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USGS2009

2008 Spawning Cisco Investigations in the Canadian Waters of Lake Superior

The Great Lakes Science Center of the United States Geological Survey (USGS) is working cooperatively with the Ontario Ministry of Natural Resources (OMNR) on a threeyear study to develop standard procedures for acoustic and midwater trawl (AC-MT) assessments of spawning cisco Coregonus artedi that the OMNR can carry forward as a management activity. In year two (2008), we conducted an AC-MT survey of the northern shore from Nipigon Bay to Thunder Bay. Spawning-cisco (> 250 mm total length) densities were lowest near Nipigon Bay (<10/ha), moderate in and around Black Bay (15- 30/ha), and highest in Thunder Bay (118/ha). Rainbow smelt Osmerus mordax densities were highest in Nipigon (2,179/ha) and Black (3,219/ha) bays, and lowest in Thunder Bay (961/ha). We combined our AC-MT survey results with commercial catch records to estimate exploitation fractions of female cisco in Thunder Bay during the 2008 fishery at 4% for ages 1-5, 8.7% for ages 6-12, and 4.4% for ages ≥ 13. Lake Superior fishery managers recently recommended that annual exploitation of adult female lake cisco be kept below 10-15%. Recruitment of cisco since 2003 has been low and there is a strong probability the Thunder Bay stock will decline into the future. Using a simple population dynamics approach we estimated that if the current total allowable catch (TAC) quota is held constant, exploitation fractions could exceed 10% by 2010 and 15% by 2011. Our 2008 collections suggested the survey of Black Bay was likely conducted before all spawners had returned there to spawn. Our data also suggested that cisco collected in Black Bay and east of this site in mid-November may be from the same stock. During November 2009 we will attempt to get better definition of the area occupied by cisco around Black Bay and also determine when surveys should be conducted at this location.

Report↗

USGS2008

Lower Methow tributaries intensive effectiveness monitoring study. Interim report

Actions have been taken to replace diversion dams in lower Beaver Creek with a series of rock vortex weirs. Some of these diversion dams have been in place for over 100 years, and they have impaired or completely blocked upstream migration of fish. Three diversion dams were replaced in 2003 (Lower Stokes, Thurlow Transfer, and Upper Stokes), and a forth diversion dam was replaced in 2004 (Fort-Thurlow). These vortex weirs were designed and installed under the supervision of U.S. Bureau of Reclamation (BOR) engineers and completed in accordance to National Marine Fisheries Service (NMFS) and Washington Department of Fisheries and Wildlife (WDFW) fish passage criteria. The projects were designed to meet fish species recovery needs described by the Endangered Species Act (ESA) and the “BiOp” issued by NMFS (2000a). Since no specific guidelines have been identified to date specifically addressing diversion dams, WDFW and NMFS guidelines are being considered as the target design and performance criteria for the sites monitored as part of this project. Where used, the vortex weirs were designed to maintain irrigation diversion capabilities while improving fish passage.

Washington↗

USGS2017

Cooperative Fish and Wildlife Research Units Program—2016 year in review

Summary The Cooperative Fish and Wildlife Research Units (CRU) Program had a productive year in 2016. Despite vacancies in our scientist ranks exceeding 20 percent, our research, training, and teaching portfolio was full and we graduated 93 students and published 398 manuscripts primarily focused on addressing the real conservation challenges of our cooperators. As I’ve stated before, our mission is our legacy: meeting the actionable science needs of our cooperators, providing them technical guidance and assistance in interpreting and applying new advances in science, and developing the future workforce through graduate education and mentoring. Our scientists and the manner in which they approach our mission continue to inspire me. The most rewarding part of my job is meeting and engaging with the students they recruit—the conservation professionals of the future. I cannot help but feel uplifted after discussions with and presentations by these young men and women. Personally, I owe my place in the profession today to the mentoring I received as a CRU student, and today’s CRU scientists have raised the bar. It gives me hope for the future of conservation, and added motivation to see our vacancies filled so that we can expand our portfolio. The National Cooperators’ Coalition has been active and is strategically working to build support on our behalf. Sincere thanks to the American Fisheries Society, the Association of Fish and Wildlife Agencies, the Boone and Crockett Club, the National Association of University Fish and Wildlife Programs, the Wildlife Management Institute, and The Wildlife Society for their efforts and those of their affiliated members. We co-sponsored a workshop at the 2016 North American Wildlife and Natural Resources Conference along with the American Fisheries Society, the Association of Fish and Wildlife Agencies, the Wildlife Management Institute, and The Wildlife Society, titled “Barriers and Bridges in Reconnecting Natural Resources Science and Management.” The workshop was well received and we have been asked to continue the dialogue with a second workshop in 2017. It was evident during the workshop that the CRU is viewed by our cooperators as an important and essential linkage between academia and practitioners. This is testament to the legacy of the CRU Program and the foundation it is built upon. In this Year in Review report, you will find details on staffing, vacancies, research funding, and other pertinent information. You will also see snapshots of CRU projects with information on how results have been or are being applied by cooperators. That is the essence of what we do: science that matters.

Circular↗

USGS1998

Low-flow water-quality characterization of the Gore Creek watershed, upper Colorado River basin, Colorado, August 1996

The Upper Colorado River Basin (UCOL) is one of 59 National Water-Quality Assessment (NAWQA) study units designed to assess the status and trends of the Nation?s water quality (Leahy and others, 1990). The UCOL study unit began operation in 1994, and surface-water-quality data collection at a network of 14 sites began in October 1995 (Apodaca and others, 1996; Spahr and others, 1996). Gore Creek, which flows through Vail, Colorado, originates in pristine alpine headwaters and is designated a gold-medal trout fishery. The creek drains an area of about 102 square miles and is a tributary to the Eagle River. Gore Creek at the mouth near Minturn (site 13 in fig. 1) is one of the 14 sites in the UCOL network. This site was selected to evaluate water quality resulting from urban development and recreational land use. The Gore Creek watershed has undergone rapid land-use changes since the 1960?s as the Vail area shifted from traditional mountain ranchlands to a four-season resort community. Residential, recreational, commercial, and transportation development continues near Gore Creek and its tributaries to support the increasing permanent and tourist population of the area. Interstate 70 runs through the watershed from Vail Pass near site 14, along the eastern side of Black Gore Creek, and along the northern side of the main stem of Gore Creek to the mouth of the watershed (fig. 1). A major local concern is how increasing urbanization/recreation affects the water quality, gold-medal trout fishery, and aesthetic values of Gore Creek. An evaluation of the spatial characteristics of water quality in the watershed upstream from site 13 at the mouth of Gore Creek (fig. 1) can provide local water and land managers with information necessary to establish water policy and make land-use planning decisions to maintain or improve water quality. Historical data collected at the mouth of Gore Creek provide information about water quality resulting from land use, but a synoptic sampling is needed to determine the distribution and sources of water-quality constituents at one point in time. In August 1996, a low-flow synoptic sampling for analyses of water-quality properties and constituents at sites in the Gore Creek watershed was done by the U.S. Geological Survey, in cooperation with the Town of Vail, Eagle River Water and Sanitation District, Upper Eagle River Water Authority, and Northwest Colorado Council of Governments, to evaluate the water quality of Gore Creek. The August low-flow period can be important from water-quality and stream ecology perspectives. There is less water available to dilute any contaminants entering the streams, and stream temperatures are highest during August. Physical habitat for aquatic plants and animals is smaller than during most other times of the year. To address these more extreme water-quality and ecological conditions, the synoptic sampling was conducted during the summer low-flow period. Specific objectives of this sampling included: 1. Establish a current data set representing the spatial characteristics of low-flow water-quality conditions in the Gore Creek watershed, and 2. Develop some understanding of land-use and water-quality relations in the watershed. This fact sheet presents hydrologic background information and an analysis of general water-quality properties and constituents, trace elements, and nutrients collected in water samples during low-flow synoptic sampling of the Gore Creek watershed. The U.S. Geological Survey also is conducting a study of the algae and macroinvertebrate communities and physical habitat of streams in the Gore Creek watershed during low flow. This study is designed to provide information about land-use and stream ecology relations in the watershed.

Colorado↗

USGS2005

The Columbia River Research Laboratory

The U.S. Geological Survey's Columbia River Research Laboratory (CRRL) was established in 1978 at Cook, Washington, in the Columbia River Gorge east of Portland, Oregon. The CRRL, as part of the Western Fisheries Research Center, conducts research on fishery issues in the Columbia River Basin. Our mission is to: 'Serve the public by providing scientific information to support the stewardship of our Nation's fish and aquatic resources...by conducting objective, relevant research'.

Washington↗

USGS2006

Investigations of the Effects of Synthetic Chemicals on the Endocrine System of Common Carp in Lake Mead, Nevada and Arizona

Introduction: Lake Mead is the largest reservoir by volume in the United States and was created by the construction of the 221-meter high Hoover Dam in 1935 at Black Canyon on the lower Colorado River between Nevada and Arizona (fig. 1). Inflows of water into the lake include three rivers, Colorado, Virgin, and Muddy; as well as Las Vegas Wash, which is now perennial because of discharges from municipal wastewater treatment plants (Covay and Leiker, 1998) and urban stormwater runoff. As the population within the Las Vegas Valley began to increase in the 1940s, the treated effluent volume also has increased and in 1993 it constituted about 96 percent of the annual discharge of Las Vegas Wash (Bevans and others, 1996). The mean flow of Las Vegas Wash into Las Vegas Bay from 1992 to 1998 was about 490,000 m3/d (Preissler and others, 1999) and in 2001 increased to 606,000 m3/d (U.S. Bureau of Reclamation, 2001). The nutrient concentration in most areas of the lake is low, but wastewater discharged into Las Vegas Bay has caused an increased level of nutrients and primary productivity (aquatic plant and algal production) in this area of the lake (LaBounty and Horn, 1997). A byproduct of this increase in productivity has been the establishment of an important recreational fishery in Las Vegas Bay. However, concentrations of chlorophyll a (a measure of algal biomass) have also increased (LaBounty and Horn, 1997). In the spring of 2001, parts of Lake Mead experienced massive algal blooms. In addition to nutrient loading by wastewater, the presence of numerous synthetic chemicals in water, bottom sediments, and in fish tissue also has been reported (Bevans and others, 1996). Synthetic chemicals discharging into Las Vegas Bay and Lake Mead (fig. 1) originate from several sources that include surplus residential-irrigation water runoff, stormwater runoff, subsurface inflow, and tertiary treated sewage effluent discharging from three sewage-treatment plants. Chemicals detected in Las Vegas Wash and Bay environments include polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), organochlorine pesticides (including DDT and DDE), and 'emerging contaminants' such as fragrances/musks, flame retardants, triclosan and its breakdown products, personal care products, and pharmaceuticals (Bevans and others, 1996; Boyd and Furlong, 2002; Leiker and others, in press). Many of these compounds are able to interact with the endocrine system of animals and potentially cause reproductive impacts. The National Park Service (NPS) manages Lake Mead National Recreation Area (LMNRA) with about 8 million yearly visitors including 500,000 anglers drawn to its world-class recreational fishery. The U.S. Fish and Wildlife Service (FWS) provides management for the federally designated, endangered razorback sucker (Xyrauchen texanus) and for more than 180 species of migratory birds that utilize LMNRA surface waters. These multiple uses of surface water in the area demonstrate their vital importance to the LMNRA as well as the need to maintain the quality of water at levels that are adequate for these uses.

Fact Sheet↗

USGS2022

Eastern Ecological Science Center — Fish and aquatic animal health

Science provided by the U.S. Geological Survey (USGS) Eastern Ecological Science Center (EESC) helps to protect fish and aquatic animal health and support disease management of our Nation’s fisheries and aquatic animal populations. Our capabilities and expertise span diverse, yet highly integrated disciplines related to all aspects of biology, ecology, and animal health. Our scientists work to identify novel and emerging pathogens and diseases to assess fish and aquatic animal responses to parasites, pathogens, adverse environmental conditions, and chemical exposures. Eastern Ecological Science Center research is conducted both in laboratories and in the field in various aquatic environments ranging from headwater streams to the ocean. The EESC team provides science leadership and support for fisheries and aquatic species specialists nationwide.

Fact Sheet↗

USGS2025

U.S. Geological Survey Cooperative Research Units Program—A hawk’s view of 2024

Introduction The U.S. Geological Survey Cooperative Fish and Wildlife Research Units (USGS CRU) program was established in 1935 and codified by Congress in 1960 to enhance graduate education in wildlife and fisheries sciences and to facilitate research and technical assistance among natural resource agencies and universities on fisheries and wildlife management topics of mutual concern. The success of the CRU program lies in its cooperative approach. State and Federal fish and wildlife agencies determine where focused, science-based studies for wildlife and natural resource management for societal benefit are needed. The CRU scientists conduct applied research to contribute results to inform and aid partners in determining best practices for managing resources. Each Unit is a unique partnership among the U.S. Geological Survey, a host university, one or more State agencies, the Wildlife Management Institute, and the U.S. Fish and Wildlife Service.

Fact Sheet↗

USGS2000

Cruise report RV Ocean Surveyor cruise O-1-00-GM the bathymetry and acoustic backscatter of the Pinnacles area, northern Gulf of Mexico May 23, through June 10, 2000 Venice, LA to Venice, LA

An extensive deep (~100 m) reef tract occurs on the Mississippi-Alabama outer continental shelf (OCS). The tract, known as "The Pinnacles", is apparently part of a sequence of drowned reef complexes along the "40-fathom" shelf edge of the northern Gulf of Mexico (Ludwick and Walton, 1957). It is critical to determine the accurate geomorphology of deep-reefs because of their importance as benthic habitats for fisheries. The Pinnacles were mapped by Ludwick and Walton (1957) using a single-beam echo sounder but the spatial extent and morphology were interpreted from a series of widely separated, poorly navigated bathymetric profiles. Other recent studies, supported by Minerals Management Service (MMS), used towed sidescan sonars and single-channel seismic-reflection profiling. None of the existing studies provide the quality of geomorphic data necessary for reasonable habitat studies. The fish faunas of shallow hermatypic reefs have been well studied, but those of deep ahermatypic reefs have relatively ignored. The ecology of deep ahermatypic reefs is fundamentally different from hermatipic reefs because autochthonous intracellular symbiotic zooxanthellae (the carbon source for hermatypic corals) do not form the base of the trophic web. Instead, exogenous plankton, transported to the reef by currents, serves as the primary carbon source. Deep OCS reefs also lie below the practical working depths for SCUBA; consequently, remote investigations from a ship or in situ investigations using submersibles or ROVs are required. Community structure and trophodynamics of demersal fishes of the Pinnacles are presently the focus of USGS reseach. A goal of the research is to answer questions concerning the relataive roles played by geomorphology and surficial geology in the interaction with and control of biological differentiation. OCS reefs are important because we now know that such areas are important coral reef fish havens, key spawning 2 sites, and a critical early larval and juvenile habitats for economically important sport/food fishes. Also, deep-reef ecosystems as well as the fish populations they sustain are impacted by intensive oil-field development. It is now known that deep OCS reefs function as a key source of re-population (via seasonal and ontogenetic migration) of already heavily impacted inshore reefs. A reflection of this realization is the recent closure by the Gulf States Fisheries Management Council of a 600 mi 2 area of the Florida Middle Grounds (another unmapped major "40-fathom" OCS reef complex) to commercial fishing to preserve grouper spawning aggregations. It is known that the Pinnacles reefs support a lush fauna of ahermatypic hard corals, soft corals, black corals, sessile crinoids and sponges—together forming a living habitat for a well-developed fish fauna. The fish fauna comprises typical Caribbean reef fishes and Carolinian shelf fishes, plus epipelagic fishes, and a few deep-sea fishes. The base of the megafaunal invertebrate food web is plankton, borne by essentially continuous semi-laminar currents flowing predominantly out of the SW, up, along and across the shelf edge. These currents are intercepted by pinnacles reefs, which lie roughly in two linear tracts, parallel to the coastline (see fig. 1 in report). USGS research initiated in 1997 (Sulak et al., in progress) has demonstrated that the Pinnacles reef fish fauna is dominated by planktivorous fishes. Ongoing food habits, trophic web and stable isotope analyses by the USGS are reinforcing a basic picture of deep OCS reefs as ecosystems based on exogenous current-borne plankton. Long-term current meter deployments have demonstrated that the >3 m, <16m relief of the Pinnacles reefs disrupts the prevailing currents, inducing local complexity (F. Kelly, Texas A&M Univ., pers. comm.) favorable to plankton and planktivores. Geodetically accurate bathymetry maps, coregistered with calibrated acoustic backscatter maps, are critical to delineate benthic biotopes, and are essential to correlate biological community differentiation with the physical environment. Previous mapping of the Pinnacles area using the TAMU towed single-beam sidescan system (Anonymous., 1999) employed technology with inherent deficiencies in backscatter calibration, bathymetric precision, and geo-referencing. The resulting bathymetric interpretations of TAMU data are further degraded by ship-track-parallel artifacts that obliterate geomorphology rendering them inadequate to provide high-resolution mapping of individual target reefs (typical maximum relief 15 m, diameter 200-500 m). The sidescan-sonar surveys of the area (Laswell et al., 1990) suffer many of the same deficiencies as the TAMU data so they add no quantitative and little qualitative information about the geomorphology and surficial geology.

Gulf of Mexico, the Pinnacles area↗

USGS2007

Longitudinal patterns of fish assemblages, aquatic habitat, and water temperature in the Lower Crooked River, Oregon

The Lower Crooked River is a remarkable groundwater-fed stream flowing through vertical basalt canyons in the Deschutes River Valley ecoregion in central Oregon (Pater and others, 1998). The 9-mile section of the river between the Crooked River National Grasslands boundary near Ogden Wayside and river mile (RM) 8 is protected under the National Wild and Scenic Rivers Act (16 U.S.C. 1271-1287) for its outstandingly remarkable scenic, recreational, geologic, hydrologic, wildlife, and botanical values (ORVs), and significant fishery and cultural values. Groundwater springs flow directly out of the canyon walls into the Lower Crooked River and create a unique hydrologic setting for native coldwater fish, such as inland Columbia Basin redband trout (Oncorhynchus mykiss gairdneri). To protect and enhance the ORVs that are the basis for the wild and scenic designation, the Bureau of Land Management (BLM) has identified the need to evaluate, among other conditions, fish presence and habitat use of the Lower Crooked River. The results of this and other studies will provide a scientific basis for communication and cooperation between the BLM, Oregon Water Resources Department, Oregon Department of Fish and Wildlife (ODFW) and all water users within the basin. These biological studies initiated by the BLM in the region reflect a growing national awareness of the impacts of agricultural and municipal water use on the integrity of freshwater ecosystems. Biological surveys are needed to better understand the aquatic ecosystem of the Lower Crooked River. This baseline information will be valuable to public land managers whose task is to balance resource use while protecting the unique attributes (that is, ORVs) of the Lower Crooked River. The habitat requirements of coldwater fishes in this section of stream are of particular interest due to state and federal regulation of water temperature in order to protect and restore fish populations. Historical data on the distribution and abundance of stream fishes in the Lower Crooked River are limited to point observations by fishermen and local biologists because steep canyon walls have limited access to most of the river. Surveys of aquatic habitat (channel morphology and substrate composition) have been conducted for the BLM by the ODFW (Oregon Department of Fish and Wildlife, 1997), U.S. Forest Service (United States Forest Service, 2003), and the U.S. Fish and Wildlife Service (USFWS), but fish surveys using electrofishing gear have never been conducted in the isolated 11-mile section of the Crooked River Gorge, and visual observations with mask and snorkel have only been made at isolated point locations where hiking trails provide access to the river (K. Jones, Steve Marx, and Brett Hodgson, ODFW; P. Lickwar, USFWS; pers. comm.). Thus, there is a poor understanding of stream fish presence and distribution throughout Lower Crooked River. Information on fish assemblages is available for the Deschutes River basin and applies generally to the Lower Crooked River because the two rivers were connected historically (Zimmerman and Ratliff 2003). The construction of dams throughout the Deschutes River basin has eliminated historic runs of salmon and steelhead and prevented migration of bull trout and Pacific lamprey into the Crooked River system. Native fish species expected to occur in the Lower Crooked River include Columbia Basin redband trout ( Oncorhynchus mykiss gairdneri ), mountain whitefish ( Prosopium williamsoni ), sculpin ( Cottus spp.), two species of dace ( Rhinichthys spp.), two species of sucker ( Catostomus spp.), northern pikeminnow ( Ptychocheilus oregonensis ), chiselmouth ( Acrocheilus alutaceus ), and redside shiner ( Richardsonius balteatus ). Threespine stickleback ( Gasterosteus aculeatus ), a species native to western Oregon, also occurs in the basin but is believed to be introduced (D. Markle, Department of Fisheries and Wildlife, Oregon State University, personnel commun.). Extensive stocking of rainbow trout has contributed to a large population of naturalized fish of hatchery origin in the Lower Crooked River. Due to the difficulty of differentiating between wild redband trout and naturalized rainbow trout of hatchery origin, the general classification of rainbow trout ( Oncorhynchus mykiss ) is used throughout this report to describe the fish that were observed in the Lower Crooked River. Exotic fish species expected to occur in the Lower Crooked River include large- and smallmouth bass ( Micropterus spp.), yellow perch ( Perca flavescens ), and brown bullhead (Ameiurus nebulosis) (Zimmerman and Ratliff 2003). The goal of this project was to examine longitudinal patterns in fish assemblages, aquatic habitat, and water temperature in the Lower Crooked River during summer conditions. Specific objectives were to (1) characterize the spatial distribution of native and non-native fishes, (2) describe variation in channel morphology, substrate composition, and water temperature, and (3) evaluate the associations between fishes, aquatic habitat, and water temperature.

Oregon↗

USGS2010

Short-Term Effects of the 2008 High-Flow Experiment on Macroinvertebrates in Colorado River Below Glen Canyon Dam, Arizona

Glen Canyon Dam has dramatically altered the physical environment (especially discharge regime, water temperatures, and sediment inputs) of the Colorado River. High-flow experiments (HFE) that mimic one aspect of the natural hydrograph (floods) were implemented in 1996, 2004, and 2008. The primary goal of these experiments was to increase the size and total area of sandbar habitats that provide both camping sites for recreational users and create backwaters (areas of stagnant flow in the lee of return-current eddies) that may be important as rearing habitat for native fish. Experimental flows might also positively or negatively alter the rainbow trout (Oncorhynchus mykiss) sport fishery in the clear tailwater reach below Glen Canyon Dam, Ariz., and native fish populations in downstream reaches (for example, endangered humpback chub, Gila cypha) through changes in available food resources. We examined the short-term response of benthic macroinvertebrates to the March 2008 HFE at three sites [river mile 0 (RM 0, 15.7 miles downriver from the dam), RM 62, and RM 225] along the Colorado River downstream from Glen Canyon Dam by sampling immediately before and then 1, 7, 14, and 30 days after the HFE. We selected these sites because of their importance to management; RM 0 has a valuable trout fishery, and RM 62 is the location of the largest population of the endangered humpback chub in the Grand Canyon. In addition to the short-term collection of samples, as part of parallel investigations, we collected 3 years of monthly (quarterly for RM 62) benthic macroinvertebrate samples that included 15 months of post-HFE data for all three sites, but processing of the samples is only complete for one site (RM 0). At RM 0, the HFE caused an immediate 1.75 g AFDM/m2 (expressed as grams ash-free dry mass, or AFDM) reduction of macroinvertebrate biomass that was driven by significant reductions in the biomass of the two dominant taxa in this reach-Potamopyrgus antipodarum (New Zealand mud snails) and Gammarus lacustris (scuds or side-swimmers)-and also biomass reductions of other common taxa (worms in the families Lumbricidae and Tubificidae). Invertebrate drift estimates during the HFE suggest that reductions in biomass of some taxa were because of export from the reach. Reductions in biomass of P. antipodarum and G. lacustris persisted at least 15 months after the HFE, when this study concluded, and coincided with a significant decline in the annual production of these taxa: P. antipodarum production of 11 to 13 g AFDM/m2/yr in two pre-HFE years versus 2 g AFDM/m2/yr in the post-HFE year, and G. lacustris production of 7 to 8 g AFDM/m2/yr in two pre-HFE years versus 3 g AFDM/m2/yr in the post-HFE year. There were not changes in invertebrate feeding habits in response to the HFE, as our 3-year dataset of invertebrate diets indicated no substantial changes. Our long-term analysis of the composition of the drift indicates that because of a reduction in P. antipodarum in the drift relative to digestible taxa, the quality of the drift as a food resource for fishes increased. At downstream sites, total assemblage biomass did not decline, likely because assemblages were dominated by blackflies (Simulium arcticum), which were not affected by the HFE. Similar to RM 0, G. lacustris and Tubificidae had significantly lower biomass after the HFE at RM 62 and RM 225. Chironomids were also significantly lower following the flood at both downstream sites. Our findings demonstrate that the effects of a HFE on invertebrates may persist up to at least 15 months in the clear tailwater below the dam, whereas in downstream reaches impacts were more short lived. If controlling the abundance of P. antipodarum is a goal of managers, our findings indicate that periodic HFEs on the order of every 2 to 3 years may be an effective strategy for meeting that goal. More frequent HFEs may cause a shift in the state of the benthic invertebrate assemblage of the tailwa

Open-File Report↗

USGS2012

Monitoring of endangered Roanoke logperch ( Percina rex ) in Smith River upstream from the Philpott Reservoir on U.S. Army Corps of Engineers property near Martinsville, Virginia

The purpose of this study was to continue annual monitoring of Roanoke logperch ( Percina rex ), an endangered fish, in the Smith River immediately upstream from Philpott Reservoir. This river reach is owned by the U.S. Army Corps of Engineers (USACE), which must ensure that appropriate actions are undertaken to aid in recovery of logperch. Monitoring of fish abundance and habitat conditions provides a means for assessing the species’ status and its responses to USACE management actions. The Roanoke logperch is a large darter (Percidae: Etheostomatinae) endemic to the Roanoke, Dan, and Nottoway River basins of Virginia and North Carolina, where it occupies third- to sixth-order streams containing relatively silt-free substrate (Jenkins and Burkhead, 1994). Because of its rarity, small range, and vulnerability to siltation, the Roanoke logperch was listed in 1989 as endangered under the U.S. Endangered Species Act (ESA) (U.S. Federal Register 54:34468-34472). Within the Dan basin, Roanoke logperch have long been known to occupy the Smith River and one of its largest tributaries, Town Creek (Jenkins and Burkhead, 1994). Logperch also recently were discovered in other tributaries of the Dan River, including North Carolina segments of the Mayo River, Cascade Creek, Big Beaver Island Creek, Wolf Island Creek (William Hester, U.S. Fish and Wildlife Service, personal commun., 2012). Within the Smith River, Roanoke logperch are present both upstream and downstream from Philpott Reservoir, a hydroelectric and water storage project owned and operated by the USACE. Although logperch have not been observed in the reservoir itself, the species is relatively abundant in a free-flowing, ≈ 2.5-km-long segment of Smith River upstream from the reservoir on USACE property (Lahey and Angermeier, 2006). This segment is bounded on the downstream end by the lentic conditions of the reservoir and on the upstream end by White Falls, a natural waterfall that presumably allows fish passage during all but the lowest streamflow (Roberts and Angermeier, 2009). The ESA stipulates that USACE must ensure that its actions do not jeopardize Roanoke logperch and ensure that appropriate actions are taken to aid in the recovery of Roanoke logperch. USACE recognized that additional information was needed to assess compliance with these stipulations, including data on baseline population levels, habitat availability, and potential threats to the species on USACE property. USACE therefore contracted with Virginia Tech (VT) and the U.S. Geological Survey via the Virginia Cooperative Fisheries and Wildlife Research Unit (VCFWRU) to continue ecological monitoring that was initiated in a pilot study in 2005 (Lahey and Angermeier, 2006). The VCFWRU is jointly sponsored by the U.S. Geological Survey, Virginia Tech, Virginia Department of Game and Inland Fisheries, and Wildlife Management Institute. This final report summarizes results of biological monitoring performed by VT and the VCFWRU in 2011, and compares these data to data collected during 2006–2010 (Roberts and Angermeier, 2011). Where appropriate, a comparison was made to data on Roanoke logperch collected previously in the study reach (Lahey and Angermeier, 2006) and in the upper Roanoke River (Roberts and Angermeier, 2011). This work was performed under the auspices of VT’s Institutional Animal Care and Use Committee (IACUC) protocol 11-035-FIW. Specifically, the following objectives were addressed: * Estimate population density of Roanoke logperch on USACE property; * Measure and map by suitability class the distribution of habitat suitable for Roanoke logperch in the project area; * Assess water quality relative to Roanoke logperch habitat in the project area; * Use the data on logperch abundance, habitat suitability, and water quality to test the general validity of correlates of logperch abundance from other locations; * Identify opportunities and threats related to protecting and enhancing Roanoke logperch habitat; and * Provide suggestions on the necessity and scale of future studies and monitoring related to logperch in and near USACE waters.

Virginia↗

USGS2012

A standard operating procedure for the surgical implantation of transmitters in juvenile salmonids

Biotelemetry is a useful tool to monitor the movements of animals and is widely applied in fisheries research. Radio or acoustic technology can be used, depending on the study design and the environmental conditions in the study area. A broad definition of telemetry also includes the use of Passive Integrated Transponder (PIT) tags, either separately or with a radio or acoustic transmitter. To use telemetry, fish must be equipped with a transmitter. Although there are several attachment procedures available, surgical implantation of transmitters in the abdominal cavity is recognized as the best technique for long-term telemetry studies in general (Stasko and Pincock, 1977; Winter, 1996; Jepsen, 2003), and specifically for juvenile salmonids, Oncorhynchus spp. (Adams and others, 1998a, 1998b; Martinelli and others, 1998; Hall and others, 2009). Studies that use telemetry assume that the processes by which the animals are captured, handled, and tagged, as well as the act of carrying the transmitter, will have minimal effect on their behavior and performance. This assumption, commonly stated as a lack of transmitter effects, must be valid if telemetry studies are to describe accurately the movements and behavior of an entire population of interest, rather than the subset of that population that carries transmitters. This document describes a standard operating procedure (SOP) for surgical implantation of radio or acoustic transmitters in juvenile salmonids. The procedures were developed from a broad base of published information, laboratory experiments, and practical experience in tagging thousands of fish for numerous studies of juvenile salmon movements near Columbia River and Snake River hydroelectric dams. Staff from the Western Fisheries Research Center's Columbia River Research Laboratory (CRRL) frequently have used telemetry studies to evaluate new structures or operations at hydroelectric dams in the Columbia River Basin, and these evaluations typically require large numbers of tagged fish. For example, a study conducted at the dams on the Columbia River and funded by the U.S. Army Corps of Engineers required tagging and monitoring of 40,000 juvenile salmon during a 3-month migration period (Counihan and others, 2006a, 2006b; Perry and others, 2006). To meet the demands of such a large study, the authors and CRRL staff refined the SOP to increase efficiency in the tagging process while maintaining high standards of fish care. The SOP has been used in laboratory and field settings for more than 15 years, and consistently has produced low mortality rates (<1 percent) and transmitter loss rates (<0.01 percent) in the 24-36 hours after tagging. In addition to describing the detailed surgical procedures required for transmitter implantation, this document provides guidance on fish collection, handling and holding, and the release of tagged fish. Although often overlooked, or at least underemphasized, these processes can have a large impact on the outcome of the tagging procedure. Stress associated with the individual steps in handling and tagging can be cumulative and lethal (Maule and others, 1988; Wedemeyer and others, 1990; Portz and others, 2006), so the goal is to provide the best possible fish care at every step in order to manage the overall effect on study fish.

Open-File Report↗

USGS2013

Conservation and Ecology of Marine Forage Fishes--Proceedings of a Research Symposium, September 2012

Locally and globally, there is growing recognition of the critical roles that herring, smelt, sand lance, eulachon, and other forage fishes play in marine ecosystems. Scientific and resource management entities throughout the Salish Sea, agree that extensive information gaps exist, both in basic biological knowledge and parameters critical to fishery management. Communication and collaboration among researchers also is inadequate. Building on the interest and enthusiasm generated by recent forage fish workshops and symposia around the region, the 2012 Research Symposium on the Conservation and Ecology of Marine Forage Fishes was designed to elucidate practical recommendations for science and policy needs and actions, and spur further collaboration in support for the precautionary management of forage fish. This dynamic and productive event was a joint venture of the Northwest Straits Commission Forage Fish Program, U.S. Geological Survey (USGS), Washington Department of Fish and Wildlife (WDFW), and The Puget Sound Partnership. The symposium was held on September 12–14, 2012, at the University of Washington, Friday Harbor Laboratories campus. Sixty scientists, graduate students, and fisheries policy experts convened; showcasing ongoing research, conservation, and management efforts targeting forage fish from regional and national perspectives. The primary objectives of this event were to: (1) review current research and management related to marine forage fish species; and (2) identify priority science and policy needs and actions for Washington, British Columbia, and the entire West Coast. Given the diversity of knowledge, interests, and disciplines surrounding forage fish on both sides of the international border, the organizing committee made a concerted effort to contact many additional experts who, although unable to attend, provided valuable insights and ideas to the symposium structure and discussions. The value of the symposium format was highlighted in the closing remarks delivered by Joseph Gaydos, SeaDoc Society and Chair of the Puget Sound Science Panel. Dr. Gaydos’ presentation referenced the 2011 paper by Murray Rudd in the journal Conservation Biology , “How research-prioritization exercises affect conservation policy.” The paper points out that policy makers and funding agencies are more likely to gain a full understanding of issues when they are presented with research findings from an aligned research program. That is, compared to unaligned research strategies, where work is not based on identified research priorities.

Open-File Report↗

USGS2014

Water quality and algal conditions in the North Umpqua River, Oregon, 1995-2007, and their response to Diamond Lake restoration

The Wild and Scenic North Umpqua River is one of the highest-quality waters in the State of Oregon, supporting runs of wild salmon, steelhead, and trout. For many years, blooms of potentially toxic blue-green algae in Diamond and Lemolo Lakes have threatened water quality, fisheries, and public health. The blooms consist primarily of Anabaena , a nitrogen (N)-fixing planktonic alga that appears to have contributed to N enrichment, which could account for changes in communities and biomass of periphyton, or attached benthic algae, in the river. Periphyton can become a nuisance in summer by affecting riffle habitat and causing high pH that fails to meet State of Oregon water-quality standards. These symptoms of nutrient enrichment in the North Umpqua River were first documented in 1995, and the symptoms have continued since then. Restoring natural ecosystem processes that store nutrients rather than fueling algae might help improve pH and water-clarity conditions. This report summarizes the results from a study in 2005–07 characterizing water quality and algal conditions in the North Umpqua River before, during, and after the 2006 rotenone treatment of Diamond Lake in the headwaters of the North Umpqua River. The treatment was part of a restoration project to eradicate Tui chub ( Gila bicolor ), a non-native invasive fish blamed for decimating the trout fishery in Diamond Lake and fueling Anabaena blooms. Diamond Lake was expected to contribute organic matter and associated nutrients to Lake Creek during the project, but it was unclear whether these nutrients would affect periphyton communities in the North Umpqua River downstream. This study also provided an opportunity to examine changes in stream conditions in the main stem North Umpqua River and its tributaries, which were previously sampled in July 1995. The 1995 study was designed to provide background data during relicensing of the upstream hydroelectric facilities, and was partly motivated by anecdotal concerns about increase periphyton growth and reduced water clarity. As part of the 2005–07 study associated with the Diamond Lake restoration project, we repeated the 1995 basinwide synoptic survey in 2005, before the rotenone treatment. Although both samplings were just a snapshot of conditions, these data were evaluated for possible changes between 1995 and 2005.

Oregon↗

USGS2014

Evaluation of the behavior and movement of adult summer steelhead in the lower Cowlitz River, Washington, following collection and release, 2013-2014

Summer steelhead ( Oncorhynchus mykiss ) produced by a hatchery on the lower Cowlitz River, Washington, support a popular sport fishery during June–September each year. Many of these fish return to the Cowlitz Salmon Hatchery and are held until they are spawned in December. In the past, fishery managers have released some of the steelhead that return to the hatchery at downstream release sites (hereafter referred to as “recycled steelhead”) to increase angling opportunity. The recycling of summer steelhead is a potential use of hatchery fish that can benefit anglers in the lower Cowlitz River, provided these fish are harvested or return to the hatchery. However, recycled steelhead that are not removed from the river could compete against or spawn with wild winter steelhead, which would be a negative consequence of recycling. The Washington Department of Fish and Wildlife (WDFW) conducted an evaluation during 1998 and recycled 632 summer steelhead. They determined that 55 percent of the recycled steelhead returned to the hatchery and 15 percent of the fish were harvested by anglers. The remaining 30 percent of recycled fish were not known to have been removed from the river. Recycling has not occurred in recent years because definitive studies have not been conducted to determine the fate of the fish that remain in the lower Cowlitz River after being recycled. The U.S. Geological Survey and WDFW conducted a 2-year study during 2012–2014 to quantify recycled steelhead that (1) returned to the hatchery, (2) were captured by anglers, or (3) remained in the river. All recycled steelhead were marked with a Floy ® tag and opercle punch, and 20 percent of the recycled fish were radio-tagged to determine post-release behavior and movement patterns, and to describe locations of tagged fish that remained in the river during the spawning period. During 2012–2013, we recycled 549 steelhead and determined that 50 percent of the fish returned to the hatchery, 18 percent of the fish were harvested by anglers, and 32 percent of the fish were not known to have been removed from the river. During October–December 2012, only 9 percent of the radio-tagged steelhead remained in the lower Cowlitz River and none of these fish entered tributaries monitored by fixed-telemetry sites. The second year of the evaluation was conducted during 2013–2014. A total of 502 steelhead were recycled during June–August and releases were conducted weekly with group sizes that ranged from 30 to 76 fish. Results from 2013–2014 were similar to results from 2012–2013. Fifty percent (251 fish) of the recycled steelhead returned to the hatchery, 20 percent (100 fish) were harvested by anglers, and 30 percent (151 fish) were unaccounted for. The median elapsed time from release to hatchery return was 13 days, and the median elapsed time from release to capture by an angler was 11 days. The percentage of unaccounted-for steelhead in the general population was moderately high (30 percent), but detection records of radio-tagged fish suggest that few recycled steelhead were present in the lower Cowlitz River during the spawning period. A total of 109 steelhead were radio-tagged during 2013–2014, and most of these fish (88 percent) moved upstream following release and entered the Trout Hatchery–Salmon Hatchery reach (river miles 44–51). The median elapsed time from release to reach entry was 4.6 days (range of 0.5–65.5 days). After fish entered this reach, they spent a considerable amount of time near the Cowlitz Trout Hatchery (median residence time of 16.7 hours) or Cowlitz Salmon Hatchery (median residence time of 146.3 hours), or they moved back and forth between these two sites. Thirty radio-tagged steelhead made at least two trips between the sites and some fish made as many as seven trips. Detection records showed that 61 percent (66 fish) of the radio-tagged fish returned to the hatchery reach and 21 percent (23 fish) of the fish were captured by anglers. The remaining 18 percent (20 fish) of the radio-tagged fish had various fates. One fish (less than 1 percent) left the Cowlitz River and nine fish (8 percent) died, were harvested, or spit their transmitter near boat launches in the river. The remaining 10 fish (9 percent) had the potential to interact with winter steelhead. Four tagged steelhead (4 percent) entered lower Cowlitz River tributaries (two fish in the Toutle River; two fish in Salmon Creek) during October and November, and five tagged fish (5 percent) were last detected in the lower Cowlitz River in October. One fish (less than 1 percent) was never detected after being released. We measured the diameter of opercle punches in recycled steelhead to determine the temporal effectiveness of these marks. A total of 116 opercle punches were measured—36 were measured at the time of tagging and 80 were measured when fish returned to the hatchery. Opercle punches remained open for less than 1 month. None of the fish that returned to the hatchery more than 30 days after release had opercle punches that were open. All recycled steelhead were marked with a Floy ® tag and opercle punch. However, if a steelhead lost its Floy ® tag and was captured by an angler, or returned to the hatchery more than 30 days after being recycled, it likely would not have been accurately identified as having been recycled because of regrowth of the opercle punch. During 2013–2014, at least 70 percent of the recycled steelhead were removed from the lower Cowlitz River by anglers, returned to the hatchery, or left the river. Radiotelemetry data indicated that a maximum of 9 percent of the radio-tagged fish remained in the lower Cowlitz River during the spawning period and only 4 percent of the radio-tagged fish entered tributaries where wild steelhead are known to spawn. These results are consistent with findings from previous studies. Overall, results from these studies suggest that about one-third of the recycled steelhead were not known to have been removed from the river. However, the radiotelemetry data indicated that only about 10 percent of the recycled steelhead were present in the lower Cowlitz River during late autumn and early winter, and few of those fish (0 in 2012–2013 and 4 in 2013–2014) entered tributaries where winter steelhead spawn. These results have management implications in the lower Cowlitz River where the risks and rewards of steelhead recycling will be weighed to determine the future of the recycling program.

Washinton↗

USGS2017

Report from the Workshop on Coregonine Restoration Science

Summary Great Lakes fishery managers have the opportunity and have expressed interest in reestablishing a native forage base in the Great Lakes consisting of various forms and species within the genus Coregonus . This report summarizes the proceedings of a workshop focused on a subset of the genus, and the term “coregonines” is used to refer to several species of deepwater ciscoes (also known as “chubs”) and the one more pelagic-oriented cisco species ( Coregonus artedi , also known as “lake herring”). As the principal conservation agency for the United States Government, the Department of Interior has unique and significant authorities and capacities to support a coregonine reestablishment program in the Great Lakes. To identify and discuss key uncertainties associated with such a program and develop a coordinated approach, the U.S. Geological Survey (USGS) and the U.S. Fish and Wildlife Service (FWS), the principal Department of the Interior bureaus to address Great Lakes fishery issues, held the first of a series of workshops on coregonine science in Ann Arbor, Michigan, on October 11–13, 2016. Workshop objectives were to identify (1) perceived key uncertainties associated with coregonine restoration in the Great Lakes and (2) DOI capacities for addressing these key uncertainties.

Open-File Report↗

USGS2018

Brown trout in the Lees Ferry reach of the Colorado River—Evaluation of causal hypotheses and potential interventions

Over the period 2014–2016, the number of nonnative brown trout (Salmo trutta) captured during routine monitoring in the Lees Ferry reach of the Colorado River, downstream of Glen Canyon Dam, began increasing. Management agencies and stakeholders have questioned whether the increase in brown trout in the Lees Ferry reach represents a threat to the endangered humpback chub (Gila cypha), to the rainbow trout (Oncorhynchus mykiss) sport fishery, or to other resources of concern. In this report, we evaluate the evidence for the expansion of brown trout in the Lees Ferry reach, consider a range of causal hypotheses for this expansion, examine the likely efficacy of several potential management interventions to reduce brown trout, and analyze the effects of those interventions on other resources of concern. The brown trout population at Lees Ferry historically consisted of a small number of large fish supported by low levels of immigration from downstream reaches. This population is now showing signs of sustained successful reproduction and is on the cusp of recruiting locally hatched fish into the spawning class, based on analysis with a new integrated population model. The proximate causes of this change in status are a large pulse of immigration in the fall of 2014 and higher reproductive rates in 2015–2017. The ultimate causes of this change are not clear. The pulse of immigrants from downstream reaches in fall 2014 may have been induced by three sequential high-flow releases from the dam in November of 2012–2014, but may also have been the result of a unique set of circumstances unrelated to dam operations. The increase in reproduction may have been the result of any number of changes, including an Allee effect, warmer water temperatures, a decrease in competition from rainbow trout, or fall high-flow releases. Correlations over space and time among predictor variables do not allow us to make a clear inference about the cause of the changes. Under a null causal model, and without any changes to management, we predict there is a 36-percent chance the brown trout population at Lees Ferry will not show sustained growth, and will remain around a mean size of 5,800 adults, near its current size; in contrast, we predict there is a 64-percent chance that the population has a positive intrinsic growth rate and will increase 3–10 fold over the next 20 years. A humpback chub population model linked to the brown trout model suggests an increase of brown trout of this magnitude could lead to declines in the minimum adult humpback chub population over the same time period. Forecasts of rainbow trout abundance, however, suggest that increased abundance of brown trout in the Lees Ferry reach does not pose a threat to the rainbow trout fishery there. There are interventions that may be effective in moderating the growth of the brown trout population in the Lees Ferry reach of the Colorado River. Across causal hypotheses, we predict that removal strategies (for example, a concerted electrofishing effort or an incentivized take program targeted at large brown trout) could reduce brown trout abundance by approximately 50 percent relative to status quo management. Reductions in the frequency or a change in the seasonal timing of high-flow releases from Glen Canyon Dam could be even more effective, but only under the causal hypotheses that involve effects of such releases on immigration or reproduction. Brown trout management flows— dam releases designed to strand young fish at a vulnerable stage—may be able to reduce brown trout abundance to some degree, but are not forecast to be the most effective strategy under any causal hypothesis. We predict that the alternative management interventions would have effects on other resource goals as well, and the pattern of these effects differs across causal hypotheses. The removal strategies would incur direct costs (on the order of $7 million over 20 years) and the mechanical removal strategy is unethical from the perspective of several tribes. The strategies that involve reducing the frequency of high-flow releases from Glen Canyon Dam would decrease the ability to transport and store sediment in the ecosystem, potentially undermining goals associated with sandbar building, recreation, and riparian vegetation, but would increase hydropower revenue. Trout management flows would reduce hydropower revenue. From the standpoint of humpback chub, the alternative strategies largely follow the effect on brown trout; when brown trout abundance is reduced, predation pressure decreases, and humpback chub viability is predicted to increase, but the variation in predicted chub viability is not large across strategies or causal hypotheses. To design a response to brown trout, management agencies will need to navigate both the tradeoffs among resources goals and the uncertainty in the causes of the brown trout expansion. Continued monitoring, possibly coupled with new research or experimental management actions that better inform demographic and ecological dynamics, can help to reduce the causal uncertainty.

Arizona↗