Geology topics

Russell W. Perry

Publications and source records attributed to Russell W. Perry.

101 records · Page 6Linked to original sources

USGS2012

Bias from false-positive detections and strategies for their removal in studies using telemetry

The use of radio and acoustic telemetry to study aquatic animals has flourished since the 1950s and 1960s (see Section 1). Electronic data-logging receivers are commonly used in both types of active telemetry to record the presence of transmitters in the detection field formed by one or more antennas or hydrophones. As described in Sections 5.1 and 7.1, the path of a transmitter signal to a telemetry receiver can be influenced by many factors and the received signal is not always detected or correctly assigned. It should be of no surprise to users of active telemetry systems that not all records in telemetry receivers are from tagged fish and not all tagged fish are recorded when present. Four types of observations are possible in data from telemetry receiving systems based on the binary nature of presence and absence (Table 1). True positives and true negatives are what one ideally expects from telemetry systems, but in most studies they are accompanied by false negatives (not recorded when present) and false positives (recorded when absent). False negatives arise due to a variety of causes, including insufficient detection area relative to transmitter pulse rate and fish travel speed, collisions between transmitters in the detection area, interference from ambient noise, or a received signal too weak to be recorded (see Sections 3, 5, and 7). The probability of false negatives can be calculated as (1–detection probability) and can be estimated with proper study design and incorporated into estimates of fish presence (see Sections 7.2 and 9.2).

Book chapter↗

USGS2012

2011 Georgiana Slough non-physical barrier performance evaluation project report

The Sacramento River and its tributaries support populations of anadromous fish species including winter-run, spring-run, fall-run, and late fall–run Chinook salmon ( Oncorhynchus tshawytscha ); and steelhead ( O. mykiss ). Several of these species are listed as threatened or endangered under the California Endangered Species Act (CESA), federal Endangered Species Act (ESA), or both. These species spawn and rear in Sacramento River tributaries; adults use the mainstem Sacramento River for primarily upstream migration and juveniles use it for downstream migration. Juvenile Chinook salmon and steelhead migrate through the lower river during winter and spring. During their downstream migration, juvenile salmonids encounter alternative pathways, such as Sutter and Steamboat Sloughs, the Sacramento–San Joaquin Delta (Delta), Delta Cross Channel (DCC), and Georgiana Slough. Likewise, sturgeon juveniles migrate downstream in the Sacramento River basin to the Delta, utilizing the distributary channels to rear within and migrate through the system. Georgiana Slough is a natural channel that allows water and fish to move into the interior Delta. Previous studies have demonstrated that juvenile Chinook salmon experience greater mortality when migrating into Georgiana Slough than those juveniles that continue to migrate downstream in the Sacramento River (Perry 2010). Movement and/or diversion of these fish into the interior and south Delta increases the likelihood of losses through predation, entrainment into non-project Delta diversions, and mortality associated with the State Water Project (SWP) and Central Valley Project (CVP) pumping facilities in the south Delta (Perry 2010; NMFS 2009). Figure ES-1 shows the migration pathways in the lower Sacramento River and Delta for outmigrating anadromous salmonids, and the location of the DCC, and the SWP and CVP pumping facilities in the south Delta. Passage of juvenile salmonids from the Sacramento River into the interior Delta through the DCC can be reduced through seasonal closure of the radial gates (February through May); however, no similar protection is available to reduce the movement of juvenile salmonids from the Sacramento River into the interior Delta through Georgiana Slough. Flows into Georgiana Slough improve water quality and flushing in the interior Delta and free access encourages use by recreational boaters. Because of these benefits, alternatives to the installation of a physical barrier (i.e. radial gates), are being investigated. Under the ESA, the National Marine Fisheries Service (NMFS) issued the 2009 Biological and Conference Opinion for the Long‐Term Operations of the Central Valley Project and State Water Project (BO) for Chinook salmon and other listed anadromous fish species (NMFS 2009). Reasonable and Prudent Alternative (RPA) Action IV.1.3 of the BO requires the California Department of Water Resources (DWR) and the U.S. Bureau of Reclamation (Reclamation) to consider engineering solutions to reduce the diversion of juvenile salmonids from the Sacramento River into the interior and south Delta. DWR implemented the 2011 Georgiana Slough NonPhysical Barrier (GSNPB) Study to test the effectiveness of using a non-physical barrier, referred to as a behavioral Bio-Acoustic Fish Fence (BAFF), that combines three stimuli to deter juvenile Chinook salmon from entering Georgiana Slough: sound, high-intensity modulated light (previously known as stroboscopic light), and a bubble curtain. This report presents the results of the experimental tests conducted in 2011.

California↗

USGS2012

Evaluation of stream flow effects on smolt survival in the Yakima River basin, Washington

Study Summary The influence of stream flow on salmon smolt emigration survival is a topic of widespread management interest. We collected smolt survival data to inform flow management decisions in the Yakima Basin. The Yakima River watershed drains the eastern slopes of the Cascade Mountain Range in central Washington State. The upper basin is comprised of two major tributaries–the Naches River and the upper Yakima River. Headwater storage reservoirs capture runoff during the winter and spring seasons to support downstream irrigation needs. During summer months, water is conveyed through the upper Yakima River and diverted at Roza Dam, a major irrigation diversion that supplies water to the Roza Irrigation District and to a hydroelectric plant located near Yakima, Washington. To assess smolt survival in the 18 km reach downstream of Roza Dam, a radio telemetry project will be carried out over a three-year timeframe. The first year of study was designed to provide baseline survival estimates at two distinct flow treatments during the spring migration period. The goal was to establish flow treatments that were as divergent as possible in order to maximize the observed effect of environmental conditions on smolt survival. In total, three experimental trials were carried out in 2012–one during low flow conditions (<600 cfs) and two during high flows (>3000 cfs). Data from the first year will be used to determine experimental design requirements to adequately address study objectives in years two and three. In the spring of 2012, fixed telemetry monitoring stations were established in strategic locations upstream and downstream of Roza Dam. Yearling Chinook salmon Oncorhynchus tshawytscha smolts originating from Cle Elum Hatchery were captured at the Roza Dam fish screen bypass facility, implanted with radio tags, and released upstream of Roza Dam. Each release group of 50 fish was paired with a high or low flow condition. Fish movements were tracked as tagged fish passed each monitoring station during their migration down the upper Yakima River, through Roza Dam, past the Naches River confluence, and eventually through Sunnyside and Prosser Dams. At the conclusion of field data collection, survival rates for each release group were calculated using Cormack-Jolly-Seber mark-recapture models. Yearling Chinook smolt survival and travel time estimates from 2012 suggest that migration rates and survival rates in the Roza Reach may be associated with stream flow, water temperature, release timing (i.e. migratory disposition), and fish size, but the extent to which each variable influenced survival is yet to be determined. The lowest survival rate (61%) and longest travel time (median 2.26 days) was observed in Release Group 1, which had the smallest size distribution and experienced the lowest flows, lowest temperatures, and earliest release date among the three groups. Release Groups 2 and 3 survived at 96% and 98% respectively and traveled through the Roza Reach in less than eight hours. The primary focus of years two and three of this study will be to collect data that minimizes the effect of confounding explanatory variables, so that flow effects on emigration survival can be quantified independent of these other influential factors.

Washington↗

USGS2012

Time-to-event analysis as a framework for quantifying fish passage performance

Fish passage is the result of a sequence of processes, whereby fish must approach, enter, and pass a structure. Each of these processes takes time, and fishway performance is best quantified in terms of the rates at which each process is completed. Optimal performance is achieved by maximizing the rates of approach, entry, and passage through safe and desirable routes. Sometimes, however, it is necessary to reduce rates of passage through less desirable routes in order to increase proportions passing through the preferred route. Effectiveness of operational or structural modifications for achieving either of these goals is best quantified by applying time-to-event analysis, commonly known as survival analysis methods, to telemetry data. This set of techniques allows for accurate estimation of passage rates and covariate effects on those rates. Importantly, it allows researchers to quantify rates that vary over time, as well as the effects of covariates that also vary over time. Finally, these methods are able to control for competing risks, i.e., the presence of alternate passage routes, failure to pass, or other fates that remove fish from the pool of candidates available to pass through a particular route. In this chapter, we present a model simulation of telemetered fish passing a hydroelectric dam, and provide step-by-step guidance and rationales for performing time-to-event analysis on the resulting data. We demonstrate how this approach removes bias from performance estimates that can result from using methods that focus only on proportions passing each route. Time-to-event analysis, coupled with multinomial models for measuring survival, provides a comprehensive set of techniques for quantifying fish passage, and a framework from which performance among different sites can be better understood.

Book chapter↗

USGS2011

Analysis of dam-passage survival of yearling and subyearling Chinook salmon and juvenile steelhead at The Dalles Dam, Oregon, 2010

We performed a series of analyses of mark-recapture data from a study at The Dalles Dam during 2010 to determine if model assumptions for estimation of juvenile salmonid dam-passage survival were met and if results were similar to those using the University of Washington's newly developed ATLAS software. The study was conducted by the Pacific Northwest National Laboratory and used acoustic telemetry of yearling Chinook salmon, juvenile steelhead, and subyearling Chinook salmon released at three sites according to the new virtual/paired-release statistical model. This was the first field application of the new model, and the results were used to measure compliance with minimum survival standards set forth in a recent Biological Opinion. Our analyses indicated that most model assumptions were met. The fish groups mixed in time and space, and no euthanized tagged fish were detected. Estimates of reach-specific survival were similar in fish tagged by each of the six taggers during the spring, but not in the summer. Tagger effort was unevenly allocated temporally during tagging of subyearling Chinook salmon in the summer; the difference in survival estimates among taggers was more likely a result of a temporal trend in actual survival than of tagger effects. The reach-specific survival of fish released at the three sites was not equal in the reaches they had in common for juvenile steelhead or subyearling Chinook salmon, violating one model assumption. This violation did not affect the estimate of dam-passage survival, because data from the common reaches were not used in its calculation. Contrary to expectation, precision of survival estimates was not improved by using the most parsimonious model of recapture probabilities instead of the fully parameterized model. Adjusting survival estimates for differences in fish travel times and tag lives increased the dam-passage survival estimate for yearling Chinook salmon by 0.0001 and for juvenile steelhead by 0.0004. The estimate was unchanged for subyearling Chinook salmon. The tag-life-adjusted dam-passage survival estimates from our analyses were 0.9641 (standard error [SE] 0.0096) for yearling Chinook salmon, 0.9534 (SE 0.0097) for juvenile steelhead, and 0.9404 (SE 0.0091) for subyearling Chinook salmon. These were within 0.0001 of estimates made by the University of Washington using the ATLAS software. Contrary to the intent of the virtual/paired-release model to adjust estimates of the paired-release model downward in order to account for differential handling mortality rates between release groups, random variation in survival estimates may result in an upward adjustment of survival relative to estimates from the paired-release model. Further investigation of this property of the virtual/paired-release model likely would prove beneficial. In addition, we suggest that differential selective pressures near release sites of the two control groups could bias estimates of dam-passage survival from the virtual/paired-release model.

Open-File Report↗

USGS2011

Simulating daily water temperatures of the Klamath River under dam removal and climate change scenarios

A one-dimensional daily averaged water temperature model was used to simulate Klamath River temperatures for two management alternatives under historical climate conditions and six future climate scenarios. The analysis was conducted for the Secretarial Determination on removal of four hydroelectric dams on the Klamath River. In 2012, the Secretary of the Interior will determine if dam removal and implementation of the Klamath Basin Restoration Agreement (KBRA) (Klamath Basin Restoration Agreement, 2010) will advance restoration of salmonid fisheries and is in the public interest. If the Secretary decides dam removal is appropriate, then the four dams are scheduled for removal in 2020. Water temperature simulations were conducted to compare the effect of two management alternatives: the no-action alternative where dams remain in place, and the action alternative where dam removal occurs in 2020 along with habitat restoration. Each management alternative was simulated under historical climate conditions (1961-2010) and six 50-year (2012-2061) climate scenarios. The model selected for the study, River Basin Model-10 (RBM10), was used to simulate water temperatures over a 253-mile reach of the Klamath River located in south-central Oregon and northern California. RBM10 uses a simple equilibrium flow model, assuming discharge in each river segment on each day is transmitted downstream instantaneously. The model uses a heat budget formulation to quantify heat flux at the air-water interface. Inputs for the heat budget were calculated from daily-mean meteorological data, including net shortwave solar radiation, net longwave atmospheric radiation, air temperature, wind speed, vapor pressure, and a psychrometric constant needed to calculate the Bowen ratio. The modeling domain was divided into nine reaches ranging in length from 10.8 to 42.4 miles, which were calibrated and validated separately with measured water temperature data collected irregularly from 1961 to 2010. Calibration root mean square errors of observed versus simulated water temperatures for the nine reaches ranged from 0.8 to 1.5 degrees C. Mean absolute errors ranged from 0.6 to 1.2 degrees C. For model validation, a k-fold cross-validation technique was used. Validation root mean square error and mean absolute error for the nine reaches ranged from 0.8 to 1.4 degrees C and 0.8 to 1.2 degrees C, respectively. Input data for the six future climate scenarios (2012-2061) were derived from historical hydrological and meteorological data and simulated meteorological output from five Global Circulation Models. Total Maximum Daily Loads or other regulatory processes that might reduce future water temperatures were not included in the simulations. Under the current climate conditions scenario, impacts of dam removal on water temperatures were greatest near Iron Gate Dam (near Yreka, California) and were attenuated in the lower reaches of the Klamath River. May and October simulated mean water temperatures increased and decreased by approximately 1-2 degrees C and 2-4 degrees C, respectively, downstream of Iron Gate Dam after dam removal. Dam removal also resulted in an earlier annual temperature cycle shift of 18 days, 5 days, and 2 days, near Iron Gate Dam, Scott River, and Trinity River, respectively. Although the magnitude of precipitation and air temperature change predicted by the five Global Circulation Models varied, all five models resulted in progressive incremental increases in water temperatures with each decade from 2012 to 2061. However, dam removal under KBRA appeared to delay the effects of climate change to some extent near Iron Gate Dam. With dam removal under KBRA, annual-mean water temperatures exceeded the 49-year historical mean temperature beginning in 2045; whereas with dams, annual-mean temperatures exceeded the historical mean beginning in 2025. Potential changes in seasonal water temperatures resulting from dam removal, with or without future climat

Open-File Report↗

USGS2010

Guidelines for conducting Smolt survival studies in the Columbia River

For more than a decade, investigators from different research groups in the Pacific Northwest have been using electronic tags to estimate survival of salmonid smolts as they migrate seaward past hydroelectric dams and through impoundments on the Snake and Columbia Rivers. Over the years, they have refined both analytical and field methods associated with such studies. In this collaborative paper, they synthesize years of experience to formulate a set of guidelines that may assist others with the design and execution of survival studies involving smolts during their migratory phase.

Report↗

USGS2009

Distribution and Joint Fish-Tag Survival of Juvenile Chinook Salmon Migrating through the Sacramento-San Joaquin River Delta, California, 2008

Acoustic telemetry was used to obtain the movement histories of 915 juvenile fall-run Chinook salmon (Oncorhynchus tshawytscha) through the lower San Joaquin River and Sacramento-San Joaquin Delta, California, in 2008. Data were analyzed within a release-recapture framework to estimate survival, route distribution, and detection probabilities among three migration pathways through the Delta. The pathways included the primary route through the San Joaquin River and two less direct routes (Old River and Turner Cut). Strong inferences about survival were limited by premature tag failure, but estimates of fish distribution among migration routes should be unaffected by tag failure. Based on tag failure tests (N = 66 tags), we estimated that only 55-78 percent of the tags used in this study were still functioning when the last fish was detected exiting the study area 15 days after release. Due to premature tag failure, our 'survival' estimates represent the joint probability that both the tag and fish survived, not just survival of fish. Low estimates of fish-tag survival could have been caused by fish mortality or fish travel times that exceeded the life of the tag, but we were unable to differentiate between the two. Fish-tag survival through the Delta (from Durham Ferry to Chipps Island by all routes) ranged from 0.05 +or- 0.01 (SE) to 0.06 +or- 0.01 between the two weekly release groups. Among the three migration routes, fish that remained in the San Joaquin River exhibited the highest joint fish-tag survival (0.09 +or- 0.02) in both weeks, but only 22-33 percent of tagged fish used this route, depending on the week of release. Only 4-10 percent (depending on week) of tagged fish traveled through Turner Cut, but no tagged fish that used this route were detected exiting the Delta. Most fish (63-68 percent, depending on week of release) migrated through Old River, but fish-tag survival through this route (0.05 +or- 0.01) was only about one-half that of fish that remained in the San Joaquin River. Once tagged fish entered Old River, only fish collected at two large water conveyance projects and transported through the Delta by truck were detected exiting the Delta, suggesting that this route was the only successful migration pathway for fish that entered Old River. The rate of entrainment of tagged juvenile salmon into Old River was similar to the fraction of San Joaquin River discharge flowing into Old River, which averaged 63 percent but varied tidally and ranged from 33 to 100 percent daily. Although improvements in transmitter battery life are clearly needed, this information will help guide the development of future research and monitoring efforts in this system.

Open-File Report↗

USGS2008

Survival and migration behavior of juvenile salmonids at Lower Granite Dam, 2006

We described behavior and estimated passage and survival parameters of juvenile salmonids during spring and summer migration periods at Lower Granite Dam in 2006. During the spring, the study was designed to examine the effects of the Behavioral Guidance Structure (BGS) by using a randomized-block BGS Stored / BGS Deployed treatment design. The summer study was designed to compare passage and survival through Lower Granite Dam using a randomized-block design during two spill treatments while the BGS was in the stored position. We used the Route Specific Survival Model to estimate survival and passage probabilities of hatchery yearling Chinook salmon, hatchery juvenile steelhead, and hatchery and wild subyearling Chinook salmon. We also estimated fish guidance efficiency (FGE), fish passage efficiency (FPE), Removable Spillway Weir passage effectiveness (RPE), spill passage effectiveness (SPY), and combined spill and RSW passage effectiveness.

Idaho, Oregon,Washington↗

USGS2007

Survival and migration behavior of juvenile salmonids at McNary Dam, 2005: Final report of research

During 2005, we used radio-telemetry at McNary Dam to estimate passage and survival parameters of juvenile salmonids. During the spring migration period, two treatments were implemented: 1) 12-h spill operations with spill occurring between 1800 hours and 0600 hours, and 2) 24-h spill with spill occurring 24 hours per day. Treatments were not implemented during the summer migration period. However, a court-order was issued by Judge James Redden, U.S. 9th District Court, mandating a maximum powerhouse discharge of 50 kcfs with the remaining discharge to be spilled over the 24-h diel cycle between 1 July and 31 August 2005. Consequently, our study was conducted during two distinct periods: 1) a short period of involuntary spill for 24-h per day that occurred between 22 June and 30 June 2005, and 2) the period of court-ordered spill that was implemented after 1 July 2005.

Oregon, Washington↗

USGS2005

Survival and migration behavior of juvenile salmonids at McNary Dam, 2004, Final report of research

During 2004, the USGS Columbia River Research Laboratory conducted a study at McNary Dam using radio telemetry to estimate passage and survival parameters of juvenile salmonids. Our primary objective was to estimate these parameters under ambient environmental and operational conditions, and thus project-wide treatments were not implemented. The primary dam operation consisted of “biop” spill, where spill occurred at night between 1800 and 0600 hours, and no spill occurred between 0600 and 1800 hours for the majority of our study period. During the spring study period, we radio-tagged and released 1,896 yearling Chinook salmon and 1,888 juvenile steelhead. During the summer study period, we radio-tagged and released 1,919 subyearling Chinook salmon. All fish were tagged using gastric techniques to implant transmitters weighing 1.58 g for yearling Chinook salmon, 1.93 g for juvenile steelhead, and 0.96 g for subyearling Chinook salmon. Minimum fish sizes were based on a 6.5% tag:fish weight ratio, and the size of tagged fish represented about 91%, 100%, and 17% of the population, respectively for yearling Chinook salmon, juvenile steelhead, and subyearling Chinook salmon. About 60% of radio-tagged fish were released 10 km upstream of McNary Dam at Hat Rock State Park, Oregon, with the remainder released as control groups 400 m downstream of the dam.

Oregon, Washington↗