dalles Dam Sluiceway, 2005

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Gary E.; Khan, Fenton; Hedgepeth, J; Mueller, Robert P.; Rakowski, Cynthia L.; Richmond, Marshall C.; Serkowski, John A.; Skalski, John R.

    2006-06-01

    The U.S. Army Corps of Engineers Portland District engaged the Pacific Northwest National Laboratory to evaluate fish passage at The Dalles Dam powerhouse in 2005. The goal of the study was to provide information on smolt passage that will inform decisions on long-term measures and operations to enhance sluiceway passage and reduce turbine passage to improve smolt survival at the dam. The study addressed one of the main programs dedicated to improving juvenile salmonid survival at The Dalles Dam: Surface Flow Bypass. The study objectives (see below) were met using a combination of hydroacoustic and hydraulic data. The study incorporated fixed-location hydroacoustic methods across the entire powerhouse, with especially intense sampling using multiple split-beam transducers at all sluiceway portals. We did not sample fish passage at the spillway in 2005. In the sluiceway nearfield, we used an acoustic camera to track fish movements. The fish data were interpreted with hydraulic data from a computational fluid dynamics (CFD) model. Fish passage data were collected in the framework of an “experiment” using a randomized block design (3-day treatments; two treatments) to compare two sluiceway operational configurations: Sluice 2+5 and Sluice 2+19 (six gates open for each configuration). Total project outflow was 76% of the 10-year average for spring and 71% of the 10-year average for summer. Based on these findings, we make the following recommendations: 1) The sluice should be operated 24 h/d from April until November. 2) Open six rather than three sluice gates to take advantage of the maximum hydraulic capacity of the sluiceway. 3) Open the three gates above the western-most operating main turbine unit and the three gates at MU 8 where turbine passage rates are relatively high. 4) Operate the turbine units below open sluice gates as a standard fish operations procedure. 5) Develop hydraulic and entrance enhancements to the sluiceway to tap the potential of The

  20. Conservation challenges and research needs for Pacific lamprey in the Columbia River Basin

    Science.gov (United States)

    Clemens, Benjamin J.; Beamish, Richard J.; Coates, Kelly C.; Docker, Margaret F.; Dunham, Jason B.; Gray, Ann E.; Hess, Jon E.; Jolley, Jeffrey C.; Lampman, Ralph T.; McIlraith, Brian J.; Moser, Mary L.; Murauskas, Joshua G.; Noakes, David L. G.; Schaller, Howard A.; Schreck, Carl B.; Starcevich, Steven J.; Streif, Bianca; van de Wetering, Stan J.; Wade, Joy; Weitkamp, Laurie A.; Wyss, Lance A.

    2017-01-01

    The Pacific Lamprey Entosphenus tridentatus, an anadromous fish native to the northern Pacific Ocean and bordering freshwater habitats, has recently experienced steep declines in abundance and range contractions along the West Coast of North America. During the early 1990s, Native American tribes recognized the declining numbers of lamprey and championed their importance. In 2012, 26 entities signed a conservation agreement to coordinate and implement restoration and research for Pacific Lamprey. Regional plans have identified numerous threats, monitoring needs, and strategies to conserve and restore Pacific Lamprey during their freshwater life stages. Prime among these are needs to improve lamprey passage, restore freshwater habitats, educate stakeholders, and implement lamprey-specific research and management protocols. Key unknowns include range-wide trends in status, population dynamics, population delineation, limiting factors, and marine influences. We synthesize these key unknowns, with a focus on the freshwater life stages of lamprey in the Columbia River basin.

  1. Comparative Performance of Acoustic-tagged and PIT-tagged Juvenile Salmonids

    Energy Technology Data Exchange (ETDEWEB)

    Hockersmith, Eric E.; Brown, Richard S.; Liedtke, Theresa L.

    2008-02-01

    Numerous research tools and technologies are currently being used to evaluate fish passage and survival to determine the impacts of the Federal Columbia River Power System (FCRPS) on endangered and threatened juvenile salmonids, including PIT tags, balloon tags, hydroacoustic evaluations, radio telemetry, and acoustic telemetry. Each has advantages and disadvantages, but options are restricted in some situations because of limited capabilities of a specific technology, lack of detection capability downstream, or availability of adequate numbers of fish. However, there remains concern about the comparative effects of the tag or the tagging procedure on fish performance. The recently developed Juvenile Salmonid Acoustic Telemetry System (JSATS) acoustic transmitter is the smallest active acoustic tag currently available. The goal of this study was to determine whether fish tagged with the JSATS acoustic-telemetry tag can provide unbiased estimates of passage behavior and survival within the performance life of the tag. We conducted both field and laboratory studies to assess tag effects. For the field evaluation we released a total of 996 acoustic-tagged fish in conjunction with 21,026 PIT-tagged fish into the tailrace of Lower Granite Dam on 6 and 13 May. Travel times between release and downstream dams were not significantly different for the majority of the reaches between acoustic-tagged and PIT-tagged fish. In addition to the field evaluation, a series of laboratory experiments were conducted to determine if growth and survival of juvenile Chinook salmon surgically implanted with acoustic transmitters is different than untagged or PIT tagged juvenile Chinook salmon. Only yearling fish with integrated and non-integrated transmitters experienced mortalities, and these were low (<4.5%). Mortality among sub-yearling control and PIT-tag treatments ranged up to 7.7% while integrated and non-integrated treatments had slightly higher rates (up to 8.3% and 7

  2. Assessment of Native Salmonids Above Hells Canyon Dam, Idaho, 2004-2005 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, Kevin A.; Lamansky, Jr., James A. (Idaho Department of Fish and Game, Boise, ID)

    2005-08-01

    In the western United States, exotic brook trout Salvelinus fontinalis frequently have a deleterious effect on native salmonids, and biologists often attempt to remove brook trout in streams using electrofishing. Although the success of electrofishing removal projects typically is low, few studies have assessed the underlying mechanisms of failure, especially in terms of compensatory responses. We evaluated the effectiveness of a three-year removal project in reducing brook trout and enhancing native salmonids in 7.8 km of an Idaho stream and looked for brook trout compensatory responses such as decreased natural mortality, increased growth, increased fecundity at length, or earlier maturation. Due to underestimates of the distribution of brook trout in the first year and personnel shortages in the third year, the multiagency watershed advisory group that performed the project fully treated the stream (i.e. multipass removals over the entire stream) in only one year. In 1998, 1999, and 2000, a total of 1,401, 1,241, and 890 brook trout were removed, respectively. For 1999 and 2000, an estimated 88 and 79% of the total number of brook trout in the stream were removed. For the section of stream that was treated in all years, the abundance of age-1 and older brook trout decreased by 85% from 1998 to 2003. In the same area, the abundance of age-0 brook trout decreased 86% from 1998 to 1999 but by 2003 had rebounded to near the original abundance. Abundance of native redband trout Oncorhynchus mykiss decreased for age-1 and older fish but did not change significantly for age-0 fish. Despite high rates of removal, total annual survival rate for brook trout increased from 0.08 {+-} 0.02 in 1998 to 0.20 {+-} 0.04 in 1999 and 0.21 {+-} 0.04 in 2000. Growth of age-0 brook trout was significantly higher in 2000 (the year after their abundance was lowest) compared to other years, and growth of age-1 and age-2 brook trout was significantly lower following the initial removal

  3. Distribution and abundance of anadromous Sea Lamprey Spawners in a fragmented stream: Current status and potential range expansion following barrier removal

    Science.gov (United States)

    Zydlewski, Joseph D.; Gardner, Cory; Coghlan, Stephen M.

    2012-01-01

    Dams fragment watersheds and prevent anadromous fishes from reaching historic spawning habitat. Sedgeunkedunk Stream, a small tributary to the Penobscot River (Maine), has been the focus of efforts to reestablish marine-freshwater connectivity and restore anadromous fishes via the removal of two barriers to fish migration. Currently, Petromyzon marinus (Sea Lamprey) is the only anadromous fish known to spawn successfully in the stream downstream of the lowermost dam. Here, we describe the distribution and abundance of a spawning population of Sea Lamprey in Sedgeunkedunk Stream, prior to and in anticipation of habitat increase after the completion of one barrier removal. In 2008, we estimated the abundance of Sea Lamprey and its nests using daily stream surveys and an open-population mark-recapture model. We captured 47 Sea Lamprey and implanted each with a PIT tag so that we could track movements and nest associations of individual fish. The spawning migration began on 18 June, and the last living individual was observed on 27 June. We located 31 nests, distributed from head-of-tide to the lowermost dam; no spawners or nests were observed in the tidally influenced zone or upstream of this dam. Mean longevity in the stream and the number of nests attended were correlated with arrival date; early migrants were alive longer and attended more nests than later migrants. Males were more likely to be observed away from a nest, or attending three or more nests, than were females, which attended usually one or two nests. We observed a negative association between nest abundance and substrate cover by fine sediment. Based on their observed movements in the system, and the extent of their habitat use, we anticipate that spawning Sea Lamprey will recolonize formerly inaccessible habitat after dam removals.

  4. Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha.

    Directory of Open Access Journals (Sweden)

    Bobbi M Johnson

    Full Text Available The Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha. Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development. Despite historical abundance, many native salmonids are now at risk of extinction. Research and management related to Chinook salmon is usually explored under what are termed "the four H's": habitat, harvest, hatcheries, and hydropower; here we explore a fifth H, history. Patterns of prehistoric and contemporary mitochondrial DNA variation from Chinook salmon were analyzed to characterize and compare population genetic diversity prior to recent alterations and, thus, elucidate a deeper history for this species. A total of 346 ancient and 366 contemporary samples were processed during this study. Species was determined for 130 of the ancient samples and control region haplotypes of 84 of these were sequenced. Diversity estimates from these 84 ancient Chinook salmon were compared to 379 contemporary samples. Our analysis provides the first direct measure of reduced genetic diversity for Chinook salmon from the ancient to the contemporary period, as measured both in direct loss of mitochondrial haplotypes and reductions in haplotype and nucleotide diversity. However, these losses do not appear equal across the basin, with higher losses of diversity in the mid-Columbia than in the Snake subbasin. The results are unexpected, as the two groups were predicted to share a common history as parts of the larger Columbia River Basin, and instead indicate that Chinook salmon in these subbasins

  5. Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha.

    Science.gov (United States)

    Johnson, Bobbi M; Kemp, Brian M; Thorgaard, Gary H

    2018-01-01

    The Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha). Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development. Despite historical abundance, many native salmonids are now at risk of extinction. Research and management related to Chinook salmon is usually explored under what are termed "the four H's": habitat, harvest, hatcheries, and hydropower; here we explore a fifth H, history. Patterns of prehistoric and contemporary mitochondrial DNA variation from Chinook salmon were analyzed to characterize and compare population genetic diversity prior to recent alterations and, thus, elucidate a deeper history for this species. A total of 346 ancient and 366 contemporary samples were processed during this study. Species was determined for 130 of the ancient samples and control region haplotypes of 84 of these were sequenced. Diversity estimates from these 84 ancient Chinook salmon were compared to 379 contemporary samples. Our analysis provides the first direct measure of reduced genetic diversity for Chinook salmon from the ancient to the contemporary period, as measured both in direct loss of mitochondrial haplotypes and reductions in haplotype and nucleotide diversity. However, these losses do not appear equal across the basin, with higher losses of diversity in the mid-Columbia than in the Snake subbasin. The results are unexpected, as the two groups were predicted to share a common history as parts of the larger Columbia River Basin, and instead indicate that Chinook salmon in these subbasins may have divergent

  6. Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha

    Science.gov (United States)

    Kemp, Brian M.; Thorgaard, Gary H.

    2018-01-01

    The Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha). Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development. Despite historical abundance, many native salmonids are now at risk of extinction. Research and management related to Chinook salmon is usually explored under what are termed “the four H’s”: habitat, harvest, hatcheries, and hydropower; here we explore a fifth H, history. Patterns of prehistoric and contemporary mitochondrial DNA variation from Chinook salmon were analyzed to characterize and compare population genetic diversity prior to recent alterations and, thus, elucidate a deeper history for this species. A total of 346 ancient and 366 contemporary samples were processed during this study. Species was determined for 130 of the ancient samples and control region haplotypes of 84 of these were sequenced. Diversity estimates from these 84 ancient Chinook salmon were compared to 379 contemporary samples. Our analysis provides the first direct measure of reduced genetic diversity for Chinook salmon from the ancient to the contemporary period, as measured both in direct loss of mitochondrial haplotypes and reductions in haplotype and nucleotide diversity. However, these losses do not appear equal across the basin, with higher losses of diversity in the mid-Columbia than in the Snake subbasin. The results are unexpected, as the two groups were predicted to share a common history as parts of the larger Columbia River Basin, and instead indicate that Chinook salmon in these subbasins may have

  7. Total mercury concentrations in anadromous Northern Dolly Varden from the northwestern Canadian Arctic: A historical baseline study

    Energy Technology Data Exchange (ETDEWEB)

    Tran, L., E-mail: l5tran@uwaterloo.ca [Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1 (Canada); Reist, J.D. [Fisheries and Oceans Canada, Winnipeg, Manitoba R3T 2N6 (Canada); Power, M., E-mail: m3power@uwaterloo.ca [Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1 (Canada)

    2015-03-15

    Previous research has documented the significance of total mercury (THg) as a northern contaminant in general and of fish in particular. While much research has been devoted to documenting both spatial and temporal changes in THg in consumed fish, little effort has been directed at understanding patterns of THg in Dolly Varden (Salvelinus malma), a prized subsistence species throughout the western North American Arctic. Here we report historical THg concentrations for anadromous Dolly Varden from 10 populations in the Yukon and Northwest Territories sampled across a range of latitudes (67–69°N) and longitudes (136–141°W) between the years 1988–91. Unadjusted mean THg concentrations ranged from 15 to 254 ng/g wet weight. Length-adjusted THg concentrations were significantly different among sites, but were not related to latitude or longitude. Within and among populations, THg was significantly related to fork-length, age, δ{sup 15}N, and δ{sup 13}C, with the variation in THg found among populations being best explained by size. The data serve as an important baseline against which future changes in THg levels in this important subsistence fishery may be compared to determine the significance of any observed trends. - Highlights: • THg were measured in Dolly Varden from the Yukon and Northwest Territories. • Length-adjusted THg concentrations were not related to latitude or longitude. • Among-population variation in THg was best explained by fork-length. • Length-adjusted THg concentrations were related to age, δ{sup 15}N, and δ{sup 13}C. • Mean THg were below Health Canada’s consumption guideline for commercial fish.

  8. Impact of Salmonid alphavirus infection in diploid and triploid Atlantic salmon (Salmo salar L.) fry.

    Science.gov (United States)

    Herath, Tharangani K; Ashby, Angela J; Jayasuriya, Nilantha S; Bron, James E; Taylor, John F; Adams, Alexandra; Richards, Randolph H; Weidmann, Manfred; Ferguson, Hugh W; Taggart, John B; Migaud, Herve; Fordyce, Mark J; Thompson, Kim D

    2017-01-01

    With increasing interest in the use of triploid salmon in commercial aquaculture, gaining an understanding of how economically important pathogens affect triploid stocks is important. To compare the susceptibility of diploid and triploid Atlantic salmon (Salmo salar L.) to viral pathogens, fry were experimentally infected with Salmonid alphavirus sub-type 1 (SAV1), the aetiological agent of pancreas disease (PD) affecting Atlantic salmon aquaculture in Europe. Three groups of fry were exposed to the virus via different routes of infection: intraperitoneal injection (IP), bath immersion, or cohabitation (co-hab) and untreated fry were used as a control group. Mortalities commenced in the co-hab challenged diploid and triploid fish from 11 days post infection (dpi), and the experiment was terminated at 17 dpi. Both diploid and triploid IP challenged groups had similar levels of cumulative mortality at the end of the experimental period (41.1% and 38.9% respectively), and these were significantly higher (p fry also displayed significantly higher levels of pancreatic and myocardial degeneration than triploids. This study showed that both diploid and triploid fry are susceptible to experimental SAV1 infection. The lower virus load seen in the triploids compared to the diploids may possibly be related to differences in cell metabolism between the two groups, however, further investigation is necessary to confirm this and also to assess the outcome of PD outbreaks in other developmental stages of the fish when maintained in commercial production systems.

  9. Phenotypic and genetic characterization of Piscirickettsia salmonis from Chilean and Canadian salmonids.

    Science.gov (United States)

    Otterlei, Alexander; Brevik, Øyvind J; Jensen, Daniel; Duesund, Henrik; Sommerset, Ingunn; Frost, Petter; Mendoza, Julio; McKenzie, Peter; Nylund, Are; Apablaza, Patricia

    2016-03-15

    The study presents the phenotypic and genetic characterization of selected P. salmonis isolates from Atlantic salmon and rainbow trout suffering from SRS (salmonid rickettsial septicemia) in Chile and in Canada. The phenotypic characterization of the P. salmonis isolates were based on growth on different agar media (including a newly developed medium), different growth temperatures, antibiotics susceptibility and biochemical tests. This is the first study differentiating Chilean P. salmonis isolates into two separate genetic groups. Genotyping, based on 16S rRNA-ITS and concatenated housekeeping genes grouped the selected isolates into two clades, constituted by the Chilean strains, while the Canadian isolates form a branch in the phylogenetic tree. The latter consisted of two isolates that were different in both genetic and phenotypic characteristics. The phylogenies and the MLST do not reflect the origin of the isolates with respect to host species. The isolates included were heterogeneous in phenotypic tests. The genotyping methods developed in this study provided a tool for separation of P. salmonis isolates into distinct clades. The SRS outbreaks in Chile are caused by minimum two different genetic groups of P. salmonis. This heterogeneity should be considered in future development of vaccines against this bacterium in Chile. Two different strains of P. salmonis, in regards to genetic and phenotypic characteristics, can occur in the same contemporary outbreak of SRS.

  10. Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids

    Directory of Open Access Journals (Sweden)

    Davidson William S

    2007-11-01

    Full Text Available Abstract Background Several genome duplications have occurred in the evolutionary history of teleost fish. In returning to a stable diploid state, the polyploid genome reorganized, and large portions are lost, while the fish lines evolved to numerous species. Large scale transposon movement has been postulated to play an important role in the genome reorganization process. We analyzed the DNA sequence of several large loci in Salmo salar and other species for the presence of DNA transposon families. Results We have identified bursts of activity of 14 families of DNA transposons (12 Tc1-like and 2 piggyBac-like families, including 11 novel ones in genome sequences of Salmo salar. Several of these families have similar sequences in a number of closely and distantly related fish, lamprey, and frog species as well as in the parasite Schistosoma japonicum. Analysis of sequence similarities between copies within the families of these bursts demonstrates several waves of transposition activities coinciding with salmonid species divergence. Tc1-like families show a master gene-like copying process, illustrated by extensive but short burst of copying activity, while the piggyBac-like families show a more random copying pattern. Recent families may include copies with an open reading frame for an active transposase enzyme. Conclusion We have identified defined bursts of transposon activity that make use of master-slave and random mechanisms. The bursts occur well after hypothesized polyploidy events and coincide with speciation events. Parasite-mediated lateral transfer of transposons are implicated.

  11. Molecular differentiation of infectious pancreatic necrosis virus isolates from farmed and wild salmonids in Ireland.

    Science.gov (United States)

    Ruane, N M; McCarthy, L J; Swords, D; Henshilwood, K

    2009-12-01

    This study investigated the genotypes and sub-groups of infectious pancreatic necrosis virus (IPNV) present in farmed and wild salmonid fish in Ireland. An 1100-bp portion of the VP2 region of segment A from each of 55 IPNV isolates collected over 2003-2007 was amplified by reverse-transcription-polymerase chain reaction and the product directly sequenced. The nucleotide sequences of each isolate were aligned and compared with each other and with the corresponding sequences of a number of reference isolates. All the 55 sequenced isolates belonged to genogroup 5 (Sp serotype) and could be divided into two subgroups. Irish subgroup 1 consisted of isolates from farmed salmon originating from an Irish salmon broodstock. Irish subgroup 2 consisted of isolates from imported farmed stock and all reported clinical outbreaks of IPN were associated with isolates from subgroup 2. Isolates from wild fish were identical to some isolates from subgroup 2, and therefore are believed to have originated from infected farms. These results highlight the importance of import risk analysis for diseases not listed under current legislation.

  12. Low temperature-dependent salmonid alphavirus glycoprotein processing and recombinant virus-like particle formation.

    Directory of Open Access Journals (Sweden)

    Stefan W Metz

    Full Text Available Pancreas disease (PD and sleeping disease (SD are important viral scourges in aquaculture of Atlantic salmon and rainbow trout. The etiological agent of PD and SD is salmonid alphavirus (SAV, an unusual member of the Togaviridae (genus Alphavirus. SAV replicates at lower temperatures in fish. Outbreaks of SAV are associated with large economic losses of ~17 to 50 million $/year. Current control strategies rely on vaccination with inactivated virus formulations that are cumbersome to obtain and have intrinsic safety risks. In this research we were able to obtain non-infectious virus-like particles (VLPs of SAV via expression of recombinant baculoviruses encoding SAV capsid protein and two major immunodominant viral glycoproteins, E1 and E2 in Spodoptera frugiperda Sf9 insect cells. However, this was only achieved when a temperature shift from 27°C to lower temperatures was applied. At 27°C, precursor E2 (PE2 was misfolded and not processed by host furin into mature E2. Hence, E2 was detected neither on the surface of infected cells nor as VLPs in the culture fluid. However, when temperatures during protein expression were lowered, PE2 was processed into mature E2 in a temperature-dependent manner and VLPs were abundantly produced. So, temperature shift-down during synthesis is a prerequisite for correct SAV glycoprotein processing and recombinant VLP production.

  13. Preventive and Prophylactic Measures in Intensive Salmonid Fish Breeding – a Review

    Directory of Open Access Journals (Sweden)

    Miroslava Palíková

    2015-01-01

    Full Text Available Aquaculture represents the fastest growing animal husbandry in many countries word-wide. Intensive fish production has increased the risk of infectious diseases all over the world. Bacterial pathogens probably cause most disease problems in aquaculture. Most infectious bacterial diseases in commercial fish species continue to be controlled by treatment with chemotherapeutic agents although they represent a potential environmental hazard and could also have negative effects on the quality of the final product. The most important problem of antibiotic treatment is the increase in resistant bacteria, the presence of their residues in aquaculture products and the resulting threat to human health. Therefore, it is most effective to prevent the introduction or onset of the disease. Beside preventing the introduction of pathogens, good water quality, reduction of environmental stressors, adequate nutrition and immunization, many substances improving the health status of fish, such as immunostimulants, probiotics, prebiotics, symbiotics and so on, are used in fish breeding. The present review gives an overview of preventive and prophylactic substances which can be used in salmonid fish breeding to improve the health status of fish.

  14. Habitat use by juvenile salmonids in Lake Ontario tributaries-species, age, diel and seasonal effects

    Science.gov (United States)

    Johnson, James H.; McKenna, James E.

    2017-01-01

    Understanding the habitat needs of fish and how these requirements may change seasonally over a 24-h period is important, especially for highly managed sport species. Consequently, we examined the diel and seasonal habitat use of four juvenile salmonid species in streams in the Lake Ontario watershed. For juvenile Atlantic salmon Salmo salarand juvenile rainbow trout Oncorhynchus mykiss, differences in day versus night habitat use were more profound than seasonal differences. Observed differences in day versus night habitat for all species and age classes were mainly due to the use of less object oriented cover at night and to a lesser extent to the use of slower velocities and smaller substrate at night. Seasonal differences in habitat use were also observed, likely due to increased fish size, and included movement to deeper and faster water and the use of larger substrate and more cover from summer to winter. Different habitat variables were important to individual species. Juvenile Atlantic salmon were associated with higher water velocities, juvenile rainbow trout with larger substrate and more cover, and subyearling Chinook salmon O. tshawytscha and subyearling coho salmon O. kisutch with small substrate and less cover. Our observations demonstrate that habitat partitioning occurs and likely reduces intraspecific and interspecific competition which may increase the potential production of all four species in sympatry. Consequently, these findings provide important information for resource managers charged with managing, protecting, and enhancing Great Lakes tributaries where all or some of these species occur.

  15. N-mix for fish: estimating riverine salmonid habitat selection via N-mixture models

    Science.gov (United States)

    Som, Nicholas A.; Perry, Russell W.; Jones, Edward C.; De Juilio, Kyle; Petros, Paul; Pinnix, William D.; Rupert, Derek L.

    2018-01-01

    Models that formulate mathematical linkages between fish use and habitat characteristics are applied for many purposes. For riverine fish, these linkages are often cast as resource selection functions with variables including depth and velocity of water and distance to nearest cover. Ecologists are now recognizing the role that detection plays in observing organisms, and failure to account for imperfect detection can lead to spurious inference. Herein, we present a flexible N-mixture model to associate habitat characteristics with the abundance of riverine salmonids that simultaneously estimates detection probability. Our formulation has the added benefits of accounting for demographics variation and can generate probabilistic statements regarding intensity of habitat use. In addition to the conceptual benefits, model application to data from the Trinity River, California, yields interesting results. Detection was estimated to vary among surveyors, but there was little spatial or temporal variation. Additionally, a weaker effect of water depth on resource selection is estimated than that reported by previous studies not accounting for detection probability. N-mixture models show great promise for applications to riverine resource selection.

  16. Incipient toxicity of lithium to freshwater organisms representing a salmonid habitat

    International Nuclear Information System (INIS)

    Emery, R.; Klopfer, D.C.; Skalski, J.R.

    1981-07-01

    Because the eventual development of fusion power reactors could increase the mining, use and disposal of lithium five-fold by the year 2000, potential effects from unusual amounts of lithium in aquatic environments were investigated. Freshwater oganisms representing a Pacific Northwest salmonid habitat were exposed to elevated conentrations of lithium. Nine parameters were used to determine the incipient toxicity of lithium to rainbow trout (Salmo gairdneri), insect larvae (Chironomus sp.), and Columbia River periphyton. All three groups of biota were incipiently sensitive to lithium at concentrations ranging between 0.1 and 1 mg/L. These results correspond with the incipient toxicity of beryllium, a chemically similar component of fusion reactor cores. A maximum lithium concentration of 0.01 mg/L occurs naturally in most freshwater environments (beryllium is rarer). Therefore, a concentration range of 0.01 to 0.1 mg/L may be regarded as approaching toxic concentrations when assessing the hazards of lithium in freshwaters

  17. Polychlorinated biphenyls in freshwater salmonids from the Kerguelen Islands in the Southern Ocean

    International Nuclear Information System (INIS)

    Jaffal, A.; Givaudan, N.; Betoulle, S.; Terreau, A.; Paris-Palacios, S.; Biagianti-Risbourg, S.; Beall, E.; Roche, H.

    2011-01-01

    The Subantarctic Kerguelen Islands (49 o S, 70 o E) contain freshwater ecosystems among the most isolated in the world. Concentrations of polychlorinated biphenyls (PCBs) were assessed in the muscle of 48 brook trout and 38 brown trout caught during summer and spring 2006 in the rivers, lakes and ponds of Kerguelen. The sum of 29 PCBs averaged 404 and 358 ng g -1 lipid, and dioxin-like PCB was 19 and 69 ng g -1 lipid, in brook and brown trout, respectively. The values showed a high variability and some fish accumulated PCBs at levels similar to those of fish from impacted areas. While inter-sex differences were limited, the season and the morphotype appeared to have the most influence. Fish captured in summer had muscle PCB concentrations about three times higher than those caught in spring and the 'river' morphotype of brook trout showed the highest PCB levels. - Highlights: → First assessment of PCB contamination of biota in Kerguelen Islands, Sub-Antarctica. → PCB bioaccumulation level in trout varies from very high to undetectable. → Habitat and morphotype are the most influential factors on the variability. → Distribution pattern of PCBs in the muscle of fish is morphotype dependent. - Salmonids in hydrosystems of the Kerguelen Islands (Southern Ocean) show a high PCB bioaccumulation.

  18. Efficiency of Portable Antennas for Detecting Passive Integrated Transponder Tags in Stream-Dwelling Salmonids.

    Directory of Open Access Journals (Sweden)

    Nolan P Banish

    Full Text Available Portable antennas have become an increasingly common technique for tracking fish marked with passive integrated transponder (PIT tags. We used logistic regression to evaluate how species, fish length, and physical habitat characteristics influence portable antenna detection efficiency in stream-dwelling brown trout (Salmo trutta, bull trout (Salvelinus confluentus, and redband trout (Oncorhynchus mykiss newberrii marked with 12-mm PIT tags. We redetected 56% (20/36 of brown trout, 34% (68/202 of bull trout, and 33% (20/61 of redband trout after a recovery period of 21 to 46 hours. Models indicate support for length and species and minor support for percent boulder, large woody debris, and percent cobble as parameters important for describing variation in detection efficiency, although 95% confidence intervals for estimates were large. The odds of detecting brown trout (1.5 ± 2.2 [mean ± SE] are approximately four times as high as bull trout (0.4 ± 1.6 or redband trout (0.3 ± 1.8 and species-specific differences may be related to length. Our reported detection efficiency for brown trout falls within the range of other studies, but is the first reported for bull trout and redband trout. Portable antennas may be a relatively unbiased way of redetecting varying sizes of all three salmonid species.

  19. Incipient toxicity of lithium to freshwater organisms representing a salmonid habitat

    Energy Technology Data Exchange (ETDEWEB)

    Emery, R.; Klopfer, D.C.; Skalski, J.R.

    1981-07-01

    Because the eventual development of fusion power reactors could increase the mining, use and disposal of lithium five-fold by the year 2000, potential effects from unusual amounts of lithium in aquatic environments were investigated. Freshwater oganisms representing a Pacific Northwest salmonid habitat were exposed to elevated conentrations of lithium. Nine parameters were used to determine the incipient toxicity of lithium to rainbow trout (Salmo gairdneri), insect larvae (Chironomus sp.), and Columbia River periphyton. All three groups of biota were incipiently sensitive to lithium at concentrations ranging between 0.1 and 1 mg/L. These results correspond with the incipient toxicity of beryllium, a chemically similar component of fusion reactor cores. A maximum lithium concentration of 0.01 mg/L occurs naturally in most freshwater environments (beryllium is rarer). Therefore, a concentration range of 0.01 to 0.1 mg/L may be regarded as approaching toxic concentrations when assessing the hazards of lithium in freshwaters.

  20. Efficiency of portable antennas for detecting passive integrated transponder tags in stream-dwelling salmonids

    Science.gov (United States)

    Banish, Nolan P.; Burdick, Summer M.; Moyer, Katherine R.

    2016-01-01

    Portable antennas have become an increasingly common technique for tracking fish marked with passive integrated transponder (PIT) tags. We used logistic regression to evaluate how species, fish length, and physical habitat characteristics influence portable antenna detection efficiency in stream-dwelling brown trout (Salmo trutta), bull trout (Salvelinus confluentus), and redband trout (Oncorhynchus mykiss newberrii) marked with 12-mm PIT tags. We redetected 56% (20/36) of brown trout, 34% (68/202) of bull trout, and 33% (20/61) of redband trout after a recovery period of 21 to 46 hours. Models indicate support for length and species and minor support for percent boulder, large woody debris, and percent cobble as parameters important for describing variation in detection efficiency, although 95% confidence intervals for estimates were large. The odds of detecting brown trout (1.5 ± 2.2 [mean ± SE]) are approximately four times as high as bull trout (0.4 ± 1.6) or redband trout (0.3 ± 1.8) and species-specific differences may be related to length. Our reported detection efficiency for brown trout falls within the range of other studies, but is the first reported for bull trout and redband trout. Portable antennas may be a relatively unbiased way of redetecting varying sizes of all three salmonid species.

  1. Development of a rapid and efficient microinjection technique for gene insertion into fertilized salmonid eggs

    Energy Technology Data Exchange (ETDEWEB)

    Chandler, D.P.; Welt, M.; Leung, F.C.

    1990-10-01

    An efficient one-step injection technique for gene insertion into fertilized rainbow trout (Oncorhynchus mykiss) eggs is described, and basic parameters affecting egg survival are reported. Freshly fertilized rainbow trout eggs were injected in the perivitelline space with a recombinant mouse metallothionein-genomic bovine growth hormone (bGH) DNA construct using a 30-gauge hypodermic needle and a standard microinjection system. Relative to control, site of injection and DNA concentration did not affect the egg survival, but injections later than 3--4 hours post fertilization were detrimental. The injection technique permitted treatment of 100 eggs/hr with survivals up to 100%, resulting in a 4% DNA uptake rate as indicated by DNA dot blot analysis. Positive dot blot results also indicated that the injected DNA is able to cross the vitelline membrane and persist for 50--60 days post hatching, obviating the need for direct injection into the germinal disk. Results are consistent with previous transgenic fish work, underscoring the usefulness of the technique for generating transgenic trout and salmonids. 24 refs., 6 figs., 3 tabs.

  2. Strategic planning for instream flow restoration: a case study of potential climate change impacts in the central Columbia River basin.

    Science.gov (United States)

    Donley, Erin E; Naiman, Robert J; Marineau, Mathieu D

    2012-10-01

    We provide a case study prioritizing instream flow restoration activities by sub-basin according to the habitat needs of Endangered Species Act (ESA)-listed salmonids relative to climate change in the central Columbia River basin in Washington State (USA). The objective is to employ scenario analysis to inform and improve existing instream flow restoration projects. We assess the sensitivity of late summer (July, August, and September) flows to the following scenario simulations - singly or in combination: climate change, changes in the quantity of water used for irrigation and possible changes to existing water resource policy. Flows for four sub-basins were modeled using the Water Evaluation and Planning system (WEAP) under historical and projected conditions of 2020 and 2040 for each scenario. Results indicate that Yakima will be the most flow-limited sub-basin with average reductions in streamflow of 41% under climate conditions of 2020 and 56% under 2040 conditions; 1.3-2.5 times greater than those of other sub-basins. In addition, irrigation plays a key role in the hydrology of the Yakima sub-basin - with flow reductions ranging from 78% to 90% under severe to extreme (i.e., 20-40%) increases in agricultural water use (2.0-4.4 times the reductions in the other sub-basins). The Yakima and Okanogan sub-basins are the most responsive to simulations of flow-bolstering policy change (providing salmon with first priority water allocation and at biologically relevant flows), as demonstrated by 91-100% target flows attained. The Wenatchee and Methow sub-basins do not exhibit similar responsiveness to simulated policy changes. Considering climate change only, we conclude that flow restoration should be prioritized first in the Yakima and Wenatchee sub-basins, and second in the Okanogan and Methow. Considering both climate change and possible policy changes, we recommend that the Yakima sub-basin receive the highest priority for flow restoration activities to sustain

  3. Instream flow characterization of upper Salmon River Basin streams, Central Idaho, 2003

    Science.gov (United States)

    Maret, Terry R.; Hortness, Jon E.; Ott, Douglas S.

    2004-01-01

    Anadromous fish populations in the Columbia River Basin have plummeted in the last 100 years. This severe decline led to Federal listing of chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) stocks as endangered or threatened under the Endangered Species Act (ESA) in the 1990s. Historically, the upper Salmon River Basin (upstream from the confluence with the Pahsimeroi River) in Idaho provided migration corridors and significant habitat for these ESA-listed species, in addition to the federally listed bull trout (Salvelinus confluentus). Human development has modified the original streamflow conditions in many streams in the upper Salmon River Basin. Summer streamflow modifications, as a result of irrigation practices, have directly affected the quantity and quality of fish habitat and also have affected migration and (or) access to suitable spawning and rearing habitat for these fish. As a result of these ESA listings and Action 149 of the Federal Columbia River Power System Biological Opinion of 2000, the Bureau of Reclamation was tasked to conduct streamflow characterization studies in the upper Salmon River Basin to clearly define habitat requirements for effective species management and habitat restoration. These studies include the collection of habitat and streamflow information for the Physical Habitat Simulation (PHABSIM) model, a widely applied method to determine relations between habitat and discharge requirements for various fish species and life stages. Model results can be used by resource managers to guide habitat restoration efforts in the evaluation of potential fish habitat and passage improvements by increasing streamflow. Instream flow characterization studies were completed on Pole, Fourth of July, Elk, and Valley Creeks during 2003. Continuous streamflow data were collected upstream from all diversions on each stream. In addition, natural summer streamflows were estimated for each study site using regression

  4. StreamNet: Report on the status of salmon and steelhead in the Columbia River Basin -- 1995

    International Nuclear Information System (INIS)

    Anderson, D.A.; Christofferson, G.; Beamesderfer, R.; Woodard, B.; Rowe, M.; Hansen, J.

    1996-04-01

    Information on fish populations, fisheries, and fish habitat is crucial to the success of ongoing program to protect, recover, enhance, and manage fish resources in the Columbia River Basin. However, pertinent data are often difficult to locate because it is scattered among many agencies and is often unpublished. The goal of this annual report is to bring many diverse data types and sources into a single comprehensive report on the status of anadromous fish runs in the Columbia River Basin and the environmental conditions that may affect that status. Brief summaries are provided to identify the type and scope of available information. This synopsis is intended to complement other more detailed reports to which readers are referred for comprehensive treatment of specific subjects. This first report focuses mainly on anadromous salmon and steelhead (primarily through 1994) but the authors intend to expand the scope of future issues to include resident species. This is the first of what the authors intend to be an annual report. They welcome constructive suggestions for improvements. This report is a product of the StreamNet (formerly Coordinated Information System and Northwest Environmental Data Base) project which is a part of the Bonneville Power Administration's program to protect, mitigate, and enhance fish and wildlife affected by the development and operation of hydroelectric facilities on the Columbia River and its tributaries. The project is called for in the Fish and Wildlife Program of the Northwest Power Planning Council. The project's objective is to promote exchange and dissemination of information in a standardized electronic format throughout the basin. This project is administered by the Pacific States Marine Fisheries Commission with active participation by tribal, state, and federal fish and wildlife agencies

  5. Summary Report for Bureau of Fisheries Stream Habitat Surveys : Umatilla, Tucannon, Asotin, and Grande Ronde River Basins, 1934-1942, Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    McIntosh, Bruce A.; Clark, Sharon E.; Sedell, James R.

    1995-01-01

    This document contains summary reports of stream habitat surveys, conducted in the Umatilla and Grande Ronde River basins, by the Bureau of Fisheries (BOF, now National Marine Fisheries Service) from 1938-1942. These surveys were part of a larger project to survey streams in the Columbia River basin that provided, or had provided, spawning and rearing habitat for salmon and steelhead (Rich, 1948). The purpose of the survey was, as described by Rich, 'to determine the present condition of the various tributaries with respect to their availability and usefulness for the migration, breeding, and rearing of migratory fishes'. Current estimates of the loss of anadromous fish habitat in the Columbia River Basin are based on a series of reports published from 1949-1952 by the U.S. Fish and Wildlife Service. The reports were brief, qualitative accounts of over 5000 miles of stream surveys conducted by the BOF from 1934-1946 (Bryant, 1949; Bryant and Parkhurst, 1950; Parkhurst, 1950a-c; Parkhurst et al 1950). Despite their brevity, these BOF reports have formed the basis for estimating fish habitat losses and conditions in the Columbia River Basin (Fulton, 1968, 1970; Thompson, 1976; NPPC, 1986). Recently, the field notebooks from the BOF surveys were discovered. The data is now archived and stored in the Forest Science DataBank at Oregon State University (Stafford et al., 1984; 1988). These records are the earliest and most comprehensive documentation available of the condition and extent of anadromous fish habitat before hydropower development in the Columbia River Basin. They provide the baseline data for quantifying changes and setting a benchmark for future restoration of anadromous fish habitat throughout the Basin. The summaries contained in this book are exact replicates of the originals. Due to discrepancies between the field data and the summaries, the database should be used to assess pool and substrate conditions. This data is available from the

  6. Yakima Fisheries Project revised Draft Environmental Impact Statement: Summary

    International Nuclear Information System (INIS)

    1995-05-01

    The Bonneville Power Administration (BPA) proposes to fund the Yakima Fisheries Project (YFP) to undertake fishery research and enhancement activities in the Yakima River Basin. The State of Washington and the Yakima Indian Nation would jointly direct the project. The Yakima River system is a promising location for mitigation and enhancement to compensate for stock losses from development and operation of hydroelectric projects elsewhere in the Columbia Basin. The YFP would help determine the role that supplementation might play in increasing natural production of anadromous salmonids throughout the Columbia Basin. In cooperation with BPA, the project managers propose to construct, operate and maintain anadromous (e.g. salmon) fish production facilities. The goal is to conduct research activities designed to increase knowledge of supplementation techniques. These techniques would be applied to rebuild naturally spawning anadromous fish stocks historically present in the Yakima River Basin and, ultimately, those throughout the Columbia River Basin. Eventually, the YFP might involve the supplementation of all stocks of anadromous fish known to have occurred in the Yakima Basin. However, at this time only two alternatives have been proposed: Alternative 1 would supplement depressed naturally spawning populations of upper Yakima spring chinook salmon; Alternative 2 (preferred) would include all actions under Alternative 1; it would also add a study to determine the feasibility of re-establishing a naturally spawning population and a significant fall fishery for coho salmon in the Yakima Basin. (Coho smolts are currently being imported from another basin under the Columbia River Basin Fish Management Plan; the stock is now virtually eliminated from the Basin.)

  7. Superimposed versus residual basin: The North Yellow Sea Basin

    Directory of Open Access Journals (Sweden)

    Wenyong Li

    2012-01-01

    Full Text Available The North Yellow Sea Basin is a Mesozoic and Cenozoic basin. Based on basin-margin facies, sedimentary thinning, size and shape of the basin and vitrinite reflectance, North Yellow Sea Basin is not a residual basin. Analysis of the development of the basin’s three structural layers, self-contained petroleum systems, boundary fault activity, migration of the Mesozoic–Cenozoic sedimentation centers, different basin structures formed during different periods, and superposition of a two-stage extended basin and one-stage depression basin, the North Yellow Sea Basin is recognized as a superimposed basin.

  8. Fish assemblages and environmental variables associated with hard-rock mining in the Coeur d'Alene River basin, Idaho

    Science.gov (United States)

    Maret, Terry R.; MacCoy, Dorene E.

    2002-01-01

    As part of the U.S. Geological Survey's National Water Quality Assessment Program, fish assemblages, environmental variables, and associated mine densities were evaluated at 18 test and reference sites during the summer of 2000 in the Coeur d'Alene and St. Regis river basins in Idaho and Montana. Multimetric and multivariate analyses were used to examine patterns in fish assemblages and the associated environmental variables representing a gradient of mining intensity. The concentrations of cadmium (Cd), lead (Pb), and zinc (Zn) in water and streambed sediment found at test sites in watersheds where production mine densities were at least 0.2 mines/km2 (in a 500-m stream buffer) were significantly higher than the concentrations found at reference sites. Many of these metal concentrations exceeded Ambient Water Quality Criteria (AWQC) and the Canadian Probable Effect Level guidelines for streambed sediment. Regression analysis identified significant relationships between the production mine densities and the sum of Cd, Pb, and Zn concentrations in water and streambed sediment (r2 = 0.69 and 0.66, respectively; P the primary metal contaminant in both water and streambed sediment. Eighteen fish species in the families Salmonidae, Cottidae, Cyprinidae, Catostomidae, Centrarchidae, and Ictaluridae were collected. Principal components analysis of 11 fish metrics identified two distinct groups of sites corresponding to the reference and test sites, predominantly on the basis of the inverse relationship between percent cottids and percent salmonids (r = -0.64; P the areas of intensive hard-rock mining in the Coeur d'Alene River basin contained fewer native fish and lower abundances as a result of metal enrichment, not physical habitat degradation. Typically, salmonids were the predominant species at test sites where Zn concentrations exceeded the acute AWQC. Cottids were absent at these sites, which suggests that they are more severely affected by elevated metals than are

  9. Hydroacoustic Evaluation of Juvenile Salmonid Passage and Distribution at Detroit Dam, 2011

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Fenton; Royer, Ida M.; Johnson, Gary E.; Ham, Kenneth D.

    2012-11-15

    Pacific Northwest National Laboratory evaluated juvenile salmonid passage and distribution at Detroit Dam (DET) on the North Santiam River, Oregon for the U.S. Army Corps of Engineers (USACE) to provide data to support decisions on long-term measures to enhance downstream passage at DET and others dams in USACE’s Willamette Valley Project. This study was conducted in response to regulatory requirements necessitated by the listing of Upper Willamette River Spring Chinook salmon (Oncorhynchus tshawytscha) and Upper Willamette River steelhead (O. mykiss) as threatened under the Endangered Species Act. The goal of the study was to provide information of juvenile salmonid passage and distribution at DET from February 2011 through February 2012. The results of the hydroacoustic study provide new and, in some cases, first-ever data on passage estimates, run timing, distributions, and relationships between fish passage and environmental variables at the dam. This information will inform management decisions on the design and development of surface passage and collection devices to help restore Chinook salmon populations in the North Santiam River watershed above DET. During the entire study period, an estimated total of 182,526 smolt-size fish (±4,660 fish, 95% CI) passed through turbine penstock intakes. Run timing peaked in winter and early spring months. Passage rates were highest during late fall, winter and early spring months and low during summer. Horizontal distribution for hours when both turbine units were operated simultaneously indicated Unit 2 passed almost twice as much fish as Unit 1. Diel distribution for smolt-size fish during the study period was fairly uniform, indicating fish were passing the turbines at all times of the day. A total of 5,083 smolt-size fish (± 312 fish, 95% CI) were estimated passed via the spillway when it was open between June 23 and September 27, 2011. Daily passage was low at the spillway during the June-August period, and

  10. Hydroacoustic Evaluation of Juvenile Salmonid Passage and Distribution at Lookout Point Dam, 2010

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Fenton; Johnson, Gary E.; Royer, Ida M.; Hughes, James S.; Fischer, Eric S.; Trott, Donna M.; Ploskey, Gene R.

    2012-05-31

    Pacific Northwest National Laboratory evaluated juvenile salmonid passage and distribution at Lookout Point Dam (LOP) on the Middle Fork Willamette River for the U.S. Army Corps of Engineers, Portland District (USACE), to provide data to support decisions on long-term measures to enhance downstream passage at LOP and others dams in USACE's Willamette Valley Project. This study was conducted in response to the listing of Upper Willamette River Spring Chinook salmon (Oncorhynchus tshawytscha) and Upper Willamette River steelhead (O. mykiss) as threatened under the Endangered Species Act. We conducted a hydroacoustic evaluation of juvenile salmonid passage and distribution at LOP during February 2010 through January 2011. Findings from this 1 year of study should be applied carefully because annual variation can be expected due to variability in adult salmon escapement, egg-to-fry and fry-to-smolt survival rates, reservoir rearing and predation, dam operations, and weather. Fish passage rates for smolt-size fish (> {approx}90 mm and < 300 mm) were highest during December-January and lowest in mid-summer through early fall. Passage peaks were also evident in early spring, early summer, and late fall. During the entire study period, an estimated total of 142,463 fish {+-} 4,444 (95% confidence interval) smolt-size fish passed through turbine penstock intakes. Of this total, 84% passed during December-January. Run timing for small-size fish ({approx}65-90 mm) peaked (702 fish) on December 18. Diel periodicity of smolt-size fish showing crepuscular peaks was evident in fish passage into turbine penstock intakes. Relatively few fish passed into the Regulating Outlets (ROs) when they were open in summer (2 fish/d) and winter (8 fish/d). Overall, when the ROs were open, RO efficiency (RO passage divided by total project passage) was 0.004. In linear regression analyses, daily fish passage (turbines and ROs combined) for smolt-size fish was significantly related to

  11. Significance of Selective Predation and Development of Prey Protection Measures for Juvenile Salmonids in the Columbia and Snake River Reservoirs: Annual Progress Report, February 1991-February 1992.

    Energy Technology Data Exchange (ETDEWEB)

    Poe, Thomas P.

    1992-12-31

    This document is the 1991 annual report of progress for the Bonneville Power Administration (BPA) research Project conducted by the US Fish and Wildlife Service (FWS). Our approach was to present the progress achieved during 1991 in a series of separate reports for each major project task. Each report is prepared in the format of a scientific paper and is able to stand alone, whatever the state of progress or completion. This project has two major goals. One is to understand the significance of selective predation and prey vulnerability by determining if substandard juvenile salmonids (dead, injured, stressed, diseased, or naive) are more vulnerable to predation by northern squawfish, than standard or normal juvenile salmonids. The second goal is to develop and test prey protection measures to control predation on juvenile salmonids by reducing predator-smolt encounters or predator capture efficiency.

  12. Designing a monitoring program to estimate estuarine survival of anadromous salmon smolts: simulating the effect of sample design on inference

    Science.gov (United States)

    Romer, Jeremy D.; Gitelman, Alix I.; Clements, Shaun; Schreck, Carl B.

    2015-01-01

    A number of researchers have attempted to estimate salmonid smolt survival during outmigration through an estuary. However, it is currently unclear how the design of such studies influences the accuracy and precision of survival estimates. In this simulation study we consider four patterns of smolt survival probability in the estuary, and test the performance of several different sampling strategies for estimating estuarine survival assuming perfect detection. The four survival probability patterns each incorporate a systematic component (constant, linearly increasing, increasing and then decreasing, and two pulses) and a random component to reflect daily fluctuations in survival probability. Generally, spreading sampling effort (tagging) across the season resulted in more accurate estimates of survival. All sampling designs in this simulation tended to under-estimate the variation in the survival estimates because seasonal and daily variation in survival probability are not incorporated in the estimation procedure. This under-estimation results in poorer performance of estimates from larger samples. Thus, tagging more fish may not result in better estimates of survival if important components of variation are not accounted for. The results of our simulation incorporate survival probabilities and run distribution data from previous studies to help illustrate the tradeoffs among sampling strategies in terms of the number of tags needed and distribution of tagging effort. This information will assist researchers in developing improved monitoring programs and encourage discussion regarding issues that should be addressed prior to implementation of any telemetry-based monitoring plan. We believe implementation of an effective estuary survival monitoring program will strengthen the robustness of life cycle models used in recovery plans by providing missing data on where and how much mortality occurs in the riverine and estuarine portions of smolt migration. These data

  13. Columbia River Basin Fish and Wildlife Program Annual Implementation Work Plan for fiscal year 1992

    International Nuclear Information System (INIS)

    1991-09-01

    The Columbia River Basin Fish and Wildlife Program Annual Implementation Work Plan (AIWP) for Fiscal Year (FY) 1992 presents Bonneville Power Administration's (BPA) plans for implementing the Columbia River Basin Fish and Wildlife Program (Program) in FY 1992. The AIWP focuses on individual Action Items found in the 1987 Program for which BPA has determined that it has authority and responsibility to implement. Each of the entries in the AIWP includes objectives, background, progress to date in achieving the objectives, and a summary of plans for implementation in FY 1992. Most Action Items are implemented through one or more BPA-funded projects. Each Action Item entry is followed by a list of completed, ongoing, and planned projects, along with objectives, results, schedules, and milestones for each project. In October 1988, BPA and the Columbia Basin Fish and Wildlife Authority (CBFWA) initiated a collaborative and cooperative Implementation Planning Process (IPP). The IPP provided opportunities in FY 1991 for the fish and wildlife agencies. Tribes, and other interested parties to be involved in planning FY 1992 Program implementation. This planing process contributed to the development of this year's AIWP. The joint BPA/CBFWA IPP is expected to continue in FY 1992. The FY 1992 AIWP emphasizes continuation of 143 ongoing, or projected ongoing Program projects, tasks, or task orders, most of which involve protection, mitigation, or enhancement of anadromous fishery resources. The FY 1992 AIWP also contains 10 new Program projects or tasks that are planned to start in FY 1992

  14. Sex Chromosome Evolution, Heterochiasmy, and Physiological QTL in the Salmonid Brook Charr Salvelinus fontinalis

    Directory of Open Access Journals (Sweden)

    Ben J.G. Sutherland

    2017-08-01

    Full Text Available Whole-genome duplication (WGD can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into nonrecombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i.e., heterochiasmy, which is also poorly understood. The family Salmonidae is a model system for these phenomena, having undergone autotetraploidization and subsequent rediploidization in most of the genome at the base of the lineage. The salmonid master sex determining gene is known, and many species have nonhomologous sex chromosomes, putatively due to transposition of this gene. In this study, we identify the sex chromosome of Brook Charr Salvelinus fontinalis and compare sex chromosome identities across the lineage (eight species and four genera. Although nonhomology is frequent, homologous sex chromosomes and other consistencies are present in distantly related species, indicating probable convergence on specific sex and neo-sex chromosomes. We also characterize strong heterochiasmy with 2.7-fold more crossovers in maternal than paternal haplotypes with paternal crossovers biased to chromosome ends. When considering only rediploidized chromosomes, the overall heterochiasmy trend remains, although with only 1.9-fold more recombination in the female than the male. Y chromosome crossovers are restricted to a single end of the chromosome, and this chromosome contains a large interspecific inversion, although its status between males and females remains unknown. Finally, we identify quantitative trait loci (QTL for 21 unique growth, reproductive, and stress-related phenotypes to improve knowledge of the genetic

  15. Seasonal occurrence of diseases in a recirculation system for salmonid fish in the Czech Republic

    Directory of Open Access Journals (Sweden)

    Miroslava Palíková

    2014-01-01

    Full Text Available Aquaculture represents the fastest growing animal husbandry in many countries. However, higher intensity of fish farming can pose higher health hazards, too. We monitored the health status of fish from one fish farm in South Bohemia and discovered the main health problems in the breeding. For two years we examined a total of 224 specimens of brook trout (Salvelinus fontinalis, 126 specimens of hybrids (S. fontinalis × S. alpinus, 49 specimens of rainbow trout (Oncorhynchus mykiss – all clinically healthy, and 100 clinically diseased or freshly dead fish. We registered skin erosions mainly in the caudal peduncle and tail fin. Two parasite species were identified (one protist Ichthyophthirius multifiliis and one nematode Raphidascaris acus by parasitological examination. The epidemiological indicators of I. multifiliis were low. The prevalence of adult R. acus was 0–86% with a maximum in June. From November, capsules with larval stages of R. acus appeared in internal organs. Their highest intensity (200 pieces and prevalence (100% were detected in October. By microbiological examination of skin and gills, we identified changes in the density of bacterial population and its species composition dependent on water temperature and fish density. The most important problem on the monitored fish farm seems to be furunculosis of salmonid fish in all clinical forms, and the high intensity of larval stages of R. acus. The originality of this study is based on the fact that the observed breeding employs the first Danish recirculation system in the Czech Republic and no recent information about health problems has been available.

  16. A comparative evaluation of crowding stress on muscle HSP90 and myostatin expression in salmonids

    Science.gov (United States)

    Galt, Nicholas J.; Froehlich, Jacob Michael; McCormick, Stephen; Biga, Peggy R.

    2018-01-01

    Stress is a major factor that contributes to poor production and animal welfare concerns in aquaculture. As such, a thorough understanding of mechanisms involved in the stress response is imperative to developing strategies to mitigate the negative side effects of stressors, including the impact of high stocking densities on growth. The purpose of this study was to determine how the muscle growth inhibitor, myostatin, and the stress-responsive gene HSP90 are regulated in response to crowding stress in rainbow trout (Oncorhynchus mykiss), cutthroat trout (Oncorhynchus clarki), brook trout (Salvelinus fontinalis), and Atlantic salmon (Salmo salar). All species exhibited higher cortisol and glucose levels following the handling stress, indicating physiological response to the treatment. Additionally, all species, except rainbow trout, exhibited higher HSP90 levels in muscle after a 48 h crowding stress. Crowding stress resulted in a decrease of myostatin-1ain brook trout white muscle but not red muscle, while, myostatin-1a and -2a levels increased in white muscle and myostatin-1b levels increased in red muscle in Atlantic salmon. In rainbow trout, no significant changes were detected in either muscle type, but myostatin-1awas upregulated in both white and red skeletal muscle in the closely related cutthroat trout. The variation in response to crowding suggests a complex and species-specific interaction between stress and the muscle gene regulation in these salmonids. Only Atlantic salmon and cutthroat trout exhibited increased muscle myostatin transcription, and also exhibited the largest increase in circulating glucose in response to crowding. These results suggest that species-specific farming practices should be carefully examined in order to optimize low stress culture conditions.

  17. Incorporating episodicity into estimates of Critical Loads for juvenile salmonids in Scottish streams

    Directory of Open Access Journals (Sweden)

    E. E. Bridcut

    2004-01-01

    Full Text Available Critical Load (CL methodology is currently used throughout Europe to assess the risks of ecological damage due to sulphur and nitrogen emissions. Critical acid neutralising capacity (ANCCRIT is used in CL estimates for freshwater systems as a surrogate for biological damage. Although UK CL maps presently use an ANC value of 0 μeq l-1, this value has been based largely on Norwegian lake studies, in which brown trout is chosen as a representative indicator organism. In this study, an ANC value specific for brown trout in Scottish streams was determined and issues were addressed such as salmon and trout sensitivity in streams, episodicity, afforestation and complicating factors such as dissolved organic carbon (DOC and labile aluminium (Al-L. Catchments with significant forest cover were selected to provide fishless sites and to provide catchment comparisons in unpolluted areas. Chemical factors were the primary determinant with land use a secondary determinant of the distribution of salmonid populations at the twenty-six study sites. ANC explained more variance in brown trout density than pH. The most significant index of episodicity was percent of time spent below an ANC of 0 μeq l-1. An ANCCRIT value of 39 μeq l-1 was obtained based on a 50% probability of brown trout occurrence. The use of this revised ANCCRIT value in the CL equation improved the relationship between trout status and exceedance of CLs. Uncertainties associated with variations in Al-L at any fixed ANCCRIT, particularly within forested catchments, and the role of DOC in modifying the toxicity of Al-L are discussed. Keywords: Critical Load, Critical acid neutralising capacity, brown trout, episodes, streams

  18. Comparative evaluation of molecular diagnostic tests for Nucleospora salmonis and prevalence in migrating juvenile salmonids from the Snake River, USA

    Science.gov (United States)

    Badil, Samantha; Elliott, Diane G.; Kurobe, Tomofumi; Hedrick, Ronald P.; Clemens, Kathy; Blair, Marilyn; Purcell, Maureen K.

    2011-01-01

    Nucleospora salmonis is an intranuclear microsporidian that primarily infects lymphoblast cells and contributes to chronic lymphoblastosis and a leukemia-like condition in a range of salmonid species. The primary goal of this study was to evaluate the prevalence of N. salmonis in out-migrating juvenile hatchery and wild Chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss from the Snake River in the U.S. Pacific Northwest. To achieve this goal, we first addressed the following concerns about current molecular diagnostic tests for N. salmonis: (1) nonspecific amplification patterns by the published nested polymerase chain reaction (nPCR) test, (2) incomplete validation of the published quantitative PCR (qPCR) test, and (3) whether N. salmonis can be detected reliably from nonlethal samples. Here, we present an optimized nPCR protocol that eliminates nonspecific amplification. During validation of the published qPCR test, our laboratory developed a second qPCR test that targeted a different gene sequence and used different probe chemistry for comparison purposes. We simultaneously evaluated the two different qPCR tests for N. salmonis and found that both assays were highly specific, sensitive, and repeatable. The nPCR and qPCR tests had good overall concordance when DNA samples derived from both apparently healthy and clinically diseased hatchery rainbow trout were tested. Finally, we demonstrated that gill snips were a suitable tissue for nonlethal detection of N. salmonis DNA in juvenile salmonids. Monitoring of juvenile salmonid fish in the Snake River over a 3-year period revealed low prevalence of N. salmonis in hatchery and wild Chinook salmon and wild steelhead but significantly higher prevalence in hatchery-derived steelhead. Routine monitoring of N. salmonis is not performed for all hatchery steelhead populations. At present, the possible contribution of this pathogen to delayed mortality of steelhead has not been determined.

  19. Corynébactériose des salmonidés : première observation en France

    Directory of Open Access Journals (Sweden)

    DE KINKELIN P.

    1974-07-01

    Full Text Available Un petit germe Gram positif, immobile, a été mis en évidence en quantités importantes (fig. 2, dans des lésions de nécrose rénale (fig. 1 et 3 survenant chez des Saumons Coho d'élevage. La morphologie de la bactérie et les lésions permettent de diagnostiquer la corynebactériose des Salmonidés, dont l'existence n'avait pas été signalée jusqu'à présent sur le continent européen.

  20. Survival Estimates for the Passage of Juvenile Salmonids through Snake River Dams and Reservoirs, 1994 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Muir, William D.

    1995-02-01

    In 1994, the National Marine Fisheries Service and the University of Washington completed the second year of a multi-year study to estimate survival of juvenile salmonids (Oncorhynchus spp.) passing through the dams and reservoirs of the Snake River. Actively migrating smolts were collected at selected locations above, at, and below Lower Granite Dam, tagged with passive integrated transponder (PIT) tags, and released to continue their downstream migration. Survival estimates were calculated using the Single-Release, Modified Single-Release, and Paired-Release Models.

  1. Summary Report for Bureau of Fisheries Stream Habitat Surveys : Clearwater, Salmon, Weiser, and Payette River Basins, 1934-1942, Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    McIntosh, Bruce A.; Clark, Sharon E.; Sedell, James R.

    1995-01-01

    This document contains summary reports of stream habitat surveys, conducted in Idaho, by the Bureau of Fisheries (BOF, now National Marine Fisheries Service) from 1938-1942.. These surveys were part of a larger project to survey streams in the Columbia River basin that provided, or had provided, spawning and rearing habitat for salmon and steelhead (Rich, 1948). The purpose of the survey was, as described by Rich, 'to determine the present condition of the various tributaries with respect to their availability and usefulness for the migration, breeding, and rearing of migratory fishes'. The Idaho portion of the survey consisted of extensive surveys of the Clearwater, Salmon, Weiser, and Payette River Subbasins. Current estimates of the loss of anadromous fish habitat in the Columbia River Basin are based on a series of reports published from 1949-1952 by the U.S. Fish and Wildlife Service. The reports were brief, qualitative accounts of over 5000 miles of stream surveys conducted by the BOF from 1934-1946 (Bryant, 1949; Bryant and Parkhurst, 1950; Parkhurst, 1950a-c; Parkhurst et al., 1950). Despite their brevity, these BOF reports have formed the basis for estimating fish habitat losses and conditions in the Columbia River Basin (Fulton, 1968, 1970; Thompson, 1976; NPPC, 1986). Recently, the field notebooks from the BOF surveys were discovered. The data is now archived and stored in the Forest Science DataBank at Oregon State University (Stafford et al., 1984; 1988). These records are the earliest and most comprehensive documentation available of the condition and extent of anadromous fish habitat before hydropower development in the Columbia River Basin. They provide the baseline data for quantifying changes and setting a benchmark for future restoration of anadromous fish habitat throughout the Basin. The summaries contained in this book are exact replicates of the originals. Due to discrepancies between the field data and the summaries, the database

  2. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume XXI; A Summary of Methods for Conducting Salmonid Fry Mark-Recapture Studies for Estimating Survival in Tributaries, Technical Report 2005-2006.

    Energy Technology Data Exchange (ETDEWEB)

    Skalski, John

    2007-02-01

    Productivity and early fry survival can have a major influence on the dynamics of fish stocks. To investigate the early life history of fish, numerous methods have been developed or adapted to these much smaller fish. Some of the marking techniques provide individual identification; many others, only class identification. Some of the tagging techniques require destructive sampling to identify a mark; other methods permit benign examination and rerelease of captured fish. Sixteen alternative release-recapture designs for conducting fry survival investigations were examined. Eleven approaches were found capable of estimating survival parameters; five were not. Of those methods capable of estimating fry survival, five required unique marks, four required batch-specific marks, and two approaches required remarking and rereleasing captured fry. No approach based on a simple batch mark was capable of statistically estimating survival.

  3. Synthesis of downstream fish passage information at projects owned by the U.S. Army Corps of Engineers in the Willamette River Basin, Oregon

    Science.gov (United States)

    Hansen, Amy C.; Kock, Tobias J.; Hansen, Gabriel S.

    2017-08-07

    The U.S. Army Corps of Engineers (USACE) operates the Willamette Valley Project (Project) in northwestern Oregon, which includes a series of dams, reservoirs, revetments, and fish hatcheries. Project dams were constructed during the 1950s and 1960s on rivers that supported populations of spring Chinook salmon (Oncorhynchus tshawytscha), winter steelhead (O. mykiss), and other anadromous fish species in the Willamette River Basin. These dams, and the reservoirs they created, negatively affected anadromous fish populations. Efforts are currently underway to improve passage conditions within the Project and enhance populations of anadromous fish species. Research on downstream fish passage within the Project has occurred since 1960 and these efforts are documented in numerous reports and publications. These studies are important resources to managers in the Project, so the USACE requested a synthesis of existing literature that could serve as a resource for future decision-making processes. In 2016, the U.S. Geological Survey conducted an extensive literature review on downstream fish passage studies within the Project. We identified 116 documents that described studies conducted during 1960–2016. Each of these documents were obtained, reviewed, and organized by their content to describe the state-of-knowledge within four subbasins in the Project, which include the North Santiam, South Santiam, McKenzie, and Middle Fork Willamette Rivers. In this document, we summarize key findings from various studies on downstream fish passage in the Willamette Project. Readers are advised to review specific reports of interest to insure that study methods, results, and additional considerations are fully understood.

  4. Summary Report for Bureau of Fisheries Stream Habitat Surveys: Cowlitz River Basin, 1934-1942 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    McIntosh, Bruce A.; Clark, Sharon E.; Sedell, James R.

    1995-01-01

    This document contains summary reports of stream habitat surveys, conducted in the Cowlitz River basin, by the Bureau of Fisheries (BOF, now National Marine Fisheries Service) from 1938-1942. These surveys were part of a larger project to survey streams in the Columbia River basin that provided, or had provided, spawning and rearing habitat for salmon and steelhead. The purpose of the survey was, as described by Rich, [open quotes]to determine the present condition of the various tributaries with respect to their availability and usefulness for the migration, breeding, and rearing of migratory fishes[close quotes]. Current estimates of the loss of anadromous fish habitat in the Columbia River Basin are based on a series of reports published from 1949-1952 by the U.S. Fish and Wildlife Service. The reports were brief, qualitative accounts of over 5000 miles of stream surveys conducted by the BOF from 1934-1946. Despite their brevity, these BOF reports have formed the basis for estimating fish habitat losses and conditions in the Columbia River Basin.

  5. Climate vulnerability of native cold-water salmonids in the Northern Rockies Region [Chapter 5

    Science.gov (United States)

    Michael K. Young; Daniel J. Isaak; Scott Spaulding; Cameron A. Thomas; Scott A. Barndt; Matthew C. Groce; Dona Horan; David E. Nagel

    2018-01-01

    During the 21st century, climate change is expected to alter aquatic habitats throughout the Northern Rocky Mountains, intermountain basins, and western Great Plains. Particularly in montane watersheds, direct changes are likely to include warmer water temperatures, earlier snowmelt-driven runoff, earlier declines to summer baseflow, downhill movement of perennial...

  6. Development of a System-Wide Predator Control Program: Stepwise Implementation of a Predation Index, Predator Control Fisheries, and Evaluation Plan in the Columbia River Basin; Northern Pikeminnow Management Program, 2001 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Porter, Russell G.; Winther, Eric C.; Fox, Lyle G.

    2003-03-01

    This report presents results for year eleven in a basin-wide program to harvest northern pikeminnow (Ptychocheilus oregonensis). This program was started in an effort to reduce predation by northern pikeminnow on juvenile salmonids during their emigration from natal streams to the ocean. Earlier work in the Columbia River Basin suggested predation by northern pikeminnow on juvenile salmonids might account for most of the 10-20% mortality juvenile salmonids experience in each of eight Columbia River and Snake River reservoirs. Modeling simulations based on work in John Day Reservoir from 1982 through 1988 indicated that, if predator-size northern pikeminnow were exploited at a 10-20% rate, the resulting restructuring of their population could reduce their predation on juvenile salmonids by 50%. To test this hypothesis, we implemented a sport-reward angling fishery and a commercial longline fishery in the John Day Pool in 1990. We also conducted an angling fishery in areas inaccessible to the public at four dams on the mainstem Columbia River and at Ice Harbor Dam on the Snake River. Based on the success of these limited efforts, we implemented three test fisheries on a system-wide scale in 1991--a tribal longline fishery above Bonneville Dam, a sport-reward fishery, and a dam-angling fishery. Low catch of target fish and high cost of implementation resulted in discontinuation of the tribal longline fishery. However, the sport-reward and dam-angling fisheries were continued in 1992 and 1993. In 1992, we investigated the feasibility of implementing a commercial longline fishery in the Columbia River below Bonneville Dam and found that implementation of this fishery was also infeasible.

  7. Characterization of untranslated regions of the salmonid alphavirus 3 (SAV3 genome and construction of a SAV3 based replicon

    Directory of Open Access Journals (Sweden)

    Rimstad Espen

    2009-10-01

    Full Text Available Abstract Salmonid alphavirus (SAV causes disease in farmed salmonid fish and is divided into different genetic subtypes (SAV1-6. Here we report the cloning and characterization of the 5'- and 3'- untranslated regions (UTR of a SAV3 isolated from Atlantic salmon in Norway. The sequences of the UTRs are very similar to those of SAV1 and SAV2, but single nucleotide polymorphisms are present, also in the 3' - conserved sequence element (3'-CSE. Prediction of the RNA secondary structure suggested putative stem-loop structures in both the 5'- and 3'-ends, similar to those of alphaviruses from the terrestrial environment, indicating that the general genome replication initiation strategy for alphaviruses is also utilized by SAV. A DNA replicon vector, pmSAV3, based upon a pVAX1 backbone and the SAV3 genome was constructed, and the SAV3 non-structural proteins were used to express a reporter gene controlled by the SAV3 subgenomic promoter. Transfection of pmSAV3 into CHSE and BF2 cell lines resulted in expression of the reporter protein, confirming that the cloned SAV3 replication apparatus and UTRs are functional in fish cells.

  8. Hydroacoustic Assessment of Downstream Migrating Salmonids at the Dalles Dam in Spring and Summer, 1985 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Steig, Tracy W.; Johnson, Ward R. (BioSonics, Inc. Seattle, WA)

    1986-02-15

    A hydroacoustic study of downstream migrating salmon and steelhead was conducted at The Dalles Dam. The primary objective was to estimate the effectiveness of the spillway and sluiceway in passing downstream migrants. The secondary goals were to provide information on the horizontal, vertical, and temporal distributions of downstream migrants. June 1, and the summer season was from July 1 to August 15, 1985. Nineteen transducers were deployed to monitor turbine, spillway, and sluiceway locations. The 10 h instantaneous spill effectiveness results showed that spill passed fish more efficiently during the summer study than during the spring study. During the period May 1-31 when the turbines, spillway, and sluiceway were all operating consistently, the sluiceway was found to be the most efficient method of passing fish on a percent flow basis. During the summer study, after the termination of spill, the sluiceway and turbines passed almost equal percentages of fish. The run timing during the spring showed steadily increasing numbers of fish until the peak of the run on May 16. Another, smaller peak occurred on May 20. Thereafter, passage gradually decreased through the end of the spring study. The spring run consisted of yearling chinook, steelhead and sockeye juvenile salmonids. During the summer study, fish passage gradually decreased, except for minor peaks near the beginning of the study. The summer migration consisted primarily of subyearling chinook juvenile salmonids.

  9. A comparison of mercury biomagnification through lacustrine food webs supporting Brook Trout (Salvelinus fontinalis and other salmonid fishes

    Directory of Open Access Journals (Sweden)

    Monica LD Finley

    2016-04-01

    Full Text Available Methyl mercury (MeHg bioaccumulation in lower-trophic-level organisms and its subsequent biomagnification through food webs differs in magnitude among lakes and results in intraspecific variability of MeHg in top predator fishes. Understanding these differences is critical given the reproductive and neurotoxic effects of MeHg on fishes and their predators, including humans. In this study we characterized the food webs of five lakes in New Brunswick, Canada, supporting Brook Trout (Salvelinus fontinalis using measures of relative trophic position (δ15N and carbon sources (δ13C, determined the concentrations of MeHg in invertebrates and total Hg (THg in fishes, and quantified MeHg biomagnification from primary to tertiary consumers. Methyl Hg and THg concentrations were highest in biota from lakes with lower pH. The trophic magnification slopes (TMS; log Hg versus δ15N varied significantly among lakes (0.12-0.20; ANCOVA, p=0.031. When combined with data from other salmonid lakes in temperate and Arctic Canada (n=36, among-system variability in TMS was best, but weakly, positively predicted by aqueous total phosphorous (p = 0.028, R2adj = 0.109. These results suggest that lake productivity directly or indirectly influences the biomagnification of MeHg through diverse food webs supporting salmonids.

  10. Genetically influenced resistance to stress and disease in salmonids in relation to present-day breeding practice - a short review

    Directory of Open Access Journals (Sweden)

    Jan Mendel

    2018-01-01

    Full Text Available While intensive fish production has many advantages, it also has a number of drawbacks as regards disease and stress. To date, there has been no conclusive review of disease resistance at Czech fish farms. The aim of the study was to describe briefly the existing salmonid breeding practice in the Czech Republic and to point out the trends and new possibilities gaining ground around Europe. However, the present situation in the Czech stocks is not rare at all and therefore it is used here as a model example representing numerous breeding practices in Europe. Stress and disease resistance in fish is polygenic and quantitative, making selection for such traits difficult. In recent years, however, fish breeding methods have developed rapidly, with the use of genetic analysis tools, for example, now allowing much greater selection accuracy. Gradual progress in understanding the importance of individual genetic markers offers many new options that can be utilised in breeding practice. New selection methods, such as quantitative trait loci (QTLs and genomic selection, are increasingly employed in European aquaculture. Next generation sequencing techniques now help in the finding of new and promising QTLs that can be used in assisted selection. This review maps the current progress in improving salmonid resistance to stress and disease in aquaculture and at the same time provides the breeders with a short overview of the latest tools of genetically controlled breeding and of the newest products available at the European market.

  11. Evaluating species-specific changes in hydrologic regimes: an iterative approach for salmonids in the Greater Yellowstone Area (USA)

    Science.gov (United States)

    Al-Chokhachy, Robert K.; Sepulveda, Adam; Ray, Andrew M.; Thoma, David P.; Tercek, Michael T.

    2017-01-01

    Despite the importance of hydrologic regimes to the phenology, demography, and abundance of fishes such as salmonids, there have been surprisingly few syntheses that holistically assess regional, species-specific trends in hydrologic regimes within a framework of climate change. Here, we consider hydrologic regimes within the Greater Yellowstone Area in the Rocky Mountains of western North America to evaluate changes in hydrologic metrics anticipated to affect salmonids, a group of fishes with high regional ecological and socioeconomic value. Our analyses assessed trends across different sites and time periods (1930–, 1950–, and 1970–2015) as means to evaluate spatial and temporal shifts. Consistent patterns emerged from our analyses indicating substantial shifts to (1) earlier peak discharge events; (2) reductions of summer minimum streamflows; (3) declines in the duration of river ice; and (4) decreases in total volume of water. We found accelerated trends in hydrologic change for the 1970–2015 period, with an average peak discharge 7.5 days earlier, 27.5% decline in summer minimum streamflows, and a 15.6% decline in the annual total volume of water (1 October–September 30) across sites. We did observe considerable variability in magnitude of change across sites, suggesting different levels of vulnerability to a changing climate. Our analyses provide an iterative means for assessing climate predictions and an important step in identifying the climate resilience of landscapes.

  12. Clinical manifestations of pancreas disease outbreaks in Norwegian marine salmon farming - variations due to salmonid alphavirus subtype.

    Science.gov (United States)

    Jansen, M D; Jensen, B Bang; Brun, E

    2015-04-01

    Pancreas disease (PD) in Norwegian salmonid aquaculture has traditionally been caused by salmonid alphavirus (SAV) subtype 3. Following the isolation of a novel SAV subtype in 2010, marine SAV2, two separate endemic areas have developed. It has been debated whether disease outbreaks due to marine SAV2 result in milder clinical manifestations compared to outbreaks caused by SAV3. The aim of this study was to descriptively investigate site-level differences in the clinical manifestations of marine SAV2 and SAV3 at Norwegian seawater sites diagnosed with PD in 2012. The findings suggest that Norwegian PD outbreaks caused by marine SAV2 result in lower mortality and milder clinical signs compared to outbreaks caused by SAV3. For sites without reported PD-related mortality, there was no difference in the mortality levels between sites infected by marine SAV2 and SAV3. The results also indicate that there are no differences in grading quality at slaughter between the SAV subtypes. © 2014 John Wiley & Sons Ltd.

  13. The impact of the Sea Empress oil spill on the abundance of juvenile migratory salmonids in West Wales

    International Nuclear Information System (INIS)

    Roberts, D.E.; Jones, F.H.; Wyatt, R.J.; Milner, N.J.

    1998-01-01

    No counting facilities for adult salmonids were operational in the rivers draining into the area of coast affected by the Sea Empress oil spill. There were therefore no direct means of determining any impact on the numbers of returning salmon and sea trout. However, a measure of salmon and trout fry abundance before and after (1997) the spill may provide evidence of an impact; on recruitment and abundance of adults. Approximately 10 years historical fry data were available from 53 sites on the Tywi and 41 sites on the Taf, as part of the Welsh Region Juvenile Salmonid Monitoring Programme (RJSMP). An assessment was undertaken by the Water Research Centre on the design of the survey and appropriate data analysis. Analysed data included: River Tywi salmon and trout fry densities 1985-1996, compared to 1997 and Teifi control 1986-1997. River Taf salmon and trout fry densities 1986-1996, compared to 1997 and Teifi control 1986-1997. The abundance of salmon and trout fry in 1997 were similar to previous years suggesting the Sea Empress oil spill did not have a major impact on recruitment. However, it is not possible to conclude unequivocally that returning salmon and sea trout were not affected by the spill. (author)

  14. Detection and quantification of Renibacterium salmoninarum DNA in salmonid tissues by real-time quantitative polymerase chain reaction analysis

    Science.gov (United States)

    Chase, D.M.; Elliott, D.G.; Pascho, R.J.

    2006-01-01

    Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids.

  15. Piscine Reovirus: Genomic and Molecular Phylogenetic Analysis from Farmed and Wild Salmonids Collected on the Canada/US Pacific Coast.

    Directory of Open Access Journals (Sweden)

    Ahmed Siah

    Full Text Available Piscine reovirus (PRV is a double stranded non-enveloped RNA virus detected in farmed and wild salmonids. This study examined the phylogenetic relationships among different PRV sequence types present in samples from salmonids in Western Canada and the US, including Alaska (US, British Columbia (Canada and Washington State (US. Tissues testing positive for PRV were partially sequenced for segment S1, producing 71 sequences that grouped into 10 unique sequence types. Sequence analysis revealed no identifiable geographical or temporal variation among the sequence types. Identical sequence types were found in fish sampled in 2001, 2005 and 2014. In addition, PRV positive samples from fish derived from Alaska, British Columbia and Washington State share identical sequence types. Comparative analysis of the phylogenetic tree indicated that Canada/US Pacific Northwest sequences formed a subgroup with some Norwegian sequence types (group II, distinct from other Norwegian and Chilean sequences (groups I, III and IV. Representative PRV positive samples from farmed and wild fish in British Columbia and Washington State were subjected to genome sequencing using next generation sequencing methods. Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4. In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State, and the sequence types were relatively stable over a 13 year period.

  16. Flow Restoration in the Columbia River Basin: An Evaluation of a Flow Restoration Accounting Framework.

    Science.gov (United States)

    McCoy, Amy L; Holmes, S Rankin; Boisjolie, Brett A

    2018-03-01

    Securing environmental flows in support of freshwater biodiversity is an evolving field of practice. An example of a large-scale program dedicated to restoring environmental flows is the Columbia Basin Water Transactions Program in the Pacific Northwest region of North America, which has been restoring flows in dewatered tributary habitats for imperiled salmon species over the past decade. This paper discusses a four-tiered flow restoration accounting framework for tracking the implementation and impacts of water transactions as an effective tool for adaptive management. The flow restoration accounting framework provides compliance and flow accounting information to monitor transaction efficacy. We review the implementation of the flow restoration accounting framework monitoring framework to demonstrate (a) the extent of water transactions that have been implemented over the past decade, (b) the volumes of restored flow in meeting flow targets for restoring habitat for anadromous fish species, and (c) an example of aquatic habitat enhancement that resulted from Columbia Basin Water Transactions Program investments. Project results show that from 2002 to 2015, the Columbia Basin Water Transactions Program has completed more than 450 water rights transactions, restoring approximately 1.59 million megaliters to date, with an additional 10.98 million megaliters of flow protected for use over the next 100 years. This has resulted in the watering of over 2414 stream kilometers within the Columbia Basin. We conclude with a discussion of the insights gained through the implementation of the flow restoration accounting framework. Understanding the approach and efficacy of a monitoring framework applied across a large river basin can be informative to emerging flow-restoration and adaptive management efforts in areas of conservation concern.

  17. Flow Restoration in the Columbia River Basin: An Evaluation of a Flow Restoration Accounting Framework

    Science.gov (United States)

    McCoy, Amy L.; Holmes, S. Rankin; Boisjolie, Brett A.

    2018-03-01

    Securing environmental flows in support of freshwater biodiversity is an evolving field of practice. An example of a large-scale program dedicated to restoring environmental flows is the Columbia Basin Water Transactions Program in the Pacific Northwest region of North America, which has been restoring flows in dewatered tributary habitats for imperiled salmon species over the past decade. This paper discusses a four-tiered flow restoration accounting framework for tracking the implementation and impacts of water transactions as an effective tool for adaptive management. The flow restoration accounting framework provides compliance and flow accounting information to monitor transaction efficacy. We review the implementation of the flow restoration accounting framework monitoring framework to demonstrate (a) the extent of water transactions that have been implemented over the past decade, (b) the volumes of restored flow in meeting flow targets for restoring habitat for anadromous fish species, and (c) an example of aquatic habitat enhancement that resulted from Columbia Basin Water Transactions Program investments. Project results show that from 2002 to 2015, the Columbia Basin Water Transactions Program has completed more than 450 water rights transactions, restoring approximately 1.59 million megaliters to date, with an additional 10.98 million megaliters of flow protected for use over the next 100 years. This has resulted in the watering of over 2414 stream kilometers within the Columbia Basin. We conclude with a discussion of the insights gained through the implementation of the flow restoration accounting framework. Understanding the approach and efficacy of a monitoring framework applied across a large river basin can be informative to emerging flow-restoration and adaptive management efforts in areas of conservation concern.

  18. Umatilla Basin Natural Production Monitoring and Evaluation; 1998-2002 Summary Report.

    Energy Technology Data Exchange (ETDEWEB)

    Contor, Craig R. (Confederated Tribes of the Umatilla Indian Reservation, Department of Natural Resources, Pendleton, OR)

    2004-07-01

    The Umatilla Basin Natural Production Monitoring and Evaluation Project (WWNPME) was funded by Bonneville Power Administration (BPA) as directed by section 4(h) of the Pacific Northwest Electric Power Planning and Conservation Act of 1980 (P. L. 96-501). This project is in accordance with and pursuant to measures 4.2A, 4.3C.1, 7.1A.2, 7.1C.3, 7.1C.4 and 7.1D.2 of the Northwest Power Planning Council's (NPPC) Columbia River Basin Fish and Wildlife Program (NPPC 1994). Work was conducted by the Fisheries Program of the Confederated Tribes of the Umatilla Indian Reservation (CTUIR) under the Umatilla Basin Natural Production Monitoring and Evaluation Project (UBNPME). Chapter One provides an overview of the entire report and shows how the objectives of each statement of work from 1999, 2000, 2001, and 2002 contract years are organized and reported. This chapter also provides background information relevant to the aquatic resources of the Umatilla River Basin. (Figure 1-1, Tables 1-1 and 1-2). Data and reports from this and previous efforts are available on the CTUIR website http://www.umatilla.nsn.us. This project was one of several subprojects of the Umatilla River Basin Fisheries Restoration Master Plan (CTUIR 1984, ODFW 1986) orchestrated to rehabilitate salmon and steelhead runs in the Umatilla River Basin. Subprojects in additions to this project include: Watershed Enhancement and Rehabilitation; Hatchery Construction and Operation; Hatchery Monitoring and Evaluation; Satellite Facility Construction and Operations for Juvenile Acclimation and Adult Holding and Spawning; Fish Passage Construction and Operation; Juvenile and Adult Passage Facility Evaluations; Evaluation of Juvenile Salmonid Outmigration and Survival in the Lower Umatilla River Basin, and Flow Augmentation to Increase Stream Flows below Irrigation Diversions.

  19. Influence of environmental factors on fish assemblages in streams of the Elbe and Oder basins

    Directory of Open Access Journals (Sweden)

    Luboš Kůra

    2015-11-01

    Full Text Available The effects of environmental parameters on changes in the structure of fish assemblages were studied in the Elbe and the Odra basin. Research was done at 819 sites surveyed in the field during the period 1993-2007. The impact of 46 factors derived from the maps through a GIS was tested as well as the impact of 10 factors recognized in the field. To evaluate the influence of these factors the indirect (DCA and direct (CCA multivariate cluster analysis were used. Analyses were performed with data on presence-absence and relative abundance of each species. DCA well reflects changes in assemblages in the longitudinal profile of streams. CCA refers to a significant influence of regional and temporal variability and influence of individual factors. The fish assemblages are best characterized by distance from the source location, stream slope, altitude of locality, representation of arable land in the basin, number of ponds in the sub-basin above the locality, type of waters (salmonid or cyprinid, and water temperature (the only of the parameters of the field. The analyzed factors better reflect the variability in fish assemblages of the Odra than of Elbe river basin. The analysis showed good practical efficiency of processing information from a large sample of data from ichthyological surveys. The tools of GIS and the use of statistical methods make possible to characterize basic ecological requirements of most species and specify conditions determining specific composition of fish assemblages.

  20. Hydroacoustic Evaluation of Juvenile Salmonid Passage at The Dalles Dam in 2004

    International Nuclear Information System (INIS)

    Johnson, Gary E.; Hanks, Michael E.; Khan, Fenton; Cook, Chris B.; Hedgepeth, J.; Mueller, Robert P.; Rakowski, Cynthia L.; Richmond, Marshall C.; Sargeant, Susan L.; Serkowski, John A.; Skalski, John R.

    2005-01-01

    The U.S. Army Corps of Engineers Portland District engaged the Pacific Northwest National Laboratory to evaluate juvenile salmon passage at The Dalles Dam in 2004 to inform decisions about long-term measures and operations to enhance sluiceway and spill passage and reduce turbine passage to improve smolt survival at the dam. PNNL used fixed-location hydroacoustic sampling across the entire project, especially at the sluiceway and spillway, using multiple split-beam transducers at selected locations. At the sluiceway nearfield, we used an acoustic camera to track fish. The fish data were interpreted and integrated with hydraulic data from a CFD model and in-field ADCP measurements. Two sluiceway operations were compared: West only (SL 1) vs. West+East (SL 1 + SL 18). Based on our findings, we concluded that The Dalles Dam sluiceway has the potential to be highly efficient and effective at passing juvenile salmonids. This potential could be tapped with hydraulic and entrance enhancements to the sluiceway. We recommended the following: (1) six rather than three sluice gates should be opened to take advantage of the maximum hydraulic capacity of the sluiceway. (2) The turbine units below open sluice gates should be operated as a standard fish operations procedure. (3) In 2005, the Corps and fisheries agencies should consider operating sluice gates in one or more of the following combinations of six gates: (a) SL 1-1, 1-2, 1-3 and SL 18-1, 18-2, 18-3 (repeat 2004 operation), (b) SL 1-1, 1-2, 1-3 and SL 11-1, 11-2, 11-3, or (c) SL 1-1, 1-2, 1-3 and SL 2-1, 2-2, 2-3. The following elements for surface flow bypasses which should be considered during design of any sluiceway enhancements at The Dalles Dam: (1) form an extensive surface flow bypass flow net (surface bypass discharge greater than ∼7% of total project discharge), (2) create a gradual increase in water velocity approaching the surface flow bypass (ideally, acceleration 3 m/s) to entrain the subject juvenile

  1. Hydroacoustic Evaluation of Juvenile Salmonid Passage at The Dalles Dam in 2004

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Gary E.; Hanks, Michael E.; Khan, Fenton; Cook, Chris B.; Hedgepeth, J; Mueller, Robert P.; Rakowski, Cynthia L.; Richmond, Marshall C.; Sargeant, Susan L.; Serkowski, John A.; Skalski, John R.

    2005-06-01

    The U.S. Army Corps of Engineers Portland District engaged the Pacific Northwest National Laboratory to evaluate juvenile salmon passage at The Dalles Dam in 2004 to inform decisions about long-term measures and operations to enhance sluiceway and spill passage and reduce turbine passage to improve smolt survival at the dam. PNNL used fixed-location hydroacoustic sampling across the entire project, especially at the sluiceway and spillway, using multiple split-beam transducers at selected locations. At the sluiceway nearfield, we used an acoustic camera to track fish. The fish data were interpreted and integrated with hydraulic data from a CFD model and in-field ADCP measurements. Two sluiceway operations were compared: West only (SL 1) vs. West+East (SL 1 + SL 18). Based on our findings, we concluded that The Dalles Dam sluiceway has the potential to be highly efficient and effective at passing juvenile salmonids. This potential could be tapped with hydraulic and entrance enhancements to the sluiceway. We recommended the following: (1) six rather than three sluice gates should be opened to take advantage of the maximum hydraulic capacity of the sluiceway. (2) The turbine units below open sluice gates should be operated as a standard fish operations procedure. (3) In 2005, the Corps and fisheries agencies should consider operating sluice gates in one or more of the following combinations of six gates: (a) SL 1-1, 1-2, 1-3 and SL 18-1, 18-2, 18-3 (repeat 2004 operation), (b) SL 1-1, 1-2, 1-3 and SL 11-1, 11-2, 11-3, or (c) SL 1-1, 1-2, 1-3 and SL 2-1, 2-2, 2-3. The following elements for surface flow bypasses which should be considered during design of any sluiceway enhancements at The Dalles Dam: (1) form an extensive surface flow bypass flow net (surface bypass discharge greater than {approx}7% of total project discharge), (2) create a gradual increase in water velocity approaching the surface flow bypass (ideally, acceleration < 1 m/s/m), (3) make water

  2. Long-term effective population sizes, temporal stability of genetic composition and potential for local adaptation in anadromous brown trout ( Salmo trutta ) populations

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Ruzzante, D.E.; Eg Nielsen, Einar

    2002-01-01

    We examined the long-term temporal (1910s to 1990s) genetic variation at eight microsatellite DNA loci in brown trout (Salmo trutta L) collected from five anadromous populations in Denmark to assess the long-term stability of genetic composition and to estimate effective population sizes (N...... temporal samples from the same populations than among samples from different populations. Estimates of N-e, using a likelihood-based implementation of the temporal method, revealed N-e greater than or equal to 500 in two of three populations for which we have historical data. A third population in a small...... adaptations resulting from strong selection were expected to occur at the level of individual populations. Adaptations resulting from weak selection were more likely to occur on a regional basis, i.e. encompassing several populations. N-e appears to have declined recently in at least one of the studied...

  3. Differential expression of gill Na+,K+-ATPase alpha- and beta-subunits, Na+,K+,2Cl- cotransporter and CFTR anion channel in juvenile anadromous and landlocked Atlantic salmon Salmo salar

    DEFF Research Database (Denmark)

    Nilsen, Tom O.; Ebbesson, Lars O. E.; Madsen, Steffen S.

    2007-01-01

    June, whereas alpha1a levels in landlocked salmon, after an initial decrease in April, remained significantly higher than those of the anadromous smolts in May and June. Following SW transfer, gill NKA-alpha1b and NKCC mRNA increased in both strains, whereas NKA-alpha1a decreased. Both strains......) and NKCC mRNA levels in anadromous salmon increased transiently, reaching peak levels in smolts in April/May, whereas no similar smolt-related upregulation of these transcripts occurred in juvenile landlocked salmon. Gill NKA-alpha1a mRNA decreased significantly in anadromous salmon from February through...... exhibited a transient increase in gill NKA alpha-protein abundance, with peak levels in May. Gill alpha-protein abundance was lower in SW than corresponding FW values in June. Gill NKCC protein abundance increased transiently in anadromous fish, with peak levels in May, whereas a slight increase...

  4. Significance of selective predation and development of prey protection measures for juvenile salmonids in the Columbia and Snake River reservoirs. Annual progress report, February 1993--February 1994

    International Nuclear Information System (INIS)

    Poe, T.P.

    1994-01-01

    This report addresses the problem of predator-prey interactions of juvenile salmonids in the Columbia and Snake River. Six papers are included on selective predation and prey protection. Attention is focused on monitoring the movements, the distribution, and the behavior of juvenile chinook salmon and northern squawfish

  5. Improved primer sequences for the mitochondrial ND1, ND3/4 and ND5/6 segments in salmonid fishes : application to RFLP analysis of Atlantic salmon

    DEFF Research Database (Denmark)

    Eg Nielsen, Einar; Hansen, Michael Møller; Mensberg, Karen-Lise Dons

    1998-01-01

    New specific primers for the mtDNA segments ND1, ND3/4 and ND5/6 designed from the rainbow trout sequence, improved PCR amplification for salmonid fishes. RFLP analysis revealed restriction site variation for all three segments in Atlantic salmon. Eleven haplotypes were detected in a screening...

  6. Quantifying the effect of predators on endangered species using a bioenergetics approach : Caspian terns and juvenile salmonids in the Columbia River estuary

    NARCIS (Netherlands)

    Roby, DD; Lyons, DE; Craig, DP; Collis, K; Visser, GH

    We estimated the consumption of juvenile salmonids (Oncorhynchus spp.) and other forage fishes by Caspian terns (Sterna caspia) nesting on Rice Island in the Columbia River estuary in 1997 and 1998 using a bioenergetics modeling approach. The study was prompted by concern that Caspian tern predation

  7. StreamNet; Northwest Aquatic Resource Information Network - Status of Salmon and Steelhead in the Columbia River Basin, 1995 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Duane A.; Beamesderfer, Raymond C. [Oregon Dept. of Fish and Wildlife, Enterprise, OR (United States); Woodard, Bob [Washington Dept. of Fish and Wildlife, Olympia, WA (United States)

    1996-04-01

    Information on fish populations, fisheries, and fish habitat is crucial to the success of ongoing program to protect, recover, enhance, and manage fish resources in the Columbia River Basin. However, pertinent data are often difficult to locate because it is scattered among many agencies and is often unpublished. The goal of this annual report is to bring many diverse data types and sources into a single comprehensive report on the status of anadromous fish runs in the Columbia River Basin and the environmental conditions that may affect that status. Brief summaries are provided to identify the type and scope of available information. This synopsis is intended to complement other more detailed reports to which readers are referred for comprehensive treatment of specific subjects. This first report focuses mainly on anadromous salmon and steelhead (primarily through 1994) but the authors intend to expand the scope of future issues to include resident species. This is the first of what the authors intend to be an annual report. They welcome constructive suggestions for improvements. This report is a product of the StreamNet (formerly Coordinated Information System and Northwest Environmental Data Base) project which is a part of the Bonneville Power Administration`s program to protect, mitigate, and enhance fish and wildlife affected by the development and operation of hydroelectric facilities on the Columbia River and its tributaries. The project is called for in the Fish and Wildlife Program of the Northwest Power Planning Council. The project`s objective is to promote exchange and dissemination of information in a standardized electronic format throughout the basin. This project is administered by the Pacific States Marine Fisheries Commission with active participation by tribal, state, and federal fish and wildlife agencies.

  8. Catchment source contributions to the sediment-bound organic matter degrading salmonid spawning gravels in a lowland river, southern England

    Energy Technology Data Exchange (ETDEWEB)

    Collins, A.L., E-mail: adrian.collins@adas.co.uk [ADAS, Pendeford House, Wobaston Road, Wolverhampton WV9 5AP (United Kingdom); Geography and Environment, University of Southampton, Highfield, Southampton SO17 1BJ (United Kingdom); Williams, L.J.; Zhang, Y.S. [ADAS, Pendeford House, Wobaston Road, Wolverhampton WV9 5AP (United Kingdom); Marius, M. [Civil Engineering and Environment, University of Southampton, Highfield, Southampton S017 1BJ (United Kingdom); Dungait, J.A.J. [Department of Sustainable Systems and Grassland Science, Rothamsted Research—North Wyke, Okehampton, Devon EX20 2SB (United Kingdom); Smallman, D.J. [Civil Engineering and Environment, University of Southampton, Highfield, Southampton S017 1BJ (United Kingdom); Dixon, E.R. [Department of Sustainable Systems and Grassland Science, Rothamsted Research—North Wyke, Okehampton, Devon EX20 2SB (United Kingdom); Stringfellow, A. [Civil Engineering and Environment, University of Southampton, Highfield, Southampton S017 1BJ (United Kingdom); Sear, D.A. [Geography and Environment, University of Southampton, Highfield, Southampton SO17 1BJ (United Kingdom); Jones, J.I. [School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS (United Kingdom); Naden, P.S. [CEH Wallingford, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB (United Kingdom)

    2013-07-01

    The ingress of particulate material into freshwater spawning substrates is thought to be contributing to the declining success of salmonids reported over recent years for many rivers. Accordingly, the need for reliable information on the key sources of the sediment problem has progressed up the management agenda. Whilst previous work has focussed on apportioning the sources of minerogenic fine sediment degrading spawning habitats, there remains a need to develop procedures for generating corresponding information for the potentially harmful sediment-bound organic matter that represents an overlooked component of interstitial sediment. A source tracing procedure based on composite signatures combining bulk stable {sup 13}C and {sup 15}N isotope values with organic molecular structures detected using near infrared (NIR) reflectance spectroscopy was therefore used to assess the primary sources of sediment-bound organic matter sampled from artificial spawning redds. Composite signatures were selected using a combination of the Kruskal–Wallis H-test, principal component analysis and GA-driven discriminant function analysis. Interstitial sediment samples were collected using time-integrating basket traps which were inserted at the start of the salmonid spawning season and extracted in conjunction with critical phases of fish development (eyeing, hatch, emergence, late spawning). Over the duration of these four basket extractions, the overall relative frequency-weighted average median (± 95% confidence limits) source contributions to the interstitial sediment-bound organic matter were estimated to be in the order: instream decaying vegetation (39 ± < 1%; full range 0–77%); damaged road verges (28 ± < 1%; full range 0–77%); septic tanks (22 ± < 1%; full range 0–50%), and; farm yard manures/slurries (11 ± < 1%; full range 0–61%). The reported procedure provides a promising basis for understanding the key sources of interstitial sediment-bound organic matter

  9. Walla Walla River Basin Fish Habitat Enhancement Project, 2000-2001 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Volkman, Jed; Sexton, Amy D. (Confederated Tribes of the Umatilla Indian Reservation, Pendleton, OR)

    2001-01-01

    In 2000, the Confederated Tribes of the Umatilla Indian Reservation (CTUIR) Fisheries Habitat Program implemented stream habitat restoration and protection efforts in the Walla Walla River Basin with funding from Bonneville Power Administration (BPA). The objective of these efforts is to protect and restore habitat critical to the recovery of weak or reintroduced populations of salmonid fish. Six projects, two on Couse Creek, two adjacent properties on Blue Creek, one on Patit Creek, and one property on the mainstem Walla Walla River were part of the exercise. Several thousand native plants as bare-root stock and cuttings were reintroduced to the sites and 18 acres of floodplain corridor was seeded with native grass seed. Pre and post-project monitoring efforts were included for all projects, incorporating methodologies from CTUIR's Draft Monitoring Plan.

  10. Umatilla River Basin Anadromus Fish Habitat Enhancement Project. 1994 Annual report

    International Nuclear Information System (INIS)

    Shaw, R.T.

    1994-05-01

    The Umatilla Basin Anadromous Fish Habitat Enhancement Project targets the improvement of water quality and restoration of riparian areas, holding, spawning and rearing habitats of steelhead, spring and fall chinook and coho salmon. The project focused on implementing cooperative instream and riparian habitat improvements on private lands on the Umatilla Indian Reservation from April 1, 1988 to March 31, 1992. These efforts resulted in enhancement of the lower 1/4 mile of Boston Canyon Creek, the lower 4 river miles of Meacham Creek and 3.2 river miles of the Umatilla River in the vicinity of Gibbon, Oregon. In 1993, the project shifted emphasis to a comprehensive watershed approach, consistent with other basin efforts, and began to identify upland and riparian watershed-wide causative factors impacting fisheries habitat and natural fisheries production capabilities throughout the Umatilla River Watershed. During the 1994--95 project period, a one river mile demonstration project was implemented on two privately owned properties on Wildhorse Creek. This was the first watershed improvement project to be implemented by the Confederated Tribes of the Umatilla Indian Reservation (CTUIR) off of the Reservation

  11. Survival Estimates for the Passage of Juvenile Salmonids through Snake River Dams and Reservoirs, 1997 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Hockersmith, Eric E.

    1999-03-01

    This report consists of two parts describing research activities completed during 1997 under Bonneville Power Administration Project Number 93-29. Part 1 provides reach survival and travel time estimates for 1997 for PIT-tagged hatchery steelhead and yearling chinook salmon in the Snake and Columbia Rivers. The results are reported primarily in the form of tables and figures with a minimum of text. More detailed information on methodology and the statistical models used in the analysis are provided in previous annual reports cited in the text. Analysis of the relationships among travel time, survival, and environmental factors for 1997 and previous years of the study will be reported elsewhere. Part 2 of this report describes research to determine areas of loss and delay for juvenile hatchery salmonids above Lower Granite Reservoir.

  12. Acoustic Telemetry Evaluation of Juvenile Salmonid Passage and Survival at John Day Dam, 2011

    Energy Technology Data Exchange (ETDEWEB)

    Weiland, Mark A.; Woodley, Christa M.; Ploskey, Gene R.; Hughes, James S.; Hennen, Matthew J.; Kim, Jin A.; Deng, Zhiqun; Fu, Tao; Skalski, J. R.; Townsend, Richard L.; Wagner, Katie A.; Fischer, Eric S.; Duncan, Joanne P.; Batten, G.; Carlson, Thomas J.; Carpenter, Scott M.; Cushing, Aaron W.; Elder, T.; Etherington, D. J.; Johnson, Gary E.; Khan, Fenton; Miracle, Ann L.; Mitchell, T. D.; Prather, K.; Rayamajhi, Bishes; Royer, Ida; Seaburg, Adam; Zimmerman, Shon A.

    2013-06-21

    This report presents survival, behavioral, and fish passage results for tagged yearling Chinook salmon and juvenile steelhead as part of a survival study conducted at John Day Dam during spring 2011. This study was designed to evaluate the passage and survival of yearling Chinook salmon and juvenile steelhead to assist managers in identifying dam operations for compliance testing as stipulated by the 2008 Federal Columbia River Power System Biological Opinion and the 2008 Columbia Basin Fish Accords. Survival estimates were based on a paired-release survival model.

  13. Acoustic Telemetry Evaluation of Juvenile Salmonid Passage and Survival at John Day Dam, 2010

    Energy Technology Data Exchange (ETDEWEB)

    Weiland, Mark A.; Woodley, Christa M.; Ploskey, Gene R.; Hughes, James S.; Kim, Jin A.; Deng, Zhiqun; Fu, Tao; Fischer, Eric S.; Skalski, J. R.; Townsend, Richard L.; Duncan, Joanne P.; Hennen, Matthew J.; Wagner, Katie A.; Arntzen, Evan V.; Miller, Benjamin L.; Miracle, Ann L.; Zimmerman, Shon A.; Royer, Ida M.; Khan, Fenton; Cushing, Aaron W.; Etherington, D. J.; Mitchell, T. D.; Elder, T.; Batton, George; Johnson, Gary E.; Carlson, Thomas J.

    2013-05-01

    This report presents survival, behavioral, and fish passage results for yearling and subyearling Chinook salmon smolts and juvenile steelhead tagged with JSATS acoustic micro-transmitters as part of a survival study conducted at John Day Dam during 2010. This study was designed to evaluate the passage and survival of yearling and subyearling Chinook salmon and juvenile steelhead to assist managers in identifying dam operations for compliance testing as stipulated by the 2008 Federal Columbia River Power System Biological Opinion and the 2008 Columbia Basin Fish Accords. Survival estimates were based on a single-release survival estimate model.

  14. Framework for Assessing Water Resource Sustainability in River Basins

    Science.gov (United States)

    Borden, J.; Goodwin, P.; Swanson, D.

    2013-12-01

    indicators to use in the analytical evaluation. A software template guides users through this process. For demonstration, the RBAF-C template has been applied to address competing irrigation demand-anadromous fish flow requirements in the Lemhi Basin, Idaho, and the increase in municipal and industrial demand in the Upper Bhima River Basin, India, which affects water supply to downstream irrigation command areas. The RBAF-A is for quantitatively evaluating the current conditions of water resources in a river basin and testing potential scenarios with respect to the sustainability criterion. The primary foundation for quantifying water movement is a river basin model. Upon this, the RBAF-A Interface organizes input data, collects output data from each discipline, and reports the HWB. Within the RBAF-A Interface, the EGS-HWB Calculator collects output time series data, processes the data with respect to space and time, and computes the ecologic, economic, and social well-being. The Reporting Tool presents the scenario output as values and trends in well-being. To demonstrate the technology, the RBAF-A was applied to the Lemhi Basin, Idaho. The RBAF supports the IWRM process by providing a structured and transparent means to understand the water related issues, analyses to conduct, and indicators to select in assessing the sustainability of water programs and policies in river basins.

  15. An epidemic model for the interactions between thermal regime of rivers and transmission of Proliferative Kidney Disease in salmonid fish

    Science.gov (United States)

    Carraro, Luca; Bertuzzo, Enrico; Mari, Lorenzo; Gatto, Marino; Strepparava, Nicole; Hartikainen, Hanna; Rinaldo, Andrea

    2015-04-01

    Proliferative kidney disease (PKD) affects salmonid populations in European and North-American rivers. It is caused by the endoparasitic myxozoan Tetracapsuloides bryosalmonae, which exploits freshwater bryozoans (Fredericella sultana) and salmonids as primary and secondary hosts, respectively. Incidence and mortality, which can reach up to 90-100%, are known to be strongly related to water temperature. PKD has been present in brown trout population for a long time but has recently increased rapidly in incidence and severity causing a decline in fish catches in many countries. In addition, environmental changes are feared to cause PKD outbreaks at higher latitude and altitude regions as warmer temperatures promote disease development. This calls for a better comprehension of the interactions between disease dynamics and the thermal regime of rivers, in order to possibly devise strategies for disease management. In this perspective, a spatially explicit model of PKD epidemiology in riverine host metacommunities is proposed. The model aims at summarizing the knowledge on the modes of transmission of the disease and the life-cycle of the parasite, making the connection between temperature and epidemiological parameters explicit. The model accounts for both local population and disease dynamics of bryozoans and fish and hydrodynamic dispersion of the parasite spores and hosts along the river network. The model is time-hybrid, coupling inter-seasonal and intra-seasonal dynamics, the former being described in a continuous time domain, the latter seen as time steps of a discrete time domain. In order to test the model, a case study is conducted in river Wigger (Cantons of Aargau and Lucerne, Switzerland), where data about water temperature, brown trout and bryozoan populations and PKD prevalence are being collected.

  16. Introduction de salmonidés en milieu vierge (Îles Kerguelen, Subantarctique : enjeux, résultats, perspectives

    Directory of Open Access Journals (Sweden)

    DAVAINE P.

    1997-01-01

    Full Text Available Les îles Kerguelen (Terres Australes et Antarctiques Françaises sont, à l'origine, vierges de toute espèce de poisson d'eau douce. Les quelques espèces de Salmonidés, introduites à la fin des années cinquante dans le cadre d'une politique d'occupation et de mise en valeur du Territoire, se sont acclimatées à l'environnement subantarctique et naturalisées avec plus ou moins de succès en fonction de leurs stratégies adaptatives respectives. Objet d'un suivi scientifique continu, ces populations apparaissent comme d'excellents modèles pour des études de génétique et de dynamique des populations. Les phénomènes de colonisation, limités dans un premier temps à l'augmentation régulière des densités de population et une extension rapide intra-rivière, ont connu un développement spectaculaire depuis les années quatre-vingt, à la suite des modifications importantes du climat local, dont l'influence sur les populations a été multiple. La vaste superficie de Kerguelen et les caractéristiques de ses réseaux hydrographiques permettent d'envisager de continuer à tirer parti positivement des introductions passées de Salmonidés, sur les plans scientifique et de mise en valeur du territoire, tout en développant une politique de protection des écosystèmes aquatiques et terrestres conforme à l'évolution actuelle des mentalités.

  17. Salmonids surveys, number of juvenile fish, fork length, and species diversity conducted in the Little Campbell Creek watershed, Alaska from 2010-11-01 to 2011-03-01 (NCEI Accession 0148761)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Over the past few years biologists and other researchers have encountered noticeable fish die-offs, mostly of young salmonid, in various stretches of Little Campbell...

  18. Great Basin insect outbreaks

    Science.gov (United States)

    Barbara Bentz; Diane Alston; Ted Evans

    2008-01-01

    Outbreaks of native and exotic insects are important drivers of ecosystem dynamics in the Great Basin. The following provides an overview of range, forest, ornamental, and agricultural insect outbreaks occurring in the Great Basin and the associated management issues and research needs.

  19. Melo carboniferous basin

    International Nuclear Information System (INIS)

    Flossdarf, A.

    1988-01-01

    This report is about of the Melo carboniferous basin which limits are: in the South the large and high Tupambae hill, in the west the Paraiso hill and the river mountains, in the North Yaguaron river basin to Candidata in Rio Grande del Sur in Brazil.

  20. K Basin safety analysis

    International Nuclear Information System (INIS)

    Porten, D.R.; Crowe, R.D.

    1994-01-01

    The purpose of this accident safety analysis is to document in detail, analyses whose results were reported in summary form in the K Basins Safety Analysis Report WHC-SD-SNF-SAR-001. The safety analysis addressed the potential for release of radioactive and non-radioactive hazardous material located in the K Basins and their supporting facilities. The safety analysis covers the hazards associated with normal K Basin fuel storage and handling operations, fuel encapsulation, sludge encapsulation, and canister clean-up and disposal. After a review of the Criticality Safety Evaluation of the K Basin activities, the following postulated events were evaluated: Crane failure and casks dropped into loadout pit; Design basis earthquake; Hypothetical loss of basin water accident analysis; Combustion of uranium fuel following dryout; Crane failure and cask dropped onto floor of transfer area; Spent ion exchange shipment for burial; Hydrogen deflagration in ion exchange modules and filters; Release of Chlorine; Power availability and reliability; and Ashfall

  1. Genomic arrangement of salinity tolerance QTLs in salmonids: A comparative analysis of Atlantic salmon (Salmo salar with Arctic charr (Salvelinus alpinus and rainbow trout (Oncorhynchus mykiss

    Directory of Open Access Journals (Sweden)

    Norman Joseph D

    2012-08-01

    Full Text Available Abstract Background Quantitative trait locus (QTL studies show that variation in salinity tolerance in Arctic charr and rainbow trout has a genetic basis, even though both these species have low to moderate salinity tolerance capacities. QTL were observed to localize to homologous linkage group segments within putative chromosomal regions possessing multiple candidate genes. We compared salinity tolerance QTL in rainbow trout and Arctic charr to those detected in a higher salinity tolerant species, Atlantic salmon. The highly derived karyotype of Atlantic salmon allows for the assessment of whether disparity in salinity tolerance in salmonids is associated with differences in genetic architecture. To facilitate these comparisons, we examined the genomic synteny patterns of key candidate genes in the other model teleost fishes that have experienced three whole-genome duplication (3R events which preceded a fourth (4R whole genome duplication event common to all salmonid species. Results Nine linkage groups contained chromosome-wide significant QTL (AS-2, -4p, -4q, -5, -9, -12p, -12q, -14q -17q, -22, and −23, while a single genome-wide significant QTL was located on AS-4q. Salmonid genomes shared the greatest marker homology with the genome of three-spined stickleback. All linkage group arms in Atlantic salmon were syntenic with at least one stickleback chromosome, while 18 arms had multiple affinities. Arm fusions in Atlantic salmon were often between multiple regions bearing salinity tolerance QTL. Nine linkage groups in Arctic charr and six linkage group arms in rainbow trout currently have no synteny alignments with stickleback chromosomes, while eight rainbow trout linkage group arms were syntenic with multiple stickleback chromosomes. Rearrangements in the stickleback lineage involving fusions of ancestral arm segments could account for the 21 chromosome pairs observed in the stickleback karyotype. Conclusions Salinity tolerance in

  2. Genomic arrangement of salinity tolerance QTLs in salmonids: a comparative analysis of Atlantic salmon (Salmo salar) with Arctic charr (Salvelinus alpinus) and rainbow trout (Oncorhynchus mykiss).

    Science.gov (United States)

    Norman, Joseph D; Robinson, Mike; Glebe, Brian; Ferguson, Moira M; Danzmann, Roy G

    2012-08-24

    Quantitative trait locus (QTL) studies show that variation in salinity tolerance in Arctic charr and rainbow trout has a genetic basis, even though both these species have low to moderate salinity tolerance capacities. QTL were observed to localize to homologous linkage group segments within putative chromosomal regions possessing multiple candidate genes. We compared salinity tolerance QTL in rainbow trout and Arctic charr to those detected in a higher salinity tolerant species, Atlantic salmon. The highly derived karyotype of Atlantic salmon allows for the assessment of whether disparity in salinity tolerance in salmonids is associated with differences in genetic architecture. To facilitate these comparisons, we examined the genomic synteny patterns of key candidate genes in the other model teleost fishes that have experienced three whole-genome duplication (3R) events which preceded a fourth (4R) whole genome duplication event common to all salmonid species. Nine linkage groups contained chromosome-wide significant QTL (AS-2, -4p, -4q, -5, -9, -12p, -12q, -14q -17q, -22, and -23), while a single genome-wide significant QTL was located on AS-4q. Salmonid genomes shared the greatest marker homology with the genome of three-spined stickleback. All linkage group arms in Atlantic salmon were syntenic with at least one stickleback chromosome, while 18 arms had multiple affinities. Arm fusions in Atlantic salmon were often between multiple regions bearing salinity tolerance QTL. Nine linkage groups in Arctic charr and six linkage group arms in rainbow trout currently have no synteny alignments with stickleback chromosomes, while eight rainbow trout linkage group arms were syntenic with multiple stickleback chromosomes. Rearrangements in the stickleback lineage involving fusions of ancestral arm segments could account for the 21 chromosome pairs observed in the stickleback karyotype. Salinity tolerance in salmonids from three genera is to some extent controlled by the

  3. Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon

    Directory of Open Access Journals (Sweden)

    Lubieniecki Krzysztof P

    2008-11-01

    Full Text Available Abstract Background Comparative genomic studies suggest that the modern day assemblage of ray-finned fishes have descended from an ancestral grouping of fishes that possessed 12–13 linkage groups. All jawed vertebrates are postulated to have experienced two whole genome duplications (WGD in their ancestry (2R duplication. Salmonids have experienced one additional WGD (4R duplication event compared to most extant teleosts which underwent a further 3R WGD compared to other vertebrates. We describe the organization of the 4R chromosomal segments of the proto-ray-finned fish karyotype in Atlantic salmon and rainbow trout based upon their comparative syntenies with two model species of 3R ray-finned fishes. Results Evidence is presented for the retention of large whole-arm affinities between the ancestral linkage groups of the ray-finned fishes, and the 50 homeologous chromosomal segments in Atlantic salmon and rainbow trout. In the comparisons between the two salmonid species, there is also evidence for the retention of large whole-arm homeologous affinities that are associated with the retention of duplicated markers. Five of the 7 pairs of chromosomal arm regions expressing the highest level of duplicate gene expression in rainbow trout share homologous synteny to the 5 pairs of homeologs with the greatest duplicate gene expression in Atlantic salmon. These regions are derived from proto-Actinopterygian linkage groups B, C, E, J and K. Conclusion Two chromosome arms in Danio rerio and Oryzias latipes (descendants of the 3R duplication can, in most instances be related to at least 4 whole or partial chromosomal arms in the salmonid species. Multiple arm assignments in the two salmonid species do not clearly support a 13 proto-linkage group model, and suggest that a 12 proto-linkage group arrangement (i.e., a separate single chromosome duplication and ancestral fusion/fissions/recombination within the putative G/H/I groupings may have occurred in

  4. Enhanced invertebrate prey production following estuarine restoration supports foraging for multiple species of juvenile salmonids (Oncorhynchus spp.)

    Science.gov (United States)

    Woo, Isa; Davis, Melanie; Ellings, Christopher S.; Nakai, Glynnis; Takekawa, John Y.; De La Cruz, Susan

    2018-01-01

    Estuaries provide crucial foraging resources and nursery habitat for threatened populations of anadromous salmon. As such, there has been a global undertaking to restore habitat and tidal processes in modified estuaries. The foraging capacity of these ecosystems to support various species of out-migrating juvenile salmon can be quantified by monitoring benthic, terrestrial, and pelagic invertebrate prey communities. Here, we present notable trends in the availability of invertebrate prey at several sites within a restoring large river delta in Puget Sound, Washington, U.S.A. Three years after the system was returned to tidal influence, we observed substantial additions to amphipod, copepod, and cumacean abundances in newly accessible marsh channels (from 0 to roughly 5,000–75,000 individuals/m2). In the restoration area, terrestrial invertebrate colonization was dependent upon vegetative cover, with dipteran and hymenopteran biomass increasing 3-fold between 1 and 3 years post-restoration. While the overall biodiversity within the restoration area was lower than in the reference marsh, estimated biomass was comparable to or greater than that found within the other study sites. This additional prey biomass likely provided foraging benefits for juvenile Chinook, chum, and coho salmon. Primary physical drivers differed for benthic, terrestrial, and pelagic invertebrates, and these invertebrate communities are expected to respond differentially depending on organic matter exchange and vegetative colonization. Restoring estuaries may take decades to meet certain success criteria, but our study demonstrates rapid enhancements in foraging resources understood to be used for estuary-dependent wildlife.

  5. Wada basin boundaries and basin cells

    NARCIS (Netherlands)

    Nusse, H.E.; Yorke, J.A.

    1996-01-01

    In dynamical systems examples are common in which two or more attractors coexist, and in such cases the basin boundary is nonempty. We consider a two-dimensional diffeomorphism F (that is, F is an invertible map and both F and its inverse are differentiable with continuous derivatives), which has at

  6. The genetic profiles of two salmonid populations from Romania obtained through nuclear markers analysis

    Directory of Open Access Journals (Sweden)

    Ramona Nechifor

    2017-05-01

    Full Text Available The Salmonidae fish family is well represented in Romanian fauna, with a total of six species in the wild and reared in fish farms. Among them, the brown trout (Salmo trutta fario can be found in all major Romanian river basins. However, anthropogenic activities might disrupt salmonids’ habitats, so that inbreeding and genetic isolation might easily occur in the wild populations. We analyzed two wild brown trout populations from rivers targeted by anthropogenic activities, by using nuclear markers and genotyping in order to observe their genetic structure. We analyzed nine microsatellites and we observed their alleles frequencies, number of private alleles, observed and expected heterozygosity, as well as their population structure. The two populations are not in Hardy-Weinberg equilibrium for most of the loci and the inbreeding coefficient for both populations suggests a heterozygote deficit. Further sequencing data are needed in order to have a better view upon their complete genetic structure.

  7. Coho Salmon Master Plan, Clearwater River Basin.

    Energy Technology Data Exchange (ETDEWEB)

    Nez Perce Tribe; FishPro

    2004-10-01

    uncertainties, the Nez Perce Tribe proposes to utilize a phased approach for coho reintroductions. This Master Plan seeks authorization and funding to move forward to Step 2 in the Northwest Power and Conservation Council 3-Step review process to further evaluate Phase I of the coho reintroduction program, which would focus on the establishment of a localized coho salmon stock capable of enduring the migration to the Clearwater River subbasin. To achieve this goal, the Nez Perce Tribe proposes to utilize space at existing Clearwater River subbasin hatchery facilities in concert with the construction of two low-tech acclimation facilities, to capitalize on the higher survival observed for acclimated versus direct stream released coho. In addition, Phase I would document the natural productivity of localized coho salmon released in two targeted tributaries within the Clearwater River subbasin. If Phase I is successful at establishing a localized coho salmon stock in an abundance capable of filling existing hatchery space, the rates of natural productivity are promising, and the interspecific interactions between coho and sympatric resident and anadromous salmonids are deemed acceptable, then Phase II would be triggered. Phase II of the coho reintroduction plan would focus on establishing natural production in a number of Clearwater River subbasin tributaries. To accomplish this goal, Phase II would utilize existing Clearwater River subbasin hatchery facilities, and expand facilities at the Nez Perce Tribal Hatchery Site 1705 facility to rear approximately 687,700 smolts annually for use in a rotating supplementation schedule. In short, this document identifies a proposed alternative (Phase I), complete with estimates of capital, operations and maintenance, monitoring and evaluation, and permitting that is anticipated to raise average smolt replacement rates from 0.73 (current) to 1.14 using primarily existing facilities, with a limited capital investment for low-tech acclimation

  8. California Air Basins

    Data.gov (United States)

    California Department of Resources — Air ResourcesCalifornia Air Resources BoardThe following datasets are from the California Air Resources Board: * arb_california_airbasins - California Air BasinsThe...

  9. BASINS Framework and Features

    Science.gov (United States)

    BASINS enables users to efficiently access nationwide environmental databases and local user-specified datasets, apply assessment and planning tools, and run a variety of proven nonpoint loading and water quality models within a single GIS format.

  10. Watershed Planning Basins

    Data.gov (United States)

    Vermont Center for Geographic Information — The Watershed Planning Basin layer is part of a larger dataset contains administrative boundaries for Vermont's Agency of Natural Resources. The dataset includes...

  11. K Basin Hazard Analysis

    International Nuclear Information System (INIS)

    PECH, S.H.

    2000-01-01

    This report describes the methodology used in conducting the K Basins Hazard Analysis, which provides the foundation for the K Basins Final Safety Analysis Report. This hazard analysis was performed in accordance with guidance provided by DOE-STD-3009-94, Preparation Guide for U. S. Department of Energy Nonreactor Nuclear Facility Safety Analysis Reports and implements the requirements of DOE Order 5480.23, Nuclear Safety Analysis Report

  12. K Basin Hazard Analysis

    Energy Technology Data Exchange (ETDEWEB)

    PECH, S.H.

    2000-08-23

    This report describes the methodology used in conducting the K Basins Hazard Analysis, which provides the foundation for the K Basins Final Safety Analysis Report. This hazard analysis was performed in accordance with guidance provided by DOE-STD-3009-94, Preparation Guide for U. S. Department of Energy Nonreactor Nuclear Facility Safety Analysis Reports and implements the requirements of DOE Order 5480.23, Nuclear Safety Analysis Report.

  13. K Basins Hazard Analysis

    International Nuclear Information System (INIS)

    WEBB, R.H.

    1999-01-01

    This report describes the methodology used in conducting the K Basins Hazard Analysis, which provides the foundation for the K Basins Safety Analysis Report (HNF-SD-WM-SAR-062/Rev.4). This hazard analysis was performed in accordance with guidance provided by DOE-STD-3009-94, Preparation Guide for U. S. Department of Energy Nonreactor Nuclear Facility Safety Analysis Reports and implements the requirements of DOE Order 5480.23, Nuclear Safety Analysis Report

  14. Salmonids, stream temperatures, and solar loading--modeling the shade provided to the Klamath River by vegetation and geomorphology

    Science.gov (United States)

    Forney, William M.; Soulard, Christopher E.; Chickadel, C. Christopher

    2013-01-01

    The U.S. Geological Survey is studying approaches to characterize the thermal regulation of water and the dynamics of cold water refugia. High temperatures have physiological impacts on anadromous fish species. Factors affecting the presence, variability, and quality of thermal refugia are known, such as riverine and watershed processes, hyporheic flows, deep pools and bathymetric factors, thermal stratification of reservoirs, and other broader climatic considerations. This research develops a conceptual model and methodological techniques to quantify the change in solar insolation load to the Klamath River caused by riparian and floodplain vegetation, the morphology of the river, and the orientation and topographic characteristics of its watersheds. Using multiple scales of input data from digital elevation models and airborne light detection and ranging (LiDAR) derivatives, different analysis methods yielded three different model results. These models are correlated with thermal infrared imagery for ground-truth information at the focal confluence with the Scott River. Results from nonparametric correlation tests, geostatistical cross-covariograms, and cross-correlograms indicate that statistical relationships between the insolation models and the thermal infrared imagery exist and are significant. Furthermore, the use of geostatistics provides insights to the spatial structure of the relationships that would not be apparent otherwise. To incorporate a more complete representation of the temperature dynamics in the river system, other variables including the factors mentioned above, and their influence on solar loading, are discussed. With similar datasets, these methods could be applied to any river in the United States—especially those listed as temperature impaired under Section 303(d) of the Clean Water Act—or international riverine systems. Considering the importance of thermal refugia for aquatic species, these methods can help investigate opportunities

  15. Mapping and validation of a major QTL affecting resistance to pancreas disease (salmonid alphavirus) in Atlantic salmon (Salmo salar).

    Science.gov (United States)

    Gonen, S; Baranski, M; Thorland, I; Norris, A; Grove, H; Arnesen, P; Bakke, H; Lien, S; Bishop, S C; Houston, R D

    2015-11-01

    Pancreas disease (PD), caused by a salmonid alphavirus (SAV), has a large negative economic and animal welfare impact on Atlantic salmon aquaculture. Evidence for genetic variation in host resistance to this disease has been reported, suggesting that selective breeding may potentially form an important component of disease control. The aim of this study was to explore the genetic architecture of resistance to PD, using survival data collected from two unrelated populations of Atlantic salmon; one challenged with SAV as fry in freshwater (POP 1) and one challenged with SAV as post-smolts in sea water (POP 2). Analyses of the binary survival data revealed a moderate-to-high heritability for host resistance to PD in both populations (fry POP 1 h(2)~0.5; post-smolt POP 2 h(2)~0.4). Subsets of both populations were genotyped for single nucleotide polymorphism markers, and six putative resistance quantitative trait loci (QTL) were identified. One of these QTL was mapped to the same location on chromosome 3 in both populations, reaching chromosome-wide significance in both the sire- and dam-based analyses in POP 1, and genome-wide significance in a combined analysis in POP 2. This independently verified QTL explains a significant proportion of host genetic variation in resistance to PD in both populations, suggesting a common underlying mechanism for genetic resistance across lifecycle stages. Markers associated with this QTL are being incorporated into selective breeding programs to improve PD resistance.

  16. A novel liquid medium for the efficient growth of the salmonid pathogen Piscirickettsia salmonis and optimization of culture conditions.

    Science.gov (United States)

    Henríquez, Mirtha; González, Ernesto; Marshall, Sergio H; Henríquez, Vitalia; Gómez, Fernando A; Martínez, Irene; Altamirano, Claudia

    2013-01-01

    Piscirickettsia salmonis is the bacterium that causes Piscirickettsiosis, a systemic disease of salmonid fish responsible for significant economic losses within the aquaculture industry worldwide. The growth of the bacterium for vaccine formulation has been traditionally accomplished by infecting eukaryotic cell lines, a process that involves high production costs and is time-consuming. Recent research has demonstrated that it is possible to culture pure P. salmonis in a blood containing (cell-free) medium. In the present work we demonstrate the growth of P. salmonis in a liquid medium free from blood and serum components, thus establishing a novel and simplified bacteriological medium. Additionally, the new media reported provides improved growth conditions for P. salmonis, where biomass concentrations of approximately 800 mg cell dry weight L(-1) were obtained, about eight times higher than those reported for the blood containing medium. A 2- level full factorial design was employed to evaluate the significance of the main medium components on cell growth and an optimal temperature range of 23-27°C was determined for the microorganism to grow in the novel liquid media. Therefore, these results represent a breakthrough regarding P. salmonis research in order to optimize pure P. salmonis growth in liquid blood and serum free medium.

  17. Spiral swimming behavior due to cranial and vertebral lesions associated with Cytophaga psychrophila infections in salmonid fishes

    Science.gov (United States)

    Kent, M.L.; Groff, J.M.; Morrison, J.K.; Yasutake, W.T.; Holt, R.A.

    1989-01-01

    C. psychrophila infections of the cranium and anterior vertebrae in salmonid fishes were associated with ataxia, spiral swimming along the axis of the fish, and death. The syndrome was observed in 2-10% of underyearling coho salmon Oncorhynchus kisutch, rainbow troutSalmo gairdneri, and steelhead trout S. gairdneri at several private, state, and federal hatcheries in Washington and Oregon, USA, between 1963 and 1987. Affected fish did not recover and ultimately died. Histological examination consistently revealed subacute to chronic periostitis, osteitis, meningitis, and ganglioneuritis. Inflammation and periosteal proliferation of the anterior vertebrae at the junction of the vertebral column with the cranium with extension into the cranial case was a consistent feature. The adjacent nervous tissue, particularly the medulla, was often compressed by the proliferative lesion, and this may have caused the ataxia. Though bacteria were seldom observed in these lesions. C. psychrophilawas isolated in culture from the cranial cavity of all affected fish that were tested. Epidemiological observations suggested that this bacterium is the causative agent because the spiral swimming behaviour and lesions were observed only in populations that had recovered from acute C. psychrophila infections.

  18. Sources of variability and comparability between salmonid stomach contents and isotopic analyses: study design lessons and recommendations

    Science.gov (United States)

    Vinson, M.R.; Budy, P.

    2011-01-01

    We compared sources of variability and cost in paired stomach content and stable isotope samples from three salmonid species collected in September 2001–2005 and describe the relative information provided by each method in terms of measuring diet overlap and food web study design. Based on diet analyses, diet overlap among brown trout, rainbow trout, and mountain whitefish was high, and we observed little variation in diets among years. In contrast, for sample sizes n ≥ 25, 95% confidence interval (CI) around mean δ15Ν and δ13C for the three target species did not overlap, and species, year, and fish size effects were significantly different, implying that these species likely consumed similar prey but in different proportions. Stable isotope processing costs were US$12 per sample, while stomach content analysis costs averaged US$25.49 ± $2.91 (95% CI) and ranged from US$1.50 for an empty stomach to US$291.50 for a sample with 2330 items. Precision in both δ15Ν and δ13C and mean diet overlap values based on stomach contents increased considerably up to a sample size of n = 10 and plateaued around n = 25, with little further increase in precision.

  19. A Polyprotein-Expressing Salmonid Alphavirus Replicon Induces Modest Protection in Atlantic Salmon (Salmo Salar Against Infectious Pancreatic Necrosis

    Directory of Open Access Journals (Sweden)

    Azila Abdullah

    2015-01-01

    Full Text Available Vaccination is an important strategy for the control and prevention of infectious pancreatic necrosis (IPN in farmed Atlantic salmon (Salmo salar in the post-smolt stage in sea-water. In this study, a heterologous gene expression system, based on a replicon construct of salmonid alphavirus (SAV, was used for in vitro and in vivo expression of IPN virus proteins. The large open reading frame of segment A, encoding the polyprotein NH2-pVP2-VP4-VP3-COOH, as well as pVP2, were cloned and expressed by the SAV replicon in Chinook salmon embryo cells (CHSE-214 and epithelioma papulosum cyprini (EPC cells. The replicon constructs pSAV/polyprotein (pSAV/PP and pSAV/pVP2 were used to immunize Atlantic salmon (Salmo salar by a single intramuscular injection and tested in a subsequent IPN virus (IPNV challenge trial. A low to moderate protection against IPN was observed in fish immunized with the replicon vaccine that encoded the pSAV/PP, while the pSAV/pVP2 construct was not found to induce protection.

  20. Survival estimates for the passage of juvenile salmonids through Snake River dams and reservoirs, 1996. Annual report

    International Nuclear Information System (INIS)

    Smith, S.G.; Muir, W.D.; Hockersmith, E.E.; Achord, S.; Eppard, M.B.; Ruehle, T.E.; Williams, J.G.

    1998-02-01

    In 1996, the National Marine Fisheries Service and the University of Washington completed the fourth year of a multi-year study to estimate survival of juvenile salmonids (Oncorhynchus spp.) passing through dams and reservoirs on the Snake River. Actively migrating smolts were collected near the head of Lower Granite Reservoir and at Lower Granite Dam, tagged with passive integrated transponder (PIT) tags, and released to continue their downstream migration. Individual smolts were subsequently detected at PIT-tag detection facilities at Lower Granite, Little Goose, Lower Monumental, McNary, John Day and Bonneville Dams. Survival estimates were calculated using the Single-Release (SR) and Paired-Release (PR) Models. Timing of releases of tagged hatchery steelhead (O. mykiss) from the head of Lower Granite Reservoir and yearling chinook salmon (O. tshawytscha) from Lower Granite Dam in 1996 spanned the major portion of their juvenile migrations. Specific research objectives in 1996 were to (1) estimate reach and project survival in the Snake River using the Single-Release and Paired-Release Models throughout the yearling chinook salmon and steelhead migrations, (2) evaluate the performance of the survival-estimation models under prevailing operational and environmental conditions in the Snake River, and (3) synthesize results from the 4 years of the study to investigate relationships between survival probabilities, travel times, and environmental factors such as flow levels and water temperature

  1. Survival Estimates for the Passage of Juvenile Salmonids through Snake River Dams and Reservoirs, 1996 Annual Report

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Steven G.

    1998-02-01

    In 1996, the National Marine Fisheries Service and the University of Washington completed the fourth year of a multi-year study to estimate survival of juvenile salmonids (Oncorhynchus spp.) passing through dams and reservoirs on the Snake River. Actively migrating smolts were collected near the head of Lower Granite Reservoir and at Lower Granite Dam, tagged with passive integrated transponder (PIT) tags, and released to continue their downstream migration. Individual smolts were subsequently detected at PIT-tag detection facilities at Lower Granite, Little Goose, Lower Monumental, McNary, John Day and Bonneville Dams. Survival estimates were calculated using the Single-Release (SR) and Paired-Release (PR) Models. Timing of releases of tagged hatchery steelhead (O. mykiss) from the head of Lower Granite Reservoir and yearling chinook salmon (O. tshawytscha) from Lower Granite Dam in 1996 spanned the major portion of their juvenile migrations. Specific research objectives in 1996 were to (1) estimate reach and project survival in the Snake River using the Single-Release and Paired-Release Models throughout the yearling chinook salmon and steelhead migrations, (2) evaluate the performance of the survival-estimation models under prevailing operational and environmental conditions in the Snake River, and (3) synthesize results from the 4 years of the study to investigate relationships between survival probabilities, travel times, and environmental factors such as flow levels and water temperature.

  2. Distribution and stability of potential salmonid spawning gravels in steep boulder-bed streams of the eastern Sierra Nevada

    International Nuclear Information System (INIS)

    Kondolf, G.M.; Cada, G.F.; Sale, M.J.; Felando, T.

    1991-01-01

    Interest in small hydroelectric development (< 5 MW) has recently focused attention on steep streams and the resident trout populations they contain. High-gradient boulder-bed streams have been the sites of relatively few studies of salmonid spawning habitat, although they have geomorphic and hydraulic characteristics - and therefore gravel distributions - that are quite different from the more commonly described lower-gradient channels. The authors documented gravel distribution in seven high-gradient stream reaches in the eastern Sierra Nevada. Gravels occurred only in locations characterized by relatively low shear stress; they formed small pockets in sites of low divergence and larger deposits upstream of natural hydraulic controls. In 1986 (a wet year), all tracer gravels placed in gravel pockets at nine sites on four streams were completely swept away, and substantial scour, fill, and other channel changes occurred at many sites. In 1987 (a dry year), tracer gravels and the channel cross sections were generally stable. Periodic mobility of gravel may explain why brown trout Salmo trutta are more abundant than rainbow trout Oncorhychus mykiss in the study reaches, where high flows occur every May and June during snowmelt. Brown trout are fall spawners, and their fry emerge long before the high snowmelt flows, whereas rainbow trout are spring spawners whose eggs are in the gravel, and thus vulnerable to scour, during snowmelt flows

  3. Assessment of Native Salmonids Above Hells Canyon Dam, Idaho, 2003-2004 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, Kevin A.; Lamansky, Jr., James A. (Idaho Department of Fish and Game, Boise, ID)

    2004-08-01

    Despite the substantial declines in distribution and abundance that the Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri has experienced over the past century, quantitative evaluations of existing population sizes over broad portions of its historical range have not been made. In this study, we estimate trout abundance throughout the Upper Snake River basin in Idaho (and portions of adjacent states), based on stratified sample extrapolations of electrofishing surveys conducted at 961 study sites, the vast majority of which (84%) were selected randomly. Yellowstone cutthroat trout were the most widely distributed species of trout (caught at 457 study sites), followed by brook trout Salvelinus fontinalis (242 sites), rainbow trout O. mykiss and rainbow x cutthroat hybrids (136 sites), and brown trout Salmo trutta (70 sites). Of the sites that contained cutthroat trout, more than half did not contain any other species of trout. Where nonnative trout were sympatric with cutthroat trout, brook trout were most commonly present. In the 11 Geographic Management Units (GMUs) where sample size permitted abundance estimates, there were about 2.2 million trout {ge}100 mm, and of these, about one-half were cutthroat trout. Similarly, we estimated that about 2.0 million trout <100 mm were present, of which about 1.2 million were cutthroat trout. The latter estimate is biased low because our inability to estimate abundance of trout <100 mm in larger-order rivers negated our ability to account for them at all. Cutthroat trout were divided into approximately 70 subpopulations but estimates could be made for only 55 subpopulations; of these, 44 subpopulations contained more than 1,000 cutthroat trout and 28 contained more than 2,500 cutthroat trout. Using a logistic regression model to predict the number of spawning cutthroat trout at a given study site, we estimate that an average of about 30% of the cutthroat trout {ge}100 mm are spawners. We compared visually

  4. Instream flow characterization of Upper Salmon River basin streams, central Idaho, 2005

    Science.gov (United States)

    Maret, Terry R.; Hortness, Jon E.; Ott, Douglas S.

    2006-01-01

    Anadromous fish populations in the Columbia River Basin have plummeted in the last 100 years. This severe decline led to Federal listing of Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) stocks as endangered or threatened under the Endangered Species Act (ESA) in the 1990s. Historically, the upper Salmon River Basin (upstream of the confluence with the Pahsimeroi River) in Idaho provided migration corridors and significant habitat for these ESA-listed species, in addition to the ESA-listed bull trout (Salvelinus confluentus). Human development has modified the original streamflow conditions in many streams in the upper Salmon River Basin. Summer streamflow modifications resulting from irrigation practices, have directly affected quantity and quality of fish habitat and also have affected migration and (or) access to suitable spawning and rearing habitat for these fish. As a result of these ESA listings and Action 149 of the Federal Columbia River Power System Biological Opinion of 2000, the Bureau of Reclamation was tasked to conduct streamflow characterization studies in the upper Salmon River Basin to clearly define habitat requirements for effective species management and habitat restoration. These studies include collection of habitat and streamflow information for the Physical Habitat Simulation System (PHABSIM) model, a widely applied method to determine relations between habitat and discharge requirements for various fish species and life stages. Model simulation results can be used by resource managers to guide habitat restoration efforts by evaluating potential fish habitat and passage improvements by increasing or decreasing streamflow. In 2005, instream flow characterization studies were completed on Big Boulder, Challis, Bear, Mill, and Morgan Creeks. Continuous streamflow data were recorded upstream of all diversions on Big Boulder. Instantaneous measurements of discharge were also made at selected sites. In

  5. Instream flow characterization of upper Salmon River basin streams, central Idaho, 2004

    Science.gov (United States)

    Maret, Terry R.; Hortness, Jon E.; Ott, Douglas S.

    2005-01-01

    Anadromous fish populations in the Columbia River Basin have plummeted in the last 100 years. This severe decline led to Federal listing of Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) stocks as endangered or threatened under the Endangered Species Act (ESA) in the 1990s. Historically, the upper Salmon River Basin (upstream of the confluence with the Pahsimeroi River) in Idaho provided migration corridors and significant habitat for these ESA-listed species, in addition to the ESA-listed bull trout (Salvelinus confluentus). Human development has modified the original streamflow conditions in many streams in the upper Salmon River Basin. Summer streamflow modifications resulting from irrigation practices, have directly affected quantity and quality of fish habitat and also have affected migration and (or) access to suitable spawning and rearing habitat for these fish. As a result of these ESA listings and Action 149 of the Federal Columbia River Power System Biological Opinion of 2000, the Bureau of Reclamation was tasked to conduct streamflow characterization studies in the upper Salmon River Basin to clearly define habitat requirements for effective species management and habitat restoration. These studies include collection of habitat and streamflow information for the Physical Habitat Simulation System model, a widely applied method to determine relations between habitat and discharge requirements for various fish species and life stages. Model results can be used by resource managers to guide habitat restoration efforts by evaluating potential fish habitat and passage improvements by increasing streamflow. In 2004, instream flow characterization studies were completed on Salmon River and Beaver, Pole, Champion, Iron, Thompson, and Squaw Creeks. Continuous streamflow data were recorded upstream of all diversions on Salmon River and Pole, Iron, Thompson, and Squaw Creeks. In addition, natural summer streamflows were

  6. A summary of 22 Years of Fish Screen Evaluation in the Yakima River Basin, Summary Report 1985-2007.

    Energy Technology Data Exchange (ETDEWEB)

    Chamness, Mickie A. [Pacific Northwest National Laboratory

    2007-12-03

    Sixty fish screen facilities were constructed in the Yakima River basin between 1985 and 2006 as part of the Northwest Power and Conservation Council plan to mitigate the effects of federal hydroelectric projects on fish and wildlife populations. This report summarizes evaluations of some of those and other fish screen facilities conducted by Pacific Northwest National Laboratory (PNNL) from 1985 through 2006. The objective of these studies was to determine if the newly designed and constructed fish screens were effective at providing juvenile salmonids safe passage past irrigation diversions. To answer that question, PNNL conducted release-and-catch studies at eight Phase I sites in the Yakima River basin. Increasing concerns about the impacts of hatchery fish releases on the wild fish population, as well as the cost and time necessary to perform these kinds of biological studies at more than 60 planned Phase II sites, required development of techniques to evaluate the effectiveness of the sites without releasing fish. The new techniques involved collecting information on screen design, operation, and effectiveness at guiding fish safely through the fish screen facility. Performance measures including water velocities and passage conditions provide a good alternative to biological studies at significantly lower cost and time. Physical techniques were used at all 10 Phase I and 28 Phase II sites evaluated by PNNL over the following 19 years. Results of these studies indicate the Phase I and II fish screen facilities are designed and capable of providing safe passage for juvenile salmonids so long as construction, maintenance, and operations meet the criteria used in the design of each site and the National Marine Fisheries Service criteria for juvenile fish screen design.

  7. Assessment of Native Salmonids Above Hells Canyon Dam, Idaho, 2001 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, Kevin A.; Lamansky, Jr., James A. (Idaho Department of Fish and Game, Boise, ID)

    2002-11-01

    We investigated factors affecting the distribution and abundance of Yellowstone cutthroat trout (YCT), the abundance of all trout, and species richness in several drainages in the upper Snake River basin in Idaho. A total of 326 randomly selected sites were visited within the four study drainages, and of these, there was sufficient water to inventory fish and habitat in 56 of the sites in the Goose Creek drainage, 64 in the Raft River drainage, 54 in the Blackfoot River drainage, and 27 in the Willow Creek drainage. Fish were captured in 36, 55, 49, and 22 of the sites, respectively, and YCT were present at 17, 37, 32, and 13 of the sites, respectively. There was little consistency or strength in the models developed to predict YCT presence/absence and density, trout density, or species richness. Typically, the strongest models had the lowest sample sizes. In the Goose Creek drainage, sites with YCT were higher in elevation and lower in conductivity. In the Raft River drainage, trout cover was more abundant at sites with YCT than without YCT. In the Blackfoot River drainage, there was less fine substrate and more gravel substrate at sites with YCT than at sites without YCT. In the Willow Creek drainage, 70% of the sites located on public land contained YCT, but only 35% of private land contained YCT. The differences in variable importance between drainages suggests that factors that influence the distribution of YCT vary between drainages, and that for the most part the variables we measured had little influence on YCT distribution. n sites containing YCT, average cutthroat trout density was 0.11/m{sup 2}, 0.08/m{sup 2}, 0.10/m{sup 2}, and 0.08/m{sup 2} in the Goose Creek, Raft River, Blackfoot River, and Willow Creek drainages, respectively. In sites containing trout in general, average total trout density in these same drainages was 0.16/m{sup 2}, 0.15/m{sup 2}, 0.10/m{sup 2}, and 0.10/m{sup 2}. Models to predict YCT density, total trout density, and species

  8. Manyame River Basin, Zimbabwe

    African Journals Online (AJOL)

    Available on website http://www.wrc.org.za. ISSN 1816-7950 (On-line) = Water SA Vol. 42 No. 1 January 2016. Published under a Creative Commons Attribution Licence. A test of the Lake Habitat Survey method in Cleveland Reservoir and. Lake Chivero (Manyame River Basin, Zimbabwe). Tatenda Dalu1*, Edwin ...

  9. The Mediterranean basin

    DEFF Research Database (Denmark)

    Tomas, Carmen; Sanchez Sanchez, Juan Jose; Barbaro, A.

    2008-01-01

    genetically from the rest of the populations in the Mediterranean area. This result supports the hypothesis of a low incidence of the south-north genetic interchange at the western shores of the Mediterranean basin. A low genetic distance was found between populations in the Middle East and the western part...

  10. Feasibility study for evaluating cumulative exposure of downstream migrant juvenile salmonids to total dissolved gas. Final report

    International Nuclear Information System (INIS)

    Abernethy, C.S.; Dauble, D.D.; Johnson, R.L.

    1997-11-01

    A feasibility study was initiated to determine if downstream migrant salmonids could be monitored to determine potential relationships between total dissolved gas (TDG) exposure and signs of gas bubble trauma (GBT). The primary objectives were to: (1) establish logistical requirements for in-river monitoring of TDG exposure, including net pen design, deployment, and navigation constraints; (2) resolve uncertainties associated with effects of the net pen on fish behavior; (3) test the accuracy and precision of in-river monitoring equipment used to measure fish distribution and water quality; and (4) determine the application of hydrologic/flow models to predictions of TDG exposure. In-river measurements included water velocity, boat position, and selected water quality parameters (temperature, dissolved oxygen, pH, depth, conductivity). Fish distribution within the net pen was monitored using scanning sonar, and a split-beam echo sounder was used to evaluate vertical distribution of fish m in the river adjacent to the net pen. Three test drifts were conducted from late July through late August. The studies demonstrated that it was feasible to assemble and deploy a large net pen for mobile monitoring of TDG exposure. Accurate monitoring of vertical and lateral distribution of smolts was performed, and diel differences in behavior were documented. Further, the fish sounded in response to researcher activity on the perimeter platform. Thus, in-transit monitoring for GBT or mortality would affect fish depth distribution and exposure to TDG. Principal recommendations for future studies are directed at improving maneuverability of the net pen in adverse weather conditions and applying new acoustics technology to simultaneously collect fish distribution data from within and outside of the pen. 6 refs., 17 figs., 2 tabs

  11. Hydrological and thermal effects of hydropeaking on early life stages of salmonids: A modelling approach for implementing mitigation strategies.

    Science.gov (United States)

    Casas-Mulet, Roser; Saltveit, Svein Jakob; Alfredsen, Knut Tore

    2016-12-15

    Alterations in hydrological and thermal regimes can potentially affect salmonid early life stages development and survival. The dewatering of salmon spawning redds due to hydropeaking can lead to mortality in early life stages, with higher impact on the alevins as they have lower tolerance to dewatering than the eggs. Flow-related mitigation measures can reduce early life stage mortality. We present a set of modelling tools to assess impacts and mitigation options to minimise the risk of mortality in early life stages in hydropeaking rivers. We successfully modelled long-term hydrological and thermal alterations and consequences for development rates. We estimated the risk of early life stages mortality and assessed the cost-effectiveness of implementing three release-related mitigation options (A,B,C). The economic cost of mitigation was low and ranged between 0.7% and 2.6% of the annual hydropower production. Options reducing the flow during spawning (B and C) in addition to only release minimum flows during development (A) were considered more effective for egg and alevin survival. Options B and C were however constraint by water availability in the system for certain years, and therefore only option A was always feasible. The set of modelling tools used in this study were satisfactory and their applications can be useful especially in systems where little field data is available. Targeted measures built on well-informed modelling tools can be tested on their effectiveness to mitigate dewatering effects vs. the hydropower system capacity to release or conserve water for power production. Environmental flow releases targeting specific ecological objectives can provide better cost-effective options than conventional operational rules complying with general legislation. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Investigating the Geomorphic and Ecologic Functions of Wood in Relationship to Habitat Type and Salmonid Redds on a Regulated California River

    Science.gov (United States)

    Senter, A. E.; Pasternack, G. B.

    2006-12-01

    Most river rehabilitation projects incorporate little to no wood in current designs, and those that do have little science to guide them. The overall goal of this research is to investigate the role of wood in a regulated, mid- sized (where river width is greater than most tree heights), Mediterranean-climate (where smaller, softer-wood trees dominate the landscape) river in order to provide a scientific foundation for the potential use of wood in rehabilitation projects within such systems. Wood structures in the active salmonid spawning reach of the Lower Mokelumne River in Central California were measured, mapped, and described during summer and fall 2006. Digital photos and GPS coordinates were used to establish wood location within the stream channel. Structural morphology was determined by measuring physical properties such as individual diameter and length, orientation to stream flow, and jam dimensions. In addition, qualitative attributes were recorded such as decay class and leaf, limb, bark, and root characteristics. A GIS wood layer will be created and added to a database of existing Mokelumne River GIS layers containing salmonid redd (salmon egg nests) densities, hydraulic conditions associated with individual redds, and sub-reach habitat types. An analysis of wood properties, redd locations and conditions, and habitat types will be used to develop a conceptual model of wood dynamics in relation to salmonid habitat on the Lower Mokelumne River. The primary products of this study will be (1) a scientific conceptual model of the role of wood in regulated gravel reaches of mid-size rivers in Mediterranean California and (2) a decision-making framework that will enable river managers to include scientifically based wood structures into rehabilitation designs, thereby enhancing spawning habitat, stream complexity, and biological diversity. These tools will be developed in collaboration with East Bay Municipal Utilities District to aid in the continuing

  13. Using Satellite Tracking and Isotopic Information to Characterize the Impact of South American Sea Lions on Salmonid Aquaculture in Southern Chile.

    Directory of Open Access Journals (Sweden)

    Maritza Sepúlveda

    Full Text Available Apex marine predators alter their foraging behavior in response to spatial and/or seasonal changes in natural prey distribution and abundance. However, few studies have identified the impacts of aquaculture that represents a spatially and temporally predictable and abundant resource on their foraging behavior. Using satellite telemetry and stable isotope analysis we examined the degree of spatial overlap between the South American sea lion (SASL and salmon farms, and quantify the amount of native prey versus farmed salmonids in SASL diets. We instrumented eight SASL individuals with SRDL-GPS tags. Vibrissae, hair and skin samples were collected for δ13C and δ15N analyses from five of the tagged individuals and from four males captured in a haul-out located adjacent to salmon farms. Tracking results showed that almost all the foraging areas of SASL are within close proximity to salmon farms. The most important prey for the individuals analyzed was farmed salmonids, with an estimated median (±SD contribution of 19.7 ± 13.5‰ and 15.3 ± 9.6‰ for hair and skin, respectively. Using vibrissae as a temporal record of diet for each individual, we observed a remarkable switch in diet composition in two SASL, from farmed salmonids to pelagic fishes, which coincided with the decrease of salmon production due to the infectious salmon anemia virus that affected salmon farms in Chile at the end of 2008. Our study demonstrates the usefulness of integrating stable isotope derived dietary data with movement patterns to characterize the impacts of a non-native prey on the foraging ecology of an apex marine predator, providing important applied implications in situations where interactions between aquaculture and wildlife are common.

  14. Biological and Physical Inventory of the Streams within the Nez Perce Reservation; Juvenile Steelhead Survey and Factors that Affect Abundance in Selected Streams in the Lower Clearwater River Basin, Idaho, 1983-1984 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Kucera, Paul A.; Johnson, David B. (Nez Perce Tribe, Lapwai, ID)

    1986-08-01

    A biological and physical inventory of selected tributaries in the lower Clearwater River basin was conducted to collect information for the development of alternatives and recommendations for the enhancement of the anadromous fish resources in streams on the Nez Perce Reservation. Five streams within the Reservation were selected for study: Bedrock and Cottonwood Creeks were investigated over a two year period (1983 to 1984) and Big Canyon, Jacks and Mission Creeks were studied for one year (1983). Biological information was collected and analyzed on the density, biomass, production and outmigration of juvenile summer steelhead trout. Physical habitat information was collected on available instream cover, stream discharge, stream velocity, water temperature, bottom substrate, embeddedness and stream width and depth. The report focuses on the relationships between physical stream habitat and juvenile steelhead trout abundance.

  15. Investigation of head burns in adult salmonids: Phase 1: Examination of fish at Lower Granite Dam, July 2, 1996. Final report

    International Nuclear Information System (INIS)

    Elston, R.

    1996-08-01

    Head burn is a descriptive clinical term used by fishery biologists to describe exfoliation of skin and underlying connective tissue of the jaw and cranial region of salmonids, observed at fish passage facilities on the Columbia and Snake Rivers. The observations are usually made on upstream migrant adult salmon or steelhead. An expert panel, convened in 1996, to evaluate the risk and severity of gas bubble disease (GBD) in the Snake and Columbia River system believed that, while head burns appeared to be distinct from GBD, the relationship between dissolved gas saturation in the rivers and head burns was uncertain

  16. Columbia River Basin Fish and Wildlife Program Work Plan for Fiscal Year 1989.

    Energy Technology Data Exchange (ETDEWEB)

    United States. Bonneville Power Administration. Division of Fish and Wildlife.

    1988-11-01

    The FY 1989 Columbia River Basin Fish and Wildlife Program Work Plan (Work Plan) presents Bonneville Power Administration's plans for implementing the Columbia River Basin Fish and Wildlife Program (Program) in FY 1989. The Work Plan focuses on individual Action Items found in the 1987 Program for which Bonneville Power Administration (BPA) has determined that it has authority and responsibility to implement. Each of the entries in the Work Plan includes objectives, background, and progress to date in achieving those objectives, and a summary of plans for implementation in FY 1989. Most Action Items are implemented through one or more BPA-funded projects. Each Action Item entry is followed by a list of completed, ongoing, and planned projects, along with objectives, results, schedules, and milestones for each project. The FY 1989 Work Plan emphasizes continuation of 113 projects, most of which involve protection, mitigation, or enhancement of anadromous fishery resources. BPA also plans to start 20 new projects in FY 1989. The number of ongoing FY 1988 projects to be continued in FY 1989 and the number of new projects planned to start in FY 1989 are based on current (September 7, 1988) procurement expectations. Several projects presently in BPA's procurement process are expected to be contracted by September 30, 1988, the last day of FY 1988. Although these projects have not yet started, they have been listed in the Work Plan as ongoing FY 1988 projects, based on projected start dates in late September 1988. Throughout the Work Plan, those projects with projected start dates in September 1988 have been noted.

  17. Adaptive Management of Bull Trout Populations in the Lemhi Basin

    Science.gov (United States)

    Peterson, James T.; Tyre, Andrew J.; Converse, Sarah J.; Bogich, Tiffany L.; Miller, Damien; Post van der Burg, Max; Thomas, Carmen; Thompson, Ralph J.; Wood, Jeri; Brewer, Donna; Runge, Michael C.

    2011-01-01

    The bull trout Salvelinus confluentus, a stream-living salmonid distributed in drainages of the northwestern United States, is listed as threatened under the Endangered Species Act because of rangewide declines. One proposed recovery action is the reconnection of tributaries in the Lemhi Basin. Past water use policies in this core area disconnected headwater spawning sites from downstream habitat and have led to the loss of migratory life history forms. We developed an adaptive management framework to analyze which types of streams should be prioritized for reconnection under a proposed Habitat Conservation Plan. We developed a Stochastic Dynamic Program that identified optimal policies over time under four different assumptions about the nature of the migratory behavior and the effects of brook trout Salvelinus fontinalis on subpopulations of bull trout. In general, given the current state of the system and the uncertainties about the dynamics, the optimal policy would be to connect streams that are currently occupied by bull trout. We also estimated the value of information as the difference between absolute certainty about which of our four assumptions were correct, and a model averaged optimization assuming no knowledge. Overall there is little to be gained by learning about the dynamics of the system in its current state, although in other parts of the state space reducing uncertainties about the system would be very valuable. We also conducted a sensitivity analysis; the optimal decision at the current state does not change even when parameter values are changed up to 75% of the baseline values. Overall, the exercise demonstrates that it is possible to apply adaptive management principles to threatened and endangered species, but logistical and data availability constraints make detailed analyses difficult.

  18. Canada Basin revealed

    Science.gov (United States)

    Mosher, David C.; Shimeld, John; Hutchinson, Deborah R.; Chian, D; Lebedeva-Ivanova, Nina; Jackson, Ruth

    2012-01-01

    More than 15,000 line-km of new regional seismic reflection and refraction data in the western Arctic Ocean provide insights into the tectonic and sedimentologic history of Canada Basin, permitting development of new geologic understanding in one of Earth's last frontiers. These new data support a rotational opening model for southern Canada Basin. There is a central basement ridge possibly representing an extinct spreading center with oceanic crustal velocities and blocky basement morphology characteristic of spreading centre crust surrounding this ridge. Basement elevation is lower in the south, mostly due to sediment loading subsidence. The sedimentary succession is thickest in the southern Beaufort Sea region, reaching more than 15 km, and generally thins to the north and west. In the north, grabens and half-grabens are indicative of extension. Alpha-Mendeleev Ridge is a large igneous province in northern Amerasia Basin, presumably emplaced synchronously with basin formation. It overprints most of northern Canada Basin structure. The seafloor and sedimentary succession of Canada Basin is remarkably flat-lying in its central region, with little bathymetric change over most of its extent. Reflections that correlate over 100s of kms comprise most of the succession and on-lap bathymetric and basement highs. They are interpreted as representing deposits from unconfined turbidity current flows. Sediment distribution patterns reflect changing source directions during the basin’s history. Initially, probably late Cretaceous to Paleocene synrift sediments sourced from the Alaska and Mackenzie-Beaufort margins. This unit shows a progressive series of onlap unconformities with a younging trend towards Alpha and Northwind ridges, likely a response to contemporaneous subsidence. Sediment source direction appeared to shift to the Canadian Arctic Archipelago margin for the Eocene and Oligocene, likely due to uplift of Arctic islands during the Eurekan Orogeny. The final

  19. Development of a System-Wide Predator Control Program: Stepwise Implementation of a Predation Index, Predator Control Fisheries, and Evaluation Plan in the Columbia River Basin; Northern Pikeminnow Management Program, 2002 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Porter, Russell G.; Winther, Eric C.; Fox, Lyle G.

    2004-01-01

    This report presents results for year twelve in a basin-wide program to harvest northern pikeminnow1 (Ptychocheilus oregonensis). This program was started in an effort to reduce predation by northern pikeminnow on juvenile salmonids during their emigration from natal streams to the ocean. Earlier work in the Columbia River Basin suggested predation by northern pikeminnow on juvenile salmonids might account for most of the 10-20% mortality juvenile salmonids experience in each of eight Columbia River and Snake River reservoirs. Modeling simulations based on work in John Day Reservoir from 1982 through 1988 indicated that, if predator-size northern pikeminnow were exploited at a 10-20% rate, the resulting restructuring of their population could reduce their predation on juvenile salmonids by 50%. To test this hypothesis, we implemented a sport-reward angling fishery and a commercial longline fishery in the John Day Pool in 1990. We also conducted an angling fishery in areas inaccessible to the public at four dams on the mainstem Columbia River and at Ice Harbor Dam on the Snake River. Based on the success of these limited efforts, we implemented three test fisheries on a system-wide scale in 1991--a tribal longline fishery above Bonneville Dam, a sport-reward fishery, and a dam-angling fishery. Low catch of target fish and high cost of implementation resulted in discontinuation of the tribal longline fishery. However, the sport-reward and dam-angling fisheries were continued in 1992 and 1993. In 1992, we investigated the feasibility of implementing a commercial longline fishery in the Columbia River below Bonneville Dam and found that implementation of this fishery was also infeasible. Estimates of combined annual exploitation rates resulting from the sport-reward and damangling fisheries remained at the low end of our target range of 10-20%. This suggested the need for additional effective harvest techniques. During 1991 and 1992, we developed and tested a modified

  20. Characterization of Gatewell Orifice Lighting at the Bonneville Dam Second Powerhouse and Compendium of Research on Light Guidance with Juvenile Salmonids

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Robert P.; Simmons, Mary Ann

    2007-12-29

    The goal of the study described in this report is to provide U.S. Army Corps of Engineers (USACE) biologists and engineers with general design guidelines for using artificial lighting to enhance the passage of juvenile salmonids into the collection channel at the Bonneville Dam second powerhouse (B2). During fall 2007, Pacific Northwest National Laboratory (PNNL) researchers measured light levels in the field at one powerhouse orifice through which fish must pass to reach the collection channel. Two light types were evaluated—light-emitting diode (LED) lights and halogen spot lights. Additional measurements with mercury lamps were made at the PNNL Aquatic Research Laboratory to determine baseline intensity of the current lighting. A separate chapter synthesizes the relevant literature related to light and fish guidance for both field and laboratory studies. PNNL will also review the Corps plans for existing lighting protocol at all of the Portland District projects and help develop a uniform lighting scheme which could be implemented. The specific objectives for this study are to 1. Create a synthesis report of existing lighting data for juvenile salmonid attraction and deterrence and how the data are used at fish bypass facilities. 2. Evaluate current B2 orifice lighting conditions with both LED and halogen sources. 3. Make recommendations as to what lighting intensity, source, and configuration would improve passage at the B2 orifices. 4. Review USACE plans for retrofit of existing systems (to be assessed at a later date).

  1. The ecology of fish parasites with particular reference to helminth parasites and their salmonid fish hosts in Welsh rivers: a review of some of the central questions.

    Science.gov (United States)

    Thomas, J D

    2002-01-01

    Ecological studies carried out in Welsh rivers on the feeding behaviour of salmonid fish, their helminth parasites and intermediate hosts in the early 1950s and in 1998 have been used as a basis to review the literature dealing with the following questions. First, how are the helminth populations dispersed in space-time? Second, to what extent are the distributional patterns and the life history strategies of the parasites influenced by physicochemical factors? Third, to what extent are populations of helmith parasites in salmonid fish influenced by host characteristics including the genome, sex, age, size, social position and Feeding behaviour? Fourth, are the populations of parasites regulated in a density-dependent manner? Fifth, do the parasites influence the survival and wellbeing of their salmonid hosts and the evolution of sex? Sixth, to what extent is the parasite community influenced by environmental changes including those of an anthropogenic nature and can the parasites be used as bioindicators of pollution? As with most parasites the helminth species found were highly overdispersed thus making it necessary to undertake a log10 (1 + x) conversion for statistical analyses. Statistical analyses confirm that the genome, age and sex of salmonid fish hosts, the station and seasonal change in radiation levels were significant factors in predicting the number of parasites. The evidence given supports the hypothesis that the feeding behaviour and habitat selection by the host fish, their position in the social hierarchy and the overdispersed nature of the transmission sites are the key factors in causing differences in the parasitic fauna related to host species, age, size and sex. Differences in the helminth parasite community related to station can be explained on the basis of differences in water types, sediments and chemistry. Although the evidence presented is in accord with the consensus view that temperature is correlated with seasonal changes in the

  2. Using 3D acoustic telemetry to assess the response of resident salmonids to strobe lights in Lake Roosevelt, Washington: Chief Joseph Kokanee Enhancement Feasibility Study, 2001-2002 annual report

    Science.gov (United States)

    Perry, R.W.; Farley, M.J.; Hansen, G.S.; Shurtleff, D.J.; Rondorf, D.W.; LeCaire, R.

    2003-01-01

    In 1995, the Chief Joseph Kokanee Enhancement Project was established to mitigate the loss of anadromous fish due to the construction of Chief Joseph and Grand Coulee dams. The objectives of the Chief Joseph Enhancement Project are to determine the status of resident kokanee (Oncorhynchus nerka) populations above Chief Joseph and Grand Coulee dams and to enhance kokanee and rainbow trout (Oncorhynchus mykiss) populations. Studies conducted at Grand Coulee Dam documented substantial entrainment of kokanee through turbines at the third powerhouse.

  3. Integrated Hydrographical Basin Management. Study Case - Crasna River Basin

    Science.gov (United States)

    Visescu, Mircea; Beilicci, Erika; Beilicci, Robert

    2017-10-01

    Hydrographical basins are important from hydrological, economic and ecological points of view. They receive and channel the runoff from rainfall and snowmelt which, when adequate managed, can provide fresh water necessary for water supply, irrigation, food industry, animal husbandry, hydrotechnical arrangements and recreation. Hydrographical basin planning and management follows the efficient use of available water resources in order to satisfy environmental, economic and social necessities and constraints. This can be facilitated by a decision support system that links hydrological, meteorological, engineering, water quality, agriculture, environmental, and other information in an integrated framework. In the last few decades different modelling tools for resolving problems regarding water quantity and quality were developed, respectively water resources management. Watershed models have been developed to the understanding of water cycle and pollution dynamics, and used to evaluate the impacts of hydrotechnical arrangements and land use management options on water quantity, quality, mitigation measures and possible global changes. Models have been used for planning monitoring network and to develop plans for intervention in case of hydrological disasters: floods, flash floods, drought and pollution. MIKE HYDRO Basin is a multi-purpose, map-centric decision support tool for integrated hydrographical basin analysis, planning and management. MIKE HYDRO Basin is designed for analyzing water sharing issues at international, national and local hydrographical basin level. MIKE HYDRO Basin uses a simplified mathematical representation of the hydrographical basin including the configuration of river and reservoir systems, catchment hydrology and existing and potential water user schemes with their various demands including a rigorous irrigation scheme module. This paper analyzes the importance and principles of integrated hydrographical basin management and develop a case

  4. Evidence for competitive dominance of Pink salmon (Oncorhynchus gorbuscha) over other Salmonids in the North Pacific Ocean

    Science.gov (United States)

    Ruggerone, G.T.; Nielsen, J.L.

    2004-01-01

    Relatively little is known about fish species interactions in offshore areas of the world's oceans because adequate experimental controls are typically unavailable in such vast areas. However, pink salmon (Oncorhynchus gorbuscha) are numerous and have an alternating-year pattern of abundance that provides a natural experimental control to test for interspecific competition in the North Pacific Ocean and Bering Sea. Since a number of studies have recently examined pink salmon interactions with other salmon, we reviewed them in an effort to describe patterns of interaction over broad regions of the ocean. Research consistently indicated that pink salmon significantly altered prey abundance of other salmon species (e.g., zooplankton, squid), leading to altered diet, reduced total prey consumption and growth, delayed maturation, and reduced survival, depending on species and locale. Reduced survival was observed in chum salmon (O. keta) and Chinook salmon (O. tshawytscha) originating from Puget Sound and in Bristol Bay sockeye salmon (O. nerka). Growth of pink salmon was not measurably affected by other salmon species, but their growth was sometimes inversely related to their own abundance. In all marine studies, pink salmon affected other species through exploitation of prey resources rather than interference. Interspecific competition was observed in nearshore and offshore waters of the North Pacific Ocean and Bering Sea, and one study documented competition between species originating from different continents. Climate change had variable effects on competition. In the North Pacific Ocean, competition was observed before and after the ocean regime shift in 1977 that significantly altered abundances of many marine species, whereas a study in the Pacific Northwest reported a shift from predation- to competition-based mortality in response to the 1982/1983 El Nino. Key traits of pink salmon that influenced competition with other salmonids included great abundance, high

  5. Assessing the First Year of a Large-Scale Salmonid River Restoration Project on the Carmel River, CA

    Science.gov (United States)

    Smith, D. P.; Chow, K.; Luna, L.; Conlen, A.; Marson, L.

    2016-12-01

    The 93 year old San Clemente Dam was removed from the Carmel River in 2015 to reduce seismic hazards and to improve steelhead migration. A new 1 km long channel was constructed with a low-gradient meandering section, and a long series of step-pools interspersed with sporadic resting pools and plane-bed reaches. Each step was constructed with approximately 1 ft drop to facilitate steelhead mobility. The channel banks were constructed of well-compacted and vegetated soil lifts encapsulated in jute geotechnical fabric. The adjacent floodplain was graded and covered with vegetated geotechnical fabric. A variety of tall large-wood structures were anchored in the floodplain for hydraulic roughness, and to capture large wood. Following one run-off season, the project shows improved fish passage, salmonids residing in new pools, robust new floodplain vegetation, a veneer of new sediment and wood on floodplain areas, and sediment transport past the former dam location. The strongest components of the project were designed to sustain flows up to the 50-yr event without significant alteration. Significant changes occurred during the first year of operation, although the flows did not exceed the 3-yr event. Many large boulders used to construct arcuate steps were dislodged into the subsequent pools. Several reaches experienced bank erosion leading to geotechnical material disturbance or removal. Several of the large wood structures were compromised by bank erosion, and some were mobilized downstream. Floodwaters locally destroyed a constructed wetland, and produced significant erosional features. If left unchecked, the floodplain alteration could lead to avulsion. Premature boulder transport may have been caused by hydraulic modeling that assumed incorrect boulder density, impact and leveraging from large wood structures liberated from the floodplain, or differences between modeled and actual boulder stacking geometry. Excessive floodplain erosion occurred where pool

  6. Impacts of road deicing salts on the early-life growth and development of a stream salmonid: Salt type matters.

    Science.gov (United States)

    Hintz, William D; Relyea, Rick A

    2017-04-01

    The use of road deicing salts in regions that experience cold winters is increasing the salinity of freshwater ecosystems, which threatens freshwater resources. Yet, the impacts of environmentally relevant road salt concentrations on freshwater organisms are not well understood, particularly in stream ecosystems where salinization is most severe. We tested the impacts of deicing salts-sodium chloride (NaCl), magnesium chloride (MgCl 2 ), and calcium chloride (CaCl 2 )-on the growth and development of newly hatched rainbow trout (Oncorhynchus mykiss). We exposed rainbow trout to a wide range of environmentally relevant chloride concentrations (25, 230, 860, 1500, and 3000 mg Cl -  L -1 ) over an ecologically relevant time period (25 d). We found that the deicing salts studied had distinct effects. MgCl 2 did not affect rainbow trout growth at any concentration. NaCl had no effects at the lowest three concentrations, but rainbow trout length was reduced by 9% and mass by 27% at 3000 mg Cl -  L -1 . CaCl 2 affected rainbow trout growth at 860 mg Cl -  L -1 (5% reduced length; 16% reduced mass) and these effects became larger at higher concentrations (11% reduced length; 31% reduced mass). None of the deicing salts affected rainbow trout development. At sub-lethal and environmentally relevant concentrations, our results do not support the paradigm that MgCl 2 is the most toxic deicing salt to fish, perhaps due to hydration effects on the Mg 2+ cation. Our results do suggest different pathways for lethal and sub-lethal effects of road salts. Scaled to the population level, the reduced growth caused by NaCl and CaCl 2 at critical early-life stages has the potential to negatively affect salmonid recruitment and population dynamics. Our findings have implications for environmental policy and management strategies that aim to reduce the impacts of salinization on freshwater organisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Survival Estimates for the Passage of Spring-Migrating Juvenile Salmonids through Snake and Columbia River Dams and Reservoirs, 2008.

    Energy Technology Data Exchange (ETDEWEB)

    Faulkner, James R.; Smith, Steven G.; Muir, William D. [Northwest Fisheries Science Center

    2009-06-23

    In 2008, the National Marine Fisheries Service completed the sixteenth year of a study to estimate survival and travel time of juvenile salmonids Oncorhynchus spp. passing through dams and reservoirs on the Snake and Columbia Rivers. All estimates were derived from detections of fish tagged with passive integrated transponder (PIT) tags. We PIT tagged and released a total of 18,565 hatchery steelhead O. mykiss, 15,991 wild steelhead, and 9,714 wild yearling Chinook salmon O. tshawytscha at Lower Granite Dam in the Snake River. In addition, we utilized fish PIT tagged by other agencies at traps and hatcheries upstream from the hydropower system and at sites within the hydropower system in both the Snake and Columbia Rivers. These included 122,061 yearling Chinook salmon tagged at Lower Granite Dam for evaluation of latent mortality related to passage through Snake River dams. PIT-tagged smolts were detected at interrogation facilities at Lower Granite, Little Goose, Lower Monumental, Ice Harbor, McNary, John Day, and Bonneville Dams and in the PIT-tag detector trawl operated in the Columbia River estuary. Survival estimates were calculated using a statistical model for tag-recapture data from single release groups (the single-release model). Primary research objectives in 2008 were to: (1) estimate reach survival and travel time in the Snake and Columbia Rivers throughout the migration period of yearling Chinook salmon and steelhead, (2) evaluate relationships between survival estimates and migration conditions, and (3) evaluate the survival estimation models under prevailing conditions. This report provides reach survival and travel time estimates for 2008 for PIT-tagged yearling Chinook salmon (hatchery and wild), hatchery sockeye salmon O. nerka, hatchery coho salmon O. kisutch, and steelhead (hatchery and wild) in the Snake and Columbia Rivers. Additional details on the methodology and statistical models used are provided in previous reports cited here. Survival

  8. Drainage basins features and hydrological behaviour river Minateda basin

    International Nuclear Information System (INIS)

    Alonso-Sarria, F.

    1991-01-01

    Nine basin variables (shape, size and topology) have been analyzed in four small basins with non-permanent run off (SE of Spain). These geomorphological variables have been selected for their high correlation with the Instantaneous unit hydrograph parameters. It is shown that the variables can change from one small basin to another within a very short area; because of it, generalizations about the behaviour of the run off are not possible. In conclusion, it is stated that the variations in geomorphological aspects between different basins, caused mainly by geological constraints, are a very important factor to be controlled in a study of geoecological change derived from climatic change

  9. Abundance, Behavior, and Habitat Utilization by Coho Salmon and Steelhead Trout in Fish Creek, Oregon, as Influenced by Habitat Enhancement, 1985 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Wolfe, John (Mount Hood National Forest, Clackamas River Ranger District, Estacada, OR); Everest, Fred H. (Oregon State University, Pacific Northwest Forest and Range Experiment Station, Corvallis, OR); Heller, David A. (Mount Hood National Forest, Gresham, OR)

    1986-09-01

    Construction and evaluation of salmonid habitat improvements on Fish Creek, a tributary of the upper Clackamas River, was continued in fiscal year 1985 by the Estacada Ranger District, Mt. Hood National Forest, and the Anadromous Fish Habitat Research Unit of the Pacific Northwest Forest and Range Experiment Station (PNW), USDA Forest Service. The study began in 1982 when PNW entered into an agreement with the Mt. Hood National Forest to evaluate fish habitat improvements in the Fish Creek basin on the Estacada Ranger District. The project was initially conceived as a 5-year effort (19824986) to be financed by Forest Service funds. Several factors limiting production of salmonids in the basin were identified during the first year of the study, and the scope of the habitat improvement effort was subsequently enlarged. The habitat improvement program and the evaluation of improvements were both expanded in mid-1983 when the Bonneville Power Administration entered into an agreement with the Mt. Hood National Forest to provide additional funding for work on Fish Creek. Habitat improvement work in the basin is designed to increase the annual number of chinook and coho salmon, and steelhead trout smolt outmigrants. The primary objectives of the evaluation include the: (1) Evaluation and quantification of changes in salmonid spawning and rearing habitat resulting from a variety of habitat Improvements. (2) Evaluation and quantification of changes in fish populations and biomass resulting from habitat improvements. (3) Evaluation of the cost-effectiveness of habitat improvements developed with BPA and Forest Service funds on Fish Creek. Several prototype enhancement projects were constructed and tested during the first three years of the study. The Intention was to identify successful techniques that could then be broadly applied within the bash. This stepwise procedure has been largely successful in identifying the most promising enhancement techniques for the Fish Creek

  10. Report on the Predation Index, Predator Control Fisheries, and Program Evaluation for the Columbia River Basin Experimental Northern Pikeminnow Management Program, 2008 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Porter, Russell [Pacific States Marine Fisheries Commission].

    2009-09-10

    This report presents results for year seventeen in the basin-wide Experimental Northern Pikeminnow Management Program to harvest northern pikeminnow1 (Ptychocheilus oregonensis) in the Columbia and Snake Rivers. This program was started in an effort to reduce predation by northern pikeminnow on juvenile salmonids during their emigration from natal streams to the ocean. Earlier work in the Columbia River Basin suggested predation by northern pikeminnow on juvenile salmonids might account for most of the 10-20% mortality juvenile salmonids experience in each of eight Columbia River and Snake River reservoirs. Modeling simulations based on work in John Day Reservoir from 1982 through 1988 indicated that, if predator-size northern pikeminnow were exploited at a 10-20% rate, the resulting restructuring of their population could reduce their predation on juvenile salmonids by 50%. To test this hypothesis, we implemented a sport-reward angling fishery and a commercial longline fishery in the John Day Pool in 1990. We also conducted an angling fishery in areas inaccessible to the public at four dams on the mainstem Columbia River and at Ice Harbor Dam on the Snake River. Based on the success of these limited efforts, we implemented three test fisheries on a system-wide scale in 1991 - a tribal longline fishery above Bonneville Dam, a sport-reward fishery, and a dam-angling fishery. Low catch of target fish and high cost of implementation resulted in discontinuation of the tribal longline fishery. However, the sport-reward and dam-angling fisheries were continued in 1992 and 1993. In 1992, we investigated the feasibility of implementing a commercial longline fishery in the Columbia River below Bonneville Dam and found that implementation of this fishery was also infeasible. Estimates of combined annual exploitation rates resulting from the sport-reward and dam-angling fisheries remained at the low end of our target range of 10-20%. This suggested the need for additional

  11. Wind energy in Mediterranean Basin

    International Nuclear Information System (INIS)

    Gaudiosi, G.

    1991-01-01

    In its examination of wind energy potential in the Mediterranean Basin, this paper provides brief notes on the Basin's geography; indicates power production and demand; describes the area's wind characteristics and wind monitoring activities; illustrates wind velocity distributions; estimates local wind power production potential; reviews the Basin's wind energy marketing situation and each bordering country's wind energy programs; surveys installed wind energy farms; and assesses national research and commercialization efforts

  12. Multiple oscillatory modes of the Argentine Basin. Part II. The spectral origin of the basin modes

    NARCIS (Netherlands)

    Weijer, W.; Vevier, F.; Gille, S.T.; Dijkstra, H.A.

    2007-01-01

    In this paper the spectrum of barotropic basin modes of the Argentine Basin is shown to be connected to the classical Rossby basin modes of a flat-bottom (constant depth), rectangular basin. First, the spectrum of basin modes is calculated for the Argentine Basin, by performing a normal-mode

  13. Instream habitat restoration and stream temperature reduction in a whirling disease-positive Spring Creek in the Blackfoot River Basin, Montana

    Science.gov (United States)

    Pierce, Ron; Podner, Craig; Marczak, Laurie B; Jones, Leslie A.

    2014-01-01

    Anthropogenic warming of stream temperature and the presence of exotic diseases such as whirling disease are both contemporary threats to coldwater salmonids across western North America. We examined stream temperature reduction over a 15-year prerestoration and postrestoration period and the severity of Myxobolus cerebralisinfection (agent of whirling disease) over a 7-year prerestoration and postrestoration period in Kleinschmidt Creek, a fully reconstructed spring creek in the Blackfoot River basin of western Montana. Stream restoration increased channel length by 36% and reduced the wetted surface area by 69% by narrowing and renaturalizing the channel. Following channel restoration, average maximum daily summer stream temperatures decreased from 15.7°C to 12.5°C, average daily temperature decreased from 11.2°C to 10.0°C, and the range of daily temperatures narrowed by 3.3°C. Despite large changes in channel morphology and reductions in summer stream temperature, the prevalence and severity of M. cerebralis infection for hatchery Rainbow Trout Oncorhynchus mykiss remained high (98–100% test fish with grade > 3 infection) versus minimal for hatchery Brown Trout Salmo trutta (2% of test fish with grade-1 infection). This study shows channel renaturalization can reduce summer stream temperatures in small low-elevation, groundwater-dominated streams in the Blackfoot basin to levels more suitable to native trout. However, because of continuous high infections associated with groundwater-dominated systems, the restoration of Kleinschmidt Creek favors brown trout Salmo trutta given their innate resistance to the parasite and the higher relative susceptibility of other salmonids.

  14. The Confederated Tribes of the Warm Springs Indian Reservation of Oregon John Day Basin Office : Watershed Restoration Projects : 2002 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Confederated Tribes of the Warm Springs Reservation of Oregon. John Day Basin Office.

    2003-06-30

    The John Day is the nation's second longest free-flowing river in the contiguous United States and the longest containing entirely unsupplemented runs of anadromous fish. Located in eastern Oregon, the basin drains over 8,000 square miles, Oregon's fourth largest drainage basin, and incorporates portions of eleven counties. Originating in the Strawberry Mountains near Prairie City, the John Day River flows 284 miles in a northwesterly direction, entering the Columbia River approximately four miles upstream of the John Day dam. With wild runs of spring Chinook salmon and summer steelhead, westslope cutthroat, and redband and bull trout, the John Day system is truly a basin with national significance. The majority of the John Day basin was ceded to the Federal government in 1855 by the Confederated Tribes of the Warm Springs Reservation of Oregon (Tribes). In 1997, the Tribes established an office in the basin to coordinate restoration projects, monitoring, planning and other watershed activities on private and public lands. Once established, the John Day Basin Office (JDBO) formed a partnership with the Grant Soil and Water Conservation District (GSWCD), also located in the town of John Day, who contracts the majority of the construction implementation activities for these projects from the JDBO. The GSWCD completes the landowner contact, preliminary planning, engineering design, permitting, construction contracting, and construction implementation phases of most projects. The JDBO completes the planning, grant solicitation/defense, environmental compliance, administrative contracting, monitoring, and reporting portion of the program. Most phases of project planning, implementation, and monitoring are coordinated with the private landowners and basin agencies, such as the Oregon Department of Fish and Wildlife and Oregon Water Resources Department. In 2002, the JDBO and GSWCD proposed continuation of their successful partnership between the two agencies

  15. Acoustic Imaging Evaluation of Juvenile Salmonid Behavior in the Immediate Forebay of the Water Temperature Control Tower at Cougar Dam, 2010

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Fenton; Johnson, Gary E.; Royer, Ida M.; Phillips, Nathan RJ; Hughes, James S.; Fischer, Eric S.; Ploskey, Gene R.

    2011-10-01

    This report presents the results of an evaluation of juvenile Chinook salmonid (Oncorhynchus tshawytscha) behavior in the immediate forebay of the Water Temperature Control (WTC) tower at Cougar Dam in 2010. The study was conducted by the Pacific Northwest National Laboratory for the U.S. Army Corps of Engineers. The overall goal of the study was to characterize juvenile salmonid behavior and movement patterns in the immediate forebay of the WTC tower for fisheries resource managers to use to make decisions on bioengineering designs for long-term structures and/or operations to facilitate safe downstream passage for juvenile salmonids. We collected acoustic imaging (Dual-Frequency Identification Sonar; DIDSON) data from February 1, 2010 through January 31, 2011 to evaluate juvenile salmonid behavior year-round in the immediate forebay surface layer of the WTC tower (within 20 m, depth 0-5 m). From October 28, 2010 through January 31, 2011 a BlueView acoustic camera was also deployed in an attempt to determine its usefulness for future studies as well as augment the DIDSON data. For the DIDSON data, we processed a total of 35 separate 24-h periods systematically covering every other week in the 12-month study. Two different 24-hour periods were processed for the BlueView data for the feasibility study. Juvenile salmonids were present in the immediate forebay of the WTC tower throughout 2010. The juvenile salmonid abundance index was low in the spring (<200 fish per sample-day), began increasing in late April and peaked in mid-May. Fish abundance index began decreasing in early June and remained low in the summer months. Fish abundance increased again in the fall, starting in October, and peaked on November 8-9. A second peak occurred on December 22. Afterwards, abundance was low for the rest of the study (through January 2011). Average fish length for juvenile salmonids during early spring 2010 was 214 {+-} 86 mm (standard deviation). From May through early November

  16. Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling

    Directory of Open Access Journals (Sweden)

    Ferguson Moira M

    2010-07-01

    Full Text Available Abstract Background Clock family genes encode transcription factors that regulate clock-controlled genes and thus regulate many physiological mechanisms/processes in a circadian fashion. Clock1 duplicates and copies of Clock3 and NPAS2-like genes were partially characterized (genomic sequencing and mapped using family-based indels/SNPs in rainbow trout (RT(Oncorhynchus mykiss, Arctic charr (AC(Salvelinus alpinus, and Atlantic salmon (AS(Salmo salar mapping panels. Results Clock1 duplicates mapped to linkage groups RT-8/-24, AC-16/-13 and AS-2/-18. Clock3/NPAS2-like genes mapped to RT-9/-20, AC-20/-43, and AS-5. Most of these linkage group regions containing the Clock gene duplicates were derived from the most recent 4R whole genome duplication event specific to the salmonids. These linkage groups contain quantitative trait loci (QTL for life history and growth traits (i.e., reproduction and cell cycling. Comparative synteny analyses with other model teleost species reveal a high degree of conservation for genes in these chromosomal regions suggesting that functionally related or co-regulated genes are clustered in syntenic blocks. For example, anti-müllerian hormone (amh, regulating sexual maturation, and ornithine decarboxylase antizymes (oaz1 and oaz2, regulating cell cycling, are contained within these syntenic blocks. Conclusions Synteny analyses indicate that regions homologous to major life-history QTL regions in salmonids contain many candidate genes that are likely to influence reproduction and cell cycling. The order of these genes is highly conserved across the vertebrate species examined, and as such, these genes may make up a functional cluster of genes that are likely co-regulated. CLOCK, as a transcription factor, is found within this block and therefore has the potential to cis-regulate the processes influenced by these genes. Additionally, clock-controlled genes (CCGs are located in other life-history QTL regions within

  17. Geophysical Investigation of the Raton Basin.

    Science.gov (United States)

    1982-05-01

    65 miles wide, the Raton Basin is divided by the Cimarron Arch into the northern Raton Basin and the Las Vegas Basin on the south. The deepest...to the east, the Cimarron Arch on the north, and was linked by a low saddle to the Tucumcari Basin to the south. The Colorado and Rowe-Mora Basins...sedimentary rock thinning near the Apishipa, Cimarron , and Sierra Grande Arches; 2) presence of volcanic rock in the southern portion of the Basin; 3

  18. Impact des aménagements sur la migration anadrome du saumon atlantique (Salmo salar L. sur le gave de Pau (France

    Directory of Open Access Journals (Sweden)

    CHANSEAU M.

    1999-04-01

    Full Text Available Le suivi par radiotélémétrie de la migration anadrome de 114 saumons atlantiques sur le Gave de Pau, réalisé de 1995 à 1997, a permis d'étudier l'impact de 31 des 37 obstacles érigés sur l'axe de migration. Cinq obstacles majeurs ont été identifiés en regard de leur faible perméabilité et/ou des retards qu'ils induisent ainsi que de leur position sur l'axe. La transparence de ces 5 aménagements permettrait à plus de 80 % (contre seulement 13 % dans la situation actuelle des saumons de parvenir sur de bonnes zones de frayères. L'accumulation des retards au niveau de chaque obstacle peut empêcher une proportion non négligeable des poissons de parvenir à temps sur les meilleures zones de frayères, notamment ceux qui se présentent à l'automne sur le gave, ou ceux qui, ralentis par les obstacles, effectuent un arrêt estival sur la partie aval du cours d'eau. Les seuils de stabilisation en enrochements de faible hauteur ( 2,5 m supérieure ont eu des impacts variables, imputables en grande partie au type de passe à poissons. Les passes à bassins et les rivières de contournement ont été les dispositifs de franchissement les plus performants. Les passés à ralentisseurs à chevrons épais se sont révélées peu performantes en raison de leur faible débit d'alimentation et de leur grande sensibilité aux variations des niveaux d'eau amont. L'impact des aménagements hydroélectriques sans dérivation dépend de l'emplacement de l'entrée de la passe à poissons et de son débit d'alimentation : des effets minimums sur la migration ont été observés lorsque les ouvrages étaient équipés d'un dispositif mobilisant des débits importants (2-4 m3/s et dont l'entrée se situait dans le canal de fuite. L'impact des aménagements hydroélectriques munis d'une dérivation, tous équipés d'un dispositif de franchissement au niveau des barrages de prise d'eau, dépend des débits réservés dans les parties court

  19. Identifying stakeholder-relevant climate change impacts: a case study in the Yakima River Basin, Washington, USA

    Science.gov (United States)

    Jenni, K.; Graves, D.; Hardiman, Jill M.; Hatten, James R.; Mastin, Mark C.; Mesa, Matthew G.; Montag, J.; Nieman, Timothy; Voss, Frank D.; Maule, Alec G.

    2014-01-01

    Designing climate-related research so that study results will be useful to natural resource managers is a unique challenge. While decision makers increasingly recognize the need to consider climate change in their resource management plans, and climate scientists recognize the importance of providing locally-relevant climate data and projections, there often remains a gap between management needs and the information that is available or is being collected. We used decision analysis concepts to bring decision-maker and stakeholder perspectives into the applied research planning process. In 2009 we initiated a series of studies on the impacts of climate change in the Yakima River Basin (YRB) with a four-day stakeholder workshop, bringing together managers, stakeholders, and scientists to develop an integrated conceptual model of climate change and climate change impacts in the YRB. The conceptual model development highlighted areas of uncertainty that limit the understanding of the potential impacts of climate change and decision alternatives by those who will be most directly affected by those changes, and pointed to areas where additional study and engagement of stakeholders would be beneficial. The workshop and resulting conceptual model highlighted the importance of numerous different outcomes to stakeholders in the basin, including social and economic outcomes that go beyond the physical and biological outcomes typically reported in climate impacts studies. Subsequent studies addressed several of those areas of uncertainty, including changes in water temperatures, habitat quality, and bioenergetics of salmonid populations.

  20. The effects of increased stream temperatures on juvenile steelhead growth in the Yakima River Basin based on projected climate change scenarios

    Science.gov (United States)

    Hardiman, Jill M.; Mesa, Matthew G.

    2013-01-01

    Stakeholders within the Yakima River Basin expressed concern over impacts of climate change on mid-Columbia River steelhead (Oncorhynchus mykiss), listed under the Endangered Species Act. We used a bioenergetics model to assess the impacts of changing stream temperatures—resulting from different climate change scenarios—on growth of juvenile steelhead in the Yakima River Basin. We used diet and fish size data from fieldwork in a bioenergetics model and integrated baseline and projected stream temperatures from down-scaled air temperature climate modeling into our analysis. The stream temperature models predicted that daily mean temperatures of salmonid-rearing streams in the basin could increase by 1–2°C and our bioenergetics simulations indicated that such increases could enhance the growth of steelhead in the spring, but reduce it during the summer. However, differences in growth rates of fish living under different climate change scenarios were minor, ranging from about 1–5%. Because our analysis focused mostly on the growth responses of steelhead to changes in stream temperatures, further work is needed to fully understand the potential impacts of climate change. Studies should include evaluating changing stream flows on fish activity and energy budgets, responses of aquatic insects to climate change, and integration of bioenergetics, population dynamics, and habitat responses to climate change.

  1. Annual Review of BPA-Funded Projects in Natural and Artificial Propagation of Salmonids, March 27-29, 1985, Holiday Inn Airport, Portland, Oregon.

    Energy Technology Data Exchange (ETDEWEB)

    United States. Bonneville Power Administration.

    1985-04-01

    The Fish and Wildlife Division of Bonneville Power Administration (BPA) hosted a meeting for contractors to present the results of fiscal year 1984 research conducted to implement the Northwest Power Planning Council's Fish and Wildlife Program. The meeting focused on those projects specifically related to natural and artificial propagation of salmonids. The presentations were held at the Holiday Inn Airport in Portland, Oregon, on March 27-29, 1985. This document contains abstracts of the presentations from that meeting. Section 1 contains abstracts on artificial propagation, fish health, and downstream migration, and Section 2 contains abstracts on natural propagation and habitat improvement. The abstracts are indexed by BPA Project Number and by Fish and Wildlife Program Measure. The registered attendees at the meeting are listed alphabetically in Appendix A and by affiliation in Appendix B.

  2. L'hybridation dans les populations naturelles de salmonidés dans le Sud-Ouest de l'Europe et en milieu expérimental

    OpenAIRE

    BEALL E.; MORAN P.; PENDAS A.; IZQUIERDO J.; GARCIA VAZQUEZ E.; GLISE S.; VIGNES J. C.; BARRIERE L.

    1997-01-01

    L'hybridation interspécifique entre le saumon atlantique et la truite commune dans la nature a été mise en évidence dans différents pays d'Europe et au Canada. Une étude a été entreprise pour examiner son incidence dans des populations de salmonidés de certaines rivières des Asturies (nord de l'Espagne) et du sud-ouest de la France. Elle a été complétée par des expériences en milieu contrôlé pour déterminer les causes et les conditions de la disparition des barrières comportementales permetta...

  3. Successive oral immunizations against Piscirickettsia salmonis and infectious salmon anemia virus are required to maintain a long-term protection in farmed salmonids

    Directory of Open Access Journals (Sweden)

    Ivan eTobar

    2015-05-01

    Full Text Available Currently, there is a growing demand to determine the protective status of vaccinated fish in order to prevent diseases outbreaks. A set of different parameters that include the infectious and immunological status of vaccinated salmonids from 622 Chilean farms were analyzed during 2011-2014. The aim of this study was to optimize the vaccination program of these centers through the determination of the protective state of vaccinated fish using oral immunizations. This state was measured by the association of the concentration of the immunoglobulin M (IgM in the serum and the mortality rate of vaccinated fish. Salmonids were vaccinated with different commercial mono- or polyvalent vaccines against SRS and ISAv, first by the intraperitoneal injection of oil-adjuvanted antigens and then by the stimulation of mucosal immunity using oral vaccines as booster. The results showed that high levels of specific IgM antibodies were observed after injectable vaccination, reaching a maximum concentration at 600-800 degree-days. Similar levels of antibodies were observed when oral immunizations were administrated. The high concentration of antibodies (above 2750 ng/mL for ISAv and 3500 ng/mL for SRS was maintained for a period of 800 degree-days after each vaccination procedure. In this regard, oral immunizations maintained a long-term high concentration of anti-SRS and anti-ISAv specific IgM antibodies. When the concentration of antibodies decreased below 2000 pg/mL, a window of susceptibility to SRS infection was observed in the farm, suggesting the close association between antibody levels and fish protective status. These results demonstrated that, in the field, several oral immunizations are essential to uphold a high level of specific anti-pathogens antibodies and, therefore, a protective status during the whole productive cycle.

  4. Comparison of pigment cell ultrastructure and organisation in the dermis of marble trout and brown trout, and first description of erythrophore ultrastructure in salmonids

    Science.gov (United States)

    Djurdjevič, Ida; Kreft, Mateja Erdani; Sušnik Bajec, Simona

    2015-01-01

    Skin pigmentation in animals is an important trait with many functions. The present study focused on two closely related salmonid species, marble trout (Salmo marmoratus) and brown trout (S. trutta), which display an uncommon labyrinthine (marble-like) and spot skin pattern, respectively. To determine the role of chromatophore type in the different formation of skin pigment patterns in the two species, the distribution and ultrastructure of chromatophores was examined with light microscopy and transmission electron microscopy. The presence of three types of chromatophores in trout skin was confirmed: melanophores; xanthophores; and iridophores. In addition, using correlative microscopy, erythrophore ultrastructure in salmonids was described for the first time. Two types of erythrophores are distinguished, both located exclusively in the skin of brown trout: type 1 in black spot skin sections similar to xanthophores; and type 2 with a unique ultrastructure, located only in red spot skin sections. Morphologically, the difference between the light and dark pigmentation of trout skin depends primarily on the position and density of melanophores, in the dark region covering other chromatophores, and in the light region with the iridophores and xanthophores usually exposed. With larger amounts of melanophores, absence of xanthophores and presence of erythrophores type 1 and type L iridophores in the black spot compared with the light regions and the presence of erythrophores type 2 in the red spot, a higher level of pigment cell organisation in the skin of brown trout compared with that of marble trout was demonstrated. Even though the skin regions with chromatophores were well defined, not all the chromatophores were in direct contact, either homophilically or heterophilically, with each other. In addition to short-range interactions, an important role of the cellular environment and long-range interactions between chromatophores in promoting adult pigment pattern

  5. Design and evaluation of a unique RT-qPCR assay for diagnostic quality control assessment that is applicable to pathogen detection in three species of salmonid fish.

    Science.gov (United States)

    Sepúlveda, Dagoberto; Bohle, Harry; Labra, Alvaro; Grothusen, Horst; Marshall, Sergio H

    2013-09-16

    The detection of pathogens at early stages of infection is a key point for disease control in aquaculture. Therefore, accurate diagnostic procedures are a must. Real-time PCR has been a mainstay in diagnostics over the years due to its speed, specificity, sensitivity, reproducibility and throughput; as such, real-time PCR is a target for improvement. Nevertheless, to validate a novel diagnostic tool, correct setup of the assay, including proper endogenous controls to evaluate the quantity and quality of the samples and to detect possible sample degradation, is compulsory. This work aims to design a unique RT-qPCR assay for pathogen detection in the three salmonid species reared in Chile. The assay uses elongation factor 1 alpha as the single endogenous control, thus avoiding the need for multiple endogenous controls, as well as multiple validations and non-comparable quality control parameters. The in vivo and in vitro analyses of samples from Salmo salar, Oncorhynchus mykiss and Oncorhynchus kisutch showed that when primers were accurately selected to target conserved regions of the elongation factor 1 alpha (ELF1α) gene, a single novel RT-qPCR assay yielding similar and reproducible Ct values between the three species could be designed. The opposite occurred when an assay originally designed for Salmo salar was tested in samples from the two species of the genus Oncorhynchus. Here, we report the design and evaluation of an accurate trans-species RT-qPCR assay that uses the elongation factor 1 alpha (ELF1α) gene as an endogenous control and is applicable for diagnostic purposes in samples obtained from the three salmonid species reared in Chile.

  6. Fine-scale foraging movements by fish-eating killer whales (Orcinus orca) relate to the vertical distributions and escape responses of salmonid prey (Oncorhynchusspp.).

    Science.gov (United States)

    Wright, Brianna M; Ford, John K B; Ellis, Graeme M; Deecke, Volker B; Shapiro, Ari Daniel; Battaile, Brian C; Trites, Andrew W

    2017-01-01

    We sought to quantitatively describe the fine-scale foraging behavior of northern resident killer whales ( Orcinus orca ), a population of fish-eating killer whales that feeds almost exclusively on Pacific salmon ( Oncorhynchus spp.). To reconstruct the underwater movements of these specialist predators, we deployed 34 biologging Dtags on 32 individuals and collected high-resolution, three-dimensional accelerometry and acoustic data. We used the resulting dive paths to compare killer whale foraging behavior to the distributions of different salmonid prey species. Understanding the foraging movements of these threatened predators is important from a conservation standpoint, since prey availability has been identified as a limiting factor in their population dynamics and recovery. Three-dimensional dive tracks indicated that foraging ( N  = 701) and non-foraging dives ( N  = 10,618) were kinematically distinct (Wilks' lambda: λ 16  = 0.321, P  killer whales dove deeper, remained submerged longer, swam faster, increased their dive path tortuosity, and rolled their bodies to a greater extent than during other activities. Maximum foraging dive depths reflected the deeper vertical distribution of Chinook (compared to other salmonids) and the tendency of Pacific salmon to evade predators by diving steeply. Kinematic characteristics of prey pursuit by resident killer whales also revealed several other escape strategies employed by salmon attempting to avoid predation, including increased swimming speeds and evasive maneuvering. High-resolution dive tracks reconstructed using data collected by multi-sensor accelerometer tags found that movements by resident killer whales relate significantly to the vertical distributions and escape responses of their primary prey, Pacific salmon.

  7. Walla Walla River Basin Fish Habitat Enhancement Project, 2002-2003 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Volkman, Jed (Confederated Tribes of the Umatilla Indian Reservation, Pendleton, OR)

    2005-12-01

    In 2002 and 2003, the Confederated Tribes of the Umatilla Indian Reservation (CTUIR) Fisheries Habitat Program implemented stream habitat restoration and protection efforts on private properties in the Walla Walla River Basin with funding from Bonneville Power Administration (BPA). The objective of this effort is to protect and restore habitat critical to the recovery of weak or reintroduced populations of salmonid fish. The CTUIR has currently enrolled nine properties into this program: two on Couse Creek, two adjacent properties on Blue Creek, one on Patit Creek, and four properties on the mainstem Walla Walla River. Major accomplishments during the reporting period include the following: (1) Secured approximately $229,000 in project cost share; (2) Purchase of 46 acres on the mainstem Walla Walla River to be protected perpetually for native fish and wildlife; (3) Developed three new 15 year conservation easements with private landowners; (4) Installed 3000 feet of weed barrier tarp with new plantings within project area on the mainstem Walla Walla River; (5) Expanded easement area on Couse Creek to include an additional 0.5 miles of stream corridor and 32 acres of upland habitat; (6) Restored 12 acres on the mainstem Walla Walla River and 32 acres on Couse Creek to native perennial grasses; and (7) Installed 50,000+ new native plants/cuttings within project areas.

  8. The Confederated Tribes of the Warm Springs Indian Reservation of Oregon John Day Basin Office: watershed restoration projects: annual report, 1999.; ANNUAL

    International Nuclear Information System (INIS)

    2001-01-01

    The John Day River is the second longest free-flowing river in the contiguous United States and one of the few major subbasins in the Columbia River basin containing entirely unsupplemented runs of anadromous fish. Located in eastern Oregon, the basin drains over 8,000 square miles, the fourth largest drainage area in Oregon. With its beginning in the Strawberry Mountains near the town of Prairie City, the John Day flows 284 miles in a northwesterly direction, entering the Columbia River approximately four miles upstream of the John Day dam. With wild runs of spring chinook salmon and summer steelhead, red band, westslope cutthroat, and redband trout, the John Day system is truly one of national significance. The entire John Day basin was granted to the Federal government in 1855 by the Confederated Tribes of the Warm Springs Reservation of Oregon (Tribes). In 1997, the Tribes established an office in the basin to coordinate restoration projects, monitoring, planning and other watershed activities on private and public lands. Once established, the John Day Basin Office (JDBO) initiated contracting the majority of its construction implementation actions with the Grant Soil and Water Conservation District (GSWCD), also located in the town of John Day. The GSWCD completes the landowner contact, preliminary planning, engineering design, permitting, construction contracting, and construction implementation phases of the projects. The JDBO completes the planning, grant solicitation/defense, environmental compliance, administrative contracting, monitoring, and reporting portion of the program. Most phases of project planning, implementation, and monitoring are coordinated with the private landowners and basin agencies, such as the Oregon Department of Fish and Wildlife and Oregon Water Resources Department. In 1999, the JDBO and GSWCD proposed continuation of a successful partnership between the two agencies and basin landowners to implement an additional eleven (11

  9. The Confederated Tribes of the Warm Springs Indian Reservation of Oregon John Day Basin Office: FY 1999 Watershed Restoration Projects : Annual Report 1999.

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, Shawn W.

    2001-03-01

    The John Day River is the second longest free-flowing river in the contiguous United States and one of the few major subbasins in the Columbia River basin containing entirely unsupplemented runs of anadromous fish. Located in eastern Oregon, the basin drains over 8,000 square miles, the fourth largest drainage area in Oregon. With its beginning in the Strawberry Mountains near the town of Prairie City, the John Day flows 284 miles in a northwesterly direction, entering the Columbia River approximately four miles upstream of the John Day dam. With wild runs of spring chinook salmon and summer steelhead, red band, westslope cutthroat, and redband trout, the John Day system is truly one of national significance. The entire John Day basin was granted to the Federal government in 1855 by the Confederated Tribes of the Warm Springs Reservation of Oregon (Tribes). In 1997, the Tribes established an office in the basin to coordinate restoration projects, monitoring, planning and other watershed activities on private and public lands. Once established, the John Day Basin Office (JDBO) initiated contracting the majority of its construction implementation actions with the Grant Soil and Water Conservation District (GSWCD), also located in the town of John Day. The GSWCD completes the landowner contact, preliminary planning, engineering design, permitting, construction contracting, and construction implementation phases of the projects. The JDBO completes the planning, grant solicitation/defense, environmental compliance, administrative contracting, monitoring, and reporting portion of the program. Most phases of project planning, implementation, and monitoring are coordinated with the private landowners and basin agencies, such as the Oregon Department of Fish and Wildlife and Oregon Water Resources Department. In 1999, the JDBO and GSWCD proposed continuation of a successful partnership between the two agencies and basin landowners to implement an additional eleven (11

  10. The Confederated Tribes of the Warm Springs Indian Reservation of Oregon John Day Basin Office: watershed restoration projects: annual report, 1998.; ANNUAL

    International Nuclear Information System (INIS)

    1999-01-01

    The John Day River is the second longest free-flowing river in the contiguous US and one of the few major subbasins in the Columbia River basin containing entirely unsupplemented runs of anadromous fish. Located in eastern Oregon, the basin drains over 8,000 square miles, the fourth largest drainage area in Oregon. With its beginning in the Strawberry Mountains near the town of Prairie City, the John Day flows 284 miles in a northwesterly direction, entering the Columbia River approximately four miles upstream of the John Day dam. With wild runs of spring chinook salmon and summer steelhead, red band, westslope cutthroat, and redband trout, the John Day system is truly one of national significance. The entire John Day basin was granted to the Federal government in 1855 by the Confederated Tribes of the Warm Springs Reservation of Oregon (Tribes). In 1997, the Tribes established an office in the basin to coordinate restoration projects, monitoring, planning and other watershed activities on private and public lands. Once established, the John Day Basin Office (JDBO) initiated contracting the majority of its construction implementation actions with the Grant Soil and Water Conservation District (GSWCD), also located in the town of John Day. The GSWCD completes the landowner contact, preliminary planning, engineering design, permitting, construction contracting, and construction implementation phases of the projects. The JDBO completes the planning, grant solicitation/defense, environmental compliance, administrative contracting, monitoring, and reporting portion of the program. Most phases of project planning, implementation, and monitoring are coordinated with the private landowners and basin agencies, such as the Oregon Department of Fish and Wildlife and Oregon Water Resources Department. In 1998, the JDBO and GSWCD proposed continuation of a successful partnership between the two agencies and basin landowners to implement an additional ten (10) watershed

  11. Climate variables explain neutral and adaptive variation within salmonid metapopulations: The importance of replication in landscape genetics

    Science.gov (United States)

    Hand, Brian K.; Muhlfeld, Clint C.; Wade, Alisa A.; Kovach, Ryan; Whited, Diane C.; Narum, Shawn R.; Matala, Andrew P.; Ackerman, Michael W.; Garner, B. A.; Kimball, John S; Stanford, Jack A.; Luikart, Gordon

    2016-01-01

    Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

  12. K-Basins design guidelines

    International Nuclear Information System (INIS)

    Roe, N.R.; Mills, W.C.

    1995-06-01

    The purpose of the design guidelines is to enable SNF and K Basin personnel to complete fuel and sludge removal, and basin water mitigation by providing engineering guidance for equipment design for the fuel basin, facility modifications (upgrades), remote tools, and new processes. It is not intended to be a purchase order reference for vendors. The document identifies materials, methods, and components that work at K Basins; it also Provides design input and a technical review process to facilitate project interfaces with operations in K Basins. This document is intended to compliment other engineering documentation used at K Basins and throughout the Spent Nuclear Fuel Project. Significant provisions, which are incorporated, include portions of the following: General Design Criteria (DOE 1989), Standard Engineering Practices (WHC-CM-6-1), Engineering Practices Guidelines (WHC 1994b), Hanford Plant Standards (DOE-RL 1989), Safety Analysis Manual (WHC-CM-4-46), and Radiological Design Guide (WHC 1994f). Documents (requirements) essential to the engineering design projects at K Basins are referenced in the guidelines

  13. Geologic Basin Boundaries (Basins_GHGRP) GIS Layer

    Data.gov (United States)

    U.S. Environmental Protection Agency — This is a coverage shapefile of geologic basin boundaries which are used by EPA's Greenhouse Gas Reporting Program. For onshore production, the "facility" includes...

  14. Marketing San Juan Basin gas

    International Nuclear Information System (INIS)

    Posner, D.M.

    1988-01-01

    Marketing natural gas produced in the San Juan Basin of New Mexico and Colorado principally involves four gas pipeline companies with significant facilities in the basin. The system capacity, transportation rates, regulatory status, and market access of each of these companies is evaluated. Because of excess gas supplies available to these pipeline companies, producers can expect improved take levels and prices by selling gas directly to end users and utilities as opposed to selling gas to the pipelines for system supply. The complexities of transporting gas today suggest that the services of an independent gas marketing company may be beneficial to smaller producers with gas supplies in the San Juan Basin

  15. Great Basin Experimental Range: Annotated bibliography

    Science.gov (United States)

    E. Durant McArthur; Bryce A. Richardson; Stanley G. Kitchen

    2013-01-01

    This annotated bibliography documents the research that has been conducted on the Great Basin Experimental Range (GBER, also known as the Utah Experiment Station, Great Basin Station, the Great Basin Branch Experiment Station, Great Basin Experimental Center, and other similar name variants) over the 102 years of its existence. Entries were drawn from the original...

  16. From salmon to shad: Shifting sources of marine-derived nutrients in the Columbia River Basin

    Science.gov (United States)

    Haskell, Craig A.

    2018-01-01

    Like Pacific salmon (Oncorhynchus spp.), nonnative American shad (Alosa sapidissima) have the potential to convey large quantities of nutrients between the Pacific Ocean and freshwater spawning areas in the Columbia River Basin (CRB). American shad are now the most numerous anadromous fish in the CRB, yet the magnitude of the resulting nutrient flux owing to the shift from salmon to shad is unknown. Nutrient flux models revealed that American shad conveyed over 15,000 kg of nitrogen (N) and 3,000 kg of phosphorus (P) annually to John Day Reservoir, the largest mainstem reservoir in the lower Columbia River. Shad were net importers of N, with juveniles and postspawners exporting just 31% of the N imported by adults. Shad were usually net importers of P, with juveniles and postspawners exporting 46% of the P imported by adults on average. American shad contributed <0.2% of the total annual P load into John Day Reservoir, but during June when most adult shad are migrating into John Day Reservoir, they contributed as much as 2.0% of the P load. Nutrient inputs by American shad were similar to current but far less than historical inputs of Pacific salmon owing to their smaller size. Given the relatively high background P levels and low retention times in lower Columbia River reservoirs, it is unlikely that shad marine-derived nutrients affect nutrient balances or food web productivity through autotrophic pathways. However, a better understanding of shad spawning aggregations in the CRB is needed.

  17. River basin management and community : the Great Ouse Basin, 1850–present

    NARCIS (Netherlands)

    Mostert, E.

    2017-01-01

    River basins are difficult units to manage. Society is generally not organized on the basis of river basins, yet river basins are important units for society and vice versa. This paper discusses the development and effectiveness of river basin management, using the Great Ouse Basin in the east of

  18. Allegheny County Basin Outlines Map

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — This basins dataset was created to initiate regional watershed approaches with respect to sewer rehabilitation. If viewing this description on the Western...

  19. Fisheries Enhancement in the Fish Creek Basin; Evaluation of In-Channel and Off-Channel Projects, 1984 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Everest, Fred H.; Sedell, James R. (Oregon State University, Pacific Northwest Forest and Range Experiment Station, Corvallis, OR); Wolfe, John (Mount Hood National Forest, Clackamas River Ranger District, Estacada, OR)

    1985-07-01

    This S-year project which began in 1983 is designed to construct and evaluate habitat improvements in the Fish Creek basin by personnel of the Estacada Ranger District, Ht. Hood National Forest, and the Pacific Northwest Forest and Range Experiment Station. The work is jointly funded by BPA and USDA-Forest Service. The evaluation has focused on activities designed to improve spawning and rearing habitat for chinook and coho salmon and steelhead trout. Specific habitat improvements being evaluated include: boulder berms, an off-channel pond, a side-channel, addition of large woody debris to stream edge habitats, and hardwood plantings to improve riparian vegetation. The initial phases of habitat work have proceeded cautiously in concert with the evaluation so that knowledge gained could be immediately applied to future proposed habitat work. The evaluation has been conducted at the basin level, rather than reach or site level, and has focused intensely on identification of factors limiting production of salmonids in Fish Creek, as well as physical and biological changes resulting from habitat improvement. Identification of limiting factors has proven to be difficult and requires several years of all-season investigation. Results of this work to date indicate that spawning habitat is not limiting production of steelhead or coho in the basin. Coho habitat is presently underseeded because of inadequate escapement. Key summer habitats for coho, age 0 and age 1+ steelhead are beaver ponds, side channels, and pools, respectively. Key winter habitats appear to be groundwater-fed side channels and boulder-rubble stream margins with 30+ cm depth and low velocity water. Additional work is needed to determine whether summer habitat or winter habitat is limiting steelhead and coho production. Chinook use of the basin appears to be related to the timing of fall freshets that control migratory access into the system. Instream habitat improvements show varying degrees of promise

  20. Sustaining Exploration in Mature Basins

    International Nuclear Information System (INIS)

    Bayo, A.

    2002-01-01

    Exploration is a business like any other business driven by opportunity, resources and expectation of profit. Therefore, exploration will thrive anywhere the opportunities are significant, the resources are available and the outlook for profit (or value creation) is good. To sustain exploration activities anywhere, irrespective of the environment, there must be good understanding of the drivers of these key investment criteria. This paper will examine these investment criteria as they relate to exploration business and address the peculiarity of exploration in mature basin. Mature basins are unique environment that lends themselves a mix of fears, paradigms and realities, particularly with respect to the perception of value. To sustain exploration activities in a mature basin, we need to understand these perceptions relative to the true drivers of profitability. Exploration in the mature basins can be as profitable as exploration in emerging basins if the dynamics of value definition-strategic and fiscal values are understood by operators, regulators and co ventures alike. Some suggestions are made in this presentation on what needs to be done in addressing these dynamic investment parameters and sustaining exploration activities in mature basins

  1. The Heidelberg Basin Drilling Project — basin analysis

    Science.gov (United States)

    Tanner, David C.; Martini, Nicole; Buness, Hermann; Gabriel, Gerald; Krawczyk, Charlotte M.

    2010-05-01

    Within the context of the Heidelberg Basin Project (Gabriel et al. 2008), we present the first results of three-dimensional structural modelling of the basin, based on interpretation of reflection seismics and decompaction using porosity data measured from core material. Firstly, we interpreted six horizons (Base Quaternary, Internal and Base Pliocene, Base Upper Miocene, Internal and Base Mid Miocene Hydrobien beds) from all available industrial (ca. 100 km) and our own reflection seismic sections (ca. 15 km), which lie within a 8 km radius around the Heidelberg UniNord 1/2 boreholes. This data was used to construct a three-dimensional geometrical model of the Heidelberg Basin. Using 300 core samples, we determined the porosity of the Quaternary sediments and constructed an exponential porosity/depth relationship for these rocks, which were then attributed to the model. Lower strata were given values from the literature. The model shows that the Heidelberg basin has a N-S and E-W areal extent of only 10 × 6 km, directly abutting the eastern fault boundary of the Upper Rhine Graben. The strongest synsedimentary tectonic subsidence occurred during the Upper Miocene, Upper Pliocene, and Quarternary. Faults are not seen within the basin at this level, but a NW-SE striking strike-slip structure is recorded to the west of the basin. Furthermore, the sedimentary depocentre shifted 2 km northwards over time to the present location, directly below the city of Heidelberg. We determined that Quaternary sediments have porosities of over 60% at the surface, but at the Base Quaternary porosity is less than 35%. This strong decrease means that 740 m of sediments were compacted to produce the present ca. 500 m thickness of Quaternary strata. Gabriel, G., Ellwanger, D., Hoselmann, C. & Weidenfeller, M. (2008): The Heidelberg Basin Drilling Project. -- Quaternary Science Journal, 57, 3-4, 253-260.

  2. Single nucleotide polymorphism (SNP discovery in duplicated genomes: intron-primed exon-crossing (IPEC as a strategy for avoiding amplification of duplicated loci in Atlantic salmon (Salmo salar and other salmonid fishes

    Directory of Open Access Journals (Sweden)

    Primmer Craig R

    2006-07-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs represent the most abundant type of DNA variation in the vertebrate genome, and their applications as genetic markers in numerous studies of molecular ecology and conservation of natural populations are emerging. Recent large-scale sequencing projects in several fish species have provided a vast amount of data in public databases, which can be utilized in novel SNP discovery in salmonids. However, the suggested duplicated nature of the salmonid genome may hamper SNP characterization if the primers designed in conserved gene regions amplify multiple loci. Results Here we introduce a new intron-primed exon-crossing (IPEC method in an attempt to overcome this duplication problem, and also evaluate different priming methods for SNP discovery in Atlantic salmon (Salmo salar and other salmonids. A total of 69 loci with differing priming strategies were screened in S. salar, and 27 of these produced ~13 kb of high-quality sequence data consisting of 19 SNPs or indels (one per 680 bp. The SNP frequency and the overall nucleotide diversity (3.99 × 10-4 in S. salar was lower than reported in a majority of other organisms, which may suggest a relative young population history for Atlantic salmon. A subset of primers used in cross-species analyses revealed considerable variation in the SNP frequencies and nucleotide diversities in other salmonids. Conclusion Sequencing success was significantly higher with the new IPEC primers; thus the total number of loci to screen in order to identify one potential polymorphic site was six times less with this new strategy. Given that duplication may hamper SNP discovery in some species, the IPEC method reported here is an alternative way of identifying novel polymorphisms in such cases.

  3. RESERVES IN WESTERN BASINS PART IV: WIND RIVER BASIN

    Energy Technology Data Exchange (ETDEWEB)

    Robert Caldwell

    1998-04-01

    Vast quantities of natural gas are entrapped within various tight formations in the Rocky Mountain area. This report seeks to quantify what proportion of that resource can be considered recoverable under today's technological and economic conditions and discusses factors controlling recovery. The ultimate goal of this project is to encourage development of tight gas reserves by industry through reducing the technical and economic risks of locating, drilling and completing commercial tight gas wells. This report is the fourth in a series and focuses on the Wind River Basin located in west central Wyoming. The first three reports presented analyses of the tight gas reserves and resources in the Greater Green River Basin (Scotia, 1993), Piceance Basin (Scotia, 1995) and the Uinta Basin (Scotia, 1995). Since each report is a stand-alone document, duplication of language will exist where common aspects are discussed. This study, and the previous three, describe basin-centered gas deposits (Masters, 1979) which contain vast quantities of natural gas entrapped in low permeability (tight), overpressured sandstones occupying a central basin location. Such deposits are generally continuous and are not conventionally trapped by a structural or stratigraphic seal. Rather, the tight character of the reservoirs prevents rapid migration of the gas, and where rates of gas generation exceed rates of escape, an overpressured basin-centered gas deposit results (Spencer, 1987). Since the temperature is a primary controlling factor for the onset and rate of gas generation, these deposits exist in the deeper, central parts of a basin where temperatures generally exceed 200 F and drill depths exceed 8,000 feet. The abbreviation OPT (overpressured tight) is used when referring to sandstone reservoirs that comprise the basin-centered gas deposit. Because the gas resources trapped in this setting are so large, they represent an important source of future gas supply, prompting studies

  4. Development of a System-Wide Predator Control Program: Stepwise Implementation of a Predation Index, Predator Control Fisheries, and Evaluation Plan in the Columbia River Basin; Northern Pikeminnow Management Program, 2000 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Porter, Russell G.; Glaser, Bryce G.; Amren, Jennifer

    2003-03-01

    This report presents results for year ten in a basin-wide program to harvest northern pikeminnow (Ptychocheilus oregonensis). This program was started in an effort to reduce predation by northern pikeminnow on juvenile salmonids during their emigration from natal streams to the ocean. Earlier work in the Columbia River Basin suggested predation by northern pikeminnow on juvenile salmonids might account for most of the 10-20% mortality juvenile salmonids experience in each of eight Columbia River and Snake River reservoirs. Modeling simulations based on work in John Day Reservoir from 1982 through 1988 indicated that, if predator-size northern pikeminnow were exploited at a 10-20% rate, the resulting restructuring of their population could reduce their predation on juvenile salmonids by 50%. To test this hypothesis, we implemented a sport-reward angling fishery and a commercial longline fishery in the John Day Pool in 1990. We also conducted an angling fishery in areas inaccessible to the public at four dams on the mainstem Columbia River and at Ice Harbor Dam on the Snake River. Based on the success of these limited efforts, we implemented three test fisheries on a system-wide scale in 1991--a tribal longline fishery above Bonneville Dam, a sport-reward fishery, and a dam-angling fishery. Low catch of target fish and high cost of implementation resulted in discontinuation of the tribal longline fishery. However, the sport-reward and dam-angling fisheries were continued in 1992 and 1993. In 1992, we investigated the feasibility of implementing a commercial longline fishery in the Columbia River below Bonneville Dam and found that implementation of this fishery was also infeasible. Estimates of combined annual exploitation rates resulting from the sport-reward and damangling fisheries remained at the low end of our target range of 10-20%. This suggested the need for additional effective harvest techniques. During 1991 and 1992, we developed and tested a modified

  5. Development of an Environmental Flow Framework for the McKenzie River Basin, Oregon

    Science.gov (United States)

    Risley, John; Wallick, J. Rose; Waite, Ian; Stonewall, Adam J.

    2010-01-01

    The McKenzie River is a tributary to the Willamette River in northwestern Oregon. The McKenzie River is approximately 90 miles in length and has a drainage area of approximately 1,300 square miles. Two major flood control dams, a hydropower dam complex, and two hydropower canals significantly alter streamflows in the river. The structures reduce the magnitude and frequency of large and small floods while increasing the annual 7-day minimum streamflows. Stream temperatures also have been altered by the dams and other anthropogenic factors, such as the removal of riparian vegetation and channel simplification. Flow releases from one of the flood control dams are cooler in the summer and warmer in the fall in comparison to unregulated flow conditions before the dam was constructed. In 2006, the Oregon Department of Environmental Quality listed a total of 112.4, 6.3, and 55.7 miles of the McKenzie River basin mainstem and tributary stream reaches as thermally impaired for salmonid rearing, salmonid spawning, and bull trout, respectively. The analyses in this report, along with previous studies, indicate that dams have altered downstream channel morphology and ecologic communities. In addition to reducing the magnitude and frequency of floods, dams have diminished sediment transport by trapping bed material. Other anthropogenic factors, such as bank stabilization, highway construction, and reductions of in-channel wood, also have contributed to the loss of riparian habitat. A comparison of aerial photography taken in 1939 and 2005 showed substantial decreases in secondary channels, gravel bars, and channel sinuosity, particularly along the lower alluvial reaches of the McKenzie River. In addition, bed armoring and incision may contribute to habitat degradation, although further study is needed to determine the extent of these processes. Peak streamflow reduction has led to vegetation colonization and stabilization of formerly active bar surfaces. The large flood control

  6. Population Genetic Structure and Life History Variability in Oncorhynchus Nerka from the Snake River Basin, 1991-1993 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Waples, Robin S.; Aebersold, Paul B.; Winans, Gary A. (Northwest and Alaska Fisheries Science Center, Coastal Zone and Estuarine Studies Division, Seattle, WA)

    1997-05-01

    A detailed examination of O. nerka from lakes in the Sawtooth Valley of Idaho was undertaken to help guide recovery planning for the endangered Redfish Lake population and to help resolve relationships between resident and anadromous forms.

  7. De novo assembly and transcriptome analysis of Atlantic salmon macrophage/dendritic-like TO cells following type I IFN treatment and Salmonid alphavirus subtype-3 infection.

    Science.gov (United States)

    Xu, Cheng; Evensen, Øystein; Munang'andu, Hetron Mweemba

    2015-02-18

    Interferons (IFN) are cytokines secreted by vertebrate cells involved in activation of signaling pathways that direct the synthesis of antiviral genes. To gain a global understanding of antiviral genes induced by type I IFNs in salmonids, we used RNA-seq to characterize the transcriptomic changes induced by type I IFN treatment and salmon alphavirus subtype 3 (SAV-3) infection in TO-cells, a macrophage/dendritic like cell-line derived from Atlantic salmon (Salmo salar L) head kidney leukocytes. More than 23 million reads generated by RNA-seq were de novo assembled into 58098 unigenes used to generate a total of 3149 and 23289 differentially expressed genes (DEGs) from TO-cells exposed to type I IFN treatment and SAV-3 infection, respectively. Although the DEGs were classified into genes associated with biological processes, cellular components and molecular function based on gene ontology classification, transcriptomic changes reported here show upregulation of genes belonging to the canonical type I IFN signaling pathways together with a broad spectrum of antiviral genes that block virus replication in host cells. In addition, the transcriptome shows a profile of genes associated with apoptosis as well as genes that activate adaptive immunity. Further, our findings show that the profile of genes expressed by TO-cells is comparable to orthologous genes expressed by mammalian macrophages and dendritic cells in response to type I IFNs. Twenty DEGs randomly selected for qRT-PCR confirmed the validity of the transcriptomic changes detected by RNA-seq by showing that the genes upregulated by RNA-seq were also upregulated by qRT-PCR and that genes downregulated by RNA-seq were also downregulated by qRT-PCR. The de novo assembled transcriptome presented here provides a global description of genes induced by type I IFNs in TO-cells that could serve as a repository for future studies in fish cells. Transcriptome analysis shows that a large proportion of IFN genes expressed

  8. Bilan des introductions de salmonidés dans les lacs et ruisseaux d'altitude des Hautes-Pyrénées

    Directory of Open Access Journals (Sweden)

    DELACOSTE M.

    1997-01-01

    Full Text Available Les introductions de Salmonidés ont été importantes au cours des 60 dernières années dans les lacs et ruisseaux d'altitude des Hautes-Pyrénées. Six espèces de Salmonidés ont été introduites dans des milieux qui, pour la plupart, étaient vierges de populations piscicoles : la truite commune (Salmo trutta L., la truite arc-en-ciel (Oncorhynchus mykiss Walbaum, l'omble de fontaine (Salvelinus fontinalis Mitchill, l'omble chevalier (Salvelinus alpinus L., le cristivomer (Salvelinus namaycush Walbaum et le splake (Salvelinus fontinalis x Salvelinus namaycush. Dans de très nombreux cas, ces introductions ont abouti à des acclimatations. En revanche, les naturalisations sont beaucoup plus rares. Seules les espèces lacustres (cristivomer et omble chevalier se sont naturalisées dans l