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John W. Beeman

Publications and source records attributed to John W. Beeman.

34 records · Page 2Linked to original sources
USGS2012

Preface

Telemetry provides a powerful and flexible tool for studying fish and other aquatic animals, and its use has become increasingly commonplace. However, telemetry is gear intensive and typically requires more specialized knowledge and training than many other field techniques. As with other scientific methods, collecting good data is dependent on an understanding of the underlying principles behind the approach, knowing how to use the equipment and techniques properly, and recognizing what to do with the data collected. This book provides a road map for using telemetry to study aquatic animals, and provides the basic information needed to plan, implement, and conduct a telemetry study under field conditions. Topics include acoustic or radio telemetry study design, tag implantation techniques, radio and acoustic telemetry principles and case studies, and data management and analysis.

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↗
USGS2010

Approach, passage, and survival of juvenile salmonids at Little Goose Dam, Washington: Post-construction evaluation of a temporary spillway weir, 2009

This report describes a study of dam passage and survival of radio-tagged juvenile salmonids after installation of a temporary spillway weir (TSW) at Little Goose Dam, Washington, in 2009. The purpose of the study was to document fish passage and survival when the dam was operated with the TSW in place. Spillway weirs are one of several methods used to improve downstream passage of juvenile salmonids. Each spillway weir design is based on the concept of providing an overflow weir with a depth more similar to the natural migration depth of juvenile salmonids than conventional spill bays. Little Goose Dam was the last of the four lower Snake River dams to have a spillway weir installed. This was the first year that some form of surface passage device was operating at all Snake River and Columbia River dams between Lewiston, Idaho, and the Columbia River estuary. The study design stipulated that a total of 30 percent of the river discharge would continuously be passed over the TSW and the conventional spill bays, and this percentage was achieved. The TSW also was to be operated at the ?low crest? elevation during the spring and the ?high crest? elevation during the summer, but the TSW was only operated at the low crest elevation during this study. Behavior, passage, and survival of spring and summer juvenile salmonid migrants passing through Little Goose Dam were examined using radio telemetry. Survival was estimated using the Route Specific Survival Model (RSSM) by releasing tagged fish near Central Ferry State Park 21 kilometers upstream of the dam and in the tailrace approximately 0.5 kilometer downstream of the dam. From April 18 to May 21, 2009, 1,520 yearling Chinook salmon (Oncorhynchus tshawytscha) and 1,517 juvenile steelhead (O. mykiss) were radio tagged and released. From June 6 to July 5, 2009, 4,251 subyearling Chinook salmon (O. tshawytscha) were radio tagged and released. Release dates of subyearling Chinook salmon were selected to avoid ?reservoir-type? fish that cease to migrate around July. Detection sites were installed in the forebay 2 kilometers upstream of the dam, on the dam, and at several sites downstream. Detection equipment was operated from April 18 to June 5, 2009, and from June 6 to July 6, 2009, hereinafter referred to as the study periods. We describe passage behaviors through the forebay, main passage routes, and tailrace, survival probabilities through the pool (release to the forebay) and forebay and passage and survival probabilities through the main passage routes (TSW, conventional spill bays, turbines, juvenile bypass), and survival passing the concrete (the dam itself) and the dam (concrete plus the forebay).

Scientific Investigations Report↗
USGS2009

Summary of Survival Data from Juvenile Coho Salmon in the Klamath River, Northern California, 2008

A study to estimate the effects of Iron Gate Dam discharge on ESA-listed juvenile coho salmon during their seaward migration to the ocean was begun in 2005. Estimates of survival through various reaches of river downstream from the dam were completed in 2006, 2007, and 2008 as part of this process. This report describes the estimates of survival during 2008, and is a complement to similar reports from 2006 and 2007. In each year, a series of models were evaluated to determine apparent survival and recapture probabilities of radio-tagged fish in several river reaches between Iron Gate Hatchery at river kilometer 309 and a site at river kilometer 33. These results indicate most trends in survival among reaches were similar to those from 2006 and 2007, but the magnitudes of the estimated survivals were lower in 2008. The differences in survivals from Iron Gate Hatchery to river kilometer 33 in 2006 (0.653 SE 0.039), 2007 (0.497 SE 0.044), and 2008 (0.406 SE 0.032) were caused primarily by differences in survival upstream from the Scott River. This report is intended as a brief description of the survivals estimated from the fish released in 2008 to be used by others interested in the data.

Open-File Report↗
USGS2009

Summary of Migration and Survival Data from Radio-Tagged Juvenile Coho Salmon in the Trinity River, Northern California, 2008

The survival of hatchery-origin juvenile coho salmon from the Trinity River Hatchery was estimated as they migrated seaward through the Trinity and Klamath Rivers. The purpose of the study was to collect data for comparison to a similar study in the Klamath River and provide data to the Trinity River Restoration Program. A total of 200 fish fitted with radio transmitters were released into the Trinity River near the hatchery (river kilometer 252 from the mouth of the Klamath River) biweekly from March 19 to May 28, 2008. Fish from the earliest release groups took longer to pass the first detection site 10 kilometers downstream of the hatchery than fish from the later release groups, but travel times between subsequent sites were often similar among the release groups. The travel times of individuals through the 239 kilometer study area ranged from 15.5 to 84.6 days with a median of 43.3 days. The data and models did not support differences in survival among release groups, but did support differences among river reaches. The probability of survival in the first 53 kilometers was lower than in the reaches farther downstream, which is similar to trends in juvenile coho salmon in the Klamath River. The lowest estimated survival in this study was in the first 10 kilometers from release in the Trinity River (0.676 SE 0.036) and the highest estimated survival was in the final 20 kilometer reach in the Klamath River (0.987 SE 0.013). Estimated survivals of radio-tagged juvenile coho salmon from release to Klamath River kilometer 33 were 0.639 per 100 kilometers for Trinity River fish and 0.721 per 100 kilometers for Klamath River fish.

Open-File Report↗
USGS2009

Summary of survival data from juvenile coho salmon in the Klamath River, northern California, 2009

A study of the effects of the discharge from Iron Gate Dam on the Klamath River on juvenile coho salmon during their seaward migration began in 2005. Estimates of fish survival through various reaches of the river downstream of the dam were completed in 2006, 2007, 2008, and 2009. This report describes the estimates of survival during 2009, and is a complement to similar reports for 2006, 2007, and 2008. For each year, a series of numerical models were evaluated to determine apparent survival and recapture probabilities of radio-tagged fish in several river reaches between Iron Gate Hatchery at river kilometer 309 and a site at river kilometer 33. The evaluations indicate that the primary differences among years are in the survivals through reaches upstream of the confluence of the Scott River with the Klamath River. Data from 2009, one of two years when fish from both hatchery and wild origins were available for analysis, indicate that survival of wild and hatchery fish are similar.

California↗
USGS2009

Pilot study to access the role of Ceratomyxa shasta infection in mortality of fall-run Chinook smolts migrating through the lower Klamath River in 2008

Apparent survival and migration rate of radio-tagged hatchery subyearling Chinook salmon released at Iron Gate Hatchery was monitored in the Klamath River to see if the timing of mortality coincided with observations of ceratomyxosis in re-captured coded wire tag cohorts. Despite rapid emigration, these relatively large (mean fork length 92 mm) smolts had a cumulative apparent survival to the estuary of 0.074 (SE 0.024) and standardized rates of survival per 100 km tended to decrease linearly with distance from the hatchery. The last fish detection occurred 26 days after release but median travel time between Iron Gate Hatchery (rkm 309) and the last receiver near the Klamath estuary (Blake’s Riffle rkm 13) was about 10 days. The majority of apparent mortality (8-10 d post-release) occurred before disease from Ceratomyxa shasta infection is expected after exposure to infectious waters. Despite numerous observations of ceratomyxosis in the Klamath R. during June, an obvious link between disease and apparent survival was not present in this study. Future studies should examine the acute (e.g., predator types and densities) and chronic (e.g., swimming performance impairment due to disease) mortality factors for juvenile Chinook salmon smolts in the Klamath River.

California↗
USGS2008

Summary of Survival Data from Juvenile Coho Salmon in the Klamath River, Northern California, 2007

A study to estimate the effects of Iron Gate Dam discharge on ESA-listed juvenile coho salmon during their seaward migration to the ocean was begun in 2005. Estimates of survival through various reaches of river downstream from the dam were completed in 2006 and 2007 as part of this process. This report describes the estimates of survival during 2007, and is a complement to a similar report from 2006. Further analyses will be included in a separate report. In 2007, a series of models were evaluated to determine what survival and capture probabilities of radio-tagged hatchery fish were in several reaches between Iron Gate Hatchery at river kilometer 309 and a site at river kilometer 33. The results indicate trends in survival among reaches were similar to those found in 2006, but the survival in 2007 was lower than in 2006. The differences in survivals from Iron Gate Hatchery to river kilometer 33 in 2006 (0.653 SE 0.039) and 2007 (0.497 SE 0.044) were caused primarily by differences in survivals upstream from the Scott River. This document is a brief summary of 2007 survival results.

Open-File Report↗
USGS2008

Survival and migration behavior of juvenile coho salmon in the Klamath River relative to discharge at Iron Gate Dam, Northern California, 2007

This report describes a study of survival and migration behavior of juvenile coho salmon in the Klamath River relative to discharge at Iron Gate Dam in 2006. This was the second year of a multi-year study with the goal of determining the effects of discharge at Iron Gate Dam on survival of juvenile coho salmon downstream. The study was a collaborative effort among U.S. Geological Survey (USGS), U.S. Fish and Wildlife Service (USFWS), and the Yurok and Karuk Tribal Fisheries Departments. The goals of the study included: 1) estimating the survival of wild and hatchery juvenile coho salmon in the Klamath River downstream from Iron Gate Dam, 2) determining the effects of discharge and other covariates on their survival and migration, and 3) determining if fish from Iron Gate Hatchery could be used as surrogates for the limited source of wild fish. The major findings of the study in 2006 include: River discharges during the 2006 study period (4 April through 21 July 2006) were among the greatest on record. Average daily discharge at Iron Gate Dam was 3,956 cubic feet per second (cfs) and ranged from 997 to 10,300 cfs. Discharge at Iron Gate Dam was positively correlated with discharges of tributaries downstream due to the above average water year and frequent occurrence of spill at Iron Gate Dam. Average daily discharge near the estuary was 25,789 cfs and ranged from 4,740 to 50,600 cfs. This study was based on hatchery fish taken directly from a tank at Iron Gate Hatchery and wild fish captured in a rotary trap on the Shasta River. Releases of both groups began on 4 April when the catch of wild fish in California Department of Fish and Game‟s Shasta River rotary trap increased, but trap catches varied throughout the study period, resulting in differences in release dates of hatchery and wild fish. A total of 211 hatchery fish were released from 4 April through 26 May. Wild and hatchery fish released on a regular schedule between 25 April and 16 May 2006 were used in comparisons of the survival and migration of hatchery (N = 120) and wild (N = 162) fish. Additional analyses were performed using hatchery fish from all dates. The data and models did not support clear differences between survivals of hatchery and wild fish released on common dates, so estimates of reach survivals were made after pooling these data. Estimates of survival were lowest in the Iron Gate Dam to Scott River reach (0.813) and greatest in the Salmon River to Trinity River reach (1.000). The overall survival from river kilometer 309 (Iron Gate Hatchery) to river kilometer 33 was 0.653 (95% CI 0.578 to 0.729). Estimates of survival based on all hatchery fish releases were similar to those from release dates common to hatchery and wild fish and are similar to those in other river systems over similar distances. The migrations of hatchery and wild fish were different in the uppermost sections of the study area and were similar thereafter. A lag between release and migration, primarily upstream from the Scott River (river kilometer 234), was present in hatchery fish to a greater extent than in wild fish, resulting in differences in migration rates. Fish from both origins spent more time between release and the Scott River than in individual reaches downstream, and this was the only reach in which travel times of fish increased as discharge decreased. The travel times of hatchery and wild fish between sites were statistically similar downstream from Indian Creek (river kilometer 178). There were differences and similarities in the analyses of the effects of covariates on survivals of hatchery and wild fish. The models of covariate effects based on hatchery and wild fish released on common dates indicated effects on wild fish survival that were not supported in data from hatchery fish. However, when the entire suite of hatchery fish releases were used the results of the analyses were similar to those based on wild fish. In both instances the effects of temperature and release date were primarily in the first reach, the reach fish of both origins spent most of their time within. The signs of the effects of these covariates differed among the fish origins (negative for wild and positive for hatchery fish), presumably due to differences in their migrations in the first reach. The effects of dam discharge on survivals of hatchery and wild fish were generally similar (positive relation), and the effects on hatchery, and to a lesser extent wild, fish were largely downstream from the Scott River. This is likely due to the prolonged residence of the naïve hatchery fish, and to a lesser extent, migrant wild fish between release and the Scott River. Inasmuch as the differences between hatchery and wild fish we observed were likely those of migrants vs. non-migrants, the use of hatchery fish captured as they are migrating downstream, rather than those directly from hatchery tanks (i.e., naïve), may improve similarities between hatchery and wild fish in future studies. The data and models used in 2006 do not support the use of naïve hatchery fish as surrogates for migrant wild fish in determining the effects of discharge on survival upstream from the Scott River. This conclusion is based on the different effects of covariates in this reach that were likely attributable to the differences in hatchery and wild migration behaviors in this reach. The results of this second year of research provide insight to the migration and survival of hatchery and wild juvenile coho salmon in the Klamath River, but the results are from a single unusual water year. The results may be different during other water year types. The current information supports a positive relation between discharge at Iron Gate Dam and survival of juvenile coho salmon downstream, but additional data should be used to refine this relation. Discharge at the dam was correlated with discharges of Klamath River tributaries during this above average water year. The data and models from the 2006 study provide the first estimates of survival of these fish in the Klamath River and can be used with data from years with other water year types to examine the effects of discharge on survival. This will only be possible over a period of years in which the correlations between discharge and other factors, such as water temperature and date, are diminished. An experimental approach in which discharges are varied at Iron Gate Dam is the most direct method to determine if survivals are affected by discharge, but this may not be feasible given the limited storage capacity of the project.

California↗
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

Summary of Survival Data from Juvenile Coho Salmon in the Klamath River, Northern California, 2006

Little is known about the survival of ESA-listed juvenile coho salmon during their seaward migration in the lower Klamath River. In 2006, the Bureau of Reclamation funded a study to estimate the survival of radio-tagged juvenile coho salmon in the Klamath River downstream of Iron Gate Dam. A series of models were evaluated to determine if survival varied between hatchery and wild fish and among several river reaches between the dam river kilometer 33, a total distance of 276 kilometers. The results from 2006, the first year of study, indicated little support for differences in survival between hatchery and wild fish and lower survival in the most upstream reach than in those farther downstream. This document is a brief summary of survival results to date.

Open-File Report↗
USGS2004

Distribution and relative abundance of fishes in littoral areas of Chief Joseph Reservoir, Columbia River

We surveyed fish assemblages in littoral areas of Chief Joseph Reservoir of the upper Columbia River to aid in understanding this ecosystem. Fish distributions and abundances were examined during April-July 1999 in relation to environmental conditions in the reservoir. We also compared the fish assemblages in Chief Joseph reservoir in 1999 to a past study conducted during 1974-1975, and to assemblages in other areas of the Columbia River. During 67 hr of electrofishing and 78 beach seine hauls in Chief Joseph Reservoir, 7460 fishes representing 8 families were collected. The majority of the catch was native – northern pikeminnow; redside shiners; longnose, bridgelip, and largescale suckers; and sculpins. The most abundant introduced species was walleye, and one species, rainbow trout, was mostly of net-pen origin. Larger sizes of suckers and northern pikeminnow were most abundant in the upper reservoir, likely due to upstream spawning migrations. The lower reservoir contained greater abundances of smaller fishes, and this area had lower flows, smaller substrates, and more complex shorelines that offered these fishes refugia. Only adult suckers displayed significant differences in abundances related to substrate. The relative abundances of species appeared to have changed since the 1970s, when the dominant fishes were northern pikeminnow, peamouth, largescale suckers, and walleye. Fish assemblage differences between Chief Joseph Reservoir and lower Columbia River reservoirs were also evident due to the morphology of the reservoir, its more northerly location, and the lack of fish passage facilities at Chief Joseph Dam. Our study is one of the few descriptions of fishes in the upper Columbia Rivers.

Washington↗
USGS1995

A non-lethal measure of smolt status of juvenile steelhead based on body morphology

A nonlethal morphometric method to assess smolt status of juvenile steelhead Oncorhynchus mykiss was validated. Fish were collected from hatcheries before release and during their seaward migration in a large river system. Fifteen anatomical landmarks were digitized from photographs of each fish, resulting in 34 morphometric characters based on a truss network. Principal component and canonical discriminant function analyses were used to assess smolt status. A single canonical variate was significantly correlated with gill Na + ,K + ‐ATPase activity, a commonly used measure of smolt status. This nonlethal method may be a useful measure of smolt status when sacrificing fish is not desirable or possible; it requires little training to perform, but it does require a larger sample size than some other methods.

Transactions of the American Fisheries Society↗
USGS1994

A microassay for gill sodium, potassium-activated ATPase in juvenile Pacific salmon

A microassay well-plate method is described for determining Na + ,K + -ATPase activities of small gill sections from juvenile Pacific salmon Oncorhynchus spp. The method differs from the established macromethod by detecting inorganic phosphate in nanomole rather than micromole concentrations. This permits the use of much smaller tissue samples, which makes it possible to release fish after sampling. Use of sonication during enzyme extraction and elimination of the need to deproteinize samples before ATPase analysis further simplify the assay. Application of the microwell-plate technique for both Na + ,K + -ATPase activity and protein analysis permits rapid processing of many samples. It also produces results equivalent to those of the macroassay; no significant differences occurred between sample duplicates run by the two methods with the same enzyme extract ( P > 0.05). The coefficient of variation (100·SD/mean) for microassay samples containing enzyme activities of at least 10 umol inorganic phosphate per milligram protein per hour was 12% or less for between-plate comparisons and 5% or less for same-plate comparisons. Monitoring of gill-clipped fish during migration indicated that small gill clips did not cause mortality or alter migration behavior of juvenile salmonids tagged with passive integrated transponders. These are important considerations in programs for monitoring species listed under the U.S. Endangered Species Act.

Transactions of the American Fisheries Society↗