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At least 91 records · Page 5Linked to original sources
USGS1992

Prevalence of Renibacterium salmoninarum among downstream-migrating salmonids in the Columbia River

Bacterial kidney disease (BKD) is an important contributor to mortality of salmonids in hatcheries in the Columbia River basin. However, the impact of BKD on the survival of downstream migrants is difficult to determine because there is little information on the disease-related mortality among these fish. In this study, the impact of BKD on juvenile salmonids was examined by determining the percentage of downriver migrants infected with Renibacterium salmoninarum (the causative agent of BKD) and evaluating the effects of salt water on the progress of the disease. During the 2 years of this study, approximately 20% of the three species of migrating hatchery and wild salmonids ( Oncorhynchus spp.) collected were infected with R. salmoninarum . Mortality caused by BKD increased when fish were held in salt water.

Journal of Aquatic Animal Health↗
USGS2005

Temporal and spatial variation of early mortality syndrome in salmonids from Lakes Michigan and Huron

To assess the extent that early mortality syndrome (EMS) impacts different Pacific salmonid stocks and the association of EMS with thiamine, we collected eggs of coho salmon Oncorhynchus kisutch from three Lake Michigan tributaries (Platte River, Thompson Creek, and Root River) in 1996-2001. We also obtained eggs of Chinook salmon O. tshawytscha from Lake Michigan (Little Manistee River) and Lake Huron (Swan River) in 1998-2001. Unfertilized eggs from individual females were frozen for thiamine analysis, and the remainder were fertilized and reared until first feeding. We observed a high incidence of EMS in offspring when total egg thiamine levels were less than 1.7 nmol/g in both coho and Chinook salmon. In Lake Michigan strain coho salmon from the Platte River, EMS occurred in more than 70% of monitored families in 1996, 1999, 2000, and 2001, while 1997 and 1998 were years when EMS was low (<25%). Hinchenbrooke strain coho salmon from Thompson Creek exhibited greater impacts from EMS in the years when EMS was low in the Lake Michigan strain coho salmon from the Platte River. Similar to coho salmon, Lake Michigan Chinook salmon also exhibited EMS (>70%) in 1999, 2000, and 2001. Chinook salmon from Lake Huron exhibited high (>70%) EMS in 2001, moderate (40-60%) EMS in 1999, and low (<25%) EMS in 1998. Our data suggest that the incidence of EMS in salmonids varies by species, location, and year. The data support the general contention that EMS in salmonids is associated with low egg thiamine content. ?? Copyright by the American Fisheries Society 2005.

Journal of Aquatic Animal Health↗
USGS2006

Juvenile salmonid use of freshwater emergent wetlands in the floodplain and its implications for conservation management

A recent trend of enhancing freshwater emergent wetlands for waterfowl and other wildlife has raised concern about the effects of such measures on juvenile salmonids. We undertook this study to quantify the degree and extent of juvenile Pacific salmon Oncorhynchus spp. utilization of enhanced and unenhanced emergent wetlands within the floodplain of the lower Chehalis River, Washington, and to determine the fate of the salmon using them. Enhanced emergent wetlands contained water control structures that provided an outlet for fish emigration and a longer hydroperiod for rearing than unenhanced wetlands. Age‐0 and age‐1 coho salmon O. kisutch were the most common salmonid at all sites, enhanced wetlands having significantly higher age‐1 abundance than unenhanced wetlands that were a similar distance from the main‐stem river. Yearling coho salmon benefited from rearing in two enhanced wetland habitats, where their specific growth rate and minimum estimates of survival (1.43%/d by weight and 30%; 1.37%/d and 57%) were comparable to those in other side‐channel rearing studies. Dissolved oxygen concentrations decreased in emergent wetlands throughout the season and approached the limits lethal to juvenile salmon by May or June each year. Emigration patterns suggested that age‐0 and age‐1 coho salmon emigrated as habitat conditions declined. This observation was further supported by the results of an experimental release of coho salmon. Survival of fish utilizing emergent wetlands was dependent on movement to the river before water quality decreased or stranding occurred from wetland desiccation. Thus, our results suggest that enhancing freshwater wetlands via water control structures can benefit juvenile salmonids, at least in the short term, by providing conditions for greater growth, survival, and emigration.

Washington↗
USGS2010

Assessing survival of Mid-Columbia River released juvenile salmonids at McNary Dam, Washington, 2008-09

Few studies have evaluated survival of juvenile salmon over long river reaches in the Columbia River and information regarding the survival of sockeye salmon at lower Columbia River dams is lacking. To address these information gaps, the U.S. Geological Survey was contracted by the U.S. Army Corps of Engineers to evaluate the possibility of using tagged fish released in the Mid-Columbia River to assess passage and survival at and downstream of McNary Dam. Using the acoustic telemetry systems already in place for a passage and survival study at McNary Dam, fish released from the tailraces of Wells, Rocky Reach, Rock Island, Wanapum, and Priest Rapids Dams were detected at McNary Dam and at the subsequent downstream arrays. These data were used to generate route-specific survival probabilities using single-release models from fish released in the Mid-Columbia River. We document trends in passage and survival probabilities at McNary Dam for yearling Chinook and sockeye salmon and juvenile steelhead released during studies in the Mid-Columbia River. Trends in the survival and passage of these juvenile salmonid species are presented and discussed. However, comparisons made across years and between study groups are not possible because of differences in the source of the test fish, the type of acoustic tags used, the absence of the use of passive integrated transponder tags in some of the release groups, differences in tagging and release protocols, annual differences in dam operations and configurations, differences in how the survival models were constructed (that is, number of routes that could be estimated given the number of fish detected), and the number and length of reaches included in the analysis (downstream reach length and arrays). Despite these differences, the data we present offer a unique opportunity to examine the migration behavior and survival of a group of fish that otherwise would not be studied. This is particularly true for sockeye salmon because little information is available about their survival as they pass hydroelectric dams in the lower Columbia River. Collecting information on fish released in the Mid-Columbia River, as well as on fish released 8 kilometers upstream of McNary Dam, allowed us to evaluate similarities and differences in passage and survival probabilities. In general, juvenile salmonids released in the Mid-Columbia River and detected at and downstream of McNary Dam showed trends in passage and survival probabilities that were similar to fish released 8 kilometers upstream of McNary Dam. This suggests that increased migration time or length of migration had little effect on behavior and survival of Mid-Columbia River released juvenile salmonids detected at McNary Dam.

Open-File Report↗
USGS2012

A Markov chain analysis of the movements of juvenile salmonids in the forebay of McNary Dam, Washington and Oregon, 2006-09

Passage and survival data for yearling and subyearling Chinook salmon and juvenile steelhead were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of the information collected at McNary Dam was in the form of three-dimensional tracks of fish movements in the forebay. These data depicted the behavior of multiple species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and test configurations of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in reporting three-dimensional results is presenting the information in a manner that allows interested parties to summarize the behavior of many fish over many different conditions across multiple years. To accomplish this, we investigated the feasibility of using a Markov chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov chain analysis is one way that can be used to summarize numerically the behavior of fish in the forebay. Numerically summarizing the behavior of juvenile salmonids in the forebay of McNary Dam using the Markov chain analysis allowed us to confirm what had been previously summarized using visualization software. For example, proportions of yearling and subyearling Chinook salmon passing the three powerhouse areas was often greater in the southern and middle areas, compared to the northern area. The opposite generally was observed for steelhead. Results of this analysis also allowed us to confirm and quantify the extent of milling behavior that had been observed for steelhead. For fish that were first detected in the powerhouse region, less than 0.10 of the steelhead, on average, passed within each of the powerhouse areas. Instead, steelhead transitioned to adjoining areas in the spillway before passing the dam. In comparison, greater than 0.20 of the Chinook salmon passed within the powerhouse areas. Less milling behavior was observed for all species for fish that first approached the spillway. Compared to the powerhouse areas, a higher proportion of fish, regardless of species, passed the spillway areas and fewer transitioned to adjoining areas in the powerhouse. In addition to quantifying what had been previously speculated about the behavior of fish in the forebay of McNary Dam, the Markov chain analysis refined our understanding of how fish behavior and passage can be influenced by changes to the operations and structure of McNary Dam. For example, the addition of TSWs to the spillway area clearly influenced the passage of fish. Previous results have been reported showing that TSWs increased the number of fish passing through non-turbine routes and the fish-track videos indicated, in general, how fish behaved before passing through the TSWs. However, the analysis presented in this report allowed us to better understand how fish moved across the face of the dam before passing the TSWs and provided a way to quantify the effect of TSW location. Installation of the TSWs in bays 22 and 20 clearly increased passage proportions through the southern one-third of the spillway area for all species, most significantly for steelhead. When the TSWs were moved to bays 19 and 20 in 2008, overall passage through the southern one-third of the spillway remained higher than 2006, but decreased from what was observed in 2007. Shifting the TSWs to the north decreased the proportion of fish passing through the TSWs and increased the number of fish that moved to adjoining areas before passing the dam. Perhaps the most interesting new information to come out of the two-step Markov chain analysis relates to how the performance of the TSWs was influenced by their proximity to the powerhouse. During 2007, the highest proportion of fish passing through TSW22 was for fish that transitioned from the powerhouse area. In contrast, a relatively low proportion of fish passed through TSW20 after coming from the powerhouse area. Instead, the proportion of fish that passed TSW20 after coming from the northern part of the spillway was twice as high as the proportion of fish that passed through TSW20 after coming from the powerhouse. During 2008, the TSW in bay 22 was moved to bay 19, leaving the TSW in bay 20 as the one closest to the powerhouse. As was the case when a TSW was located in bay 22; the proportion of fish passing TSW20 after coming from the powerhouse was greater than the proportion of fish passing through TSW20 after coming from the northern part of the spillway. Passage proportions for fish passing through TSW19, the farthest north of the two TSWs during 2008, was higher for fish that came from the northern part of the spillway compared to the proportion of fish that passed through TSW19 after coming from the powerhouse. The Markov chain analysis provided a mathematical way to characterize fish behavior in the forebay of McNary Dam and helped refine our understanding of how fish movements were influenced by operational and structural changes at McNary Dam. The Markov chain analysis also could be used to examine how future structural and operational changes proposed for McNary Dam might influence the passage of juvenile salmonids.

Oregon;Washington↗
USGS2012

A multi-year analysis of spillway survival for juvenile salmonids as a function of spill bay operations at McNary Dam, Washington and Oregon, 2004-09

We analyzed 6 years (2004-09) of passage and survival data collected at McNary Dam to examine how spill bay operations affect survival of juvenile salmonids passing through the spillway at McNary Dam. We also examined the relations between spill bay operations and survival through the juvenile fish bypass in an attempt to determine if survival through the bypass is influenced by spill bay operations. We used a Cormack-Jolly-Seber release-recapture model (CJS model) to determine how the survival of juvenile salmonids passing through McNary Dam relates to spill bay operations. Results of these analyses, while not designed to yield predictive models, can be used to help develop dam-operation strategies that optimize juvenile salmonid survival. For example, increasing total discharge typically had a positive effect on both spillway and bypass survival for all species except sockeye salmon ( Oncorhynchus nerka ). Likewise, an increase in spill bay discharge improved spillway survival for yearling Chinook salmon ( Oncorhynchus tshawytscha ), and an increase in spillway discharge positively affected spillway survival for juvenile steelhead ( Oncorhynchus mykiss ). The strong linear relation between increased spill and increased survival indicates that increasing the amount of water through the spillway is one strategy that could be used to improve spillway survival for yearling Chinook salmon and juvenile steelhead. However, increased spill did not improve spillway survival for subyearling Chinook salmon and sockeye salmon. Our results indicate that a uniform spill pattern would provide the highest spillway survival and bypass survival for subyearling Chinook salmon. Conversely, a predominantly south spill pattern provided the highest spillway survival for yearling Chinook salmon and juvenile steelhead. Although spill pattern was not a factor for spillway survival of sockeye salmon, spill bay operations that optimize passage through the north and south spill bays maximized spillway survival for this species. Bypass survival of yearling Chinook salmon could be improved by optimizing conditions to facilitate bypass passage at night, but the method to do so is not apparent from this analysis because photoperiod was the only factor affecting bypass survival based on the best and only supported model. Bypass survival of juvenile steelhead would benefit from lower water temperatures and increased total and spillway discharge. Likewise, subyearling Chinook salmon bypass survival would improve with lower water temperatures, increased total discharge, and a uniform spill pattern.

Oregon;Washington↗
USGS2017

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

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 programs During 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), broodstock management and history, and potential constraints (that is, Endangered Species Act [ESA] listing, Evolutionarily Significant Unit concerns, pathogens, and availability). During the workshops, a group of regional fisheries and topic experts subjectively ranked the relative risks of pathogens, genetic effects, predation, and competition to resident fish and reintroduced salmonids. We assessed the pathogen risk of each potential donor for introducing new pathogens and the increased burden to existing pathogens for resident species upstream of the dams. We considered genetic risks to resident and downstream conspecifics and ecological impacts, including competition for food and space, predator-prey interactions, and ecosystem benefits/impacts. Each reintroduced species donor source was ranked based on abundance/viability (demographic risk to source and feasibility of collection), ancestral/genetic similarity (evolutionary similarity to historical populations), local adaptation (geographic proximity/similarity of source conditions to reintroduction conditions), and life history compatibility (including migration; spawn timing; and relative usage of reservoir, main-stem, or tributary habitats) with environmental conditions in the reintroduction area. We synthesized this information by species for all potential donors, in which an overall score and ranking system was established for decision support in donor selection for reintroduction into the upper Columbia River. We also provided information outside the ranking process by: Identifying predator-prey interactions and competition for food and space among species, Developing a decision support framework for donor selection, and Providing decision support for reintroduction strategies.

Washington↗
USGS1989

Developments in the control of bacterial kidney disease of salmonid fishes

Bacterial kidney disease of salmonid fishes, caused by Renibactenum salrnoninarum, was first reported more than 50 yr ago; nevertheless, large gaps persist in our knowledge of the infection - particularly in methods for its control. In the 1950's, principal control measures consisted of prophylactic or therapeutic feeding of sulfonamides, which were later supplanted by the antibiotic erythromycin. Chemotherapy has effected some reduction of mortality, but benefits are typically transient and mortality usually resumes after the drug is withdrawn. Some studies have indicated that diet composition affects the prevalence and severity of the disease. Although tests of chemotherapeutants and diet modification have continued, research emphasis has shifted partly toward prevention of the disease by breaking the infection cycle. It is now generally accepted that R. salrnoninarum can be transmitted both vertically and horizontally. Experimental evidence indicates that immersion of newly fertilized eggs in iodophor or erythromycin does not prevent vertical transmission. However, the injection of female salmon with erythromycin before they spawn shows promise as a practical means of interrupting vertical transmission. The results of attempts to prevent infection of juvenile salmonids by vaccination against bacterial kidney disease have been disappointing, thus underscoring a basic need for a better understanding of protective mechanisms in salmonids. The recent development of more sensitive and quantitative detection methods should aid in evaluating the efficacy of current and future control strategies.

Diseases of Aquatic Organisms↗
USGS2025

Environmental conditions influencing the abundance of the salmonid ectoparasite Salmincola californiensis across upper Willamette River Reservoirs, Oregon

The freshwater copepod Salmincola californiensis is an ectoparasite of Pacific salmon and trout ( Oncorhynchus spp.). High levels of infection by this parasite can significantly damage gills and result in blood loss, affecting the fitness and survival of hosts, and it may hinder recovery efforts of threatened and endangered salmonids. Juvenile salmonids that rear in reservoirs have been reported to experience higher rates of infection than their stream-dwelling counterparts. To date, the relationship between reservoir environmental conditions and infection rates remains poorly understood. Here, we evaluated sampling methods designed to capture S. californiensis copepodids, the free-swimming infectious life stage of this parasitic copepod, and develop predictive models of parasite abundance in reservoirs . We used light traps to collect 675 zooplankton samples from various sites and depths in Cougar, Lookout Point, and Fall Creek reservoirs, Oregon, USA during five months in 2020. We tested several predictive models of parasite abundance using environmental covariates obtained concurrently during plankton surveys ( e.g. , temperature, ambient light and water clarity, reservoir plankton profiles, and water flow). Our models showed a strong influence of water temperature on abundance of copepodids, with maximum initial abundance occurring at the mean water temperature 15.2 °C. At that temperature, August abundance was estimated to be 58.6 copepodids per site in Cougar Reservoir, 43.8 copepodids per site in Fall Creek Reservoir, and 3.5 copepodids per site in Lookout Point Reservoir. Water temperature and reservoir outflow both affected population growth of copepodids: increased water temperature was associated with an increase in population growth rate while an increased reservoir outflow was associated with a decrease in population growth rate. The efficacy of our sampling method was influenced by percent of moon fullness, whether the sample site was above or below the thermocline, water temperature, and number of juvenile sculpin fishes ( Cottus spp.) captured in the trap. The mean probability of detecting a single copepodid if one was present was 0.042, but detection probability increased to 0.29 under ideal trap set conditions of warmer water, location above the thermocline, and a full moon. Biologists and managers could use these methods to assess the presence and abundance of S. californiensis in other locations, or to inform reservoir operations to reduce potential salmonid infections.

Oregon↗
USGS2001

Predation by northern pikeminnow on juvenile salmonids in The Dalles Dam tailrace: field, laboratory, and habitat modeling studies (FY2000)

Predation by resident fish is known to be a substantial cause of juvenile salmonid mortality, especially in dam tailraces and outfall locations. Conditions in The Dalles Dam tailrace are unique compared to other projects on the Columbia or Snake rivers, having a complex basin with a series of downriver islands where predators are known to reside. In May-June of 1999, northern pikeminnow and smallmouth bass were sampled in the tailrace of The Dalles Dam during periods immediately following the release of PIT-tagged juvenile salmonids for survival studies. Over twice as many smallmouth bass (N = 101) were collected as northern pikeminnow (N = 40), but none of the predators had PIT tags within their gut. A laboratory study was conducted to estimate the time required for PIT tags in juvenile salmonids to be evacuated from the gut of northern pikeminnow after consuming a tagged preyfish. Evacuation rate was sensitive to temperature, with median evacuation time being 21 h at 18 oC and 30 h at 14 oC. These results suggest that field studies to estimate predator population sizes, feeding rates, or predation on specific release groups would require considerably more effort than we allocated during 1999.

Oregon, Washington↗
USGS1977

Virion RNA polymerases of two salmonid rhabdoviruses

RNA-dependent RNA polymerases were found to be associated with two salmonid rhabdoviruses: infectious hematopoietic necrosis (IHN) virus and the virus of hemorrhagic septicemia (VHS). The protein composition of these rhabdoviruses closely resembles that of rabies virus rather than that of vesicular stomatitis virus (McAllister and Wagner, 1975). The optimal temperature for in vitro transcription was found to be approximately 18 degrees C for IHN virus and approximately 15 degrees for VHS, closely approximating optimal temperatures for growth of these viruses in salmonid cells. Unlike vesicular stomatitis virus, manganese ion (1 mM) could be used as a divalent cation substitute for magnesium ion (5 mM). The in vitro transcription products of IHN and VHS viruses hybridized completely to the homologous genome but not at all to the heterologous genome.

Journal of Virology↗
USGS1993

Osmoregulatory actions of growth hormone and its mode of action in salmonids: A review

Osmoregulatory actions of growth hormone (GH) and its mode of action in salmonids are reviewed. We present evidence suggesting that insulin-like growth factor I (IGF-I) mediates some of the actions of GH on seawater acclimation. Plasma concentration and turnover of GH rise following exposure to seawater. Exogenous GH ( in vivo ) increases gill Na + ,K + -ATPase activity and the number of gill chloride cells, and inhibits an increase in plasma osmolarity and ions following transfer of fish to seawater. A single class of high affinity GH receptors is present in the liver, gill, intestine, and kidney. The levels of IGF-I mRNA in the liver, gill and kidney increased after GH-injection. After transfer to seawater, IGF-I mRNA increased in the gill and kidney following the rise in plasma GH, although no significant change was seen in the liver. Injection of IGF-I improved the ability of the fish to maintain plasma sodium levels after transfer to seawater. GH treatment also sensitizes the interrenal to adrenocorticotropin (ACTH), increasing cortisol secretion. Both cortisol and IGF-I may be involved in mediating the action of GH in seawater adaptation, although studies on the effect of GH on osmoregulatory physiology of non-salmonid species are limited. An integrated model of the osmoregulatory actions of GH is presented, and areas in need of research are outlined.

Fish Physiology and Biochemistry↗
USGS1979

Tolerance of developing salmonid eggs and fry to nitrate exposure

This paper reports on tests which show significant effects on early salmonid life stages of nitrates at levels commonly found in groundwaters in geographical areas that are influenced by fertilizer application. It has long been known, from fish cultural experience, that in certain site specific locations, chronic problems can be expected with salmonid egg development and early fry mortality. However, fingerlings which survive usually grow normally. A complete explanation is lacking although several environmental factors have been proposed to account for this phenomenon. One, which has so far received little attention, is that nitrate levels in the ground and surface waters of many areas have been increasing significantly over historical background levels. Ammonia, urea, and other potential sources of nitrate can enter natural waters from a variety of sources, such as domestic or industrial sewage, animal feedlots, or seepage and return flows from agricultural lands. The latter may be the largest contributor, since billions of tons of nitrate fertilizers are applied to agricultural crops on a worldwide basis each year. In addition, intensive forest management techniques include the aerial application of nitrate fertilizer to increase the yield of wood products, while range management practices call for use of nitrates to increase forage production. The nitrate that is not taken up by plants ultimately appears in ground or surface waters.

Bulletin of Environmental Contamination and Toxico↗
USGS2017

Evaluating species-specific changes in hydrologic regimes: an iterative approach for salmonids in the Greater Yellowstone Area (USA)

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.

Greater Yellowstone Area↗
USGS2020

Review of trap-and-haul for managing Pacific salmonids (Oncorhynchus spp.) in impounded river systems

High-head dams are migration barriers for Pacific salmon Oncorhynchus spp. in many river systems and recovery measures for impacted stocks are limited. Trap-and-haul has been widely used in attempts to facilitate recovery but information from existing programs has not been synthesized to inform improvements to aid recovery of salmonids in systems with high-head dams. We reviewed 17 trap-and-haul programs regarding Pacific salmon to: (1) summarize information about facility design, operation and biological effects; (2) identify critical knowledge gaps; and (3) evaluate trap-and-haul as a current and future management tool. Existing programs are operated to address a range of management goals including restoring access to historical habitats, temporarily reducing exposure to dangerous in-river conditions, and reintroducing ecological processes upstream from dams. Information gathered from decades of operation on facility design criteria and fish handling protocols, and robust literature on fish collection and passage are available. While many aspects of trap-and-haul have been evaluated, effects on population productivity and sustainability remain poorly understood. Long-term and systematic studies of trap-and-haul outcomes are rare, and assessments can be confounded by concurrent management actions and broad ecological and climatic effects. Existing data suggest that performance and effectiveness vary among programs and over various time scales within programs. Although critical information gaps exist, trap-and-haul is an important management and conservation tool for providing Pacific salmonids access to historical habitats. Successful application of trap-and-haul programs requires long-term commitment and an adaptive management approach by dam owners and stakeholders, and careful planning of new programs.

California, Idaho, Oregon, Washington↗
USGS1991

Developmental differences in the responsiveness of gill Na+, K+ and -ATPase to cortisol salmonids

The ability of cortisol to increase gill Na + , K + -ATPase activity was examined in several salmonid species during development. Coho salmon ( Oncorhynchus kisutch ) parr were unresponsive to cortisol in vitro (10 μg/ml for 2 days) in November. Responsiveness was significant from January to March, peaking in January just prior to seasonal increases in gill Na + , K + -ATPase activity. Gill tissue became unresponsive to in vitro cortisol in April when in vivo gill Na + , K + -ATPase activity peaked. The ability of cortisol to stimulate gill, Na + , K + -ATPase activity in postemergent fry (2–3 months after hatching) was examined in chum ( O. keta ), chinook ( O. tschawytscha ), coho, and Atlantic salmon ( Salmo salar ). Initial levels of gill Na + , K + -ATPase activity were elevated in chum salmon, which normally migrate as fry. Cortisol (10 μg/ml for 4 days in vitro ) increased gill Na + , K + -ATPase activity in chum salmon fry (48% above initial levels), had a limited but significant effect in chinook salmon fry, and had no effect in coho and Atlantic salmon fry. In an in vivo experiment, Atlantic salmon previously exposed to simulated natural photoperiod (SNP) and continuous light (L24) received four cortisol injections of 2 μg · g −1 every third day. SNP fish responded with increased gill Na + , K + -ATPase activity (+66%), whereas L24 fish were not affected. Atlantic salmon presmolts with initially low levels of gill Na + , K + -ATPase activity responded to cortisol in vitro , whereas smolts with initially high levels of gill Na + , K + -ATPase activity were unresponsive. Triiodothyronine (0.01–10 μg/ml), prolactin (0.1–10 μg/ml), growth hormone (0.1–10 μg/ml), insulin (0.01–10 μg/ml), and bovine insulin-like growth factor I (0.01–1 μg/ml) did not affect gill Na + , K + -ATPase activity in vitro , individually or with cortisol (1–10 μg/ml). Thus, changes in responsiveness to cortisol occur during salmonid development, vary among species, and may be important in the heterochrony that characterizes the parr-smolt transformation.

General and Comparative Endocrinology↗
USGS2018

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

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 cohort-sites experienced self-exposure by infected juvenile fish, this transmission route had the greatest probability of infection (0.22). Increased testing and/or determining whether transmission can occur from cohort-sites without testing records (e.g., determining there was no testing record because there were no fish at the cohort-site) are expected to improve inference about infection probabilities. Increased use of secure water supplies and continued use of biosecurity protocols may reduce IHNV transmission from adult fish and juvenile fish within the site, respectively, to juvenile salmonids at hatcheries. Models and conclusions from this study are potentially relevant to understanding the relative importance of transmission routes for other important aquatic pathogens in salmonids, including the agents of bacterial kidney disease and coldwater disease, and the basic approach may be useful for other pathogens and hosts in other geographic regions.

Ecological Modelling↗
USGS2017

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

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.

Geomorphology↗