Geology topics

Noah S. Adams

Publications and source records attributed to Noah S. Adams.

At least 19 recordsLinked to original sources

USGS2022

Monitoring fish abundance and behavior, using multi-beam acoustic imaging sonar, at a Selective Water Withdrawal structure in Lake Billy Chinook, Deschutes River, Oregon, 2020

Collection of juvenile salmonids at Round Butte Dam is a critical part of the effort to enhance populations of anadromous fish species in the upper Deschutes River because fish that are not collected at the dam may either incur increased mortality during dam passage or remain landlocked and lost to the anadromous fish population. Adaptive resolution imaging sonar systems were used to assess the behavior, abundance, and timing of fish at the entrance to the Selective Water Withdrawal (SWW) intake and fish collection structure located in the forebay of Round Butte Dam during the spring of 2020. The purpose of the SWW is to direct surface currents in the forebay to attract and collect downriver migrating juvenile salmonid smolts (Chinook salmon [ Oncorhynchus tshawytscha ], sockeye salmon [ O. nerka ], and steelhead [ O. mykiss ]) from Lake Billy Chinook and to enable operators of the SWW to withdraw water from surface and benthic elevations in the reservoir to manage downriver water temperatures. The objective of this study was to assess the abundance and behaviors of smolt-size fish (95–300 millimeters) observed near the SWW and to determine if the presence of bull trout ( Salvelinus confluentus; >350 millimeters), the predominant predator of juvenile salmonids, influenced the behavior of downriver migrants. Two imaging sonar units were deployed during the spring of 2020 smolt out-migration period. One unit monitored fish movements near the entrances and one unit monitored in one of the collection flumes of the SWW. The imaging sonar technology was informative for assessing abundance and spatial and temporal behaviors of smolt and bull trout-size fish. Smolt and bull trout-size fish were regularly observed near the entrance to and in the collection flume. Increased abundances were observed during the night, with corresponding increased discharge through the SWW, compared to during the day when discharge was reduced. Behavioral differences also were observed at different discharge rates, with smolt-size fish exhibiting more directed movement toward the collector during periods of increased discharge. Additionally, the presence of bull trout-size fish may have affected the behavior of smolt-size fish because a greater percentage of smolt-size fish were observed traveling away from the SWW when bull trout-size fish were present than when bull trout-size fish were absent. Increased counts of bull trout-size fish coincided with the increased abundances of smolt-size fish. Overall, the results indicate that smolt-size fish are more abundant near the entrance and in the flume of the SWW during periods of increased discharge, and bull trout-size fish were present at the SWW and may have affected smolt collection.

Oregon↗

USGS2021

Predator and prey events at the entrance of a surface‐oriented fish collector at North Fork Dam, Oregon

Quantifiable estimates of predator–prey interactions and relationships in aquatic habitats are difficult to obtain and rare, especially when individuals cannot be readily observed. To overcome this observational impediment, imaging sonar was used to assess the cooccurrence of predator‐size fish and juvenile salmonids, Oncorhynchus spp., at the entrance to a floating surface collector (FSC) in the forebay of North Fork Dam on the Clackamas River, Oregon (USA). Imaging sonar can be used to transform active sound waves into visual data, making it possible to obtain continuous underwater observations on the presence and interspecific interactions between predator‐size fish and prey (juvenile salmonids). Hourly counts of smolt‐size fish tracks, diel phase, water clarity and river discharge were used as covariates within a zero‐inflated Poisson model to determine how these factors may influence the number of predators in front of the FSC. Both the number of smolt‐size fish tracks and diel phase had the strongest effects on the number of predator‐size fish tracks, with more predator‐size fish tracks observed during the daytime, and as the number of smolt‐size fish tracks increased. Additionally, the presence of predator‐size fish may affect the abundance and direction of travel of juvenile salmonids, as fewer smolt‐size fish were observed when predators were present, and a greater proportion of smolt‐size fish were observed travelling away from the FSC when predator‐size fish were present. This study provides estimates of predator and prey fish abundance in the vicinity of surface collection systems at moderate‐sized hydropower projects and could help resource managers better understand mechanisms that can influence the survival and passage behaviour of juvenile salmonids using surface collection structures at dams.

Oregon↗

USGS2019

Movement and apparent survival of acoustically tagged juvenile late-fall run chinook salmon released upstream of Shasta Reservoir, California

Stakeholder interests have spurred the reintroduction of the critically endangered populations of Chinook Salmon to tributaries upstream of Shasta Dam, in northern California. We released two groups of acoustically tagged, juvenile hatchery, late-fall Chinook Salmon to determine how juvenile salmon would distribute and survive. We measured travel times to Shasta Dam, and the number of fish that moved between locations within Shasta Reservoir. We used mark-recapture methods to determine detection and apparent survival probabilities of the tagged fish as they traveled through five reaches of the Sacramento River from the McCloud River to San Francisco Bay (~590 km) over the two 3-month observation periods. After our first (February) release of 262 tagged fish, 182 fish (70%) were detected at least once at the dam, 41 (16%) were detected at least once downstream of Shasta Dam, and 3 (1%) traveled as far as San Francisco Bay. After the second (November) release of 355 tagged fish, only 4 (1%) were detected at Shasta Dam. No fish were detected below Shasta Dam, so we could not estimate survival for this second release group. The first release of fish was fortuitously exposed to exceptionally high river flows and dam discharges, which may have contributed to the more distant downstream migration and detection of these fish — though other factors such as season, diploid versus triploid, and fish maturation and size may have also contributed to release differences. The reported fish travel times as well as detection and survival rates are the first estimates of juvenile salmon emigration from locations above Shasta Dam in more than 70 years. This information should help inform resource managers about how best to assess juvenile winter-run Chinook Salmon and assist in their reintroduction to watersheds upstream of Shasta Dam.

California↗

USGS2018

Fish behavior and abundance monitoring near a floating surface collector in North Fork Reservoir, Clackamas River, Oregon, using multi-beam acoustic imaging sonar

An imaging sonar was used to assess the behavior and abundance of fish sized the same as salmonid smolt and bull trout ( Salvelinus confluentus ) at the entrance to the juvenile fish floating surface collector (FSC) at North Fork Reservoir, Oregon. The purpose of the FSC is to collect downriver migrating juvenile salmonids (Chinook salmon [ Oncorhynchus tshawytscha ], Coho salmon [ Oncorhynchus kisutch ], and steelhead [ Oncorhynchus mykiss ]) at the North Fork Dam and to safely route them around the hydroelectric projects. The objective of the imaging sonar component of this study was to assess the behaviors of both smolt and predator-size fish (smolt [60–250 millimeter] and predator 350–650 [millimeter]) observed near the FSC and to determine if the presence of predator-size fish influenced the abundance of smolt-size fish. An imaging sonar was deployed near the entrance to the FSC during the spring smolt out-migration period. The imaging sonar technology was an informative tool for assessing abundance and spatial and temporal behaviors of both smolt and predator-size fish near the entrance of the FSC. Both smolt and predator-size fish were regularly observed near the entrance, with greater abundances observed during day than during night. Behavioral differences were also observed between the two fish-size classes, with smolt-size fish traveling straighter with more directed movement, and predator-size fish generally showing more milling behavior. Additionally, the presence of predator-size fish may be effecting the abundance and direction of travel of smolt-size fish, as counts of smolt-size fish were reduced in conjunction with the presence of predator-size fish and a greater proportion of smolt-size fish were observed traveling away from the FSC when predator-size fish were present than when predator-size fish were absent. Results of modeling potential predator-prey interactions and influences indicated that both the number of juvenile fish tracks and photoperiod had the strongest effects on the number of predator fish tracks, with more predator-size fish tracks observed as the number of smolt-size fish tracks increased. Overall, the results indicate that predator-size fish are present near the entrance of the FSC, concomitant with smolt-size fish, and their abundances and behaviors indicate that they may be drawn to the entrance of the FSC because of the abundance of prey-sized fish found there.

Oregon↗

USGS2018

Emigration and transportation stress of juvenile Chinook salmon relative to their reintroduction upriver of Shasta Dam, California, 2017–18

The Bureau of Reclamation supports the Shasta Dam Fish Passage Evaluation (SDFPE; Yip, 2015) program, and in 2016 set out to determine the feasibility of reintroducing winter-run and spring-run Chinook salmon ( Oncorhynchus tshawytscha ) and steelhead ( O. mykiss ) to tributaries upstream of Shasta Dam. Ideally, reintroduction strategy includes trapping naturally produced downstream-migrating juvenile fish at the head of Lake Shasta (upstream of Shasta Dam), or near the mouth of the tributaries where they flow into the lake. However, evaluations of a juvenile collection system in one of the target tributaries (McCloud River) was delayed because of concerns about the fish source to be used as surrogate for winter-run Chinook salmon and the location and impact of the trap-and-haul operations. In 2017, the U.S. Geological Survey (USGS) was contracted to evaluate the reintroduction of winter-run salmon into tributaries upstream of Shasta Dam, and the McCloud River, having the most suitable spawning and rearing habitat for salmon adjacent to Shasta Reservoir (Lake) was the chosen study area. The first stage of the project was to assess the feasibility using a head-of-reservoir fish trap to collect juvenile salmon, but these efforts were delayed, so efforts were used to assess how juvenile Chinook salmon would distribute within the McCloud River and Shasta Reservoir and help determine the feasibility of collecting fish at Shasta Dam. Importantly, NOAA fisheries was also conducting an acoustic telemetry project through the Sacramento River, and they provided the additional acoustic detection data on our tagged fish to San Francisco Bay. These data were collected beyond original study goals, but added a large contribution to the findings and inferences from this study.

California↗

USGS2017

Spatial and temporal distribution of bull trout ( Salvelinus confluentus )-size fish near the floating surface collector in the North Fork Reservoir, Oregon, 2016

Acoustic cameras were used to assess the behavior and abundance of bull trout ( Salvelinus confluentus )-size fish at the entrance to the North Fork Reservoir juvenile fish floating surface collector (FSC). The purpose of the FSC is to collect downriver migrating juvenile salmonids at the North Fork Dam, and safely route them around the hydroelectric projects. The objective of the acoustic camera component of this study was to assess the behaviors of bull trout-size fish observed near the FSC, and to determine if the presence of bull trout-size fish influenced the collection or abundance of juvenile salmonids. Acoustic cameras were deployed near the surface and floor of the entrance to the FSC. The acoustic camera technology was an informative tool for assessing abundance and spatial and temporal behaviors of bull trout-size fish near the entrance of the FSC. Bull trout-size fish were regularly observed near the entrance, with greater abundances on the deep camera than on the shallow camera. Additionally, greater abundances were observed during the hours of sunlight than were observed during the night. Behavioral differences also were observed at the two depths, with surface fish traveling faster and straighter with more directed movement, and fish observed on the deep camera generally showing more milling behavior. Modeling potential predator-prey interactions and influences using collected passive integrated transponder (PIT) -tagged juvenile salmonids proved largely unpredictable, although these fish provided relevant timing and collection information. Overall, the results indicate that bull trout-size fish are present near the entrance of the FSC, concomitant with juvenile salmonids, and their abundances and behaviors indicate that they may be drawn to the entrance of the FSC because of the abundance of prey-sized fish.

Oregon↗

USGS2016

Evaluation of the hydraulic and biological performance of the portable floating fish collector at Cougar Reservoir and Dam, Oregon, 2014

The biological and hydraulic performance of a new portable floating fish collector (PFFC) located in a cul-de-sac within the forebay of Cougar Dam, Oregon, was evaluated during 2014. The purpose of the PFFC was to explore surface collection as a means to capture juvenile salmonids at one or more sites using a small, cost-effective, pilot-scale device. The PFFC used internal pumps to draw attraction flow over an inclined plane about 3 meters (m) deep, through a flume at a design velocity of as much as 6 feet per second (ft/s), and to empty a small amount of water and any entrained fish into a collection box. Performance of the PFFC was evaluated at 64 cubic feet per second (ft 3 /s) (Low) and 109 ft 3 /s (High) inflow rates alternated using a randomized-block schedule from May 27 to December 16, 2014. The evaluation of the biological performance was based on trap catch; behaviors, locations, and collection of juvenile Chinook salmon ( Oncorhynchus tshawytscha ) tagged with acoustic transmitters plus passive integrated transponder (PIT) tags; collection of juvenile Chinook salmon implanted with only PIT tags; and untagged fish monitored near and within the PFFC using acoustic cameras. The evaluation of hydraulic performance was based on measurements of water velocity and direction of flow in the PFFC. The PFFC collected 156 juvenile Chinook salmon and 280 individuals of other species, primarily dace (Cyprinidae) and largemouth bass ( Micropterus salmoides ). The collection included one of the 212 acoustic+PIT-tagged fish detected near the PFFC and two of the 1,505 PIT-tagged fish released near the head of the reservoir. No juvenile salmonids were collected between early July and early September when water temperatures near the water surface were greater than about 16 degrees Celsius (°C). Depths of acoustic+PIT-tagged fish indicated a preferential selection of water temperature of 13–15 °C, which was often deeper than the entrance to the PFFC, and those fish rarely were at depths with water temperatures greater than 16 °C. Dam passage of acoustic+PIT-tagged fish was similar to previous years, but much of the passage occurred prior to the date the PFFC began operation. Discovery Efficiency, the proportion of acoustic+PIT-tagged fish detected in the cul-de-sac that were within 10 m of the PFFC entrance and 0–6 m deep (the Discovery Zone), was 0.736 during the Low treatment and 0.639 during the High treatment. Entrance Efficiency, the proportion of fish in the Discovery Zone that were collected by the PFFC, was 0.007 during the Low treatment and 0.000 during the High treatment. Fish Collection Efficiency, the proportion of acoustic+PIT-tagged fish collected of those detected in the cul-de-sac, was 0.005 and 0.000 during the Low and High treatments, respectively. The areas of highest use by acoustic+PIT-tagged fish were between the stern of the PFFC and the outlet of the reservoir (a water temperature control tower), with the greatest use being near the tower. Results from untagged fish detected with acoustic cameras indicated that most fish near and within the PFFC were in the 90–250-millimeter length bin and few were less than 60 millimeters long; most fish were present during crepuscular periods; trajectories of fish outside the PFFC were rarely directed toward the entrance; and many fish entering the PFFC swam back out before they could be collected. The hydraulic performance of the PFFC did not achieve the design goals of smooth acceleration of inflow culminating in a peak water velocity of 6 ft/s and, as a result, the hydraulic performance likely contributed to the low biological performance. The greatest water velocity measured in the PFFC (1.87 ft/s) was lower than designed due at least in part to the PFFC being lower in the water column than expected. Additionally, difficulties during anchor deployment prevented placement of the PFFC as near to the reservoir outlet as planned, resulting in a PFFC position outside the prevailing flow field and known areas of high fish densities. Overall, the results indicate that location, hydraulic conditions, water temperature, and shallow depth of the entrance were among the factors contributing to the low biological performance of the PFFC in 2014.

Oregon↗

USGS2015

An evaluation of fish behavior upstream of the water temperature control tower at Cougar Dam, Oregon, using acoustic cameras, 2013

This report describes the initial year of a 2-year study to determine the feasibility of using acoustic cameras to monitor fish movements to help inform decisions about fish passage at Cougar Dam near Springfield, Oregon. Specifically, we used acoustic cameras to measure fish presence, travel speed, and direction adjacent to the water temperature control tower in the forebay of Cougar Dam during the spring (May, June, and July) and fall (September, October, and November) of 2013. Cougar Dam is a high-head flood-control dam, and the water temperature control tower enables depth-specific water withdrawals to facilitate adjustment of water temperatures released downstream of the dam. The acoustic cameras were positioned at the upstream entrance of the tower to monitor free-ranging subyearling and yearling-size juvenile Chinook salmon ( Oncorhynchus tshawytscha ). Because of the large size discrepancy, we could distinguish juvenile Chinook salmon from their predators, which enabled us to measure predators and prey in areas adjacent to the entrance of the tower. We used linear models to quantify and assess operational and environmental factors—such as time of day, discharge, and water temperature—that may influence juvenile Chinook salmon movements within the beam of the acoustic cameras. Although extensive milling behavior of fish near the structure may have masked directed movement of fish and added unpredictability to fish movement models, the acoustic-camera technology enabled us to ascertain the general behavior of discrete size classes of fish. Fish travel speed, direction of travel, and counts of fish moving toward the water temperature control tower primarily were influenced by the amount of water being discharged through the dam.

Oregon↗

USGS2015

Fine-scale pathways used by adult sea lampreys during riverine spawning migrations

Better knowledge of upstream migratory patterns of spawning Sea Lampreys Petromyzon marinus , an invasive species in the Great Lakes, is needed to improve trapping for population control and assessment. Although trapping of adult Sea Lampreys provides the basis for estimates of lake-wide abundance that are used to evaluate the Sea Lamprey control program, traps have only been operated at dams due to insufficient knowledge of Sea Lamprey behavior in unobstructed channels. Acoustic telemetry and radiotelemetry were used to obtain movement tracks for 23 Sea Lampreys in 2008 and 18 Sea Lampreys in 2009 at two locations in the Mississagi River, Ontario. Cabled hydrophone arrays provided two-dimensional geographic positions from acoustic transmitters at 3-s intervals; depth-encoded radio tag detections provided depths. Upstream movements occurred at dusk or during the night (2015–0318 hours). Sea Lampreys were closely associated with the river bottom and showed some preference to move near banks in shallow glide habitats, suggesting that bottom-oriented gears could selectively target adult Sea Lampreys in some habitats. However, Sea Lampreys were broadly distributed across the river channel, suggesting that the capture efficiency of nets and traps in open channels would depend heavily on the proportion of the channel width covered. Lack of vertical movements into the water column may have reflected lamprey preference for low water velocities, suggesting that energy conservation was more beneficial for lampreys than was vertical searching in rivers. Improved understanding of Sea Lamprey movement will assist in the development of improved capture strategies for their assessment and control in the Great Lakes.

Mississagi River↗

USGS2015

Diel activity patterns of juvenile late fall-run Chinook salmon with implications for operation of a gated water diversion in the Sacramento–San Joaquin River Delta

In the Sacramento-San Joaquin River Delta, California, tidal forces that reverse river flows increase the proportion of water and juvenile late fall-run Chinook salmon diverted into a network of channels that were constructed to support agriculture and human consumption. This area is known as the interior delta, and it has been associated with poor fish survival. Under the rationale that the fish will be diverted in proportion to the amount of water that is diverted, the Delta Cross Channel (DCC) has been prescriptively closed during the winter out-migration to reduce fish entrainment and mortality into the interior delta. The fish are thought to migrate mostly at night, and so daytime operation of the DCC may allow for water diversion that minimizes fish entrainment and mortality. To assess this, the DCC gate was experimentally opened and closed while we released 2983 of the fish with acoustic transmitters upstream of the DCC to monitor their arrival and entrainment into the DCC. We used logistic regression to model night-time arrival and entrainment probabilities with covariates that included the proportion of each diel period with upstream flow, flow, rate of change in flow and water temperature. The proportion of time with upstream flow was the most important driver of night-time arrival probability, yet river flow had the largest effect on fish entrainment into the DCC. Modelling results suggest opening the DCC during daytime while keeping the DCC closed during night-time may allow for water diversion that minimizes fish entrainment into the interior delta.

California↗

USGS2015

In-reservoir behavior, dam passage, and downstream migration of juvenile Chinook salmon and juvenile steelhead from Detroit Reservoir and Dam to Portland, Oregon, February 2013-February 2014

In the second year of 2 years of study, the movements of juvenile spring Chinook salmon ( Oncorhynchus tshawytscha ) and juvenile summer steelhead ( Oncorhynchus mykiss ) through Detroit Reservoir, passing Detroit Dam, and migrating downstream to Portland, Oregon, were studied during a 1-year-long period beginning in February 2013. The primary purpose of the study was to provide empirical data to inform decisions about future alternatives for improving downstream passage of salmonids at Detroit Dam. A secondary purpose was to design and assess the performance of a system to detect juvenile salmonids implanted with acoustic transmitters migrating in the Willamette River. Inferences about fish migration were made from detections of juvenile fish of hatchery origin at least 95 millimeters in fork length surgically implanted with an acoustic transmitter and released during the spring (March–May) and fall (September–November) of 2013. Detection sites were placed throughout the reservoir, near the dam, and at two sites in the North Santiam River and at three sites in the Willamette River culminating at Portland, Oregon. We based most inferences on an analysis period up to the 90th percentile of tag life (68–78 days after release, depending on species and season), although a small number of fish passed after that period as late as April 8, 2014. Chinook salmon migrated from the tributaries of release to the reservoir in greater proportion than steelhead, particularly in the fall. The in-reservoir migration behaviors and dam passage of the two species were similar during the spring study, but during the fall study, few steelhead reached the reservoir and none passed the dam within the analysis period. Migrations in the reservoir were directed and non-random, except in the forebay. Depths of fish within 25 meters of the dam were deeper in the day than at night for Chinook salmon and similar in the day and night for steelhead; steelhead generally were at shallower depths than Chinook salmon. The primary factors affecting dam passage rates were seasonal dam operating conditions and diel period. Fish passage rates were much greater during the spring and summer than in the fall and winter, and the difference was attributed to the availability and use of the spillway near the top of the dam during the spring and summer. The flood-control purpose of the reservoir prevented spillway use during much of the fall and winter because of the low forebay elevation. Passage rates at night were greater than in the day during spring and summer (4.2 times) and during the fall and winter (14.9 times). Fish length, dam discharge, and forebay elevation also affected dam passage rates. Travel times from Detroit Dam passage to the downstream sites were shorter during the fall and winter than during the spring and summer, and were less than a median of 8.68 days to Portland. The estimated survival in the 11 kilometers (km) between Detroit Dam and the Minto Dam forebay was lower than in the remaining 241 km to the Portland site. Estimated survival per 100 km in the free-flowing reach from Minto Dam to Portland was 0.675–0.836, depending on species and season, and was similar to other free-flowing rivers in the Western United States. The high probability of fish in the reservoir reaching the dam, the chance for repeated presence near the dam, the fish depths, and the factors known to affect passage rates suggest that a properly designed surface passage route could be a viable downstream passage alternative for juvenile Chinook salmon and steelhead at Detroit Dam. As part of the evaluations conducted at Detroit Dam, we continued to refine and improve methods for monitoring fish movements in the Willamette River. The goal was to develop stable, cost-effective, long-term monitoring arrays suitable for detection of any Juvenile Salmon Acoustic Telemetry System (JSATS)-tagged fish in the Willamette River. These data then could be used to estimate timing, migration rates, and survival of JSATS-tagged fish from various studies in the Willamette River Basin. The challenge, however, is that acoustic telemetry generally performs poorly in shallow, turbulent water, like that found in the Willamette River. We successfully designed, deployed, and maintained a series of monitoring sites near the Oregon cities of Salem, Wilsonville, and Portland. In the spring, detection probabilities at these sites ranged from 0.900 to 1.000. In the fall, the detection probabilities decreased and ranged from 0.526 to 1.000. The lower detection probabilities, particularly at the Salem site (0.526), were owing to loss of data caused by abnormally high flows as well as the 2013 Federal government shutdown, which prevented us from servicing the equipment. The monitoring sites that we installed seem to be robust and enable the efficient use of acoustic-tagged fish for studies of migration or survival in the Willamette River and similar environments.

Oregon↗

USGS2014

Performance of a surface bypass structure to enhance juvenile steelhead passage and survival at Lower Granite Dam, Washington

An integral part of efforts to recover stocks of Pacific salmon Oncorhynchus spp. and steelhead O. mykiss in Pacific Northwest rivers is to increase passage efficacy and survival of juveniles past hydroelectric dams. As part of this effort, we evaluated the efficacy of a prototype surface bypass structure, the removable spillway weir (RSW), installed in a spillbay at Lower Granite Dam, Washington, on the Snake River during 2002, 2003, 2005, and 2006. Radio-tagged juvenile steelhead were released upstream from the dam and their route of passage through the turbines, juvenile bypass, spillway, or RSW was recorded. The RSW was operated in an on-or-off condition and passed 3–13% of the total discharge at the dam when it was on. Poisson rate models were fit to the passage counts of hatchery- and natural-origin juvenile steelhead to predict the probability of fish passing the dam. Main-effect predictor variables were RSW operation, diel period, day of the year, proportion of flow passed by the spillway, and total discharge at the dam. The combined fish passage through the RSW and spillway was 55–85% during the day and 37–61% during the night. The proportion of steelhead passing through nonturbine routes was <88% when the RSW was off during the day and increased to >95% when the RSW was on during the day. The ratio of the proportion of steelhead passed to the proportion of water passing the RSW was from 6.3:1 to 10.0:1 during the day and from 2.7:1 to 5.2:1 during the night. Steelhead passing through the RSW exited the tailrace about 15 min faster than fish passing through the spillway. Mark–recapture single-release survival estimates for steelhead passing the RSW ranged from 0.95 to 1.00. The RSW appeared to be an effective bypass structure compared with other routes of fish passage at the dam.

Idaho, Oregon, Washington↗

USGS2014

Investigation of methods for successful installation and operation of Juvenile Salmon Acoustic Telemetry System (JSATS) hydrophones in the Willamette River, Oregon, 2012

Acoustic telemetry equipment was installed at three sites in the Willamette River during October 2012 to test the effectiveness of using the Juvenile Salmon Acoustic Telemetry System to monitor the movements of fish in a high-flow, high-velocity riverine environment. Hydrophones installed on concrete blocks were placed on the bottom of the river, and data cables were run from the hydrophones to shore where they were attached to anchor points. Under relatively low-flow conditions (less than approximately 10,000 cubic feet per second) the monitoring system remained in place and could be used to detect tagged fish as they traveled downstream during their seaward migration. At river discharge over approximately 10,000 cubic feet per second, the hydrophones were damaged and cables were lost because of the large volume of woody debris in the river and the increase in water velocity. Damage at two of the sites was sufficient to prevent data collection. A limited amount of data was collected from the equipment at the third site. Site selection and deployment strategies were re-evaluated, and an alternate deployment methodology was designed for implementation in 2013.

Oregon↗

USGS2013

Comparing effects of transmitters within and among populations: application to swimming performance of juvenile Chinook salmon

The sensitivity of fish to a transmitter depends on factors such as environmental conditions, fish morphology, life stage, rearing history, and tag design. However, synthesizing general trends across studies is difficult because each study focuses on a particular performance measure, species, life stage, and transmitter model. These differences motivated us to develop simple metrics that allow effects of transmitters to be compared among different species, populations, or studies. First, we describe how multiple regression analysis can be used to quantify the effect of tag burden (transmitter mass relative to fish mass) on measures of physiological performance. Next, we illustrate how the slope and intercept parameters can be used to calculate two summary statistics: θ, which estimates the tag burden threshold above which the performance of tagged fish begins to decline relative to untagged fish; and k, which measures the percentage change in performance per percentage point increase in tag burden. When θ = 0, k provides a single measure of the tag's effect that can be compared among species, populations, or studies. We apply this analysis to two different experiments that measure the critical swimming speed (U crit) of tagged juvenile Chinook Salmon Oncorhynchus tshawytscha. In both experiments, U crit declined as tag burden increased, but we found no significant threshold in swimming performance. Estimates of θ ranged from −0.6% to 2.1% among six unique treatment groups, indicating that swimming performance began to decline at a relatively low tag burden. Estimates of k revealed that U crit of tagged fish declined by −2.68% to −4.86% for each 1% increase in tag burden. Both θ and k varied with the tag's antenna configuration, tag implantation method, and posttagging recovery time. Our analytical approach can be used to gain insights across populations to better understand factors affecting the ability of fish to carry a transmitter.

Transactions of the American Fisheries Society↗

USGS2013

The Regional Salmon Outmigration Study--survival and migration routing of juvenile Chinook salmon in the Sacramento-San Joaquin River Delta during the winter of 2008-09

Juvenile Chinook salmon (Oncorhynchus tshawytscha) emigrating from natal tributaries of the Sacramento River may use a number of migration routes to navigate the Sacramento-San Joaquin River Delta (hereafter called “the Delta”), each of which may influence their probability of surviving. We applied a mark-recapture model to data from acoustically tagged juvenile late fall-run Chinook salmon that migrated through the Delta during the winter of 2008–09 to estimate route entrainment, survival, and migration times through the Delta. A tag-life study was conducted to determine the potential for premature tag failure. Tag failure began after 12 days and continued until the 45th day. Travel times of tagged fish exceeded minimum tag-failure times, indicating that survival estimates obtained from this study were negatively biased due to tag failure prior to fish exiting the Delta. Survival estimates were not adjusted and represent the joint probability of tag survival and fish survival. However, relative comparisons of survival among Chinook salmon choosing different routes appeared to be robust to tag failure, and migration-routing parameters were unaffected by tag failure. Migration-routing patterns were consistent among release groups. The Sacramento River was the primary migration route for all release groups except one. The percentage of fish entering the Sacramento River ranged from 33 to 55 percent. Sutter and Steamboat Sloughs were the secondary migration route for 9 of the 10 releases. The percentage of fish migrating through this route ranged from 10 to 35 percent. Entrainment into the interior Delta ranged from 15 to 33 percent. The Delta Cross Channel gates were open for 7 of the 10 releases. Entrainment into the interior Delta through the cross channel ranged from 1 to 27 percent. We estimated route-specific survival for 10 release groups that were released between November 14, 2008, and January 19, 2009. Population-level survival through the Delta (S Delta ) ranged from 0.019 (standard error of 0.012) to 0.277 (standard error of 0.041) among releases, which represent the probability of a fish surviving from Sacramento to Chipps Island with an operational transmitter. Sacramento River flows throughout the study period were approximately 8,000–15,000 cubic feet per second at Freeport, suggesting that variability in flow contributed little to differences in survival between releases. Fish migrating through the Sacramento River had the highest survival for most releases. Survival in Sutter and Steamboat Sloughs was slightly lower than survival in the Sacramento River for 7 of the 10 releases, but higher than survival in the Sacramento River for 3 releases. Survival in the interior Delta was lowest for all release groups except for one release in November. With the exception of this November release, survival patterns across release groups were similar to those of previous studies.

California↗

USGS2013

Review of a model to assess stranding of juvenile salmon by ship wakes along the Lower Columbia River, Oregon and Washington

Long period wake waves from deep draft vessels have been shown to strand small fish, particularly juvenile Chinook salmon Oncorhynchus tschawytcha, in the lower Columbia River (LCR). The U.S. Army Corps of Engineers is responsible for maintaining the shipping channel in the LCR and recently conducted dredging operations to deepen the shipping channel from an authorized depth of 40 feet(ft) to an authorized depth of 43 ft (in areas where rapid shoaling was expected, dredging operations were used to increase the channel depth to 48 ft). A model was developed to estimate stranding probabilities for juvenile salmon under the 40- and 43-ft channel scenarios, to determine if channel deepening was going to affect wake stranding (Assessment of potential stranding of juvenile salmon by ship wakes along the Lower Columbia River under scenarios of ship traffic and channel depth: Report prepared for the Portland District U.S. Army Corps of Engineers, Portland, Oregon). The U.S. Army Corps of Engineers funded the U.S. Geological Survey to review this model. A total of 30 review questions were provided to guide the review process, and these questions are addressed in this report. In general, we determined that the analyses by Pearson (2011) were appropriate given the data available. We did identify two areas where additional information could have been provided: (1) a more thorough description of model diagnostics and model selection would have been useful for the reader to better understand the model framework; and (2) model uncertainty should have been explicitly described and reported in the document. Stranding probability estimates between the 40- and 43-ft channel depths were minimally different under most of the scenarios that were examined by Pearson (2011), and a discussion of the effects of uncertainty given these minimal differences would have been useful. Ultimately, however, a stochastic (or simulation) model would provide the best opportunity to illustrate uncertainty within a given set of model predictions, but such an approach would require a substantial amount of additional data collection. Several review questions focused on the accuracy and precision of the model estimates, but we were unable to address these questions because of the limited data that currently exists regarding wake stranding in the LCR. Additional field studies will be required to validate findings from Pearson (2011), if concerns regarding accuracy and precision remain a priority. Although the Pearson (2011) model provided a useful examination of stranding under pre-construction and post-construction conditions, future research will be required to better understand the effects of wake stranding on juvenile salmonids throughout the entire LCR. If additional information on wake stranding is desired in the future, the following topics may be of interest: (1) spatial examination of wake stranding throughout the entire LCR; (2) additional evaluation of juvenile salmonid behavior and population dynamics; (3) assessing and integrating predicted changes in ship development; and (4) assessing and integrating predicted changes in climate on environmental factors known to cause stranding.

Oregon;Washington↗

USGS2012

Estimating and predicting collection probability of fish at dams using multistate modeling

Dams can be equipped with a bypass that routes a portion of the fish that enter the turbine intakes away from the powerhouse into flumes, where they can be counted. Daily passage abundance can be estimated by dividing the number of fish counted in the bypass by the sampling rate and then dividing the resulting quotient by the collection probability (i.e., the proportion of the fish population passing the dam that is bypassed). We used multistate mark–recapture modeling to evaluate six candidate models for predicting the collection probabilities of radio-tagged subyearling fall Chinook salmon (n = 3,852) as a function of 1–2-d time periods (general model), four different combinations of outflow (i.e., the total volume of water passing the dam) and turbine allocation (i.e., the proportion of outflow directed through the turbines), and a null (intercept only) model. The best-fit model was the additive combination of turbine allocation and outflow, which explained 71% of the null deviance. Cross validation of the best-fit model accounted for the variation that may arise from different data sets and the ensuing parameter values on the collection probability estimates and yielded a standard error of 0.613 that can be used to construct approximate 95% prediction intervals in nonstudy years. Such estimates have been unavailable and will be useful anywhere estimates of daily passage abundance at dams with bypasses are needed to manage migratory fishes.

Transactions of the American Fisheries Society↗

USGS2012

Adjusting survival estimates for premature transmitter failure: A case study from the Sacramento-San Joaquin Delta

In telemetry studies, premature tag failure causes negative bias in fish survival estimates because tag failure is interpreted as fish mortality. We used mark-recapture modeling to adjust estimates of fish survival for a previous study where premature tag failure was documented. High rates of tag failure occurred during the Vernalis Adaptive Management Plan’s (VAMP) 2008 study to estimate survival of fall-run Chinook salmon ( Oncorhynchus tshawytscha ) during migration through the San Joaquin River and Sacramento-San Joaquin Delta, California. Due to a high rate of tag failure, the observed travel time distribution was likely negatively biased, resulting in an underestimate of tag survival probability in this study. Consequently, the bias-adjustment method resulted in only a small increase in estimated fish survival when the observed travel time distribution was used to estimate the probability of tag survival. Since the bias-adjustment failed to remove bias, we used historical travel time data and conducted a sensitivity analysis to examine how fish survival might have varied across a range of tag survival probabilities. Our analysis suggested that fish survival estimates were low (95% confidence bounds range from 0.052 to 0.227) over a wide range of plausible tag survival probabilities (0.48–1.00), and this finding is consistent with other studies in this system. When tags fail at a high rate, available methods to adjust for the bias may perform poorly. Our example highlights the importance of evaluating the tag life assumption during survival studies, and presents a simple framework for evaluating adjusted survival estimates when auxiliary travel time data are available.

California↗