California Research: Projects, Research Publications, Presentations, Thesis and Dissertations, Technical Publications

California Research Activities

The Alsea River. Credit: Sarah Beldin, USGS

Most of the research projects undertaken by the California Unit are field oriented and conducted by graduate students in close cooperation with our Unit, other University and agency biologists.

Projects

Project	Completion Date
Klamath Basin S3 Model	September 2019	The U.S. Fish & Wildlife Service has been working in close collaboration with the U.S. Geological Survey Columbia River Research Laboratory and Dr. Thomas Hardy from Watershed Systems Group, Inc. and Texas State University to develop Decision Support Systems such as the Stream Salmonid Simulator or S3 model. The S3 model currently under development for the Klamath River represents an integrated set of sub models that predict the effects of water management alternatives on the production of juvenile Chinook Salmon. This synchronized series of sub-models reflects the array of physical and biological processes that interact to affect the growth, movement, and survival of fish at a given lifestage. A benefit to this method of model construction lies in the ability to update sub-models as new data, new analyses, or new scientific discoveries arise. The current S3 model in development for the Klamath River tracks causes of mortality throughout the sub-adult life history of Chinook Salmon (redd scour, habitat limitations, disease, water quality, etc.) over time within 233-mile section of the mainstem Klamath River spanning from Keno Dam in Oregon to its confluence with the Pacific Ocean in California. The model is also being extended into the Trinity Basin, with the addition of an ocean component and IBM-type upstream adult migration sub module. These improvements will transform the S3 model into a basin-wide, full life cycle model. Future development of the S3 model will also include its expansion to incorporate Coho Salmon, as requested by NOAA Fisheries and the Bureau of Reclamation.	Research objectives are two-fold: 1. to evaluate the best practices for assigning flow-to-habitat relationships for large river systems; and 2. to extend the Klamath River stream salmonid simulator model, which was developed to track population dynamics of juvenile Chinook Salmon as they move from tributary to the main channel; to apply to juvenile Coho salmon.
Eel River Monitoring	July 2015	CalTrout and the Eel River Forum are in process of drafting and editing the Eel River Action Plan. The final Action Plan shall include a chapter describing ongoing and proposed basin-wide monitoring activities. These monitoring activities include fisheries, water quality, and citizen-based monitoring. The existing draft Action Plan Monitoring chapter will be revised with Coop Unit staff, CalTrout and several state and federal agency staff who participate in the Eel River Action Plan monitoring subcommittee.	None
Shasta River Coho	April 2014	The purpose of this contract was to identify areas where juvenile coho salmon were rearing and document how the used habitat and responded to changing conditions throughout their residence in the Shasta River. Identify life history patterns and identify the proportion of tagged fish that exhibited those tactics. Estimate summer survival of tagged juvenile coho salmon and compare estimates among spatially, temporally or behaviorally different tag groups. Estimate survival of smolts over river segments as they migrated from rearing areas out of the Shasta River in the spring of 2012. Document and compare growth of physically recaptured individuals from various rearing habitats.	None
Establish & Operated Cooperative Fish & Wildlife Research	March 2017	The objective for this agreement is to create cooperative research for the purpose of developing adequate, coordinated research and education relating to fish and wildlife. This agreement will provide technical and professional education on the graduate and professional levels, in the fields of renewable natural resource sciences. The current projects are Prairie Creek juvenile salmonid abundance study, which continues long-term monitoring of juvenile coho salmon abundance in the Prairie Creek basin, and the "Five basin study", which is attempting to assess the commonality of habitat factors limiting production of juvenile coho salmon on a region-wide scale.	None
Prairie Creek Fisheries and Aquatic Ecosystem Synthesis	September 2015	The 104km2 Prairie Creek watershed is almost entirely situated within Redwood National and State Parks, which is a World Heritage Site and part of the California Coast Range Biosphere Reserve. Although the lower half of the watershed has been impacted by highway construction, timber harvest, and other land use, the creek in the upper watershed flows through undisturbed forest of late seral coast redwood and provides outstanding habitat for fisheries and aquatic resources. The upper watershed often serves as a reference site in studies evaluating land use impacts on aquatic resources. Prairie Creek and its tributaries support populations of Chinook salmon, Coho salmon, steelhead, coastal cutthroat trout and other valued fish and aquatic vertebrates. Many studies of watershed conditions, stream habitat and aquatic resources have been conducted in the Prairie Creek watershed over the last 65 or more years, by diverse groups including university researchers, federal and state agency scientists, and others. Unfortunately much of the data from these studies remain buried in files and reports which are not publicly available. The overall objective of this project is to identify, locate, and compile existing datasets and reports, develop an annotated bibliography, and to synthesize information on fisheries and aquatic resources into a "State of the Knowledge" report. This information will be used to evaluate fisheries health and function of sub-watersheds and guide restoration opportunities/alternatives in lower Prairie Creek. The project encompasses two tasks: data compilation; and development of a synthesis report.	None
Phase II: Monitoring the endangered Tidewater Goby using environmental DNA in water samples: Field tests	June 2019	This project proposes to assess the potential of using environmental DNA in water samples as a tool for monitoring the endangered Tidewater Goby in lagoon and bay habitats. Environmental DNA is a cost-effective and noninvasive technique that has been successfully applied to a broad range of taxonomic groups, including fishes. Studies show that environmental DNA can closely track presence/absence and can be useful for monitoring species that cannot be detected using conventional field approaches. Despite apparent promise, insufficient testing has been conducted to determine the suitability of environmental DNA (eDNA) approaches for monitoring Tidewater Goby. This project has two major phases: 1. develop and test eDNA techniques, and 2. apply eDNA techniques for presence/absence detection in natural settings. This proposal is for the second phase. During this second phase, Humboldt State University and USFWS will collaborate to survey 15 water bodies in northern California to 1. employ traditional field surveys techniques for Tidewater Goby, 2. collect 1-5 water samples from each site and test water samples for tidewater presence/absence of Tidewater Goby DNA, and 3. evaluate suitability of QPCR for determining the presence/absence and/or relative abundance of Tidewater Goby.	This project proposes to assess the potential of using environmental DNA in water samples as a tool for monitoring the endangered Tidewater Goby in lagoon and bay habitats. Environmental DNA is a cost-effective and noninvasive technique that has been successfully applied to a broad range of taxonomic groups, including fishes. Studies show that environmental DNA can closely track presence/absence and can be useful for monitoring species that cannot be detected using conventional field approaches. Despite apparent promise, insufficient testing has been conducted to determine the suitability of environmental DNA (eDNA) approaches for monitoring Tidewater Goby. This project has two major phases: 1. develop and test eDNA techniques, and 2. apply eDNA techniques for presence/absence detection in natural settings. This proposal is for the second phase. During this second phase, Humboldt State University and USFWS will collaborate to survey 15 water bodies in northern California to 1. employ traditional field surveys techniques for Tidewater Goby, 2. collect 1-5 water samples from each site and test water samples for tidewater presence/absence of Tidewater Goby DNA, and 3. evaluate suitability of QPCR for determining the presence/absence and/or relative abundance of Tidewater Goby.
Redwood Creek Life Cycle Monitoring - DIDSON	March 2015	The primary objective of this study is to estimate escapement for three species of ESA listed anadromous salmonids in Redwood Creek, California Chinook salmon (Oncorhynchus tshawytscha), coho salmon (O. kisutch) and steelhead (O. mykiss).	None
Upper and Lower Redwood Creek Juvenile Salmon (Smolt) Abundance Project	March 2017	Redwood Creek supports self-sustaining populations of coho salmon, Chinook salmon, steelhead trout and other native fishes. These salmonids are listed as threatened under the Federal Endangered Species Act and are recognized as being important for recovering populations throughout northern California. This study will determine and track smolt abundances in time and space, estimate abundance structure, collect data on life history attributes, collect genetic samples of smolts and play a key role in the life cycle monitoring station by determining smolt abundances in conjunction with operation of the DIDSON which counts adults entering lower Redwood Creek.	Project objectives for the two trap design include determining smolt population abundances for coho salmon, Chinook salmon and steelhead trout in Redwood Creek in northern California.
Prairie Creek Juvenile Salmonid (Smolt) Abundance Project	March 2017	The Prairie Creek sub-basin of Redwood Creek drains an old growth redwood forest and supports self-sustaining populations of coho salmon, Chinook salmon, steelhead trout and cutthroat throat. These salmonids, with the exception to cutthroat trout, are listed as threatened under the Federal Endangered Species Act. Prairie Creek is a stronghold for coho salmon production within the Redwood Creek basin, and produces more coho salmon than Redwood Creek and other tributaries to Redwood Creek combined. Salmon and steelhead trout within the Prairie Creek sub-basin are recognized as being important for recovery of coho salmon, Chinook salmon and steelhead trout within Redwood Creek. Recently Redwood Creek has been identified as a core stream for coho salmon by NMFS Draft Recovery Plan for SO/NCC coho salmon and implicit in this designation is that Prairie Creek is the core for production of coho salmon within the Redwood Creek basin. The project's objectives will be to 1. determine smolt population abundances for coho salmon, Chinook salmon, steelhead trout and cutthroat trout in Prairie Creek, 2. determine over-winter survival of juvenile coho salmon in Prairie Creek, and 3. incorporate data into Redwood Creek life cycle monitoring project.	Determine smolt population abundances for coho salmon, Chinook salmon, steelhead trout and cutthroat trout in Prairie Creek, determine over-winter survival of juvenile coho salmon in Prairie Creek, and to incorporate data into Redwood Creek life cycle monitoring project.
Genetic Analysis of Tidewater Goby Tissue Samples	May 2014	The tidewater goby (Eucyclogobius newberryi) is a federally endangered fish species ranging from the Smith River in northern California to Agua Hedionda Lagoon in southern California. The tidewater goby inhabits brackish/freshwater lagoons and estuaries that are positioned linearly along the California coast. Lagoons and estuaries inhabited by tidewater goby are separated from one another by 1 - 20 km. Tidewater gobies have no explicit marine stage and ocean inhabitants between these estuaries and lagoons are not inhabited by a stable populations of goby; however, rare periodic migrants occur in ocean habitats. There is only one known record of tidewater goby from coastal oceanic waters. Many coastal lagoons inhabited by tidewater gobies are physically isolated from the ocean by sand bars that rarely open to the ocean (~0 - 5 openings annually) making dispersal into and out of the lagoons contingent upon lagoon openings. Given the fragmented nature of tidewater goby geographic distribution it is convenient to view this species as composed of metapopulations experiencing periodic local extirpation with subsequent recolonization from regional source populations. Currently, there is uncertainty regarding metapopulation dynamics of tidewater goby populations from Humboldt Bay, California. Previous investigations of the federally endangered tidewater goby in the north coast region of California showed that artificially fragmented populations within Humboldt Bay exhibited higher genetic differentiation and lower genetic diversity relative to naturally fragmented populations. It was unclear whether these patterns were the result of multidecadal isolation and lack of migration among geographically separated populations or if periodic recolonization of fragmented habitats combined with founder effects (e.g., metapopulation dynamics) were responsible. Determining which process is operating will provide insights into the extent of migration between discrete and isolated Humboldt Bay tidewater goby populations. Such information is key for management because it would indicate the likelihood of re-colonization of extirpated populations.	The project will be an extension of past work recently published by McCraney et al. (2010). The objective will be to determine levels of genetic diversity, genetic structure, and stability in genetic structure through time (2006 to 2010 or 5 - 6 generations) in the north coast tidewater goby (eucyclogobius newberryi).
Salmon in the Redwood Creek Basin	March 2016	The study will provide information about the spatial distribution and relative abundance of juvenile coho salmon in the Redwood Creek basin by conducting snorkel surveys in sections of stream selected according to a spatially balanced, randomized sampling design. The project design will allow statistical inferences to be made regarding the entire basin based on data collected in the selected survey reaches. The Redwood Creek population of coho salmon was listed as threatened under the Federal Endangered Species Act (ESA) in 1997 and the California Endangered Species Act (CESA) in 2004. To address the ESA listing requirements, the National Marine Fisheries Service (NMFS) classified coho populations into reproductively isolated, evolutionarily important groups called Evolutionarily Significant Units (ESUs). Redwood Creek coho salmon, which have been characterized as a functionally independent population, were included within the Southern Oregon/Northern California (SONCC) ESU. For functionally independent, core populations, NMFS recommends performing juvenile distribution surveys during the initial phase of recovery based monitoring.	The project will evaluate spatial distribution and relative abundance of juvenile coho salmon in the Redwood Creek basin by performing surveys as specifically recommended in the Draft Recovery Plan for Southern Oregon/Northern California Coast Coho Salmon and according to a study design and methods consistent with California Coastal Salmonid Monitoring: Strategy, Design, and Methods (CDFW Fish Bulletin 180). The main goal of this project is to collect scientifically defensible data that can be used with data from existing projects to evaluate the status of coho salmon in the Redwood Creek basin. Information provided by this study will assist planning efforts associated with population recovery and delisting of coho salmon in the Redwood Creek basin
Monitoring the endangered Tidewater Goby using water samples	December 2013	The core objective of the tidewater goby recovery plan is the development of standardized survey methods for population monitoring. We propose assessing the potential of using environmental DNA in water samples as a tool for monitoring the endangered tidewater goby in lagoon and bay habitats. Environmental DNA is a cost-effective and noninvasive technique that has been successfully applied to a broad range of taxonomic groups, including fish. Studies have shown that environmental DNA can closely track presence/absence and can be useful for monitoring species that cannot be detected using conventional field approaches. Despite apparent promise insufficient testing has been conducted to determine the suitability of environmental DNA approaches for monitoring tidewater goby. We propose experiments in controlled conditions to assess the suitability of environmental DNA techniques for tidewater goby presence/absence detection. The future goal is to incorporate environmental DNA into site occupancy modeling design to allow robust monitoring of tidewater goby. This approach has the advantage of costing a fraction of field surveys, eliminates issues thwarting field studied (permits, landowner access, and inaccessibility due to weather), and could be used to monitor tidewater in coastal habitats throughout California.	None
Disease Reduction in Klamath River Salmon	December 2012	Ceratomyxa shasta is a myxozoan parasite of salmonids that produces the disease ceratomyxosis. Infected fish can be found throughout the Klamath Basin but the stage infective to fish appears largely limited to the main stem of the Klamath River. Recent studies monitoring prevalence of selected fish pathogens in smolts sampled during outmigration implicated C. shasta as the direct cause of extensive losses in Chinook salmon. Fott et al. (2002) suggested that ceratomyxosis appeared to be the leading cause of disease and death in juvenile Chinook salmon in the Klamath River estuary during summer of 2001. Williamson and Foott (1998) and Foott et al. (1999) suggested that reduced levels of infection in the Klamath River estuary as compared to the main river was due to death of infected fish prior to reaching the estuary. One management action being considered to control C. shasta in the Klamath Basin is the removal of spawned out carcasses. However, we do not have a very clear understanding as to what this might accomplish. We need to know (1) what percentage of carcasses are infected, (2) if all infected carcasses produce myxospores, (3) when myxospores are released from decaying carcasses, and (4) how many myxospores are produced by a single decaying carcass. The overall goal of this project is to answer some of these questions. With this information we can determine whether or not carcass removal might be an effective management option and how it might best be applied in the Klamath Basin. This information would also be valuable for building a mathematical model that might suggest management strategies that might be successfully in reducing mortalities due of C. shasta in the Klamath River Basin.	Our work suggests that myxospore production in the Klamath River Basin is most related to the number of large, myxospore bearing carcasses present and less related to carcass sex and date. Prevalence of myxospores in a given carcass is strongly tied to location. Thus, overall myxospore production will vary considerably between stretches of river.
Assessing the Benefits of USDA Conservation Programs in the Upper Klamath River Basin and Central Valley of California on Ecosystem Services	June 2015	Deteriorating water quality in Upper Klamath Lake has a negative effect on the entire Klamath Basin ecosystem. Annual cyanobacteria blooms dominated by Aphanozoamenon flos-aquae result in severe dissolved oxygen fluctuations, basic pH, elevated ammonia concentrations and increased levels of algal hepato-toxins. The upper Klamath Basin contains the largest remaining habitat for the federally listed endangered Lost River and shortnose suckers, as well as redband and bull trout. Declining lake water quality has been implicated with juvenile sucker mortality and occasional adult fish kills. Poor water quality in upper Klamath Lake also influences the lower Klamath River, impacting federally listed coho salmon, Chinook salmon and other fish species. Upper Klamath Lake receives over half of its inflow from the Sprague, Williamson and Wood Rivers. Reaches of the Sprague River are listed as impaired under section 303(d) of the Clean Water Act for degraded water quality, which may be associated with increased sediment and phosphorus loading. Although Upper Klamath Lake was historically eutrophic because of phosphorus-rich volcanically derived soils, today Upper Klamath Lake and adjoining Agency Lake are both hyper-eutrophic due to algal blooms from high nutrient loading. The drainage of 10,000 ha of former wetlands that historically surrounded the lake is thought to have contributed to eutrophication. A variety of restoration programs and projects have been implemented along the UKRB to improve the health of the ecosystem. These include Klamath Watershed Partnership assessments of site-specific riparian and upland conditions; USDA administered Wetlands Reserve Program (WRP), Conservation Reserve Program, and Environmental Quality Incentives Program; and USFWS-funded restoration of floodplain connectivity, fence construction for livestock management, and streambank stabilization. These efforts are believed to provide direct and indirect benefits to aquatic ecosystem health. However, their effectiveness at mitigating impacts to water quality and habitat have not been evaluated. In addition, quantification of restoration effects will provide important justification for continued financial and community support in the watershed. Regional climate change models forecast increases in air temperature and changes in precipitation and vegetation patterns in the Klamath River Basin in the future. Summer air temperature was predicted to increase 1.2 - 2.7 degrees C over the next 20-30 years and 3.2 - 6.6 degrees C by 2075. Changes in precipitation are less certain, however, snowpack is expected to decline and summers are expected to be drier than they currently are. The potential impacts to regional water quality and endangered fish populations from climate change are unknown. The objectives of this project are to use the Soil and Water Assessment Tool (SWAT) model to estimate reductions in soil and nutrient loading to Upper Klamath Lake that could potentially be achieved through WRP or other wetland restoration programs in the Upper Klamath River Basin.	None
Upper Redwood Creek Juvenile Salmonid Abundance Project	March 2014	Redwood Creek is one of the major rivers in Humboldt County, California and supports salmon and steelhead trout that are federally listed as threatened under the Endangered Species Act. Redwood Creek is currently listed as sediment and temperature impaired, and various restoration efforts (and plans) in the basin are on-going. Prior to this study there was no information on the population size of anadromous salmonids (adults or juveniles) utilizing upper to middle Redwood Creek. This juvenile smolt abundance study is a cooperative effort with California Department of Fish and Game (CDFG), Redwood Creek Landowners Association (RCLA), Doug Parkinson and Associates, and the private landowner where the trap is located. Redwood National Park (RNP) also assists our study via their estuary sampling. This study was designed to be long term, and collects data that can be used to assess watershed conditions and restoration activities. This project's main focus is to continue collecting data to determine the current population size, status, and trends of salmon (Coho, Chinook), cutthroat trout, and steelhead trout in middle to upper Redwood Creek in relation to restoration activities and current habitat conditions.	None
The Role of Barriers in the Conservation of McCloud Redband Trout	August 2011	In 1994, the U.S. Fish and Wildlife Service determined that potential threats to the McCloud River redband trout (Oncorhynchus mykiss spp.) and its habitat were sufficient to warrant classification as a Candidate species under the federal Endangered Species Act of 1973, as amended. This status reflected concern over threats to its genetic integrity from genetic introgression with stocking of hatchery strains of rainbow trout. In 1998, a multiple-signatory conservation agreement was established to ensure that steps are taken to reduce or remove threats that could cause it to be listed as threatened or endangered. Due to commitments made to protect and conserve McCloud redband through this agreement, candidate status was discontinued in 2000. Among potential strategies to achieve conservation goals is isolation management, employing the use of natural or artificial barriers to protect upstream populations from direct contact with hatchery or exotic salmonids. This approach has been adopted for other threatened species or populations, and may be particularly appropriate in river ecosystems where movement corridors are well-defined and animal passage easier to control. The success of this approach hinges on providing sufficient resources in the isolated reach to meet all life history requirements, as well as on maintenance of a sufficiently large population to promote long-term persistence. To assist in conservation efforts, this study seeks to explore the feasibility of adopting an isolation management strategy for redband trout by identifying barriers and evaluating their functional roles in streams within its established refugium. With a goal of evaluating the potential effectiveness of isolation management as a conservation strategy for redband trout populations, the objective of the proposed research are: 1) to identify existing and potential barriers in selected streams within the established redband trout refugium, and to establish the range of flows within which barriers are operational; and 2) to evaluate the extent to which an existing barrier in Moosewood Creek limits redband trout productivity in the isolated section and/or protects if from threats imposed by the presence of hatchery or exotic salmonids. Implications of the study to redband trout populations in Sheepheaven Creek, recently identified as the primary location of the source population, will be explored.	Existing and potential barriers to fish movement were located, habitat was evaluated and minimum stream lengths required to maintain genetically viable populations of McCloud River redband trout (Oncorhynchus mykiss spp) were estimated in two streams, Trout and Tate creeks, in the upper McCloud River basin in northern California. The goal of this research was to evaluate the potential effectiveness of isolation management to protect and restore populations of redband trout. Minimum stream length requirements were based on reach-scale estimates of fish density and survival. Population estimates were obtained using a modification of the Hankin and Reeves (1988) approach and from spotlight surveys. Redband trout were the only salmonid species observed in Trout Creek while Tate Creek contained redband trout and brook trout (Salvelinus fontinalis). Redband trout densities in summer 2009 were approximately 378 km-1 and 652 km-1 in Trout and Tate creeks respectively. Estimates of minimum stream length needed to maintain a population of 2,500 individuals with densities observed in 2009 ranged from 7.35 to 13.23 km on Trout Creek and from 4.26 to 7.67 km on Tate Creek. Abundance differences in streams were probably due to availability of warm, retentive, high productivity habitat in the lower reaches of the larger Tate Creek watershed. Trout Creek was determined to be a poor candidate for deliberate isolation because a percolation barrier isolates it from the upper McCloud River and further barriers would fragment already limited habitat. Although trout from the lower reach of Tate Creek showed morphological evidence of hybridization, the stream supported a higher trout density and available habitat exceeded estimated minimum stream length. As such, it may represent a viable isolation candidate, with sufficient resources to support growth of translocated populations with greater genetic purity. Existing culverts on both streams do not appear to significantly fragment habitat.
Lower Redwood Creek Juvenile Salmonid Abundance Project	March 2014	Redwood Creek is one of the major rivers in Humboldt County, California and supports salmon and steelhead trout that are federally listed as threatened under the Endangered Speicies Act. Redwood Creek is currently listed as sediment and temperature impaired, and various restoration efforts (and plans) in the basin have occurred, or on-going. Prior to this study there was little to no information on the population size of anadromous salmonids (adults or juveniles) utilizing the majority of the Redwood Creek basin. For the past five years we have successfully determined smolt population estimates for listed salmonid species migrating to the ocean from the majority of the Redwood Creek watershed; the production that we are missing (Prairie Creek watershed) is monitored by Humboldt State University. This study is a cooperative effort with California Department of Fish and Game (CDFG), Redwood National Park (RNP), the landowner where the trap is located, and trapping efforts in the upper basin (Redwood Creek Landowners Association, CDFG, and Fisheries Restoration Grant Program). RNP assists this study via estuary sampling. This study was designed to be long term, and collects data that can be used to assess watershed conditions and restoration activities.	None
Prairie Creek Sub-Basin Life Cycle Monitoring Project, 2011	March 2014	The Prairie Creek sub-basin of Redwood Creek supports self-sustaining populations of coho salmon, Chinook salmon, steelhead and coastal cutthroat trout in addition to occasional chum salmon. It was recognized as an excellent "field laboratory" for the study of andromous salmonids in California by the Coastal Watershed Planning and Assessment Program (Cannata et al. 2006). Studies of fisheries in the Prairie Creek sub-basin began in the late 1940's and extend to the present. Nearly continuous estimates of adult salmon returning to Prairie Creek have been made since 1990, while estimates of juvenile abundance and smolt production have been made each year since 1998. This project is a monitoring project and will not remediate limiting factors for salmonids. However, as anticipated by Recovery Strategy for California Coho Salmon (CDFG 2004), monitoring is necessary to track the performance of recovery efforts, to follow trends in population status and identify benchmarks for delisting. One element of the monitoring envisioned in California was the establishment of watersheds where the complete life cycle could be monitored. The Prairie Creek sub-basin of Redwood Creek offers the opportunity to establish such a life cycle monitoring program. First, the sub-basin supports self-sustaining populations of coho salmon, Chinook salmon, steelhead and costal cutthroat trout. Second, historical data on sub-basin fisheries is available. Third, data gathered continuously over the past decade is of high quality and could be used immediately in a monitoring framework. Fourth, land use within the basin will not change since 98.2 percent of the sub-basin is in state or federal ownership. Last, the largest land holder, Redwood National Park, is committed to restoring watersheds and protecting fish populations.	None
Prairie Creek Sub-Basin Life Cycle Monitoring Project	March 2012	The Prairie Creek sub-basin of Redwood Creek supports self-sustaining populations of coho salmon, Chinook salmon, steelhead and coastal cutthroat trout in addition to occasional chum salmon. It was recognized as an excellent "field laboratory" for the study of andromous salmonids in California by the Coastal Watershed Planning and Assessment Program (Cannata et al. 2006). Studies of fisheries in the Prairie Creek sub-basin began in the 1940's (Hallock 1952, Brigss 1953) and extend to the present (Duffy and Bjorkstedt 2007). Nearly continuous estimates of adult salmon returning to Prairie Creek have been made since 1990 while estimates of juvenile abundance and smolt production have been made each year since 1998. The Prairie Creek sub-basin may be considered as a life cycle monitoring station in the California Anadromous Salmonid Monitoring Plan for several reasons. First, it supports self sustaining populations of coho and Chinook salmon, steehead and coastal cutthroat trout. Second, stream habitats in the sub-basin are relatively undisturbed, although portions of the basin flow through park lands representative of northern California coastal streams and land use will not likely change in the future. Three primary tasks this project will continue are monitoring to estimate the annual abundance of: (1) Adult coho salmon, Chinook salmon, steehead and coastal cutthroat trout. (2) Juvenile coho salmon, ssteelhead and coastal cutthroat trout. (3) Migrating coho salmon, steelhead and coastal cutthroat smolts as well as pre-smolting Chinook salmon. (4) Write report analyzing trends in salmonid abundance and survival in Prairie Creek over the previous decade.	None
Polychaete Laboratory Work	May 2011	Fish diseases are widespread in the mainstream Klamath River and strong evidence suggests that disease levels are adversely affecting the freshwater production of salmonid fishes. In recent years, researchers have documented large numbers of emigrating juvenile Chinook salmon and coho salmon infected by one or both myxosporen parasites - Ceratomxya shasta and Parvicapsula minibicornis. The high infectivity rates observed in native salmonid species in the Klamath River suggests a parasite-host imbalance where environmental conditions have favored these parasites. Lifecycles of C. shasta and P. minibicornis are complex, but both parasites are dependent on the freshwater polychaete worm Manayunkia speciosa, and on salmonid fishes as alternate hosts to perpetuate their life cycle. Potential management strategies to reduce disease prevalence have centered on identifying factors that may interrupt some segment of the parasite lifecycles in order to bring the parasite-host equilibrium back into balance. Whereas several studies have examined factors affecting fish infectivity within the Klamath River basin, studies on the ecology, distribution, abundance, and infection prevalence of the polychaete host are in their infancy. Polychaete colonies exhibit a patchy distribution within the Klamath River and occur in low velocity areas comprised of sand-silt embedded with fine organic matter. The polychaete also often occurs in association with mats of filamentous algae, particularly Cladophora, and beds of vascular plants. In addition to further study of polychaete life history and factors limiting their distribution, there is a critical need to more accurately and further document the infection prevalence of polychaete populations throughout the Klamath River mainstem before proceeding to develop or implement management strategies.	None
Evaluating Dynamics of Grassland and Wetland Ecosystems in the Northern Great Plains	December 2015	The U.S. Geological Survey (USGS), Northern Prairie Wildlife Research Center (NPWRC) is engaged in an on-going research effort to better understand grassland, wetland and riverine ecosystems and their associated biotic communities in the northern Great Plains (NGP). NPWRC's research programs specifically focus on identifying and understanding threats to NGP ecosystems and developing and evaluating conservation measures that abate those threats. Examples of threats of current concern are climate change, invasive plant and animal species, runoff of chemicals and sediments, and landscape modification to support agriculture, and habitat fragmentation. Moreover, many threats to ecosystems and populations can interact; for example there is concern that landscape modifications, climate change, and invasive species have interacting effects upon ecosystem health and services. The proposed effort will allow collaboration with NPWRC to expand research efforts in these diverse prairie ecosystems.	None
Production of myxospores of Ceratomyxa shasta in Chinook salmon carcasses	September 2011	Ceratomyxa shasta is a myxozoan parasite of salmonids that produces the disease ceratomyxosis. Infected fish can be found throughout the Klamath Basin but the stage infective to fish appears largely limited to the main stem of the Klamath River (Hendrickson et al. 1989, Stocking et al. 2006). Recent studies monitoring prevalence of selected fish pathogens in smolts sampled during outmigration implicated C. shasta as the direct cause of extensive losses in Chinook salmon (Williamson and Foott 1998, Foott et al. 1999, 2002, 2003). Foott et al. (2002) suggested that ceratomyxosis appeared to be the leading cause of disease and death in juvenile Chinook salmon in the Klamath River and estuary during summer of 2001. Williamson and Foott (1998) and Foott et al. (1999) suggested that reduced levels of infection the the Klamath River estuary as compared to the main river was due to death of infected fish prior to reaching the estuary. One management action being considered to control C. shasta in the Klamath Basin is the removal of spawned out carcasses. However, we do not have a very clear understanding as to what this might accomplish. We need to know (1) what percentage of carcasses are infected, (2) if all infected carcasses produce myxospores, (3) when myxospores are released from decaying carcasses, and (4) how many myxospores are produced by a single decaying carcass. The overall goal of this project is to answer some of these questions. With this information we can determine whether or not carcass removal might be an effective management option and how it might best be applied in the Klamath Basin. This information would also be valuable for building a mathematical model that might suggest management strategies that might be successful in reducing mortalities due of C. shasta in the Klamath River Basin.	None
Redwood Creek Life Cycle Monitoring - DIDSON	March 2014	The Redwood Creek watershed in Humboldt County is considered an important watershed for anadromous salmonids in northern California. It supports self-sustaining populations of coho salmon, Chinook salmon, steelhead and coastal cutthroat trout in addition to other native fishes. There are no hatcheries in the watershed, although hatchery stocks of salmon and steelhead do stray into the stream each winter. Salmon and steelhead in the Redwood Creek watershed are recognized as important for recovering populations of anadromous salmonids throughout northern California (Cannata et al. 2006). The pattern of land ownership within the Redwood Creek watershed presents opportunities for restoration. Ninety-six percent of the land area of the lower basin is in state and federal park ownership, and watershed restoration is being actively implemented on these lands. Although 51% of the upper basin is in private ownership, a small number of land owners control most of these lands making restoration planning simpler than in watersheds having complex ownership patterns. Watershed restoration actions have and are also being implemented in the upper watershed. An understanding how the environmental influences salmon and steelhead is necessary to inform restoration actions. The environmental influences on salmon and steelhead include those operating on freshwater environments as well as on marine environments. Understanding the response of salmon and steelhead to these factors requires monitoring of at least two life stages. Due to its size and compliment of ssteelhead and salmon species, Redwood Creek offers opportunities for monitoring and developing techniques for monitoring. The Redwood Creek watershed, at 285 m2, is representative of northern California watersheds, being near the median size of rivers in the SONCC coho domain. It is large enough to support a diversity of species of salmonids, with some having moderate population size. It is also large enough to present challenges in monitoring fish populations. Our objective is to monitor escapement of adult salmon and steelhead to Redwood Creek. Escapement estimates will be made using dual frequency identification sonar (DIDSON) imaging system.	None
Myxozoan Fish Disease Research and Monitoring	December 2012	The freshwater polychaete Manayunkia speciosa is the intermediate host for two myxozoan parasites (Ceratomyxa shasta and Parvicapsula minibicornis) that infect and cause mortality in out-migrating juvenile salmon in the Klamath River. Studies have established that the polychaete populations in the lower Klamath River are patchily distributed but concentrated below Iron Gate Dam, where they are usually associated with organically-rich fine sediments that accumulate within beds of Cladophora and other macrophytes, or in epilithic biofilms (Stocking and Bartholomew 2007, Wilzbach and Cummins 2009). Increased abundance of the worm below Iron Gate Dam, particularly in the stretch of river between the Shasta and Scott Rivers, coincides with the section of river that has been found to be highly infectious for salmonids (e.g. Bartholomew et al. 2007, Hallett and Bartholomew 2006). Polychaete densities have been found to be highly variable among seasons and years, and are likely strongly affected by hydrologic events and sediment transport. M. speciosa is small, reaching a maximum body length of only 4 mm, and it lacks morphological structures for directing its movement within the water column or for anchoring itself to the substrate. Because of its small size and morphological features, the polychaete is likely susceptible to displacement at high flows and mortality from bedload movement or sediment abrasion. Recognition of the probable importance of flow and sediment dynamics in affecting distribution and abundance of polychaete populations has generated keen interest among scientists and managers in the potential for using flow and sediment manipulations as a strategy for reducing polychaete populations to enhance salmon survival. Reduction in densities of infected polychaetes would result in reduced production of the parasitic actinospores that are infectious to fish, and thus disrupt disease dynamics. One strategy that has been proposed for impacting polychaete populations has been gravel augmentation. Gravel would be introduced upstream of dense patches of polychaetes where increased flows would move the bedload over the patches. Flow and sediment manipulations, however, are likely to be effective only if polychaetes are killed by the manipulations rather than simply re-distributed as viable animals elsewhere within the system. Effects of varying velocities and particle sizes of transported sediments on viability and displacement of the polychaete are unknown.	We quantified micro-scale flow forces and their ability to entrain the freshwater polychaete, Manayunkia speciosa, which is the intermediate host for two myxozoan parasites (Ceratomyxa shasta and Parvicapsula minibicornis) that cause substantial mortalities in salmonid fishes in the Pacific Northwest. In a laboratory flume, we measured the shear stress associated with two flow levels and three substrates and quantified associated dislodgement of polychaetes, evaluated survivorship of dislodged worms, and observed behavorial responses of the worms in response to increased flow. Logistic regression modeling was used to evaluate the probability of worm dislodgement for treatment combinations of velocity (mean flow velocity of 55 cm/s with a shear velocity of 3 cm/s, and mean flow velocity of 140 cm/s with a shear velocity of 5 cm/s) and substrate type (depositional sediments and analogues of rock faces and filamentous alga, Cladophora). Few worms were dislodged at shear velocities below 3 cm/s on any substrate. Above this level of shear, probability of dislodgement was strongly affected by both substrate type and velocity. After accounting for substrate, odds of dislodgement were 6x greater at the higher flow. After accounting for velocity effects, probability of dislodgement was greatest from fine sediments, intermediate from rock faces, and negligible for Cladophora. Survivorship of dislodged polychaetes was high. Observations revealed that polychaetes exhibited a variety of behaviors for avoiding increases in flow, including extrusion of mucus, burrowing into sediments, and movement to lower flow microhabitats. Taken together, our findings suggest that polychaete populations likely exhibit high resiliency to flow-mediated disturbance events.
Effects of conservation programs on amphibian communities in seasonal wetlands of the Prairie Pothole Region's glaciated plains	June 2008	Human perturbations have altered the health and sustainability of modern ecosystems. In the Prairie Pothole Region of North America, an area of considerable value to wildlife and agriculture, the primary human perturbation has been land development to facilitate agriculture production. In response to concern regarding the fate of fish and wildlife habitat and various ecosystem functions (e.g. water quality, sediment and chemical infiltration, erosion, nutrient transport, floodwater retention, ground-water recharge and biological diversity), private and governmental entities have implemented numerous conservation programs to restore basic ecosystem services within the modern agricultural landscape.	None
Klamath REMS, Fisheries	September 2013	Declining populations of Pacific salmon (Oncorhynchus spp.) in the Klamath River have led to concerns about water quality in the river. Water temperature in the river during summer months often approaches or exceeds physiological tolerance limits of most Pacific salmon species. Reliance of these fish on cold water has been studied extensively. While temperatures at which the physiological performance of Pacific salmon is optimal is typically 14.0 - 17.0 o C, salmon are also frequently are found occupying habitats where water temperatures reach 23.0 - 24.0 o C on a daily basis. Much of the variation in tolerance to warmer water temperature in Pacific salmon is attributed to acclimation temperature. In the Klamath River, water temperature regularly exceeds 25.0 o C during July and August. Pockets of cool water that form at tributary mouths are believed to be critical to the survival of Pacific salmon during these periods. Re-analysis of data gathered by the Yurok Tribe during 1998 confirms use of cold water patches at temperatures > 22.0 o C, but also reveals a strong temporal component in use. Furthermore, spatial distribution of refuges having high abundance (> 1000 juvenile Chinook salmon) are clumped at a few stream mouths. The periodicity in heavy use of cold water patches by Chinook salmon and their spatial clumping at limited sites suggest that habitat selection is governed by more than water temperature alone. The objectives of this study are: 1) To determine if juvenile Chinook salmon and steelhead use cold water patches in the Klamath River preferentially over other habitats. 2) To determine if juvenile Chinook salmon and steelhead use specific cold water patches in the Klamath River for extended periods or for short periods during migration. 3) To determine the physiological benefit of cold water refuges to juvenile Chinook salmon and steelhead in the Klamath River.	None
Assessing the effects of USDA conservation practices on wetland ecosystem services in CA's Central Valley	August 2011	The California Central Valley (CCV) was historically an ecosystem consisting of grassland, prairie, and oak-grass savanna habitats. Interspersed within these primary habitats were riparian woodland, freshwater marsh, and vernal pool wetlands. These wetlands were integral in supporting the diverse flora and fauna of the historic CCV. Riparian forest wetlands supported many neotropical migratory birds, Chinook salmon and other woodland associated species. Freshwater marshes in the CCV once supported enormous populations of wintering waterfowl, while vernal pool wetlands supported unique plant and invertebrate communities. Most, if not all, these habitats in the CCV have been altered by human activity. Area of wetland habitats in the CCV prior to 1900 has been estimated to be 1.6-2.0 million ha. In the 1980's, wetland area in the CCV had been reduced to 153,000 ha. Human activities leading to wetland loss in the CCV are many and varied, but agricultural development and urbanization are chief among them. The USDA, Natural Resource Conservation Service (NRCS) administers a variety of programs intended to assist farmers and ranchers in addressing natural resource concerns on private lands. Among these programs is the Wetland Reserve Program (WRP) which focuses on restoring degraded wetlands or those that have been converted to agricultural production. In California, NRCS has focused their WRP activities on restoring a variety of wetlands, including seasonal wetlands, semi-permanent marshes, vernal pools, riparian and tidally-influenced wetlands. Recent information suggests that at least 52 CCV wetlands totaling more than 11,000 ha have been at least partially restored. The NRCS initiated an assessment of the effects of conservation practices on wetland ecosystem services. This conservation effects assessment of wetland ecosystems (CEAP-Wetlands) objectives are to: Produce estimates of wetland ecosystem services, Quantify effects (of agriculture on wetlands), with and without implementation of USDA conservation practices, Develop predictive wetland functional condition indicator models, Quantify and compare effects of alternative environmental or program scenarios on regional wetland services, and Develop scientific and technological tools that improve the sustainability of wetlands on agricultural landscapes. CEAP-Wetland assessments will be conducted in 10 regions throughout the coterminous United States (USDA-NRCS 2006) and the CCV is one of these regions. The research described here supports the CEAP-Wetland assessment in the CCV. Objectives: 1. Organize and conduct a regional workshop involving multiple agencies and collaborators. The purpose of this workshop will be to identify ecosystem functions and services most important in CCV wetlands. 2. Complete preliminary research to identify and select wetland assessment sampling sites to be used in a CCV wetlands assessment. 3. Develop a study plan for completing a CEAP-Wetlands assessment of the CCV.	None
Research and development of a suitable method for estimating weekly-stratified abundances of migrating juvenile salmonids in the absence of mark-recpature experiments	January 2026	This project will develop new methods for computing statistically valid abundance estimates without mark-recapture data. Innumerable fish monitoring projects rely upon mark-recapture data to track various population metrics, such as long-term trends in abundance, fish health, and outmigration timing. However, marking and recapturing fish is an invasive process that causes fish stress. Furthermore, this becomes more difficult as populations decline and become threatened and endangered. The objective of this study is to develop new methods for estimating abundances that does not depend on mark-recapture data. These methods must be biologically and technically sound, since these monitoring data are often subject to intense scrutiny and relied on in court cases.	For several decades, the U. S. Fish and Wildlife Service (USFWS) has been working in close collaboration with tribal partners to run juvenile salmonid outmigration monitoring stations on the Klamath and Trinity rivers of north-western California. The monitoring stations employ the use of rotary screw traps that capture juvenile salmonids during their seasonal emigration from, or spatial redistribution within, the Klamath Basin. The various data products generated from this monitoring program are evaluated to track long-term trends in abundance, fish health, and outmigration timing, and provide vital real-time status data to inform water management decision making in a landscape with many interests competing for scare water resources. The annual outmigrant abundance estimates generated by this study have also been relied on extensively in various court documents and mandates (i.e. population-level prevalence of infection, 80% outmigration date predictor, etc.), particularly with regard to the Service’s use of the estimates in calculating population-level effects of disease and mortality of juvenile Chinook and Coho salmon in the Klamath River. In recent years, adult returns of fall-run Chinook Salmon have been so low that Iron Gate Hatchery has not been able to meet its annual egg take goal, resulting a dramatic reduction in hatchery production. Given this trend, it is becoming increasingly likely that there will not be a sufficient number of hatchery fish available to meet the defined mitigation goals of the hatchery program, as well as to provide hatchery fish for the mark-recapture experiments. Additionally, four dams on the Klamath River mainstem are slated for removal that is tentatively proposed to occur in January 2023. A hatchery associated with one of these dams will also be decommissioned. Hence, regardless of the abundance of returning adult salmon stocks in the near future, it is assured that there will not be a sufficient number of hatchery fish available to conduct the mark-recapture experiments needed to estimate annual abundance of outmigrating juvenile salmonids. Given the importance of the estimates generated from this monitoring program, it is essential that a new method for computing statistically valid abundance estimates be developed that is biologically and technically sound, cost efficient to implement, and externally peer reviewed. The objective of this study is to develop this new methodology for estimating abundances that does not depend on the availability of hatchery fish for mark-recapture experiments.
Using environmental DNA to monitor abundances of juvenile Central Valley Chinook salmon	December 2023	The Sacramento River is unique in that it supports four different ecotypes of Chinook salmon, <i>Oncorhynchus tshawytscha</i>, including spring, fall, late fall, and winter runs. Unfortunately, due to a combination of anthropogenic actions the spring and winter runs are listed as threatened and endangered, respectively. Monitoring for juveniles in these imperiled populations on the Sacramento River uses a network of monitoring sites with varying reliability. In the upper river, a rotary screw trap located at the Red Bluff Diversion Dam can produce population-level abundance estimates for juvenile Chinook salmon. However, in the lower river monitoring sites are unable to produce population-level abundances due to the unreliability of run identification, low juvenile catch rates, and the inability to estimate gear efficiencies. Environmental DNA (eDNA) techniques could be used to more effectively sample in the lower river, where salmon densities are lower. This data would ultimately facilitate a better understanding of the timing, survival, abundance, and movement of juvenile Chinook Salmon throughout the river. <br><br>This research will focus on utilizing eDNA to develop a quantitative method for estimating juvenile Chinook salmon abundance in the Sacramento River. We will be looking at the correlation between eDNA concentrations and juvenile out-migrating trap abundances at the Red Bluff Diversion Dam site. Ideally, out of the four run types of Chinook salmon in the Sacramento River the focus will be on the spring and winter run types. In addition to the correlation between eDNA concentrations and abundance, we will examine if these eDNA abundances estimates are a function of environmental covariates (i.e. temperature, flow, turbidity, etc).<br>	The Sacramento River is unique in that it manages four different ecotypes of Chinook salmon (i.e., spring run, fall run, late-fall run, and winter run) each exhibiting varying life history traits consisting of the timing of adult immigration, spawning, juvenile rearing, and smolt outmigration. Over the past century, multiple anthropogenic stressor have contributed to the decline of these populations, resulting in two ecotypes being ESA listed. We will develop a system specific environmental DNA calibration curve for threatened and endangered salmon in California's Central Valley that will be a cost-effective technique to modernize sampling methods and provide water managers with valuable information necessary to prevent excess mortality of these fish. This project is a collaboration between Humboldt State University, the US Fish and Wildlife Service, U.S. Bureau of Reclamation, and the California Department of Fish and Wildlife.
Using genomics to elucidate local adaptation among isolated populations of the endangered tidewater goby	December 2022	This study will conduct genome scans of tidewater goby (<i>Eucyclogobius newberryi</i>) from across the geographic range of the species to determine if there is evidence of local adaptation. Local adaptation is defined as when populations of a species have evolved higher fitness in a local environment than other members of the same species. Using the first ever de novo genome assembly that we will develop for tidewater goby, we will compare tidewater goby samples from the extremes of geographic range (3 populations from northern and southern California, respectively) for evidence of local adaptation. For this project, we will partner with researchers at Humboldt State University and the University of California Los Angeles. Determining if tidewater goby exhibit local adaptation is important for conservation and management because this information is needed to determine if isolated tidewater goby populations warrant recognition as conservation units. Also, this information is needed to inform reintroduction or augmentation programs and assess the extent that tidewater goby populations will be able to respond to climate change.	This study will conduct genome scans of tidewater goby (<i>Eucyclogobius newberryi</i>) from across the geographic range of the species to determine if there is evidence of local adaptation. Local adaptation is defined as when populations of a species have evolved higher fitness in a local environment than other members of the same species. Using the first ever de novo genome assembly that we will develop for tidewater goby, we will compare tidewater goby samples from the extremes of geographic range (3 populations from northern and southern California, respectively) for evidence of local adaptation. For this project, we will partner with researchers at Humboldt State University and the University of California Los Angeles. Determining if tidewater goby exhibit local adaptation is important for conservation and management because this information is needed to determine if isolated tidewater goby populations warrant recognition as conservation units. Also, this information is needed to inform reintroduction or augmentation programs and assess the extent that tidewater goby populations will be able to respond to climate change.
Development of environmental DNA assays for Central Valley Chinook salmon ecotypes	December 2020	The objective of this project is to develop a CRISPR assay to differentiate between the four Central Valley Chinook (CVC) salmon ecotypes using environmental DNA methods. Two of the four CVC salmon ecotypes (winter, spring, fall, and late-fall) are listed on the Endangered Species Act as either threatened or endangered, and this project will make use of an existing DNA alignment of whole genome sequence data from 128 Chinook salmon representative of all four Chinook salmon run-time ecotypes. It is hoped that by screening such a large extent of genomic variation we will be able to identify a sequence region suitable for development of an eDNA assay that is specific for the endangered winter-run Chinook salmon. By using CRISPR technology, instead of quantitative PCR (qPCR), we have the potential advantage of differentiating between closely related species due to the three levels of sequence complementarity required. To achieve this goal, we will partner with researchers at NOAA and Humboldt State University. This study will develop a method to quickly and efficiently identify winter-run rearing habitats, and when they outmigrate from the Sacramento River, which will greatly improve the ability of managers to conserve this species.	The objective of this project is to develop a CRISPR assay to differentiate between the four Central Valley Chinook (CVC) salmon ecotypes using environmental DNA methods. Two of the four CVC salmon ecotypes (winter, spring, fall, and late-fall) are listed on the Endangered Species Act as either threatened or endangered, and this project will make use of an existing DNA alignment of whole genome sequence data from 128 Chinook salmon representative of all four Chinook salmon run-time ecotypes. It is hoped that by screening such a large extent of genomic variation we will be able to identify a sequence region suitable for development of an eDNA assay that is specific for the endangered winter-run Chinook salmon. By using CRISPR technology, instead of quantitative PCR (qPCR), we have the potential advantage of differentiating between closely related species due to the three levels of sequence complementarity required. To achieve this goal, we will partner with researchers at NOAA and Humboldt State University. This study will develop a method to quickly and efficiently identify winter-run rearing habitats, and when they outmigrate from the Sacramento River, which will greatly improve the ability of managers to conserve this species.
Integration of molecular methods into predator diet analysis to advance understanding of juvenile Chinook salmon predation mortality in the Delta	December 2022	The objective of this project is to measure the detectability half-life of juvenile Chinook Salmon DNA within the digestive tract of two common predators in the Sacramento-San Joaquin Delta and use this information to compare consumption estimates based on visual and molecular analyses from field collected stomachs. High mortality rates of juvenile Chinook in the Sacramento – San Joaquin Delta have been considered a result of non-native species predation on migrating smolts. Although this is the most common hypothesis, it has been difficult to test because predator stomach contents quickly becomes unidentifiable. In contrast, molecular analyses of gut content can identify species and estimate number of individuals in a mixture for a longer duration. For this project, we have partnered with researchers at the University of California Davis, USGS, and NOAA. The results from this project will provide information necessary to assist managers in understanding the impact of predation on salmon populations in the Delta. This is extremely valuable, since it has been difficult to quantify the effect of these predators on the population level.	The objective of this project is to measure the detectability half-life of juvenile Chinook Salmon DNA within the digestive tract of two common predators in the Sacramento-San Joaquin Delta and use this information to compare consumption estimates based on visual and molecular analyses from field collected stomachs. High mortality rates of juvenile Chinook in the Sacramento – San Joaquin Delta have been considered a result of non-native species predation on migrating smolts. Although this is the most common hypothesis, it has been difficult to test because predator stomach contents quickly becomes unidentifiable. In contrast, molecular analyses of gut content can identify species and estimate number of individuals in a mixture for a longer duration. For this project, we have partnered with researchers at the University of California Davis, USGS, and NOAA. The results from this project will provide information necessary to assist managers in understanding the impact of predation on salmon populations in the Delta. This is extremely valuable, since it has been difficult to quantify the effect of these predators on the population level.
Standardizing Environmental DNA methodologies for Coho Salmon	December 2023	This research is designed to provide guidance for the application of environmental DNA (eDNA) approaches for monitoring the presence, distribution, and abundance of Coho Salmon. While eDNA has the potential to revolutionize our ability to detect fish and to conduct monitoring in larger areas with higher efficiency and lower cost, it is not generally applied in standardized survey protocols developed by federal and state regulatory agencies. The initial steps involve conducting a series of laboratory and field experiments to study the ecological dynamics of eDNA, such as production, decay, and transit rates. Using the information from these initial experiments, a predictive statistical model will be developed and applied for estimating local- and broad-scale species distribution and abundance in river networks using eDNA. We are partnering with the California Department of Transportation and Humboldt State University for this project. Federal and state resource management and conservation groups will benefit from the development of eDNA approaches that allow efficient and high accuracy predictions of species geographic distribution at local- and broader scales that are not achievable using currently applied field approaches. Development of eDNA distribution and monitoring methodologies will enable efficient, no-take approaches to establish environmental baseline conditions at culvert and bridge project sites, evaluate mitigation for project impacts, and demonstrate the efficacy of mitigation projects in aquatic habitats and at fish passage remediation project locations.	This research is designed to provide guidance for the application of environmental DNA (eDNA) approaches for monitoring the presence, distribution, and abundance of Coho Salmon. While eDNA has the potential to revolutionize our ability to detect fish and to conduct monitoring in larger areas with higher efficiency and lower cost, it is not generally applied in standardized survey protocols developed by federal and state regulatory agencies. The initial steps involve conducting a series of laboratory and field experiments to study the ecological dynamics of eDNA, such as production, decay, and transit rates. Using the information from these initial experiments, a predictive statistical model will be developed and applied for estimating local- and broad-scale species distribution and abundance in river networks using eDNA. We are partnering with the California Department of Transportation and Humboldt State University for this project. Federal and state resource management and conservation groups will benefit from the development of eDNA approaches that allow efficient and high accuracy predictions of species geographic distribution at local- and broader scales that are not achievable using currently applied field approaches. Development of eDNA distribution and monitoring methodologies will enable efficient, no-take approaches to establish environmental baseline conditions at culvert and bridge project sites, evaluate mitigation for project impacts, and demonstrate the efficacy of mitigation projects in aquatic habitats and at fish passage remediation project locations.
Modeling the density of a parasite impacting salmonids in the Klamath River	November 2023	The objective of this project is to generate a predictive model of weekly waterborne <i>Ceratonova shasta </i>parasite spore density to improve estimates of mortality risk for juvenile salmonids in the Klamath River. <i>C. shasta </i>is a parasite endemic to the Klamath River basin that has been linked to population declines in native salmonids. High densities of waterborne spores of the parasite are known to cause increasing infection and mortality risk for juvenile salmonids. A recently constructed population dynamics model for Klamath River salmonids, the Stream Salmonid Simulator (S3 model), includes a sub-model to simulate <i>C. shasta </i>disease and mortality risk for outmigrating juveniles in response to potential management alternatives. We have partnered with the U.S. Fish and Wildlife Agency for this project. Developing models that are able to better estimate mortality risk for juvenile salmonids will provide a means to incorporate these models into the S3 model. This then provides an adaptive management tool for managers to understand how different management decisions (e.g. flow) might affect the population.	The objective of this project is to generate a predictive model of weekly waterborne <i>Ceratonova shasta </i>parasite spore density to improve estimates of mortality risk for juvenile salmonids in the Klamath River. <i>C. shasta </i>is a parasite endemic to the Klamath River basin that has been linked to population declines in native salmonids. High densities of waterborne spores of the parasite are known to cause increasing infection and mortality risk for juvenile salmonids. A recently constructed population dynamics model for Klamath River salmonids, the Stream Salmonid Simulator (S3 model), includes a sub-model to simulate <i>C. shasta </i>disease and mortality risk for outmigrating juveniles in response to potential management alternatives. We have partnered with the U.S. Fish and Wildlife Agency for this project. Developing models that are able to better estimate mortality risk for juvenile salmonids will provide a means to incorporate these models into the S3 model. This then provides an adaptive management tool for managers to understand how different management decisions (e.g. flow) might affect the population.
Large wood restoration effectiveness for salmonids in Pudding Creek, California: A before-after-control-impact experiment	June 2021	The object of this project is to evaluate the growth and survival response of endangered Central California Coast Coho Salmon (<i>Oncorhynchus kisutch</i>) and threatened Northern California steelhead (<i>Oncorhynchus mykiss</i>) to large woody debris (LWD) treatments on Pudding Creek in Fort Bragg, California using a before-after-control-impact design. This analysis comes from data collected in a Before-After-Control-Impact (BACI) study initiated in 2012 based on monitoring salmon populations on both Caspar and Pudding creeks. In 2015, LWD was strategically placed in 80% of mainstem Pudding Creek while Caspar Creek was the untreated control. The standardized mean abundance estimates of Coho Salmon parr captured in outmigrant traps followed a similar trend in both creeks, suggesting the creeks work well as paired watersheds for the BACI design. A growth analysis using summer and fall electrofishing data found that steelhead have not been greatly impacted by wood treatment while Coho Salmon growth per day (mm•d-1) after treatment was significantly higher in Pudding Creek than Caspar Creek. Billions of dollars have been spent on watershed restoration in California in recent decades, yet relatively few studies have linked habitat improvements with any effects on fish survival, growth, or abundance. This study will quantitatively measure the effect of large woody debris supplementation on the survival, growth, and abundance of Coho salmon and Steelhead trout so that managers can make informed decisions on how to most efficiently spend the limited amount of restoration funds available.	The object of this project is to evaluate the growth and survival response of endangered Central California Coast Coho Salmon (<i>Oncorhynchus kisutch</i>) and threatened Northern California steelhead (<i>Oncorhynchus mykiss</i>) to large woody debris (LWD) treatments on Pudding Creek in Fort Bragg, California using a before-after-control-impact design. This analysis comes from data collected in a Before-After-Control-Impact (BACI) study initiated in 2012 based on monitoring salmon populations on both Caspar and Pudding creeks. In 2015, LWD was strategically placed in 80% of mainstem Pudding Creek while Caspar Creek was the untreated control. For this project, we have partnered with the California Department of Fish and Wildlife (CDFW), Pacific States Marine Fisheries Commission (PSMFC), Lyme Redwood Forest Company, and Trout Unlimited. Billions of dollars have been spent on watershed restoration in California in recent decades, yet relatively few studies have linked habitat improvements with any effects on fish survival, growth, or abundance. This study will quantitatively measure the effect of large woody debris supplementation on the survival, growth, and abundance of Coho salmon and Steelhead trout so that managers can make informed decisions on how to most efficiently spend the limited amount of restoration funds available.
Research and development of a predictive model for Ceratonova shasta waterborne parasites in support of Klamath River water management decisions and the Klamath Basin Stream Salmonid Simulator (S3 Model)	September 2023	Develop a model to predict the weekly concentration of C. Shasta waterborne parasites in the Klamath River.	<i>Ceratonova shasta</i> is a parasite endemic to the Klamath River basin that has been linked to population declines in native salmonids. High densities of waterborne spores of the parasite are known to cause increasing infection and mortality risk for juvenile salmonids. A recently constructed population dynamics model for Klamath River salmonids, the Stream Salmonid Simulator (S3 model), includes a sub-model to simulate <i>C. shasta</i> disease and mortality risk for outmigrating juveniles in response to potential management alternatives. This sub-model uses inputs of spore density, however, spores vary spatially and temporally within years, and vary over several orders of magnitude among years. Through the development of the spore model, associations between peaks in spore density and the prevalence of infection in hatchery-origin juveniles were found. Developing models that are able to better estimate mortality risk for juvenile salmonids will provide a means to incorporate these models into the S3 model. This then provides an adaptive management tool for managers to understand how different management decisions (e.g. flow) might affect the population. The project is a collaboration of researchers between the USGS and the US Fish and Wildlife Service.
Juvenile rearing distribution of threatened coho salmon at habitat restoration sites on the Hoopa reservation	August 2022	A study to examine when and how Coho Salmon are utilizing creeks on the Hoopa tribal reservation using eDNA and snorkel surveys.	As Coho Salmon are thought to be at very low abundance in the study streams, relying only on visual observation and in-hand capture of Coho Salmon is likely to underestimate the extent of their distribution. Therefore, project sampling efforts will combine standard visual surveys (via snorkeling) with environmental DNA (eDNA) sampling (via water samples analyzed for presence of Coho Salmon DNA). This multi-method approach will also provide insight into the potential for eDNA surveys to evaluate small-scale patterns in Coho Salmon distribution associated with restoration activities. The Hoopa Tribe recently made substantial investments in habitat restoration and improvement projects to aid in Coho Salmon recovery in streams on tribal land. Results of this project will provide information necessary to assess Coho Salmon use of restored and unrestored sites to guide future restoration efforts. This project is a collaboration between the Hoopa tribe, USGS, and Humboldt State University.
Comparison of standard and eDNA methods for estimating Chinook Salmon smolt abundance in the Klamath River (CA)	April 2020	The objective of this study is to compare standard and eDNA-based estimates of weekly and season totals of Chinook Salmon at the Kinsman site, Klamath River. The project will: (1) Evaluate specificity and sensitivity of existing Chinook Salmon qPCR assays and if necessary design Chinook-specific qPCR assays. (2) Generate biweekly estimates of Chinook Salmon eDNA concentration using qPCR at the Kinsman site. (3) Evaluate the Chinook Salmon eDNA plume emanating from Iron Gate Hatchery (IGH) during periods of high, medium, and low flow. At each flow level water samples will be collected at IGH and progressively downstream at 10 km intervals until the Kinsman site is reached. These data will provide insights regarding the extent to which IGH eDNA output may bias estimates of natural-orgin smolt outmigrant abundance at the Kinsman site. (4) Statistical assessment of the relationship between the weekly eDNA concentrations and Chinook Salmon smolt abundance estimated using standard methods. Our study will leverage existing smolt abundance estimates in the Klamath River at Kinsman where weekly and season Chinook Salmon estimates have been generated since the early 1990s. The data from standard monitoring will provide a foundation for comparison of the eDNA-based estimates. Use of eDNA approaches for determining smolt abundance during seaward migration has at least three distinct advantages in comparison to standard monitoring. First, eDNA approaches are non-invasive in the sense that they do not involve direct handling and/or tagging of Chinook Salmon smolts or cause delays in their downstream migration. Second, eDNA approaches are less likely to be constrained by high water flows and debris that can result in flawed sets and/or make it dangerous for staff to implement field survey methods. Third, eDNA-based methods may provide a less expensive alternative for salmon abundance monitoring than standard methods. This study will provide eDNA-based estimates of weekly smolt abundance of Chinook Salmon within the mainstem of the Klamath River, but it could also serve as a foundation and justification for applying the eDNA methods in other areas within the Klamath-Trinity Basin and across the entire Pacific northwest where similar approaches are applied for salmon. Further, if the approaches developed herein are proven effective for monitoring Chinook Salmon, they could be easily expanded for monitoring of other commercially, recreationally, and tribally important species, such as Coho Salmon, steelhead, green sturgeon, and Pacific lamprey. Also, the same water samples collected for determination of salmon abundance could also be used for disease monitoring in the mainstem Klamath River, which is currently evaluated, in part, using environmental DNA analysis (Hallett and Bartholomew 2006). If successful, our project will generate eDNA-based estimates of Chinook Salmon smolt abundance that could be used to supplement or potentially replace standard methods in the future. Our project results should be of interest to two distinct groups of scientists. First, federal, state and tribal resource management and conservation groups should receive benefits from our anticipated project results: empirical information concerning the abundance of Chinook Salmon smolts using a non-invasive tool that is potentially less expensive than standard methods. Second, molecular ecologists should be interested in our project results, especially our application of eDNA monitoring for determination of aquatic species abundance during migration.	The objective of this study is to compare standard and eDNA-based estimates of weekly and season totals of Chinook Salmon at the Kinsman site, Klamath River. The project will: (1) Evaluate specificity and sensitivity of existing Chinook Salmon qPCR assays and if necessary design Chinook-specific qPCR assays. (2) Generate biweekly estimates of Chinook Salmon eDNA concentration using qPCR at the Kinsman site. (3) Evaluate the Chinook Salmon eDNA plume emanating from Iron Gate Hatchery (IGH) during periods of high, medium, and low flow. At each flow level water samples will be collected at IGH and progressively downstream at 10 km intervals until the Kinsman site is reached. These data will provide insights regarding the extent to which IGH eDNA output may bias estimates of natural-orgin smolt outmigrant abundance at the Kinsman site. (4) Statistical assessment of the relationship between the weekly eDNA concentrations and Chinook Salmon smolt abundance estimated using standard methods. Our study will leverage existing smolt abundance estimates in the Klamath River at Kinsman where weekly and season Chinook Salmon estimates have been generated since the early 1990s. The data from standard monitoring will provide a foundation for comparison of the eDNA-based estimates. Use of eDNA approaches for determining smolt abundance during seaward migration has at least three distinct advantages in comparison to standard monitoring. First, eDNA approaches are non-invasive in the sense that they do not involve direct handling and/or tagging of Chinook Salmon smolts or cause delays in their downstream migration. Second, eDNA approaches are less likely to be constrained by high water flows and debris that can result in flawed sets and/or make it dangerous for staff to implement field survey methods. Third, eDNA-based methods may provide a less expensive alternative for salmon abundance monitoring than standard methods. This study will provide eDNA-based estimates of weekly smolt abundance of Chinook Salmon within the mainstem of the Klamath River, but it could also serve as a foundation and justification for applying the eDNA methods in other areas within the Klamath-Trinity Basin and across the entire Pacific northwest where similar approaches are applied for salmon. Further, if the approaches developed herein are proven effective for monitoring Chinook Salmon, they could be easily expanded for monitoring of other commercially, recreationally, and tribally important species, such as Coho Salmon, steelhead, green sturgeon, and Pacific lamprey. Also, the same water samples collected for determination of salmon abundance could also be used for disease monitoring in the mainstem Klamath River, which is currently evaluated, in part, using environmental DNA analysis (Hallett and Bartholomew 2006). If successful, our project will generate eDNA-based estimates of Chinook Salmon smolt abundance that could be used to supplement or potentially replace standard methods in the future. Our project results should be of interest to two distinct groups of scientists. First, federal, state and tribal resource management and conservation groups should receive benefits from our anticipated project results: empirical information concerning the abundance of Chinook Salmon smolts using a non-invasive tool that is potentially less expensive than standard methods. Second, molecular ecologists should be interested in our project results, especially our application of eDNA monitoring for determination of aquatic species abundance during migration.
Tracking Coho Salmon using eDNA	December 2019	Coho Salmon (Oncorhynchus kisutch) populations in northern California are valuable ecologically and culturally and they comprise a fundamental component of redwood forest ecosystems. Coho Salmon populations within northern California have been listed as "threatened" under the Endangered Species Act (NMFS, 2011). Recovery of these populations requires effective management actions that are dependent on the collection of reliable and timely survey information on Coho Salmon abundance and distribution. Further, the success of restoration efforts is contingent upon the ability to effectively measure the response of salmon populations post-restoration. In this project, we will examine the potential of using a new monitoring method to assess salmon populations, which could be used to improve population management and assess the effectiveness of restoration efforts. Our goal is to use the availability of existing fish monitoring infrastructure in Prairie Creek to compare daily measurements of abundance and biomass of out-migrating Coho Salmon with eDNA concentrations taken from water samples at the trap site.	Coho Salmon (Oncorhynchus kisutch) populations in northern California are valuable ecologically and culturally and they comprise a fundamental component of redwood forest ecosystems. Coho Salmon populations within northern California have been listed as "threatened" under the Endangered Species Act (NMFS, 2011). Recovery of these populations requires effective management actions that are dependent on the collection of reliable and timely survey information on Coho Salmon abundance and distribution. Further, the success of restoration efforts is contingent upon the ability to effectively measure the response of salmon populations post-restoration. In this project, we will examine the potential of using a new monitoring method to assess salmon populations, which could be used to improve population management and assess the effectiveness of restoration efforts. Our goal is to use the availability of existing fish monitoring infrastructure in Prairie Creek to compare daily measurements of abundance and biomass of out-migrating Coho Salmon with eDNA concentrations taken from water samples at the trap site.
Basal Hollow Roost Selection	June 2019	Basal Hollow Roost Selection project addresses a lack of information and roosting habitat for Townsend's big-eared bat (Corynorhinus townsendii, COTO) and other bat species identified as Species of Greatest Conservation Need in the California Department of Fish and Wildlife 2015 State Wildlife Action Plan. The purpose of this study is to determine the extent of use of basal hollows by COTO and other bat species and to provide land managers with specific criteria to identify and protect COTO roosting habitat.	Basal Hollow Roost Selection project addresses a lack of information and roosting habitat for Townsend's big-eared bat (Corynorhinus townsendii, COTO) and other bat species identified as Species of Greatest Conservation Need in the California Department of Fish and Wildlife 2015 State Wildlife Action Plan. The purpose of this study is to determine the extent of use of basal hollows by COTO and other bat species and to provide land managers with specific criteria to identify and protect COTO roosting habitat. This is a collaboration with California Department of Fish and Wildlife, U.S. Geological Service, and Humboldt State University.
Prairie Creek Coho Salmon Life Cycle Monitoring	March 2020	Project objectives are three-fold: 1) to count the number of live adult fish, redds (nests), and carcasses of Coho Salmon and other anadromous salmonids which are returning to Prairie Creek to spawn; 2) to estimate freshwater survival and outmigration timing of tagged juvenile Coho Salmon; and 3) to estimate the population sizes of outmigrating Coho Salmon and other salmonids. Enumeration is adult salmon will be achieved by ground survey (on foot) of stream reaches by a survey crew of 2-4 people every two weeks during the spawning migrating period (mid-November through mid-March each year), as stream conditions allow. Freshwater survival and outmigration timing of juvenile Coho Salmon will be estimated using mark-recapture methods by a) sampling fish using seines each fall; b) tagging a subset of the juvenile Coho with PIT tags and releasing them at the location of capture; and c) detecting the fish at fixed in-stream antenna arrays or recapturing them in a downstream migrant trap, as the fish move downstream in the fall or during the spring outmigration period (March – June). Fish captured in the downstream migrant trap will be identified, enumerated, scanned for the presence of tags, and released. The long-term goals of the project are to determine baseline and status/trend population information for Coho Salmon and other anadromous salmonids which can be used to identify factors limiting species recovery and to identify restoration needs in the basin. The adult counts and outmigrant smolt counts will provide estimates of fish in and fish out, that can be used to provide relative estimates of freshwater and marine survival. This information is essential to understanding whether changes in salmonid numbers are due to recovery from improvements in freshwater habitat coniditons or changes in ocean conditions. The freshwater survival and abundance and size of yearling Coho Salmon smolts emigrating from Prairie Creek can be used as the benchmark for other streams because much of Prairie Creek is in pristine condition. This project continues a 9-yr data set in Prairie Creek of adult Coho Salmon counts, and a 6-yr data set of smolt counts.	Project objectives are three-fold: 1) to count the number of live adult fish, redds (nests), and carcasses of Coho Salmon and other anadromous salmonids which are returning to Prairie Creek to spawn; 2) to estimate freshwater survival and outmigration timing of tagged juvenile Coho Salmon; and 3) to estimate the population sizes of outmigrating Coho Salmon and other salmonids. Enumeration is adult salmon will be achieved by ground survey (on foot) of stream reaches by a survey crew of 2-4 people every two weeks during the spawning migrating period (mid-November through mid-March each year), as stream conditions allow. Freshwater survival and outmigration timing of juvenile Coho Salmon will be estimated using mark-recapture methods by a) sampling fish using seines each fall; b) tagging a subset of the juvenile Coho with PIT tags and releasing them at the location of capture; and c) detecting the fish at fixed in-stream antenna arrays or recapturing them in a downstream migrant trap, as the fish move downstream in the fall or during the spring outmigration period (March – June). Fish captured in the downstream migrant trap will be identified, enumerated, scanned for the presence of tags, and released. The long-term goals of the project are to determine baseline and status/trend population information for Coho Salmon and other anadromous salmonids which can be used to identify factors limiting species recovery and to identify restoration needs in the basin. The adult counts and outmigrant smolt counts will provide estimates of fish in and fish out, that can be used to provide relative estimates of freshwater and marine survival. This information is essential to understanding whether changes in salmonid numbers are due to recovery from improvements in freshwater habitat coniditons or changes in ocean conditions. The freshwater survival and abundance and size of yearling Coho Salmon smolts emigrating from Prairie Creek can be used as the benchmark for other streams because much of Prairie Creek is in pristine condition. This project continues a 9-yr data set in Prairie Creek of adult Coho Salmon counts, and a 6-yr data set of smolt counts. Cooperating organizations are the California Department of Fish and Wildlife, National Marine Fisheries Service, U.S. Geological Survey, Redwood National and State Parks, and Humboldt State University.
Monitoring threatened Coho Salmon populations in Humboldt Bay tributaries	September 2020	The objective of this project is to provide annual juvenile and adult abundance estimates for the Coho salmon population in Freshwater Creek, which is includes in the threatened Southern Oregon Northern California Coho Salmon ESU.	This project will incorporate juvenile tagging and detection efforts in streams adjacent to Freshwater Creek, California to characterize dispersal among tributaries and use these parameters, in combination with estimates of population synchrony across basins from the time series of escapement data, to evaluate potential metapopulation dynamics of Humboldt Bay tributaries. In addition, the expanded tagging and detection efforts will allow us to compare the life history diversity that we have characterized in Freshwater Creek across basins that differ in habitat and restoration status. This project is a cooperation with the California Department of Fish and Wildlife, Humboldt Fish Action Council, Humboldt State University, Pacific Coast Fish Wildlife Wetland Restoration Association, Pacific States Marine Fisheries Commission, Redwood Community Action Agency, and U.S. Geological Survey. Continuing the long-term monitoring of adult abundance in these populations is essential for status and trends assessment of regional salmon stocks. As habitat restoration and enhancement projects proceed in the Humboldt Bay watershed ongoing monitoring will provide insight into the response of Coho Salmon populations to these conservation efforts.
Monitoring Chinook Salmon in Redwood Creek to assess the impacts of a modified estuary	June 2020	The project will provide funds to continue monitoring adult and juvenile salmonids in Redwood Creek, California to provide sufficient data to build a life cycle model for the Chinook Salmon population. The objectives of this project are to: 1. Enumerate total numbers of Chinook returning to spawn in the Redwood Creek basin using DIDSON sonar; 2. conduct spawning ground surveys in Redwood Creek above Prairie Creek to estimate total numbers of redds which are constructed; and 3. install and operate a rotary screw trap in Redwood Creek to monitor the abundance and condition of juvenile salmonids outmigrating from Redwood Creek. Monitoring data will be used to parameterize a life-cycle model to assess the impact of restoration efforts and climate change on the abundance of the Chinook Salmon population in Redwood Creek.	Effective fisheries management relies on understanding how populations respond to habitat modifications resulting from environmental changes and restoration efforts. Pacific Salmon (Oncorhynchus spp.) rely on both freshwater and marine habitats during different phases of their life history; thus, it is necessary to monitor both adult and smolt abundances to differentiate how conditions in these different habitats influence demographic rates (i.e., survival). If monitoring data is collected over a sufficiently long time series, encompassing a range of environmental and biological conditions, it is possible to develop a robust life cycle model that can be used to discern the impact of restoration efforts and estimate the resiliency of a population to stressors, such as increased temperatures due to climate change or decreased flow due to drought. This is a collaborative effort which includes the California Department of Fish and Wildlife, U.S. Geological Survey and Humboldt State University. Using data from the project we developed a life-cycle model that incorporated various environmental (e.g., temperature, flow) covariates to estimate freshwater and marine survival of Chinook Salmon and evaluated the impact of restoration actions on Chinook Salmon populations. Results from this model suggest there is a minimal contribution of estuary-rearing juveniles to the spawning adult population and point out current limitations associated with rearing in the Redwood Creek estuary.
Linking predation mortality to predator density and survival for out-migrating Chinook Salmon and steelhead in the lower San Joaquin and South Delta	December 2018	Abundance data for fish predators is in the Delta is lacking, and has been identified as a primary research need in the Delta. The limited abundance data currently available for predators in the Delta cover relatively few locations and periods during the year, and fishery independent population estimates are unavailable. Both native and non-native species of predator fishes inhabit the South Delta and feed on migrating smolts and there is likely significant annual and seasonal variation in the presence of absence of individual predators. Predators are likely to exhibit positive selectivity for salmonid species because they are highly caloric, are likely naive to invasive predators and have no physical defense structures; therefore are easily eaten and handled. Our ability to make qualitative inferences about the scale and effects of fish predation on the salmonid population are greatly hindered by this lack of information. Through a combination of paired electrofishing sampling and results from acoustic surveys conducted using Dual-frequency identification sonar (DIDSON), we will be able to quantify the abundance of potential predatory fish throughout our study region.	Abundance data for fish predators is in the Delta is lacking, and has been identified as a primary research need in the Delta. The limited abundance data currently available for predators in the Delta cover relatively few locations and periods during the year, and fishery independent population estimates are unavailable. Both native and non-native species of predator fishes inhabit the South Delta and feed on migrating smolts and there is likely significant annual and seasonal variation in the presence of absence of individual predators. Predators are likely to exhibit positive selectivity for salmonid species because they are highly caloric, are likely naive to invasive predators and have no physical defense structures; therefore are easily eaten and handled. Our ability to make qualitative inferences about the scale and effects of fish predation on the salmonid population are greatly hindered by this lack of information. Through a combination of paired electrofishing sampling and results from acoustic surveys conducted using Dual-frequency identification sonar (DIDSON), we will be able to quantify the abundance of potential predatory fish throughout our study region.
Humboldt Bay Invertebrate	August 2019	Numerous studies on the U.S. West Coast have documented differences in species diversity and abundance associated with estuarine habitat types with and without oyster culture. However, due to the relatively recent transition to off-bottom culture, few studies have addressed how and whether off-bottom oyster culture affects species use and abundance or whether these differences affect the overall food web ecology of the system. We will examine how off-bottom oyster culture influences the benthic invertebrate community in Humboldt Bay, California's second largest estuary.	The project will examine the environmental impacts of shellfish aquaculture by furthering the understanding of how benthic invertebrate communities are affected by the presence of Cultch-on-Longline oyster aquaculture.
Characterizing the foraging ecology of marbled murrelets in coastal waters adjacent to old growth redwoods	June 2018	Marbled murrelets (Brachyramphus marmoratus) are highly threatened in the redwood region due to a number of factors including the loss of their old-growth nesting habitat, nest predation, and changes in marine prey resources. While extensive nesting habitat management and predator control programs have been implemented by the state and federal agencies responsible for murrelet conservation, it is increasingly recognized that changes in marine foraging conditions may interact with declines in nesting habitat to cause sustained low murrelet recruitment in California. Ensuring that adequate prey resources exist near nesting habitat and, more broadly, integrating forest and marine ecosystem management will be essential for maintaining viable populations of marbled murrelets in redwood ecosystems. Our objective is to characterize the species-level diet of marbled murrelets breeding in redwood forests by sequencing fecal material collected from individuals captured at sea. This work will continue our 15-year research project on the ecology and conservation of murrelets in the redwood region.	None
Rangewide Giant Kangaroo Rat Surveys & Monitoring Optimization	December 2018	The goal of this project will be to determine the current range and status of the state- and federally-endangered Giant Kangaroo Rat (GKR). Due to the ongoing drought, and concerns over long-term permanent changes in climate within GKR habitat, there is a critical need to understand population dynamics within all GKR colonies across their range. As the five-year review in 2010, the status of GKR in many parts of its range was unknown and the most recent surveys of the satellite colonies occurred in the late 1980s. Acquiring baseline data throughout the range of GKR is necessary for long-term management and recovery of the species as well as assessing the potential impacts of development projects.	The objectives of the project are to: 1. Identify potential giant kangaroo rat habitat based on habitat models and aerial and satellite imagery 2. Document giant kangaroo rat occurrence throughout their potential range 3. Develop monitoring methods based on existing demographic data and aerial surveys of population extent. These monitoring methods will be optimized to detect changes described in the Recovery Criteria for GKR: "During 5-year period no greater than 20 percent change in population size..." in the Carizzo Plain, and "stable or increasing populations for the Carrizo, Panoche, and western Kern Co. metapopulations through one precipitation cycle."
Giant Kangaroo Rat Population Monitoring in Panoche Valley	June 2016	Giant kangaroo rats (GKR) are a keystone species throughout their range including the Carrizo Plain. The current four year drought and the associated lack of vegetative growth have resulted in precipitous declines in GKR populations, especially during the past two years. Kit fox populations have followed this decline and now fewer than 200 kit foxes are estimated to reside on the Carrizo Plain National Monument. The objective of the project will be to increase giant kangaroo rat survival and production by providing supplemental food at three locations in the Ciervo-Panoche Natural Area. The overall project concept is to reduce the population declines for GKR and to test the effectiveness of a supplemental feeding program. Supplemental feeding will no longer be needed when more normal rainfall returns and GKR numbers recover. Giant kangaroo rats will be the primary target species; however, given the role of GKR as ecosystem engineers, benefits to GKR populations will cascade throughout the ecosystem and provide direct benefits to a wide array of San Joaquin Valley species including San Joaquin kit fox, San Joaquin antelope squirrel, blunt-nosed leopard lizard, and the California jewelflower.	None
Tidewater Goby Survey	September 2018	The goal of this research is the development of environmental DNA (eDNA) techniques and methods for monitoring endangered tidewater goby presence/absence to provide an innovative and improved set of tools for detecting tidewater goby in Caltrans project areas and perform specified surveys. The new eDNA techniques and methods will help develop a survey protocol that detects tidewater goby with higher confidence. Improved survey techniques will help Caltrans save money and avoid delays during maintenance and construction by reducing time spent in minimizing endangered species consultations to those situations where they are necessary.	California Department of Transportation (Caltrans) Districts are often required to initiate Endangered Species Act (ESA) Section 7 consultation with U.S. Fish and Wildlife Service (USFWS), on behalf of the Federal Highway Administration, for projects that may affect the federally listed Tidewater Goby, a fish species whose current range is patchy and fragmented along the entire coastline of California. Current field survey approaches required by USFWS have relatively low detection rates for Tidewater Goby. Researchers at Humboldt State University are in the initial stages of developing an innovative approach for monitoring Tidewater Goby using eDNA techniques. This research will produce a validated eDNA protocol for use in determining the presence or absence of the Tidewater Goby at or near a project site. The improved survey techniques will help CalTrans save money and avoid delays during maintenance and construction by minimizing the work done for endangered species consultations for this fish.
Habitat selection in an Arctic Seabird: Implications for Climate Change	December 2019	Climate change is projected to have its greatest impact in arctic regions where temperature increases are forecasted to cause rapid changes to ecosystems and the wildlife dependent on them. These changes range from phenological mismatches (i.e/, between the timing of emergence of invertebrate prey and the arrival and breeding of shorebird predators; Liebezeit et al. 2014) to altered habitats where warmer climates favor successional changes in plant communities. The Semipalmated Sandpiper (Calidris pusilla; hereafter "sandpiper") is an abundant, arctic shorebird whose breeding range extends across nearly all of the Nearctic. The sandpiper breeds in wet coastal tundra that is likely to be strongly affected by climate change. Recent evidence suggests a decline in population size of the Semipalmated Sandpiper (Andres et al. 2012), but the cause of this decline is unknown. Despite its abundance, little is known regarding nest site selection by breeding Semipalmated Sandpipers (Jehl 2006). In the face of global climate change, it is likely that the population of sandpipers will be affected by changing habitats. The goal of this research is to investigate current aspects of habitat selection by Semipalmated Sandpipers in order to predict how future changes will affect their habitats and population.	The California Cooperative Fish & Wildlife Research Unit will be collaborating with the U.S. Geological Survey, Alaska to examine habitat selection by Semipalmated Sandpipers in the Colville River delta, Alaska. Specific objectives are to: 10 quantify nest site selection of sandpipers breeding in the coastal plain of arctic Alaska; and 2) discuss implications in relation to changing habitats as influenced by global climate change.
Townsend's Big-Eared Bat Statewide Assessment	December 2017	The goal of this project is to quantify the current status of the Townsend's big-eared bat (Corynorhinus townsendii, COTO) in California. This task will provide the first state-wide assessment of the number and status of COTO colonies in California in more than two decades. It will provide a comprehensive report on the distribution, abundance, and condition of historic and currently occupied sites, a regional assessment of the species' status, and recommendations for maintaining or enhancing existing populations, as well as a discussion of likely future threats. Ancillary benefits of this study will be information on other bat species found in association with COTO, and additional public education on the status and value of bats through our contacts during surveys.	The goal of this project is to quantify the current status of the Townsend's big-eared bat (Corynorhinus townsendii, COTO) in California. This task will provide the first state-wide assessment of the number and status of COTO colonies in California in more than two decades. It will provide a comprehensive report on the distribution, abundance, and condition of historic and currently occupied sites, a regional assessment of the species' status, and recommendations for maintaining or enhancing existing populations, as well as a discussion of likely future threats. Ancillary benefits of this study will be information on other bat species found in association with COTO, and additional public education on the status and value of bats through our contacts during surveys.
Redwood Creek Life Cycle Monitoring DIDSON 2015-2017	March 2017	This project will use a DIDSON sonar imaging system to estimate the number of adult steelhead migrating into and out of Redwood Creek during the 2015/2016 spawning season, to provide status and trend information for this ESA-listed fish. A DIDSON has been deployed on Redwood Creek since 2009 to test its potential for monitoring escapement of adult salmon. Previous research has demonstrated that analysis of images captured by DIDSON can be used effectively to enumerate migrating salmonids over a wide range of conditions. When combined with existing smolt monitoring data, these data will alllow smolt to adult and adult to smolt survival to be estimated. The project will also describe migration timing of steelhead in Redwood Creek, and evaluate relationships with environmental conditions (streamflow, temperature, tides) using standard statistical techniques.	None
Export of Invertebrate Drift From Headwater Streams	June 2018	This study is part of a larger multidisciplinary project investigating stream ecosystem response to riparian management an includes scientists from Green Diamond Resource Company, Humboldt State University, Oregon State University and the U.S. Forest Service. The study will be conducted on Green Diamond lands in tributaries of the lower Klamath River in coastal northern California. Sites will be chosen that differ in percentage of coniferous riparian trees, but which are similar in confluence with a fish-bearing reach. Objectives of this study are to: 1) Quantify the magnitude, composition, and energy content of invertebrate subsidies of terrestrial and aquatic origin from Class II (fish-less) streams to downstream fish-bearing waters at different times of year and from streams differing in riparian canopy; and 2) Evaluate use of these invertebrate subsidies by fish and their potential contribution to fish growth.	This study is part of a larger multidisciplinary project investigating stream ecosystem response to riparian management an includes scientists from Green Diamond Resource Company, Humboldt State University, Oregon State University and the U.S. Forest Service. The study will be conducted on Green Diamond lands in tributaries of the lower Klamath River in coastal northern California. Sites will be chosen that differ in percentage of coniferous riparian trees, but which are similar in confluence with a fish-bearing reach. Objectives of this study are to: 1) Quantify the magnitude, composition, and energy content of invertebrate subsidies of terrestrial and aquatic origin from Class II (fish-less) streams to downstream fish-bearing waters at different times of year and from streams differing in riparian canopy; and 2) Evaluate use of these invertebrate subsidies by fish and their potential contribution to fish growth.

Research Publications

Research Publications	Publication Date
Zimmer, K. D., M. A. Hanson, M. G. Butler and W. G. Duffy. 2001. Size distribution of aquatic invertebrates in two prairie wetlands, with and without fish, with implications for community production. Freshwater Biology 46:1-14.	February 2001
Zimmer, K. D., M. A. Hanson, M. G. Butler and W. G. Duffy. 2001. Influence of fathead minnows on nutrient cycling, nutrient partitioning and ecosystem structure in prairie wetlands. Achives fur Hydrobiologia 150:411-433.	June 2001
Winship A.J., Thorson J., Clarke E., Coleman H., Costa B., Georgian S., Gillett D., Grüss A., Henderson M., Hourigan T.F., Huff D., Kreidler N., Pirtle J., Olson J.V., Poti M., Rooper C.N., Sigler M.F., Viehman S., and Whitmire C.E. in review . Good practices for species distribution modeling of deep-sea corals and sponges: data collection, analysis, validation, and communication. Submitted to Frontiers in Marine Science. \| Abstract	May 2020	Resource managers in the United States and worldwide are tasked with identifying and mitigating trade-offs between human activities in the deep sea (e.g., fishing, energy development, and mining) and their impacts on habitat-forming invertebrates, including deep-sea corals and sponges (DSCS). Related management decisions require information about where DSCS occur and in what densities. Species distribution modeling (SDM) provides a cost-effective means of identifying potential DSCS habitat over large areas to inform these management decisions and data collection. Here we provide recommendations of good practices for DSCS SDM, especially in the context of data collection and management applications. Managers typically need information regarding DSCS encounter probabilities, densities, and sizes, defined at sub-regional to basin-wide scales and validated using subsequent, targeted data collections. To realistically achieve these goals, we recommend integrating available data sources in SDMs including fine-scale visual sampling and broad-scale resource surveys (e.g., fisheries trawl surveys). When possible, we recommend models fitted to presence-absence and density data rather than models fitted only to presence data, which are difficult to validate and can confound estimated probability of occurrence or density with sampling effort. Ensembles of models can provide robust predictions, while multi-species models leverage information across taxa and facilitate community inference. We also recommend that analysts include environmental predictor variables representing multiple spatial scales, model residual spatial autocorrelation, and quantify prediction uncertainty. To facilitate the use of models by managers, predictions should be expressed in units that are widely understood and should be validated at an appropriate spatial scale using a sampling design that provides strong statistical inference. We present three case studies for the Pacific Ocean that illustrate good practices with respect to data collection, modeling, and validation; these case studies demonstrate it is possible to implement our recommendations in real-world settings.
Wilzbach,M., M.J. Ashenfelter, S.J. Ricker. 2012. Movement of Resident Rainbow Trout Transplanted below a Barrier to Anadromy. Transactions of the American Fisheries Society. 141:2, 294-304. \| Abstract \| Download \| Publisher Website	March 2012	We tracked the movement of resident coastal rainbow trout Oncorhynchus mykiss irideus that were experimentally transplanted below a migration barrier in a northern California stream. In 2005 and 2006, age-1 and older rainbow trout were captured above a 5-m-high waterfall in Freshwater Creek and individually marked with passive integrated transponder tags. Otolith microchemistry confirmed that the above-barrier trout were the progeny of resident rather than anadromous parents, and genetic analysis indicated that the rainbow trout were introgressed with cutthroat trout O. clarkii. At each of three sampling events, half of the tagged individuals (n = 22 and 43 trout in 2005 and 2006, respectively) were released 5 km downstream from the waterfall (approximately 10 km upstream from tidewater), and an equal number of tagged individuals were released above the barrier. Tagged individuals were subsequently relocated with stationary and mobile antennae or recaptured in downstream migrant traps, or both, until tracking ceased in October 2007. Most transplanted individuals remained within a few hundred meters of their release location. Three individuals, including one rainbow trout released above the waterfall, were last detected in the tidally influenced lower creek. Two additional tagged individuals released above the barrier were found alive in below-barrier reaches and had presumably washed over the falls. Two of seven tagged rainbow trout captured in downstream migrant traps had smolted and one was a presmolt. The smoltification of at least some individuals, coupled with above-barrier “leakage” of fish downstream, suggests that above-barrier resident trout have the potential to exhibit migratory behavior and to enter breeding populations of steelhead (anadromous rainbow trout) within the basin.
Wilzbach, P., and K. W. Cummins. 2000. Profitable stream positions differ for brook trout and cutthroat trout. Pg. 265-266 in Wild Trout VII. Management in the New Millenium: are we ready?	October 2000
Wilzbach, M. A., K. W. Cummins, T. K. Barnes, and J. C. Trexler. 2002. Channel-floodplain coupling in the Kissimmee River, Florida (USA): invertebrate movement and fish feeding. Vereinigung fur theoretische und angewandte Limnologie, Verhandlungen. 28: 164-172.	February 2002
Wilzbach, M. A., B. C. Harvey, J. L. White, and R. J. Nakamoto. 2005. Effects of riparian canopy opening and salmon carcass addition on the abundance and growth of resident salmonids. Canadian Journal of Fisheries and Aquatic Sciences 62: 58-67.	March 2005
Wilzbach, M. 2001. Review of "Wildstream: a natural history of the free flowing river". Fisheries 28(8):43.	March 2001
Wilzbach M. A., and K. W. Cummins. Rivers and Streams: Physical Setting and Adapted Biota. In Sven Erik Jorgensen and Brian D. Fath (Editor-in-Chief), Ecosystems. Vol. [4] of Encyclopedia of Ecology, 5 vols. pp. [3095-3106] Oxford: Elsevier.	June 2008
Williams, T. H., B. C. Spence, W.G. Duffy, D. Hillemeier, G. Kautsky, T. Lisle, M. McCain, T. Nickelson, G. Garman, E. Mora, and T. Pearson. 2008. Framework for assessing viability of threatened coho salmon in the Southern Oregon/Northern California Coast Evolutionarily Significant Unit. U.S. Department of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC 432. \| Publisher Website	December 2008
Van Vleet, N. P., Ward, D. M., Som, N. A., Barton, D. C., Anderson, C., & Henderson, M. J. (2024). It's about time: A multistate semicontinuous time mark–recapture model to evaluate seasonal survival and movement rates of juvenile Coho Salmon in a small coastal watershed. Transactions of the American Fisheries Society, 153, 541–1. https://doi.org/10.1002/tafs.10471 \| Abstract	August 2024	It is important to have an accurate understanding of species habitat use and demographics as managers prioritize restoration efforts and develop recovery plans for depleted salmon populations. Previous research on threatened populations of Coho Salmon has suggested that overwinter survival is a major limiting factor for population recovery in some watersheds, but these survival estimates are often confounded with emigration to alternative rearing habitats, such as estuaries. Furthermore, emigration to alternative rearing habitats can occur continuously throughout the fall and winter, which is ignored by most types of mark-recapture models. To refine previous survival estimates, we developed a multi-state mark-recapture model that allows separately estimated emigration and survival rates throughout the year. To do this, we used weekly time-varying occasions paired with discrete spatial states. We conducted extensive simulation trials to validate the use of a multi-state model on an existing 4-year PIT tag dataset in a northern California watershed. Results from our model suggest that overwinter survival rate for fish that overwinter in stream habitat and migrate as spring smolts ranged from 0.72-0.83, which is higher than expected for Coho Salmon in this region. We estimate that a substantial proportion of smaller juveniles (0.21-0.28 annually) are emigrating from upstream rearing habitat before the spring smolt migration. This implies that previous estimates of low overwinter survival of Coho Salmon could be due to high emigration rates to alternative rearing locations. Given the apparent juvenile life-history diversity of Coho Salmon, multiple emigration patterns should be considered in the design of future research, monitoring, and restoration projects.
Thorsteinson, L., VanderKooi, S., and Duffy, W., eds., 2011, Proceedings of the Klamath Basin Science Conference, Medford, Oregon, February 1–5, 2010: U.S. Geological Survey Open-File Report 2011-1196, 312 p.	July 2011
Thorsteinson, L., Grimes, C., and Duffy, W., 2011, An overview of the Klamath Basin Science Conference, Pages 1-30 in: Proceedings of the Klamath Basin Science Conference, Medford, Oregon, February 1–5, 2010: U.S. Geological Survey Open-File Report 2011-1196, 312 p.	July 2011
Takekawa, J. Y., A. K. Miles, D. H. Schoelhamer, N. D. Athearn, M. K. Saiki, W. G. Duffy, S. Kleinschmidt, G. G. Shellenbarger and C. A. Jannusch. 2006. Trophic structure of avian communities across a salinity gradient in evaporation ponds of the San Francisco Bay estuary. Hydrobiologia 567:307-327.	April 2006
Stanford, J., Duffy, W., Asarian, E., Cluer, B., Detrich, P., Eberle, L., Edmondson, S., Foott, S., Hampton, M., Kann, J., Malone, K., and Moyle, P., 2011, Conceptual Model for Restoration of the Klamath River, Pages 151-184 in: An overview of the Klamath Basin Science Conference, Pages 1-30 in: Proceedings of the Klamath Basin Science Conference, Medford, Oregon, February 1–5, 2010: U.S. Geological Survey Open-File Report 2011-1196, 312 p.	July 2011
Spence, B.C., W.G. Duffy, J.C. Garza, B.C. Harvey, S.M. Sogard, L.A. Weitkamp, T.H. Williams, and D.A. Bouthton. 2011. Historical occurrence of coho salmon (Oncorhynchus kisutch) in streams of the Santa Cruz Mountain region of California: response to an Endangered Species Act petition to delist coho salmon south of San Francisco Bay. Technical Memorandum, National Marine Fisheries Service, Southwest Fisheries Science Center, Santa Cruz, CA.	July 2011
Som, N.A. 2024. Applications of a disease-induced mortality model to inform regulatory compliance of the Klamath Project. \| Download	March 2024
Smit, R. B., Goodman, D. H., Boyce, J., & Som, N. A. 2024. Effects of 2D hydrodynamic model resolution on habitat estimates for rearing Coho Salmon in contrasting channel forms. River Research and Applications 40(10): 1912-1924. https://doi.org/10.1002/rra.4341	July 2024
Rub, A.M., Som, N.A., Henderson, M.J., Sandford, B.P., Van Doornik, D.M., Teel, D.J., Tennis, M, Langness, O., van der Leeuw, B., Huff, D.D. 2019. Changes in adult Chinook salmon (Oncorhynchus tshawytscha) survival with the lower Columbia River amid increasing pinniped abundance. Canadian Journal of Fisheries and Aquatic Sciences 76: 1862-1873. dx.doi.org/10.1139/cjfas-2018-0290 \| Abstract	September 2019	We conducted a comprehensive mark-recapture tagging study to examine the behavior and survival of spring run Chinook salmon (Oncorhynchus tshawytscha) returning to the Interior Columbia River Basin. Our study included adult salmon returning to the Upper Columbia and Snake Rivers, two fish populations that have been protected under the Endangered Species Act for greater than 15 years. This study was prompted by concern that pinnipeds present within the estuary and lower CR during spring may be detrimentally affecting the recovery of these salmon stocks. Over a five-year period we injected adult salmon with Passive Integrated Transponder Tags as they returned to the estuary. We used these data to fit a mixed effects logistic regression model and identify covariates that influence survival to Bonneville Dam (Rkm 235). Modelling indicated sea lion exposure, the abundance of adult shad (Alosa sapidissima) within the lower Columbia River, and whether or not fish had intact adipose fins all influenced survival. Survival ranged from 0.46 to 0.80 annually over the course of the study and was lowest during the last two years.
Robinson, H.E., Strickler, J.R., Henderson, M.J., Hartline, D.K., Lenz, P.H. 2019. Predation strategies of larval clownfish capturing evasive copepod prey. Marine Ecology Progress Series, 614: 125-146. DOI: 10.3354/meps12888 \| Abstract	April 2019	Fish larvae depend on finding and capturing enough prey for rapid growth during the planktonic phase. The diet of many fish larvae is dominated by copepods, small crustaceans that are highly sensitive to hydrodynamic disturbances and possess strong escape responses. We examined how fish larvae with immature jaws, musculature and fins capture such evasive prey. The kinematics of feeding attempts by larval clownfish (Amphiprion ocellaris) on three developmental stages of copepod (Bestiolina similis) were investigated using high-speed videography. A stealthy approach brought the fish larva within ca. 1 mm of the copepod; shortest distances were observed in early larvae (1 5 days post-hatch [dph]) attacking immature copepods. Peak speeds during strikes increased with fish age and copepod developmental stage (150 to 250 mm s-1) with time to capture <8 ms on average. Most successful captures (70%) were of copepods that failed to initiate an escape response during the strike. If a copepod initiated an escape, capture success decreased to ca. 50% for nauplii and copepodites, and 25% for adults. Adult copepods were more likely to attempt an escape response than copepodites or nauplii. Prey stage and the interaction between strike distance and speed were the parameters that best fit a logistic regression model to the observed captures and escapes. The successful switch to larger and more evasive copepod prey by A. ocellaris larvae did not occur until 7 dph and coincided with ontogenetic changes (post-flexion) and a predatory strategy that included shorter approach phases and greater strike speeds.
Robinson, D.H., Henderson, M.J., H.E., Goodman, Perry, R.W., Som, N.A. From site to system: approaches for producing system-wide estimates of fish habitat in large rivers. To be submitted to River Research and Applications. \| Abstract	October 2021	Worldwide, many productive rivers are dam-regulated and rely on flow management strategies that must balance support of ecological processes with human water use. One component of evaluating this balance is to understand ecological consequences of alternative flow management strategies, which has often been accomplished by coupling population dynamics models with models that relate streamflow to habitat availability and quality. Numerous methods assign habitat availability to locations within a river basin: these include fine-scale field-measured values that are extrapolated to other locations within the basin having similar physical characteristics, or equation-driven values created by functions of model-predicted values of physical characteristics. The array of options for creating habitat models is evolving rapidly as high-resolution remote sensing data becomes more accessible and computational capacity improves. Our objective was to identify tradeoffs among approaches that assign habitat relationships to large rivers, and to create a decision support tool to supplement choices of extent and granularity. Using a selection of case studies that represent a breadth of scales and diverse tradeoffs, we demonstrate the need for a transparent process of data evaluation and assessment to determine the appropriate fit for model scope or context that best supports management needs and recognize sources of uncertainty. The structured approach proposed here aims to improve future model development and refine population dynamics models that inform management of rivers.
Railsback, S. F., R. H. Lamberson, B. C. Harvey and W. G. Duffy. 2001. Reply to discussion on movement reules for individual-based models of stream fish. Ecological Modeling 143:249-251.	December 2001
Pope, K. L., J. L. Brown, W. G. Duffy and P. H. Michaletz. 2001. A caloric-based evaluation of diet indices. Environmental Biology of Fishes. 61:329-339.	August 2001
Okun, N., McGuire, J., Henderson, M., Gallagher, S., Lang, E. and Mackey, E. Large Wood Restoration Effectiveness Monitoring in a Coastal Northern California Stream: A Paired Watershed Before-After-Control-Impact Study. Final Report to California Department of Fish and Wildlife Fisheries Restoration Grant Program May 2021.	August 2021
Notch J.J., McHuron A.S., Michel C.J., Cordoleani F., Johnson M., Henderson M.J., and Ammann A.J. (in press) Outmigration survival of wild Chinook salmon smolts through the Sacramento River during historic drought and high water conditions. environmental biology of fishes. \| Abstract	May 2020	Populations of wild spring-run Chinook salmon (Oncorhynchus tshawytscha) in California’s Central Valley, once numbering in the millions, have dramatically declined to record low numbers in recent years. Dam construction, habitat degradation, and altered flow regimes have all contributed to depress populations of spring-run salmon, which currently persist in only a few tributaries to the Sacramento River. Mill Creek (Tehama County) continues to support these threatened fish, and contains some of the most pristine spawning and rearing habitat available in the Central Valley. Despite this pristine habitat, the number of spring-run salmon returning to spawn has declined to record low numbers, and is likely attributed to poor outmigration survival rates. Using miniature acoustic tags, it is now possible to track out-migrating juveniles throughout the freshwater migration corridor. From 2013-2017 we captured and acoustic tagged 334 smolts out-migrating from Mill Creek, tracking their movement and survival rates over 250 kilometers through the Sacramento River. During this study California experienced both an unprecedented drought and record rainfall, resulting in dramatic fluctuations in year-to-year river flows and water temperature. Cumulative survival of tagged smolts from Mill Creek through the Sacramento River was 9.5% (±1.6) during the study, with relatively low survival during historic drought conditions in 2015 (4.9% ± 1.6) followed by increased survival during high flows in 2017 (42.3% ± 9.1). From these data, we modeled survival in Mill Creek and the Sacramento River over a range of flow values, which indicated that higher flows in each region result in increased survival rates. Data gathered in this study can help focus management and restoration actions over a relatively long migration corridor to specific regions of low survival, and provide guidance for management actions in the Sacramento River aimed at restoring populations of threatened Central Valley spring-run Chinook salmon.
Mull, K. E., and M. A. Wilzbach. Selection of spawning sites by coho salmon in a northern California stream. North American Journal of Fisheries Management 27:1343-1354.	November 2007
Moore, J. W., S. A. Hayes, W. G. Duffy, S. Gallagher, S. Ricker, and D. Wright. Nutrient fluxes and the recent collapse of coastal California salmon populations \| Abstract	July 2011	Pacific salmon are well known for transporting nutrients from the ocean to coastal freshwaters. However, migratory salmon move nutrients both in and out freshwaters during the different parts of their life-cycle. There have been surprisingly few quantifications of the actual import and export of nutrients by salmon from coastal freshwaters. We used a mass-balance approach to quantify recent changes in phosphorus fluxes in 6 coastal California watersheds that have recently experienced dramatic decreases in salmon populations. Semelparous Chinook and coho salmon imported 8.3 and 10.4 times more phosphorus, respectively, than they exported, while iteroparous steelhead imported only 1.57 times more than they exported. The semelparous species whose life-histories led them to import more nutrients were also the species that decreased the most dramatically. In addition, the relationship between import and export was nonlinear, with export being proportionally more important at lower levels of import. This pattern was driven by two density-dependent processes—smolts were larger and disproportionately more abundant at lower spawner abundances. Thus, density-dependent processes decrease net import disproportionately rapidly as salmon populations decline. In fact, in two of the study streams, we calculated that salmon drive net export of P in the most recent year and model fitting suggested that this net export can occur in two additional streams. In other words, salmon may reverse their ecological function at low abundances. Differential vulnerability and density-processes can exacerbate the loss of net nutrient import as salmon populations decline.
Michel, CJ, Henderson, MJ, Loomis, CM, Smith, JM, Demetras, NJ, Iglesias, IS, Lehman, BM, Huff, DD. Fish Predation on a Landscape Scale. Submitted to Ecological Applications. \| Abstract	June 2020	Spatial patterns and environmental predictors of predator-prey dynamics are often investigated at discrete locations, limiting our ability to extrapolate to broader landscape scales. At these broader scales, landscapes often contain multiple complex and heterogeneous habitats, thus a spatially balanced sample throughout the different habitats is necessary to sufficiently represent them. This challenge is especially pronounced in California’s Sacramento-San Joaquin River Delta, where the landscape scale impact of fish predators on native prey fish is information needed by managers to protect multiple imperiled populations. During the spring of 2017, we quantified relative predation risk in the southern half of the Delta (South Delta) using floating baited tethers that record the exact time and location of predation events. We selected 20 study sites (1-km long) using a generalized random tessellation stratified survey design, which allowed us to infer relationships between the environment and predation across a broader spatial scale compared to previous studies. In addition to estimating relative predation risk at each study site, we also collected relevant environmental covariates including distance to nearest predators, water temperature, turbidity, depth, bottom slope, bottom roughness, water velocity, and distance to nearest riverbank and nearest submerged aquatic vegetation. We employed model selection to determine the environmental covariates that best predicted predation risk. Our most parsimonious model included water temperature, time of day, mean predator distance, and river bottom roughness. Using this model, we estimated predation risk for the entire South Delta at a 1-km resolution. This effort identified certain predation risk hotspots - the most important of which was corroborated by other studies - and allowed us to generate predicted survival rates for migrating fish transiting the South Delta. Because the 2017 water year was unusually wet, this methodology should be repeated across a suite of hydrologically distinct years to further develop the relationships.
Malakauskas, D. M., and M. Wilzbach. 2012. Invertebrate assemblages in the lower Klamath River, with reference to Manayunkia speciosa. California Fish and Game 98(4):214-235; 2012. \| Abstract \| Download	December 2012	The freshwater polychaete, Manayunkia speciosa Leidy (Canalipalpata Sabellidae), is the intermediate host for two myxozoan pathogens (Ceratomyxa shasta and Parvicapsula minibicornis) that cause substantial mortalities of juvenile salmon in the Pacific Northwest, particularly in the Klamath River below Iron Gate Dam in California. Information on the distribution of M. speciosa in the Klamath River may facilitate targeted control of polychaete populations to disrupt the parasites that affect fish populations. We sampled invertebrate assemblages in the lower Klamath River in the summer and fall of 2005 and 2006 to estimate distribution patterns of M. speciosa and to characterize assemblage structure of invertebrates in reaches where the polychaete was both collected and not collected. The polychaete was most often found in a reach of river extending 100 km downstream from the Shasta River (river km 185-287). The reach in which it was found supported high taxonomic richness of invertebrates and a high abundance of filtering collectors including marine relicts such as sponges, unioinid mussels, and bryozoans. We suggest that the large, stable substrate on which these were found represents primary, optimal habitat for the polychaete, also a marine relict. Reaches above and below the zone where we collected polychaetes showed a general trend of reduced taxonomic richness as distance away from the polychaete zone increased, and also showed differing relative abundances of non-insect taxa and functional feeding groups. Differences in invertebrate assemblages between years were coincident with large differences in water flows. We suggest flows and food resources may play important roles in invertebrate distribution patterns.
Malakauskas, D. M., Willson, S. J., M. A. Wilzbach, and N. A. Som. 2013. Flow variation and substrate type affect dislodgement of the freshwater polychaete, Manayunkia speciosa. Freshwater Science 2013, 32(3):862-873 \| Download	June 2013
Madej, M. A., M. A. Wilzbach, K. W. Cummins, C. Ellis, and S. Hadden. 2002. The contribution of suspended organic sediments to turbidity and sediment flux. Proceedings, 8th Federal Interagency Sedimentation Conference. April 2002, Reno, Nevada.	October 2002
K W Cummins and M A Wilzbach. Rivers and Streams: Ecosystem Dynamics and Integrating Paradigms. In Sven Erik Jorgensen and Brian D. Fath (Editor-in-Chief), Ecosystems. Vol. [4] of Encyclopedia of Ecology, 5 vols. pp. [3084-3095] Oxford: Elsevier.	June 2008
Hodge, B.W., M.A. Wilzbach, W.G. Duffy, R.M. Quiñones, and J.A. Hobbs. Life history diversity in Klamath River steelhead. Transactions of the American Fisheries Society 145:227-238, 2016. \| Download	February 2016
Hodge, B., M.A. Wilzbach, and W.D. Duffy. 2013. Potential fitness benefits of the half-pounder life history in Klamath River steelhead. Transactions of the American Fisheries Society, 2014. 143:864-875, 2014. \| Abstract \| Download	June 2014	Steelhead Oncorhynchus mykiss from several of the world’s rivers display the half-pounder life history: a variant characterized by an amphidromous, and less often anadromous, return to freshwater in the year of initial ocean entry. We evaluated factors related to expression of the half-pounder life history in wild steelhead from the lower Klamath River basin, California. We also evaluated fitness consequences of the half-pounder phenotype using a simple life history model that was parameterized with our empirical data and outputs from a regional survival equation. Incidence of the half-pounder life history differed among sub-basins of origin and with smolt age. Precocious maturation occurred in approximately 8% of half-pounders and was best predicted by individual length in freshwater preceding ocean entry. Adult steelhead of the half-pounder phenotype were smaller and less fecund at age than adult steelhead of the alternate (ocean contingent) phenotype. However, data suggest that fish of the half-pounder phenotype are more likely to spawn repeatedly than are fish of the ocean contingent phenotype. Models predicted that if lifetime survivorship was equal between alternate phenotypes, fitness of the half-pounder phenotype would be 17 – 28 % lower than that of the ocean contingent phenotype. To meet the condition of equal fitness between alternate phenotypes would require that first-year ocean survival is 21 - 40% higher among half-pounders in freshwater than among their cohorts at sea. We conclude that continued expression of the half-pounder phenotype is favored by precocious maturation and increased survival relative to that of the ocean contingent phenotype.
Henderson, M.J., Iglesias, I.S., Michel, C.J., Ammann, A.J., Huff, D.D. 2019. Estimating spatial-temporal differences in Chinook salmon outmigration survival with habitat and predation related covariates. Canadian Journal of Fisheries and Aquatic Sciences, 76: 1549-1561. dx.doi.org/10.1139/cjfas-2018-0212	September 2019
Henderson, M.J., Huff, D.D., and Yoklavich, M.M. 2018. Deep-Sea Coral and Sponge Taxa Increase Demeral Fish Diversity and the Probability of Fish Presence. Frontiers in Marine Science 7:593844. doi: 10.3389/fmars.2020.593844 \| Abstract \| Download	November 2020	Fish are known to use deep-sea coral and sponge (DSCS) species as habitat, but it is uncertain whether this relationship is facultative (circumstantial and not restricted to a particular function) or obligate (required for a species to persist). To address this uncertainty, we analyzed underwater video transects collected over a ten-year period, documenting the locations and abundance of DSCS and demersal fishes in the Southern California Bight. Non-metric multidimensional scaling, indicator species, and cluster analyses revealed six distinct DSCS assemblages based on depth and substratum, and we identified 44 fish taxa that were predominantly associated with a particular assemblage. We then used logistic regression to identify the ecological drivers most associated with the presence of individual fish taxa throughout the study area. Factors related to fish presence included depth, substratum relief, latitude, fish density, coral cover, coral height, and the abundance of individual coral and sponge taxa. Even after controlling for depth and substratum relief, multiple fish taxa were much more likely to be found in locations containing specific DSCS taxa. Of particular interest, young-of-the-year rockfishes (Sebastes spp.) were more than twice as likely to be found in locations with Placogorgia spp., suggesting that this gorgonian coral serves as nursery habitat. Our results provide valuable information on the relationships between environmental conditions and demersal community assemblages, which is necessary to understand how future oceanic conditions may influence the abundance and distribution of DSCS and associated fishes.
Henderson, M.J., Fiechter, J., Huff, D.D., and Wells, B. 2019. Spatial Variability in ocean-mediated growth potential is linked to Chinook salmon survival. Fisheries Oceanography, 3: 334-344. DOI: 10.1111/fog.12415	May 2019
Gleason, R. A., N. H. Euliss, Jr., D. E. Hubbard and W. G. Duffy. 2004. Invertebrate egg banks of restored, natural, and drained wetlands in the Prairie Pothole Region of the United States. Wetlands 24:562-572.	September 2004
Gleason, R. A., N. H. Euliss, Jr., D. E. Hubbard and W. G. Duffy. 2003. Effects of sediment load on emergence of aquatic invertebrates and plants from wetland soil egg and seed banks. Wetlands 23:26-34.	April 2003
Frazey, S. L., and M. A. Wilzbach. The relationship between productivities of salmonids and forest stands in northern California watersheds. Western Journal of Applied Forestry. 22 (2) 2007:73-80.	April 2007
Euliss, N. H., Jr., L. M. Smith, S. Liu, W. G. Duffy, S. P. Faulkner, R. A. Gleason and S. D. Eckles. 2008. Integrating estimates of ecosystem services from conservation programs and practices into models for decision makers: The vision for CEAP Wetlands. Ecological Applications (In Press). \| Abstract \| Publisher Website	March 2011	Most government agencies involved in land management are seeking consistent approaches to evaluate the effects of specific management actions on ecological change, and concurrent changes on ecosystem services. This is especially true within the context of anthropogenic influences, such as land-use and climate change. The Conservation Effects Assessment Project-Wetlands National Component (CEAP Wetlands) was developed by the USDA to evaluate effects of conservation practices ecosystem services including carbon sequestration for climate stability, groundwater recharge, nutrient retention, runoff and flood attenuation, water storage, nutrient and contaminant retention, and wildlife habitat. A primary purpose of CEAP Wetlands is to provide science-based information in an adaptive monitoring framework for use by USDA to facilitate policy and management decisions and to document effects of conservation programs and practices to the federal Office of Management and Budget using an adaptive monitoring framework to facilitate policy and management decisions. Herein, we propose a model to allow estimation of conservation practice and program effects on various ecosystem services at different temporal and spatial scales. This modeling approach provides the broad view needed by decision makers to avoid unintended negative environmental outcomes, and also communicate to society the positive effects of conservation actions on a broad suite of ecosystem services.
Duffy, W.G., Kahara, S.N. and Records, R.M., eds., 2011, Conservation Effects Assessment Project-Wetlands assessment in California's Central Valley and Upper Klamath River Basin: U.S. Geological Survey Open-File Report 2011-1290, 128 p. \| Abstract \| Download \| Publisher Website	October 2011	The Wetlands Reserve Program (WRP) is one of several programs implemented by the U.S. Department of Agriculture (USDA). Since the WRP's inception in 1990, it has resulted in the restoration of approximately 29,000 hectares in California's Central Valley (CCV) and roughly 12,300 hectares in Oregon's Upper Klamath River Basin (UKRB). Both the CCV and UKRB are agricultural dominated landscapes that have experienced extensive wetland losses and hydrological alteration. Restored habitats in the CCV and UKRB are thought to provide a variety of ecosystem services, but little is known about the actual benefits afforded. The U.S. Geological Survey (USGS) California Cooperative Fish and Wildlife Unit in collaboration with the USDA Natural Resources Conservation Service surveyed 70 WRP sites and 12 National Wildlife Refuge sites in the CCV, and 11 sites in the UKRB to estimate ecosystem services provided. In the CCV, sites were selected along three primary gradients: (1) restoration age, (2) management intensity, and (3) latitude (climate). Sites in the UKRB were assessed along restoration age and management intensity gradients where possible. The management intensity gradient included information about the type and frequency of conservation practices applied at each site, which was then ranked into three categories that differentiated sites primarily along a hydrological gradient. Information collected was used to estimate the following ecosystem services: Soil and vegetation nutrient content, soil loss reduction, floodwater storage as well as avian, amphibian, fish and pollinator use and habitat availability. Prior to this study, very little was known about WRP habitat morphology in the CCV and UKRB. Therefore in this study, we described these habitats and related them to ecosystem services provided. Our results indicate that although WRP in the CCV and UKRB provide a number of benefits, there may be management mediated trade-offs among ecosystem services. In this report, we considered ecosystem services at the site-specific scale; however, future work will extend to include effects of WRP relative to surrounding cropland.
Duffy, W. and Thorsteinson, L., 2011, Synthesis of information needs and science priorities, Pages 185-198 in: Proceedings of the Klamath Basin Science Conference, Medford, Oregon, February 1–5, 2010: U.S. Geological Survey Open-File Report 2011-1196, 312 p.	July 2011
Duffy, W. G., and S. N. Kahara. 2008. Wetland ecosystems in California's Central Valley and impications for wetland reserve program conservation practices. Ecological Applications (Preprint on line 8/5/2010). \| Abstract \| Publisher Website	March 2011	Primary ecosystem services provided by freshwater wetlands in the California’s Central Valley include water quality improvement, biodiversity support and flood storage capacity. We describe these services for freshwater marshes, vernal pools and riparian wetlands and the implications for wetlands restored under USDA programs in the Central Valley. California’s Central Valley is a large sedimentary basin that was once covered by grasslands, extensive riparian forests and freshwater marshes that today have been converted to one of the most intensive agriculture areas on earth. Remaining freshwater wetlands have been heavily altered and most are intensively managed. Nitrogen loading from agriculture to surface and groundwater in the Central Valley was estimated to be 34.7 X 106 kg N/yr. Atmospheric deposition of nitrogen in the Central Valley was estimated to be 44.3 X 106 kg N/yr, of which about 1.5 X 106 kg N/yr was introduced directly to wetlands. Our analysis indicates that wetlands enrolled in the USDA Wetland Reserve Program may potentially denitrify the NO3-N load from relatively unpolluted source water in less than 18 days, but the potential to denitrify the NO3-N load from highly polluted source water is uncertain. Water management strongly influences use, diversity and abundance of avian fauna as well as other biota. Nevertheless, freshwater marshes in the region continue to support important populations of breeding and wintering waterfowl and shorebirds whose populations fluctuate seasonally. Avian diversity in the little remaining area of Central Valley riparian wetlands is also high and is influenced by stand maturity, heterogeneity and diversity. USDA conservation practices that promote these characteristics may support avian diversity. Effects of USDA conservation practices on non-avian fauna are poorly understood and warrant further study.
Duffy, W. G., and E. P. Bjorkstedt. Demographics of Coastal Cutthroat Trout, Oncorhynchus clarki clarki, in Prairie Creek, California. In Press. Proceedings of the 2nd Conference on Sea Run Cutthroat Trout, Port Townsend, WA, 29 Sept - 1 Oct, 2005. \| Abstract	August 2008	The southern distribution of coastal cutthroat trout Oncorhynchus clarkii clarkii terminates in northern California. Coastal cutthroat trout have received less attention in this region than they have further north and less is known of their ecology and abundance. We monitored population abundance in and gathered basic biological data from fish in three coastal streams in northern California during 2000-2004. Density ranged from 107-983 fish/ha during the period and varied among streams and years, although strong temporal trends were not apparent. Density was greater in pool and run habitats than in riffle habitats. Density was correlated with abundance of juvenile coho salmon, O. kisutch, in pool habitats, but not in run or riffle habitats. The size of 1,220 coastal cutthroat trout measured during the period ranged from 50-269 mm. Size of fish sampled differed among streams, years, and habitat types. Condition of coastal cutthroat trout also did not differ among streams or between seasons, but did differ among years. Our principal finding was that coastal cutthroat trout population abundance in northern California streams sampled appears stable, although abundance varies with habitat condition.
Deibner-Hanson, J.D. and Henderson, M. Life Cycle Monitoring of Coho Salmon in Prairie Creek 2017-2020. Final Report to Fisheries Restoration Grant Program Project Number P1610520. April 2021. \| Abstract	October 2021	Prairie Creek, tributary to Redwood Creek in norther Humboldt County, California, drains an extremely important watershed acting as a stronghold for many plant and animal species living in its pristine old-growth redwood forest. Vital to the ecology of the forest are several keystone salmonid species including Coho Salmon, Chinook Salmon, steelhead and coastal cutthroat trout. This report summarizes the cumulative work we accomplished across three years of monitoring juvenile and adult populations of Coho Salmon in Prairie Creek. The primary purpose of this project was to provide estimates of the four critical Coho Salmon population parameters needed to maintain the status of Prairie Creek as a Life Cycle Monitoring station including (1) adult salmonid redd abundance, (2) outmigrant smolt abundance, (3) freshwater survival and (4) marine survival. Each year, we PIT tagged juveniles throughout Prairie Creek in October, we conducted spawning ground surveys in Prairie Creek from November through March, we trapped and tagged smolts on their way to the ocean from March through July, and we operated several PIT tag antenna arrays year-round. Additionally, data collected in our monitoring projects enabled us to describe other life cycle attributes including early emigration analysis and overwinter growth estimation. During the three monitoring seasons, total redd estimates for Coho Salmon ranged from very low (127 in 2019-20) to high (429 in 2017-18) and outmigrant smolt abundance ranged from average (17,036 in 2018) to extremely high (34,807 in 2020). Apparent overwinter survival estimates were mostly consistent with previous years between 0.30-0.35, though a record high of 0.44 was estimated in 2019-20. We estimated smolt-to-adult return rates for the Coho Salmon smolt cohorts that emigrated in 2018 (1.06%) and 2019 (1.16%) which were consistent and fell within the expected range. Our three seasons of work from 2017-2020 extended the monitoring period in Prairie Creek to more than a decade.
Cummins, K. W., and M. A. Wilzbach. 2005. The inadequacy of the fish-bearing criterion for stream management. Aquat. Sci. 67:486-491	September 2005
Chen, E.K. and Henderson, M.J. 2021. Reduced recruitment of Chinook salmon in a leveed bar-built estuary. Canadian Journal of Fisheries and Aquatic Sciences 78: 894-904. \| Abstract \| Download	July 2021	Estuaries are commonly touted as nurseries for salmonids, providing numerous advantages for smolts prior to ocean entry. In bar-built estuaries, sandbars form at the mouth of rivers during periods of low stream flow, closing access to the ocean and disrupting outmigration. We evaluated how summer residency in a leveed bar-built estuary affects the growth, survival, and recruitment of a Chinook salmon (<i>Oncorhynchus tshawytscha</i>) population. We performed a mark-recapture study on outmigrants to determine juvenile estuary abundance, growth, and survival. We used returning adult scales and otoliths to determine the relative abundance of summer estuary residence in spawning adults. Juveniles in the estuary grew less after mouth closure, and ultimately summer estuary residents had lower smolt-to-adult survival and contributed disproportionately less to the spawning population than fish rearing in the ocean. Mouth closure may lower food availability and deteriorate estuary conditions by reducing marine prey influx and estuary circulation. This research demonstrates the complexity of estuary dynamics and function as salmonid nurseries, particularly when considering the extensive modification of estuaries.
Bell, E., and W. G. Duffy. 2007. Previously undocumented two-year freshwater residency of juvenile coho salmon in California. Transactions of the American Fisheries Society 136:966-970. \| Abstract	January 2008	Over 2,000 juvenile coho salmon Oncorhynchus kisutch were tagged with passive integrated transponder (PIT) tags during the fall of 1998 and 1999 in Prairie Creek, California, as part of a study on individual winter growth rates and movement of juvenile coho salmon. During this study, age-2 out-migrants were incidentally observed. Previously, it had been generally assumed that all juvenile coho salmon in northern California streams spend only 1 year in freshwater before out-migrating at age 1 and that a 2-year freshwater life history pattern was found only in the more northerly portions of the species’ range. Subsequently, scale analysis of PITtagged fish recaptured during spring out-migration was used as a basis for estimating the proportion of out-migrants displaying a 1- or 2-year freshwater residency life history. Twenty-eight percent (28%) of out-migrants captured in spring 2000 displayed a 2-year freshwater residency life history, apparently related to low winter growth rates documented in related research in the study stream.
Bell, E., W. G. Duffy and T. D. Roelofs. 2001. Fidelity and survival of juvenile coho salmon in response to a flood. Transactions of the American Fisheries Society. 130:450-458.	October 2001
Ambrose, H. E., M. A. Wilzbach, and K. W. Cummins. 2004. Periphyton response to increased light and salmon carcass introduction in northern California streams. Journal of the North American Benthological Society, 23: 701-712	November 2004

Presentations

Presentations	Presentation Date
Wright, K.A. and W.G. Duffy. 2007. Monitoring Chinook and coho salmon escapement in Prairie Creek, California. 28th Annual Meeting, Pacific Ecology and Evolution Conference, University of Washington Pack Experimental Forest, WA. March 2007.	March 2007
Wright, K. A. and W. G. Duffy. 2007. Escapement estimation of adult coho and Chinook salmon in Prairie Creek, California. 137th Annual Meeting, American Fisheries Society, San Francisco, CA, September 2007.	September 2007
Winship, Thorson, Henderson et. al (2019) Best practices for spatial predictive modeling to support effective management of deep-sea corals and sponges. 7th International Symposium on Deep-Sea Corals. July 29-August 2, 2019, Cartagena, Colombia.	July 2019	Resource managers in the USA and worldwide are tasked with identifying and mitigating trade-offs between human activities in the deep sea (e.g., fishing, energy development, and mining) and their impacts on corals and sponges.
Wilzbach, P. and K. Cummins. 2008. Reproduction and development of Manayunkia speciosa. 4th Annual Klamath River Fish Health Workshop, sponsored by the USFWS, Fortuna, CA, January 2008.	January 2008
Wilzbach, P. 2008. Movement of resident trout transplanted below a barrier to anadromy. 11th Annual Pacific Coast Steelhead Management Meeting, sponsored by Pacific States Marine Fisheries Commission, Boise, ID, March 2008.	March 2008
Wilzbach, M.A., K.W. Cummins, T.K. Barnes, and J.C. Trexler. Feb 2001. Channel-floodplain coupling in the Kissimmee River, Florida (USA): invertebrate movement and fish feeding. International Limnological Society Meeting, Melbourne, Australia	February 2001
Wilzbach, M.A., K.W. Cummins, S. Willson, M. Yost, and D. Malakauskas. 2007. Field and lab studies on the distribution and ecology of Manayunkia speciosa. Klamath River Fish Health Conference, Fortuna, CA. January 2007.	January 2007
Wilzbach, M.A., B.C. Harvey, J. L. White, and R.J. Nakamoto. 2003. Relative effects of carcass addition and light enhancement on salmonid biomass and growth. Western Division American Fisheries Society Annual Meeting, San Diego, CA.	April 2003
Wilzbach, M.A. and M.A. Madej, July 2001, Composition of Suspended Sediments and Stream Health, California Department of Forestry Monitoring Study Group	July 2001
Wilzbach, M.A. and K.W. Cummins. 2006. Relative contribution of autotrophic and heterotrophic food pathways to salmonid growth. 54th annual Meeting, North American Benthological Society, Anchorage, AK. June 2006	June 2006
Wilzbach, M.A. and B.W. Hodge. 2015. Life history variation in Klamath River steelhead.	August 2015	We identified 36 life history trajectories in Klamath River steelhead using scale and otollith strontium isotope analyses. The rich life history diversity we observed likely contributes to resilience, and can help jump start recolonization of formerly anadromous habitats after planned dam removal.
Wilzbach, M.A. 2016. Fisheries and Aquatic Resources of Prairie Creek. Prairie Creek Technical Advisory Committee for Redwood National Park. Orick, California. April 5, 2016.	April 2016	This work synthesized previous research conducted on fisheries and aquatic resources of Prairie Creek, assessed factors limiting salmonid production in the creek, and identified data gaps relevant to management needs. The work will assist managers in planning restoration activities.
Wilzbach, M.A. 2015. Role and source of macroinvertebrates in fish growth. Riparian Summit Conference. Korbel, California. 29-30 August 2015.	April 2015	This work synthesized literature and previous work on the riparian v. aquatic origin of macroinvertebrate prey for stream salmonids, and its importance in salmonid production. The work will help guide riparian management strategies.
Wilzbach, M. A., Nov 2001. Importance of Light and Nutrients to Salmonid Growth	November 2001
Wilzbach, M. A., May 2002. Suspended organic sediments, Caspar Creek Annual Meeting, Jackson Demonstration State Forest, Fort Bragg, CA.	May 2002
Wilzbach, M. A., May 2002. Stream ecosystem response to light enhancement and salmon carcass introduction, 50th Ann. Meeting, North American Benthological Society, Pittsburg, PA.	June 2002
Wilzbach, M. A. and S. L. Frazey. 2005. Linking forests and fish:the relationship between productivities of salmonids and forest stands in northern California. Poster presentation, NABS Ann. Mtng., New Orleans, LA.	May 2005
Wilzbach, M. A. and K. W. Cummins. Alternative riparian management. Univ. Idaho Extension Workshop for Family Foresters, Jan. 20, 2006, Spokane, WA.	January 2006
Wilzbach, M. A. Riparian canopy openings and salmon carcass additions to increase salmonid growth. Western Forestry Conference on the Science and Policy of Wildlife and Salmon, Dec. 6, 2006, Portland, OR.	December 2005
Wilzbach, M. A. 2007. Should deep, dark, and dense riparian canopy coverage be the target for salmonid fishes? Symposium on Forestry and Anadromy in California, sponsored by the California Licensed Foresters Association. Redding, CA, October 2007.	October 2007
Wilzbach, M. A. 2005. Riparian management and fish productivity. National Council for Stream and Air Improvement, September 29, 2005.	September 2005
Wilzbach, M. A. 2005. Research against the grain. CRU National Meeting, 03/03/2005.	March 2005
Wilzbach, M. A. 2003. Riparian canopy opening overrides salmon carcass addition in affecting salmonid growth. Smith River Colloquium, Crescent City, CA.	November 2003
Williams, T.H., E.P. Bjorksted, W. Duffy, D. Hillemeier, G. Kautsky, T. Lisle, M. McCain, T. Nickelson, E. Mora, and T. Pearson. 2006. Historical population structure of coho salmon in the southern Oregon/northern California evolutionary significant unit. 42nd Annual Meeting, Oregon Chapter, American Fisheries Society, Sunriver, OR. February 2006.	February 2006
Walden, M.A. and N.A. Som. 2024. Evaluating alternative methods for modeling trap efficiencies of outmigrating juvenile salmonids. Ecological Society of American Annual Meeting. Long Beach, CA.	August 2024	Klamath dam removal is opening 400 river miles to salmon. Abundance monitoring of Chinook Salmon using rotary screw traps has been performed by USFWS and tribal partners since the 1990s. Dam removal also removes the hatchery providing fish for mark-recapture experiments to estimate fish abundance. Future estimation of trap efficiency will require model-based estimates so abundances can be generated without trap efficiency trials, to maintain this important time series of abundance information.
Van Vleet, Nicholas and Henderson, Mark. A novel approach to estimate winter movement and survival of juvenile Coho Salmon. 37th Annual Salmonid Restoration Conference. April 23-26, 2019. Santa Rosa, CA.	April 2019	Previous mark-recapture models using passive integrated transponder data have ignored temporal variation in survival (i.e., detection date is irrelevant) in order to estimate movement and survival rates at particular locations within the study area over a period of time. Condensing these data into a single point in time violates an assumption of the mark-recapture model model and results in a loss of information. In this study, we develop a novel multi-state model that accounts for this tempora
Van Vleet N., Henderson M.J., Ward, D. 2018. Winter movement and survival of juvenile Coho Salmon in Freshwater Creek, California. Oregon Chapter of the American Fisheries Society 54nd Annual Meeting, Eugene, OR. March 13-16, 2018.	March 2018	This project uses a multi-state model to provide estimates of early emigration rates for fall/winter migrant juvenile Coho Salmon, as well as survival rates for spring smolt migrants. We developed models to examine the effect of various individual and environmental covariates (e.g., streamflow, gradient, fork length at fall tagging) on survival and migration probabilities.
Van Vleet N., Henderson M.J., Ward, D. 2018. Winter movement and survival of juvenile Coho Salmon in Freshwater Creek, California. 52nd Annual California-Nevada American Fisheries Society meeting, San Luis Obispo, CA. Feb 28 - March 2, 2018.	March 2018	This project uses a multi-state model to provide estimates of early emigration rates for fall/winter migrant juvenile Coho Salmon, as well as survival rates for spring smolt migrants. We developed models to examine the effect of various individual and environmental covariates (e.g., streamflow, gradient, fork length at fall tagging) on survival and migration probabilities.
Som, N.A. 2024. Monitoring to science to management: science-informed decision making to combat an aquatic parasite. Trinity River Restoration Program Science Symposium.	May 2024	This presentation summarizes the efforts to uncover the the lifecycle of C. shasta, a parasite causing substantive mortality in Klamath River juvenile salmonids. The discoveries discussed have also informed management decisions to improve fish survival.
Som, N.A. 2024. Modeling Habitat of an Invertebrate Host of Salmonid Parasites to Inform Management Decision Making. American Fisheries Society Annual Meeting. Honolulu, HI. September.	September 2024	In this talk, I describe how collaborative monitoring and research projects made substantive progress to describe the full lifecycle of <i>Ceratonova shasta</i>, a parasite endemic to the Klamath River, and how this scientific information was used to create water management actions to reduce this risk in the future.
Solinger L., Bjorkstedt E., Buchheister A., Henderson M., and Field J. 2018. Developing spatially-explicit stock assessment models to explore spatial variability in recruitment of Chilipepper Rockfish (Sebastes goodei). 13th National Stock Assessment Workshop. Irvine, CA. May 22-24, 2018.	May 2018	Stock Synthesis 3 (SS3) was used to build seven spatially explicit stock assessment models for Chilipepper Rockfish (Sebastes goodei) that represented the coast of California and the majority of the population. . Results from this work are intended to inform efforts to incorporate spatial structure and oceanographic influence on recruitment and population dynamics in west coast rockfishes.
Sascha L. Hallett Jerri L. Bartholomew, Julie D. Alexander, Justin Alvarez, Stephen D. Atkinson, Michael Belchik, Sarah J. Bjork, J. Scott Foott, Alex Gonyaw, Mark E. Hereford, Richard A. Holt, Barry McCovey Jr., Nicholas A. Som, Toz Soto, Anne Voss, Thomas H.Williams, Ted G. Wise. 2024. Disease risk for salmonids after reconnection of the Klamath Basins. American Fisheries Society Western Fish Disease Workshop. Boise, ID. July 30 - August 1, 2024.	August 2024	This work discusses implications and predicted impacts to fish species for a suite of fish health issues in the Klamath Basin after removal of 4 dams.
Sascha L. Hallett Jerri L. Bartholomew, Julie D. Alexander, Justin Alvarez, Stephen D. Atkinson, Michael Belchik, Sarah J. Bjork, J. Scott Foott, Alex Gonyaw, Mark E. Hereford, Richard A. Holt, Barry McCovey Jr., Nicholas A. Som, Toz Soto, Anne Voss, Thomas H.Williams, Ted G. Wise. 2024. Dam Removal and Ecological Transformation on the Klamath River. American Fisheries Society Annual Meeting. Honolulu, HI. September 2024.	September 2024	This work discusses implications and predicted impacts to fish species for a suite of fish health issues in the Klamath Basin after removal of 4 dams.
Rizza, S., A.P. Kinziger, J.C. Garza, and M.A. Wilzbach. 2015. Asymmetric introgression between Coastal Cutthroat Trout and steelhead in the Smith River Basin, California. 145th Annual Meeting of the American Fisheries Society. Portland, Oregon. August 16-20, 2015.	August 2015	Analysis of introgression between sympatric Coastal Cutthroat Trout and steelhead within a large, relatively pristine basin in northern California revealed a sparse occurrence of first generation hybrids and that backcrosses were driven by sneak-mating of male cutthroat with female steelhead. Results are of interest to managers seeking means to visually distinguish between the two species in the field.
Pope, K. L., M. P. Carey, D. R. DeVries, J. E. Garvey, M. Henderson, S. Hitchman, M. E. Mather, J. M. Smith, and R. W. Tingley. 2022. Researchers and managers: co-development of science-based management. Joint Aquatic Sciences Meeting, Grand Rapids, Michigan (Virtual).	May 2022	Adapting how manager-researcher teams frame questions may advance the co-development process. Considering progress made for science-based management, using examples, we review key obstacles and prerequisites for building collaborative research-management relationships in the aquatic arena.
Okun, N. and Henderson, M. Large wood restoration effectiveness for salmonids in Pudding Creek, CA: a before-after-control-impact experiment. 37th Annual Salmonid Restoration Conference. April 23-26, 2019. Santa Rosa, CA.	April 2019	Substantial resources are invested in large woody debris (LWD) restoration projects with the intention of improving at-risk salmonid populations, but assessments of population response to LWD projects are largely lacking. This study will use a Before-After-Control-Impact (BACI) complete watershed experimental design to provide quantitative evidence to support, or refute, whether large woody debris is an effective restoration technique. This study is the first of it's kind in California and coul
Okun, N. and Henderson, M. Large Wood Restoration Effectiveness for Salmonids in Pudding Creek, CA: A before-after-Control-Impact Experiment. 149th annual meeting of the American Fisheries Society. Reno, NV. September 29 - October 3, 2019.	September 2019	Substantial resources are invested in large woody debris (LWD) restoration projects with the intention of improving at-risk salmonid populations, but assessments of population response to LWD projects are largely lacking. This study will use a Before-After-Control-Impact (BACI) complete watershed experimental design to provide quantitative evidence to support, or refute, whether large woody debris is an effective restoration technique. This study is the first of it's kind in California and coul
Nissa Kreidler, Dave Huff, Jerome Fiechter, Andre Buchheister, Mark Henderson. Species Distributions Modeling of Deep-Sea Coral and Sponge Taxa in the Southern California Bight. Ocean Sciences Meeting. Honolulu HI February 27 - March 4 2022.	March 2022	Predictions of where Deep-Sea Coral and Sponge taxa (DSCS) may occur are needed for the management and protection of DSCS taxa and the fauna (e.g. juvenile rockfish) that rely on them for habitat. This study provides predictive models and maps for three ecologically important DSCS<i> </i>in Southern California: <i>Antipathes dendochristos, Plumarella longispina, </i>and an unidentified Porifera<i> </i>sponge.
Naman, S. W. and M. A. Wilzbach. 2007. Predation by hatchery-reared steelhead on natural salmonid fry in the upper Trinity River, California. Annual Meeting of the American Fisheries Society, San Francisco, CA, September 2007.	September 2007
Mull, K. E. and M. A. Wilzbach. 2007. Selection of spawning sites by coho salmon in Freshwater Creek, California. Annual Meeting of the American Fisheries Society, San Francisco, CA, September 2007.	September 2007
Michel C., Smith, J., Demetras N., Iglesias I., Lehman B., Loomis C., Henderson M., Huff D. 2018. Spatial patterns and environmental associations of piscivorous predation throughout the south Sacramento-San Joaquin River Delta in 2017. 10th biennial Bay-Delta Science Conference, Sacramento, CA. September 10-12, 2018.	September 2018	It is currently not clear what proportion of juvenile salmonid mortality can be directly attributed to fish predation, and it is difficult to interpret results regarding population‐level salmonid predation in the Delta because empirical data have only been collected at limited spatial scales. During the spring of 2017, we quantified predation mortality rates, predator abundance and composition, and relevant environmental covariates in 21 randomly selected 1-km long field sites in the south Delt
Michel C., Loomis C., Henderson M., Smith J., Demetras N., Iglesias I., Lehman B., Huff D., and Hayes S. Fish predation on a landscape scale. OneNOAA Science Seminar Series.	August 2020	Predator-prey dynamics can have landscape-level impacts on ecosystems, and yet, spatial patterns and environmental predictors of predator-prey dynamics are often investigated at discrete locations, limiting our understanding of the broader impacts.
McLaughlin, K. D. and W. G. Duffy. 2007. Condition of juvenile steelhead in northern California streams. 137th annual Meeting, American Fisheries Society, San Francisco, CA, September 2007.	September 2007
Malakauskas, D., S. Willson, M.A., M.A. Wilzbach, N. Som. Effect of flow manipulation on polychaete dislodgement in a laboratory flume. Klamath River Fish Disease Workgroup. March 27, 2012, Klamath Falls, OR.	March 2012
Madej, M. A., M. A. Wilzbach, K. W. Cummins, C. C. Ellis and S. J. Hadden. 2004. The significance of suspended organic sediments to turbidity, sediment flux, and fish-feeding behavior. Redwood Region Forest Sciences Symposium. Rohnert Park, CA.	March 2004
Loomis, C. and Henderson, M. Estimating predator fish density and abundance in the Sacramento-San Joaquin Delta using DIDSON Acoustic cameras. 37th Annual Salmonid Restoration Conference. April 23-26, 2019. Santa Rosa, CA.	April 2019	Juvenile salmonids may experience substantial predation mortality while transiting through the Sacramento-San Joaquin Delta, yet we lack empirical evidence linking mortality to predation. This study used an experimental method to estimate piscivore populations with DIDSON acoustic cameras in the context of a Delta-wide predation study.
Loomis, C and Henderson, M. Density and Distribution of Piscivorous Fishes in the Sacramento-San Joaquin Delta. 149th annual meeting of the American Fisheries Society. Reno, NV. September 29 - October 3, 2019.	October 2019	Non-native predatory fish are common to the Sacramento – San Joaquin Delta, but abundance data for most species is insufficient to determine the Delta-wide distribution and ecological associations of these species. In this study, we present a novel method to assess predator fish populations across the southern Delta using DIDSON acoustic cameras and analyze the environmental associations that form the landscape and fine-scale distribution of predatory fishes.
Loomis C. and Henderson M., 2018. Estimating Delta predatory fish abundance with DIDSON acoustic cameras. 10th biennial Bay-Delta Science Conference, Sacramento, CA. September 10-12, 2018.	September 2018	The relationship between predatory fish abundance and predation of juvenile salmonids in the Sacramento -San Joaquin Delta (the Delta) has been obscured by the relatively unknown populations and distributions of predator fish. This study focuses on an experimental approach to estimate predator fish density in multiple habitats within the Delta using DIDSON acoustic cameras.
Kreidler, Buchheister, and Mark Henderson (2019) Habitat Suitability Mapping for Fish Indicative Deep Sea Corals and Sponges in the Southern California Bight. International deep sea coral symposium.	July 2019	Deep-sea coral and sponge species (DSCS) are some of the longest-lived marine species and their complex, three-dimensional structure provides habitat for demersal fish and invertebrates. Habitat suitability maps, which predict where these DSCS species may occur, are needed to understand what areas of suitable habitat are currently protected and what areas are still exposed to potential destruction. Until recently, the relationship between DSCS and fish species in the Southern California Bight w
Kreidler N., Buchheister A., and Henderson M. 2018. Habitat Suitability Mapping for Southern California Bight Deep Sea Corals and Sponges. 15th Deep-Sea Biology symposium. Monterey, CA. Sept 9-14, 2018	September 2018	Habitat suitability maps, which predict where Deep-Sea Coral and sponge species may occur, are needed to understand what areas of suitable habitat are currently protected and what areas are still exposed to potential destruction. In this study, we used Generalized Additive Models (GAMs) to identify environmental factors that are the best proxies for predicting Deep-Sea Coral and sponge occurrence.
King, B., O'Dowd, A., Laskodi, C., Ward, D., Som, N.A. 2024. Effects of scour and marginal habitat inundation of Trinity River Invertebrate communities. Salmon Restoration Federation Annual Meeting. Santa Rosa, CA.	March 2024	This presentation summarizes results from a study evaluating impacts scour occurrence and inundation duration to a subset of benthic macroinvertebrates, specifically known to constitute the majority food for juvenile salmonids, in the Trinity River, CA. Results can impact flow management decision making and improve food resources for fish.
Kanawi, E., Kinziger, A., and Henderson, M. Using environmental DNA water samples to determine the timing and abundance of outmigrating Coho Salmon. 55th Annual Meeting of the Oregon Chapter of the American Fisheries Society. March 4-8, 2019. Bend, OR.	March 2019	We examined the potential of using an environmental DNA (eDNA) sampling program to assess migrating salmon populations in conjunction with a traditional monitoring approach. Environmental DNA has the potential to dramatically increase the quality and volume of information available to resource managers, however, knowing its limitations will lead to more appropriate use of this technology.
Kanawi, E., Kinziger, A., and Henderson, M. Using environmental DNA water samples to determine the timing and abundance of outmigrating Coho Salmon. 37th Annual Salmonid Restoration Conference. April 23-26, 2019. Santa Rosa, CA.	April 2019	We examined the potential of using an environmental DNA (eDNA) sampling program to assess migrating salmon populations in conjunction with a traditional monitoring approach. Environmental DNA has the potential to dramatically increase the quality and volume of information available to resource managers, however, knowing its limitations will lead to more appropriate use of this technology.
Kahara, S. K. and W. G. Duffy. Ecosystem services influence of USDA farm conservation practices on wetlands in California's Central Valley. annual Meeting, Society of Wetland Scientists, Washington, D.C., May 2008.	May 2008
Justice, C. and W. G. Duffy. 2007. Response of juvenile salmonids to placement of large wood debris in California coastal streams. 43rd Annual Meeting, Oregon Chapter, American Fisheries Society, Eugene, OR, February 2007.	February 2007
Hollis, J. and M.A. Wilzbach. 2016. Export of invertebrate drift from fishless headwater streams of the lower Klamath River Basin, California, and its use by trout. Annual Meeting, Society for Freshwater Science. Sacramento, California. May 21-26, 2016.	May 2016	We described the magnitude and composition of invertebrate drift exported from fishless headwater streams and evaluated its contribution to diets of trout feeding downstream. The work is of importance in developing riparian management strategies to meet aquatic conservation goals.
Hollis, J. and M. A. Wilzbach. 2016. Export of invertebrate drift from fishless headwater streams in the lower Klamath River Basin, California, and its use by trout. Coast Redwood Forest Symposium, Eureka, California.	September 2016	We described the magnitude and composition of invertebrate drift exported from fishless headwater streams and evaluated its contribution to diets of trout feeding downstream. The work is of importance in developing riparian management strategies to meet aquatic conservation goals.
Hodge, B., P. Wilzbach, W.Duffy. The steelhead half-pounder life history: paradox or hedge bet? Western Division American Fisheries Society, March 29, 2012, Jackson WY.	March 2012
Hernandez, O., M.A. Wilzbach, K.W. Cummins, and R.W. Merritt. 2006. Red alder (Alnus rubra) breakdown rates in light and nutrient augmented second order streams of northern California. 54th Annual Meeting, North American Benthological Society, Anchorage, AK. June 2006.	June 2006
Henderson, M.J., Kreidler, N, Yoklavich, M., Buchheister, A., Fiechter J., Huff, D. 2021. The importance of accounting for spatial autocorrelation in habitat analyses. 151st meeting of the American Fisheries Society, Baltimore, MD, USA, November 6-10, 2021.	November 2021	Fisheries biologist spend an extraordinary amount of time collecting data on species distributions, and associated habitat related covariates, to develop models to predict how these distributions may change relative to climate change. Unfortunately, many of the common species distribution models ignore spatial autocorrelation. In this talk we demonstrate how using models that account for spatial autocorrelation can produce considerably different, and more realistic, results than those more comm
Henderson, M.J., I. Iglesias, C. Michel, D. Huff, E. Danner, and S. Hayes. 2018. Processes influencing outmigrating Chinook Salmon survival in the Sacramento River. 148th Annual Meeting, American Fisheries Society, Atlantic City, NJ, 19-23 August 2018.	August 2018	We used a mark-recapture model to estimate survival of outmigrating Chinook Salmon as a function of environmental, and individual, covariates. Our results provide valuable information to water resource and fisheries managers on how to reduce salmon mortality under different environmental conditions.
Henderson, M.J., Huff, D.D., and Yoklavich, M. 2018. Associations between deep-sea coral and sponge assemblages and demersal fishes in the Southern California Bight. 2018 Ocean Sciences Meeting, Portland OR, 11-16 September 2018.	February 2018	To protect the sensitive deep-sea coral, sponge, and demersal fish species in the Southern California Bight it is first necessary to understand their biotic and physical relationships. We used a multivariate analysis to understand the relationships between deep sea coral/sponge assemblages and associated demersal fish species.
Henderson, M., Iglesias, I., Michel, C., Huff, D., Pike, A., Danner, E., and Hayes, S. 2017. Mortality of Central Valley Chinook Salmon smolts relative to physical habitat features. 51st Annual meeting, Cal-Neva Chapter of the American Fisheries Society, Eureka, California, April 5-7, 2017.	April 2017	We utilized five-years of acoustic telemetry data for late-fall run Chinook Salmon in the Sacramento River to evaluate the effect of temporally stable physical habitat features (e.g., diversion density), individual specific spatio-temporal factors (e.g., flow), and individual fish attributes (e.g., condition) on overall survival during their outmigration to sea. Our results indicate that smolt survival increased in the lower, more modified, regions of the river which may have been due to decrea
Harvey, B. C. and M. A. Wilzbach. 2007. Carcass addition fails to affect abundance and growth of resident salmonids in northern California streams. Annual Meeting of the American Fisheries Society, San Francisco, CA, September 2007.	September 2007
Hadden, S. J. and M. A. Wilzbach. 2004. Effect of organic and inorganic suspended load concentration on the foraging efficiency of juvenile salmonids in the field and artificial stream channels. Annual Meeting of the Cal-Neva Chapter of the American Fisheries Society, Redding, CA, April 22-24, 2004.	April 2004
H. Eve Robinson, J. Rudi Strickler, Mark J. Henderson, Daniel K. Hartline, Petra H. Lenz	June 2018	Fish larvae depend on finding and capturing prey for rapid growth during the larval phase. We developed feeding experiments to elucidate how specific characteristics of both fish and their prey affect predation strategies and capture success.
Feyrer, F., Perry, R., Clause, J., Young, M., Huntsman, B., Larwood, V. Enos, E. Henderson, M., Dick, C., Larson, W., Shi, Y., Michel, C., and Nelson, T.R.. Quantifying the Role of Predation by Piscivorous Fishes as a Source of Juvenile Chinook Salmon Mortality in the Sacramento-San Joaquin Delta. Interagency Ecological Program annual workshop, March 22-24, 2022	March 2022	place holder
Euliss, N. H., L. M. Smith, W. G. Duffy and S. Faulkner. 2007. Beyond CEAP: Integrating delivery of concurrent goods and services attributable to conservation programs into models for decision makers to evaluate ecological change. Annual Meeting, Society of Soil and Water Conservation, Tampa, FL, June 2007.	June 2007
Duffy, Walter G. , Bjorkstedt, Eric P. and Ellings, Christopher S.(2011) 'Predation on Juvenile Pacific Salmon Oncorhynchus spp. in Downstream Migrant Traps in Prairie Creek, California, American Fisheries Society Meeting, Seattle, WA	September 2011
Duffy, W.G. 2011. Regional update on the status of coho salmon. Joint Committee on Fisheries and Aquaculture, California Legislature.	August 2011
Duffy, W.G. 2010. Potential effects of suction dredging for gold on fish. California Department of Fish and Game, Advisory Committee on Gold Dredging, Sacramento, Ca	February 2010
Duffy, W.G. 2010. Ecosystem services provided by Wetland Reserve Program wetlands of California's Central Valley.	March 2011
Duffy, W.G. 2007. Fish in wetlands: the good, the bad and the ugly. Workshop on Wetland Assessment in California, USDA-NRCS, Davis, CA. March 2007.	March 2007
Duffy, W. G., D. Schultz and M. Brown. 2004. Using relative weight of coho salmon to evaluate fish response to watershed restoration. Annual Meeting Salmonid Restoration Federation, Davis, CA.	March 2004
Duffy, W. G. and S. A. Gough. 2006. Influence of turbidity on bioenergetics of coastal cutthroat trout. California-Nevada Chapter, American Fisheries Society, Annual Meeting, March 31, 2006, San Luis Obispo, CA.	March 2006
Duffy, W. G. and S. A. Gough. 2006. Comparison of methods for estimating adult salmon escapement. Salmonid Restoration Federation Conference, Santa Barbara, CA.	February 2006
Duffy, W. G. and E. P. Bjorksted. 2005. Demographics of coastal cutthroat trout in northern California. Second Coastal Cutthroat Trout Symposium, Port Townsend, WA	September 2005
Duffy, W. G. 2008. Influence of freshwater habitat quality on coho salmon populations: evidence from nine years of investigations in Redwood National Park. Aquatic Resources in Redwood Creek. Redwood National Park, Orick, CA April, 2008.	April 2008
Duffy, W. G. 2007. Life history of anadromous fishes in California. California Licensed Foresters Association, Redding, California, 25 October 2007.	October 2007
Duffy, W. G. 2007. Influence of Wetlands Reserve Program on California. Annual Meeting, Society of Soil and Water Conservation, Tampa, FL, June 2007.	June 2007
Duffy, W. G. 2005. Status of salmon and steelhead in coastal rivers of California. Presented to California State Legislature, Staff. Sacramento, California.	June 2005
Duffy, W. G. 2004. The Historical and Current Fish Community of the Klamath River, California. Lower Klamath Basin Science Conference, Arcata, CA.	June 2004
Duffy, W. G. 2008. Response of wetlands in California's Central Valley to global change. annual Meeting, Society of Wetland Scientists, Washington, D.C., May 2008.	May 2008
Duffy, W. G. 2008. Mortality of juvenile salmon associated with downstream migrant traps: a concern for monitoring. Annual meeting, California/Nevada Chapter, American Fisheries Society, Lake Tahoe, CA April 2008.	April 2008
Dockham, A., M.A. Wilzbach, and G. Horton. 2015. Comparison of benthic invertebrate community structure and diet composition of steelhead trout in Dry Creek, California. 33rd Annual Meeting Salmonid Restoration Federation. Santa Rosa, California. Mar 11-14, 2015.	March 2015	Longitudinal patterns of invertebrate prey abundance in this regulated river did not correspond with longitudinal patterns in steelhead growth. This study is important for managers seeking to design effective restoration projects to increase salmonid production.
Dockham, A. and M.A. Wilzbach. 2014. Comparison of benthic invertebrate community structure and diet composition of steelhead trout (Oncorhynchus mykiss) in Dry Creek, California. 1st Ann. Meeting California Chapter Society of Freshwater Science.	November 2014	We sampled macrinvertebrate benthos and diets of steelhead trout to evaluate prey availability for juvenile salmonids in a river undergoing habitat restoration. The study will be used to inform managers whether prey availability is contributing to factors restricting the success of juvenile salmonids in this location.
Dick, C., Larson, W., and Henderson, M. How many salmon smolts are consumed in the Sacramento-San Joaquin Delta: quantifying predation with molecular methods. 151st annual meeting of the American Fisheries Society, Baltimore, MD, USA. November 6-10, 2021	November 2021	Juvenile Chinook Salmon (<i>Onchorhynchus tshawytscha</i>) migrating through the Sacramento – San Joaquin Delta (the Delta) have higher mortality rates than salmonids migrating through other west coast estuaries, and invasive predators are considered one of the main drivers of these high mortality rates. In this study, we show the potential to use a novel molecular approach to quantify the abundance of Chinook salmon in the stomachs of invasive predators in the Delta.
DeYoung, C.J. and M.A. Wilzbach. 2007. Effects of turbidity on foraging efficiency and growth of salmonids in natural settings. Annual Meeting, Oregon Chapter, American Fisheries Society, Eugene, Or. February 2007.	February 2007
Damon Goodman, Nicholas A. Som, Cyril Michel, Keith Denton. 2023. Evaluating the effectiveness of dam removal on the Klamath River through sonar and radio telemetry. Klamath Basin Monitoring Program Annual Meeting. Klamath Falls, OR.	November 2023	We're on the precipice of the largest dam removal project in history with four Klamath River dams set to be removed in 2024. In this presentation, we outline steps to evaluate the impacts of dam removal on the abundance and spatial distribution of spawning salmon.
Cummins, K.W., M.A. Wilzbach, and G.L. Hendrickson. 2006. Studies of the freshwater polychaete Manayunkia speciosa, andd intermediate host for myxozoan parasites that infect Pacific salmon in the Klamath River, CA. 54th Annual Meeting, North American Benthological Society, anchorage, AK. June 2006.	June 2006
Cummins, K.W., M.A. Wilzbach, and D. Hankin. Development of a research plan for quantifying the abundance of the invertebrate host of salmonid parasites in the lower Klamath River. Klamath River Fish Health Workshop, sponsored by the USFWS and Humboldt State University. Arcata, CA. February 2006. Invited.	February 2006
Cummins, K. and P. Wilzbach. 2008. Recommendations for polychaete monitoring. 4th Annual Klamath River Fish Health Workshop, sponsored by the USFWS, Fortuna, CA, January 2008.	January 2008
Cummins, K. W., S. J. Hadden, and M. A. Wilzbach. 2005. The effect of turbidity on the efficiency of prey capture by juvenile salmonids. The Water Quality Conference II; Turbidity & Suspended Sediment Concentration, sponsored by California Dept. of Forestry and Fire Protection and University of California Cooperative Extension and The Center for Forestry. Redding, California.	April 2005
Colombano, P.A. and W.G. Duffy. 2007. Response of coastal steelhead streams to fire disturbance. 28th Annual Meeting, Pacific Ecology and Evolution Conference, University of Washington Pack Experimental Forest, WA. March 2007.	March 2007
Colombano, P. A. and W. G. Duffy. 2007. Response of coastal steelhead streams to fire disturbance. 137th Annual Meeting, American Fisheries Society, San Francisco, CA, September 2007.	September 2007
Chen, Emily and Henderson, Mark. Contribution of estuarine rearing in a bar-built estuary to recruitment of Chinook salmon using a hierarchical life cycle model. 55th Annual Meeting of the Oregon Chapter of the American Fisheries Society. March 4-8, 2019. Bend, OR.	March 2019	Estuaries are commonly touted as important habitats to juvenile salmonids, yet the diversity of estuaries complicates the effects they have on salmonid recruitment. We evaluated the prevalence, survival, and growth of Chinook salmon (Oncorhynchus tshawytscha) estuarine juveniles and compared them to ocean rearing juveniles. The results of our study provide insight into the efficacy of bar-built estuaries, an estuary type that may become more prevalent with the rise in frequency of drought condi
Chen, Emily and Henderson, Mark. Barred from the Ocean: Consequences of a Unique Estuary Phenomenon on Juvenile Growth and Population Recruitment of Chinook Salmon in Redwood Creek. 37th Annual Salmonid Restoration Conference. April 23-26, 2019. Santa Rosa, CA.	April 2019	Estuaries are commonly touted as important habitats to juvenile salmonids, yet the diversity of estuaries complicates the effects they have on salmonid recruitment. We evaluated the prevalence, survival, and growth of Chinook salmon (Oncorhynchus tshawytscha) estuarine juveniles and compared them to ocean rearing juveniles. The results of our study provide insight into the efficacy of bar-built estuaries, an estuary type that may become more prevalent with the rise in frequency of drought condi
Chen, E. and Henderson, M. Barred from the Ocean: Consequences of a Unique Estuary Phenomenon on Recruitment of Chinook Salmon. 149th annual meeting of the American Fisheries Society. Reno, NV. September 29 - October 3, 2019.	October 2019	Estuaries are commonly touted as important habitats to juvenile salmonids, yet the diversity of estuaries complicates the effects they have on salmonid recruitment. We evaluated the prevalence, survival, and growth of Chinook salmon (Oncorhynchus tshawytscha) estuarine juveniles and compared them to ocean rearing juveniles. The results of our study provide insight into the efficacy of bar-built estuaries, an estuary type that may become more prevalent with the rise in frequency of drought condi
Chen E. K., Henderson M.J. 2018 Contribution of juvenile estuarine residency to Chinook Salmon recruitment in Redwood Creek, California. Oregon Chapter of the American Fisheries Society 54nd Annual Meeting, Eugene, OR. March 13-16, 2018.	March 2018	In this study, we develop a life cycle model to investigate how different juvenile life history strategies relative to estuarine residency contribute to the recruitment of a cohort. The goal of this study is both to understand the importance of estuarine use to a population of Chinook Salmon and to assist local managers in assessing the value of estuarine restoration.
Chen E. K., Henderson M.J. 2018 Contribution of juvenile estuarine residency to Chinook Salmon recruitment in Redwood Creek, California. Cal-Neva Chapter of the American Fisheries Society 52nd Annual Meeting, San Luis Obispo, CA. Feb 28-March 2, 2018.	March 2018	In this study, we develop a life cycle model to investigate how different juvenile life history strategies relative to estuarine residency contribute to the recruitment of a cohort. The goal of this study is both to understand the importance of estuarine use to a population of Chinook Salmon and to assist local managers in assessing the value of estuarine restoration.
Caught in the middle: Top-down impact of seabirds on Chinook Salmon (Oncorhynchus tshawytscha) is dependent on bottom-up mechanisms	November 2016	For waters of coastal central California from 1983-2012, we related time series of environmental conditions, forage species availability, juvenile Chinook Salmon (Oncorhynchus tshawytscha) survivorship, and the abundance of a predator, common murre (Uria aalge), to show that prey switching can have significant consequences to salmon.
Bjorkstedt, E.P., B.C. Spence, T.H. Williams, W.G. Duffy, D. Fuller, J.C. Garza, D. Hankin, D. Hillemeir, W. Jones, G. Kautsky, T. Lisle, R. Macedo, M. McCain, M. Rode, J. Smith, R.G. Szerlong, R. Schick, T. Pearson, E. Mora, M. Goslin and A. Agrawal. 2007. Historical population structure of ESA-listed Pacific salmonids in the Southern Oregon/Northern California Coast and North-Central California Coast recovery domains. 137th Annual Meeting, American Fisheries Society, San Francisco, CA, September 2007.	September 2007
Associations between deep-sea coral/sponge assemblages and demersal fishes in the Southern California Bight	September 2016	To protect the sensitive deep-sea coral, sponge, and demersal fish species in the Southern California Bight it is first necessary to understand their biotic and physical relationships. We used a multivariate analysis to understand the relationships between deep sea coral/sponge assemblages and associated demersal fish species.
Ashenfelter, M. J. and M. A. Wilzbach. 2007. Movement of resident trout transplanted below a barrier to anadromy. Annual Meeting of the American Fisheries Society, San Francisco, CA, September 2007.	September 2007

Theses and Dissertations

Theses and Dissertations	Publication Date
Wright, K. A. 2011. Escapement, migration timing, and spatial distribution of adult chinook and coho salmon in Prairie Creek, California. M.S. Thesis, Humboldt State University, Arcata, California. 127 pp.	May 2011
Willey, W.S. 2004. Energetic response of juvenile coho salmon (Oncorhynchus kisutch) to varying water temperature regimes in northern California streams. 82 pp.	May 2004
Wheeler, M. 2009. Seasonal Patterns of Anabolism and Catabolism in Juvenile Steelhead; Energy Partitioning in Growth. M.S. Thesis, Humboldt State University, Arcata, California. 60 pp.	December 2009
Van Vleet, Nicholas. 2019. A time- and state-based approach to estimate winter movement and survival of juvenile coho salmon (Oncorhynchus kisutch) in Freshwater Creek, California. Humboldt State University Masters thesis. Arcata, California.	July 2019
Sparkman, M.D. 2003. Negative influences of predacious egg-eating worms, Haplotaxis ichthyophagus, and fine sediments on coho salmon, Onchorhynchus kisutch, in natural and artificial redds. 64 pp.	December 2003
Rizza, S. F. 2015. Asymmetric Introgression Between Coastal Cutthroat Trout and Steelhead: Variable Introgression by Linkage Group. 72 pp.	July 2015
Ransom, B.O. 2007. Extended freshwater rearing of juvenile coho salmon (Oncorhynchus kisutch) in northern California streams. 81 pp.	December 2007
Poxon, B. 2012. An investigation into the efficiency of observers to visually detect adult salmon spawning in the Prairie Creek Watershed, Humboldt County, California. 52 pp.	June 2012
Pittman, R.G. 2011. Minimum stream length requirements for McCloud River redband trout Oncorhynchus mykiss spp in Trout and Tate creeks, Siskiyou County, California. 62 pp.	June 2011
Okun, Natalie B. Effects of Large Wood Restoration on Coho Salmon in a Northern California Watershed: A Before-After-Control-Impact Experment. Humboldt State University.	December 2021
Naman, S.W. 2008. Predation by hatchery steelhead on natural salmon fry in the upper-Trinity River, California. 66 pp.	December 2008
Metheny, M. 2012. Use of Dual Frequency Identification Sonar to estimate salmonid escapement to Redwood Creek, Humboldt County, California. 97 pp.	December 2012
McLaughlin, K.D. 2009. Development of a standard weight equation for juvenile steelhead trout and effects of temperature, turbidity, and steelhead trout biomass on relative weight. 63 pp.	May 2009
McCoy, B.L. 2008. Effect of rearing location on escapement of coho salmon (Oncorhynchus kisutch) at Freshwater Creek, California. 41 pp.	November 2008
Malakauskas, D. M. 2013. Ecology of Manayunkia Speciosa. 127 pp.	May 2013
Loomis, Christopher M. 2019. Density and distribution of piscivorous fishes in the Sacramento-San Joaquin Delta. Humboldt State University masters thesis. Arcata, California.	July 2019
Kreidler, Nissa. 2020. Species Distribution Models for Three Deep-Sea Coral and Sponge Taxa in the Southern California Bight. Humboldt State University M.S. Thesis., Arcata, CA.	December 2020
Kanawi, E.K. 2020. Comparing Environmental DNA and Traditional Monitoring Approaches to Assess the Abundance of Outmigrating Coho Salmon (Oncorhynchus kisutch) in California Coastal Streams. M.S. Thesis. Humboldt State University. Arcata, CA. USA.	July 2020
Justice, C. 2007. Response of juvenile salmonids to placement of large woody debris in California coastal streams. 121 pp.	August 2007
Hodge, B. 2010. Life history variation in Oncorhynchus mykiss from the lower Klamath River basin. 113 pp.	July 2010
Gough, S. A. 2010. A comparison of escapement estimate methods plus escapement-recruitment relationships for chinook salmon and coho salmon in a coastal stream. M.S. Thesis, Humboldt State University, Arcata, California. 105 pp.	August 2010
Gonzales, E.J. 2006. Diet and prey consumption of juvenile coho salmon (Oncorhynchus kisutch) in three northern California streams. 66 pp.	December 2006
Frazey, S. L. 2005. The relationship between productivities of salmonids and forest stands in northern California streams. 45 pp.	December 2005
Feola, J.E. 2007. Environmental variables influencing downstream migration of juvenile coho salmon (Oncorhynchus kisutch) in three northern California streams. 82 pp.	August 2007
Engle, R.O. 2005. Distribution and summer survival of juvenile steelhead trout (Oncorphynchus mykiss) in two streams within the King Range National Conservation Area, California. 97 pp.	December 2005
Drobny, P. Y. 2016. Influence of body size, intra-and inter-specific salmonid densities, and habitat on overwinter survival of juvenile Coho Salmon (Oncorhynchus kisutch) in Prairie Creek, California. 80 pp.	May 2016
Dockham, A. S. 2016. Comparison of benthic invertebrate community structure and diet composition of steelhead (Oncorhynchus mykiss) in Dry Creek, California. 80 pp.	May 2016
Dick, C. Comparing Molecular Methods to Estimate Fish Stomach Contents and Gastric Evacuation Rates: Implications for Measuring the Impacts of Predation on Central Valley Chinook Salmon. M.Sc thesis. California State Polytechnic University, Humboldt	July 2022
Deibner-Hanson, J.D. 2019. Overwinter Survival and Movement of Juvenile Coho Salmon (Oncorhynchus kisutch) in Relation to Large Woody Debris and Low-Velocity Habitat in Northern California Streams. MS Thesis. Humboldt State University, Arcata, CA, USA.	December 2019
DeYoung, C. 2007. Effects of turbidity on foraging efficiency and growth of salmonids in natural settings. 58 pp.	August 2007
Colombano, P. 2012. Response of coastal stream habitat and juvenile steelhead to the Honeydew Fire in Humboldt County, California. 121 pp.	December 2012
Coe, Hannah C. 2019. Effects of longline oyster aquaculture on benthic invertebrate communities in Humboldt Bay, California. Humboldt State University masters thesis. Arcata, California.	July 2019
Chen, Emily Katherine. 2019. Contribution of juvenile estuarine residency in a bar-built estuary to recruitment of chinook salmon (Oncorhynchus tshawytscha). Humboldt State University masters thesis. Arcata, California.	July 2019
Benson, S. 2014. Ceratomyxa Shasta: Timing of Myxospore release from juvenile Chinook Salmon. 68 pp.	July 2014
Balas, C.J. 2008. Effects of conservation programs on amphibian communities in seasonal wetlands of the Prairie Pothole Region's glacial plains.	June 2008
Ashenfelter, M.J. 2012. Movement of resident rainbow trout Oncorhynchus mykiss transplanted below barriers to anadromy in Freshwater Creek, California. 55 pp.	April 2012
Adams, C. A. 2013. Survival and movement of juvenile coho salmon (Oncorhynchus kisutch) in the Shasta River, California. 79 pp.	December 2013

Technical Publications

Technical Publications	Publication Date
Wilzbach. M.A. 2016. State of the fisheries and aquatic resources of Prairie Creek. Final Report to Redwood National and State Park, Cooperative Agreement P13AC00848.	January 2016
Wilzbach, P., D.M. Malakauskas, S.J. Willson. 2013. Myxozoan Fish Disease Research and Monitoring, Final Project Report. National Fish and Wildlife Foundation.	January 2013
Wilzbach, P. 2008. Movement of resident trout transplanted below a barrier to anadromy. IN Summary of the Eleventh annual Pacific coast Steelhead Management Meeting. http://www.psmfc.org/steelhead2008.	January 2008
Wilzbach, M.A., M.D. Sparkman, P.Y. Drobny, M.E. Gordon, and C.M.G. Boone. 2016. Prairie Creek Monitoring Project, 2015 Season: a report to the Fisheries Restoration Grants Program Project P1210321. 98 pg.	February 2016
Wilzbach, M. A. 2005. Using riparian canopy opening and salmon carcass addition to increase salmonid growth. Western Forester, Society of American Foresters 50(2):6-7.	March 2005
Williams, T.H., B. Spence, W. Duffy, D. Hillemeier, G. Kautsky, T. Lisle, M. McCain, T. Nickelson, E. Mora, and T. Pearson. 2007. Framework for assessing viability of threatened coho salmon in the southern Oregon/northern California coasts evolutionarily significant units. National Marine Fisheries Service, Southwest Fisheries Science Center, Santa Cruz, CA.	February 2007
Williams, T. H., E. P. Bjorkstedt, W. G. Duffy, D. Hillemeir, G. Kautsky, T. Lisle, M. McCain, M. Rhode, R. G. Szerlong, R. Schick, M. Goslin and A. Agrawal. 2006. Historical population structure of coho salmon in the Southern Oregon/Northern California coasts evolutionarily significant unit. U. S. Department of Commerce, NOAA Technical Memorandum NMFS-SWFSC-390.	October 2006
Williams, T. H., B. C. Spence, W. G. Duffy, D. Hillemeier, G. Kautsky, T. Lisle, M. McCain, T. Nickelson, G. Garman, E. Mora, and T. Pearson. 2008. Framework for assessing viability of threatened coho salmon in the Southern Oregon/Northern California Coast Evolutionarily Significant Unit. U. S. Department of Commerce, NOAA Technical Memorandum NMFS-SWFSC (In Press).	January 2008
Sparkman, M.D., R. Park, L. Osborn, and M.A.Wilzbach. 2016. Lower Redwood Creek juvenile salmonid (smolt) abundance project, study year 2015: a report to the Fisheries Restoration Grants Program, Project No. P1210322. 85 pp.	January 2016
Sparkman, M.D. 2012. Lower Redwood Creek Juvenile salmonid (smolt) abundance project 2004 - 2011 seasons.	January 2012
Sparkman, M.D. 2011. Lower Redwood Creek Juvenile salmonid (smolt) abundance project 2004-2010 Seasons	October 2011
Moore, T.L. and M.A. Wilzbach. 2016. Distribution and relative abundance of juvenile Coho Salmon in the Redwood Creek Basin, Humboldt County, California. Final report to the California Department of Fish and wildlife Fisheries Restoration Grant Program, Project P1210320.	March 2016
Limberg, K., Gibson, J., Haskill, C., Henderson, M., Huynh, Q. 2020. American Shad Benchmark Stock Assessment Peer Review Report. Stock Assessment Report of the Atlantic States Marine Fisheries Commission.	August 2020
Kahara, S.N., Duffy, W., DiGaudio, R. and Records, R. 2012. Climate, Management, and Habitat Associations of Avian Fauna in Restored Wetlands of California's Central Valley, USA. Appraisal of Approaches for the Management of Biodiversity and Life Support Systems. Diversity, ISSN 1424-2818, 23 pp.	November 2012
Iglesias I.S., Henderson M.J., Michel C.J., Ammann A.J., and Huff D.D. 2017. Chinook salmon smolt mortality zones and the influence of environmental factors on out-migration success in the Sacramento River Basin. Final report to USFWS - Agreement Number F15PG00146. 30 pgs.	April 2017
Hendrickson, G.L., N.E. Campise 2013. Production of Myxospores of Ceratomyxa shasta in Chinook Salmon Carcasses, Final Project Report, Oregon State University.	February 2013
Duffy, W.G., M.A. Wilzbach, M. Wheeler and S. Frazey. 2003. Watershed restoration validation monitoring protocols for California. California Department of Fish and Game, Sacramento.	February 2003
Duffy, W.G. and M.A. Wilzbach. 2004. A standard weight equation for juvenile coho salmon. California Department of Fish and Game, Sacramento.	July 2004
Duffy, W. G., M. A. Wilzbach, M. Wheeler and S. Frazey. 2003. Watershed restoration validation monitoring protocols for California. California Department of Fish and Game, Sacramento.	February 2003
Duffy, W. G. and M. A. Wilzbach. 2004. A standard weight equation for juvenile coho salmon. California Department of Fish and Game, Sacramento.	July 2004

Cooperative Fish and Wildlife Research Units Program: California Education, Research and Technical Assistance for Managing Our Natural Resources

California Research Activities

Cooperative Fish and Wildlife Research Units Program: California
Education, Research and Technical Assistance for Managing Our Natural Resources