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Environmental DNA calibration study interim technical review report December 2014

The Environmental DNA Calibration Study (ECALS) is a multi-year study to improve the understanding and interpretation of the detection of Asian carp DNA in environmental samples (eDNA) used in early detection monitoring. eDNA surveillance programs seek to detect the presence of genetic material (DNA in cells sloughed off in slime, feces, urine, etc.) extracted from water samples; the detection of genetic material is linked to the possible presence of Asian carp. The study involves collaboration between the U.S. Army Corps of Engineers, the U.S. Geological Survey, and the U.S. Fish and Wildlife Service. ECALS addresses three major Action Items from the Asian Carp Regional Coordinating Committee (ACRCC) Asian Carp Control Strategy Framework, of which results to date are presented below. Initial ECALS efforts focused on eDNA vectors whereas marker development and calibration experiments received greater attention in 2013.

Report

Characterization of water-resource threats and needs for U.S. Fish and Wildlife Service National Wildlife Refuges in the Legacy Mountain-Prairie Region, 2020

The U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service (FWS), began a study in 2019 to complete the compilation and quality assurance of water-resource threats and needs data for the 117 National Wildlife Refuges (NWRs) in the FWS Legacy Mountain-Prairie Region (LMPR) and to characterize the water-resource threats and needs of each refuge and of the LMPR itself. The LMPR encompasses the states of Colorado, Kansas, Montana, Nebraska, North Dakota, South Dakota, Utah, and Wyoming. This report includes the compilation and quality assurance of current (April 2020) water-resource threats and needs data for the refuges in the LMPR and a statistical, graphical, and spatial characterization, including the ranking and prioritization of threat types, threat causes, and needs by the number of occurrences in the LMPR as a whole and by refuges, states, and select U.S. Environmental Protection Agency Level III Ecoregions. A total of 540 unique threat occurrences were identified for 109 refuges in the LMPR. No threats were identified for eight refuges. About 43 percent of the threat occurrences, for 59 refuges, had a high-severity threat rating. Of the 10 most common threat types, 8 were also among the most common high-severity threat types. Water-resource threats had 72 different causes. About 83 percent of the overall common causes for threats and for high-severity threats were the same. The most common threat types overall and the most common high-severity threat types were compromised water management capability, habitat shifting/alteration, and altered flow regimes. The 20 water-resource threat types for Long Lake NWR were the most for refuges in the LMPR. Other refuges with the greatest number of threat types included Marais des Cygnes NWR (18) and Arapaho and Lee Metcalf NWRs (16 each). About 54 percent of refuges with threats had high-severity threats. Arapaho and Quivira NWRs each had 10 high-severity threat types, the maximum number of high-severity threat types for LMPR refuges. A total of 637 unique need occurrences were identified for 114 refuges. No needs were reported for three refuges. The most common need type, a Water Resource Inventory and Assessment, was reported for 78 refuges. Two of the most common need types, repair and replace water management infrastructure and water supply/quantity monitoring, were the most common high-priority need types. Bear River Migratory Bird Refuge had the most (39) unique water-resource need types for refuges in the LMPR. Other refuges with the greatest number of need types were Baca (38), Alamosa (36), and Monte Vista (36) NWRs. The most high-priority need types for a refuge was 23, at Monte Vista NWR. Alamosa (22), Baca (22), and Lake Andes (19) NWRs were also among the top 4 refuges with the greatest number of high-priority need types. An overall ranking scheme was developed to identify refuges that have the highest-ranking priority for conservation efforts to fulfill refuges’ statutory purposes. The count of occurrences of high-severity threats and high-priority needs were summed to determine the overall ranking value for a refuge. The 10 refuges with the highest overall ranking values, in order of ranking from higher to lower, were Alamosa, Baca, and Monte Vista NWRs (tied for highest); Lake Andes NWR, Ouray and Quivira NWRs, Bear River Migratory Bird Refuge and Flint Hills NWR, Cokeville Meadows NWR, and Arapaho NWR. About 33 percent of overall threat occurrences were reported as under the control of the FWS to mitigate, as were 37 percent of all threat occurrences with a high-severity rating. The most common overall threat types and high-severity threat types under FWS control were compromised water management capability; habitat shifting/alteration; altered flow regimes; loss/alteration of wetland habitat; and legal challenges or fines for non-compliance with water policy, law, or regulation. A total of 68 percent of overall need occurrences and 67 percent of all high-priority need occurrences were under the control of the FWS. The most common overall need types and high-priority needs types under control were repair or replace water management infrastructure, water supply/quantity monitoring, water quality baseline monitoring, and protect habitat from invasive species. A Water Resource Inventory and Assessment was also a common overall need under FWS control, as was the high-priority need of water level monitoring.

Colorado, Kansas, Montana, Nebraska, North Dakota,

Surveillance for Asian H5N1 avian influenza in the United States

Increasing concern over the potential for migratory birds to introduce the Asian H5N1 strain of avian influenza to North America prompted the White House Policy Coordinating Committee for Pandemic Influenza Preparedness to request that the U.S. Departments of Agriculture (USDA) and Interior (DOI) develop a plan for the early detection of highly pathogenic avian influenza (HPAI) in the United States. To promote coordination among wildlife, agriculture, and human health agencies on HPAI surveillance efforts, the two Departments worked with representatives from the U.S. Department of Health and Human Services, the International Association of Fish and Wildlife Agencies, and the Alaska Department of Fish and Game to develop the U.S. Interagency Strategic Plan for Early Detection of Asian H5N1 Highly Pathogenic Avian Influenza in Wild Migratory Birds.

Fact Sheet

Partnering in search of answers: Seabird die-offs in the Bering and Chukchi Seas

Prior to 2015, seabird die-offs in Alaskan waters were rare; they typically occurred in mid-winter, linked to epizootic disease events or above-average ocean temperatures associated with strong El Nino-Southern Oscillation events (Bodenstein et al. 2015, Jones et al. 2019, Romano et al. 2020). Since 2015, the U.S. Fish and Wildlife Service (USFWS) has monitored mortality events that have become annual occurrences in Alaska (Fig. 1). Since 2017, communities on the coasts of the northern Bering and southern Chukchi Seas have annually observed dead and dying seabirds along their coasts, although such die-offs have not been reported from communities north of Point Hope. (Fig. 2). Affected species included planktivorous birds such as auklets ( Aethia spp.) and shearwaters ( Ardenna spp.), piscivorous murres ( Uria spp.), puffins ( Fratercula spp.), and kittiwakes ( Rissa spp.), as well as low numbers of benthic feeding sea ducks ( Somateria spp.). The range of seabird species and the different prey species involved, with localized events throughout summer and over widespread areas, indicate environmental causes at multiple trophic levels. Such wildlife mortality events are a public health concern for coastal communities that rely on ocean resources for their nutritional, cultural, and economic well-being. They have also been seen as a harbinger of concern for the state of the Arctic Ocean itself.

Alaska

Cooperative Fish and Wildlife Research Units program—2019 year in review postcard

Acting Chief’s Message Dear friends, I invite you to take a look at U.S. Geological Survey Circular 1463, “Cooperative Fish and Wildlife Research Units Program—2019 Year in Review,” now available at https://doi.org/10.3133/cir1463 . In this report, you will find details about the Cooperative Fish and Wildlife Research Units (CRU) program concerning fish and wildlife science, students, staffing, vacancies, research funding, outreach and training, awards, accolades, and professional services. You will also see examples of unit projects with information on how results have been or are being applied by our cooperators. Throughout the year, keep up with our research projects at https://www1.usgs.gov/coopunits/Headquarters/ . Regards, John D. Thompson

General Information Product

Application of sediment characteristics and transport conditions to resource management in selected main-stem reaches of the Upper Colorado River, Colorado and Utah, 1965-2007

The Colorado River Basin provides habitat for 14 native fish, including 4 endangered species protected under the Federal Endangered Species Act of 1973. These endangered fish species once thrived in the Colorado River system, but water-resource development, including the building of numerous diversion dams and several large reservoirs, and the introduction of non-native fish, resulted in large reductions in the numbers and range of the four species through loss of habitat and stream function. Understanding how stream conditions and habitat change in response to alterations in streamflow is important for water administrators and wildlife managers and can be determined from an understanding of sediment transport. Characterization of the processes that are controlling sediment transport is an important first step in identifying flow regimes needed for restored channel morphology and the sustained recovery of endangered fishes within these river systems. The U.S. Geological Survey, in cooperation with the Upper Colorado River Endangered Fish Recovery Program, Bureau of Reclamation, U.S. Fish and Wildlife Service, Argonne National Laboratory, Western Area Power Administration, and Wyoming State Engineer’s Office, began a study in 2004 to characterize sediment transport at selected locations on the Colorado, Gunnison, and Green Rivers to begin addressing gaps in existing datasets and conceptual models of the river systems. This report identifies and characterizes the relation between streamflow (magnitude and timing) and sediment transport and presents the findings through discussions of (1) suspended-sediment transport, (2) incipient motion of streambed material, and (3) a case study of sediment-transport conditions for a reach of the Green River identified as a razorback sucker spawning habitat (See report for full abstract).

Colorado;Utah

Yellowstone grizzly bear investigations: Annual report of the Interagency Grizzly Bear Study Team, 2003

The contents of this Annual Report summarize results of monitoring and research from the 2003 field season. The report also contains a summary of nuisance grizzly bear ( Ursus arctos horribilis ) management actions. The study team continues to work on issues associated with counts of unduplicated females with cubs-of-the-year (COY). These counts are used to establish a minimum population size, which is then used to establish mortality thresholds for the Recovery Plan (U.S. Fish and Wildlife Service [USFWS] 1993). A computer program that defines the rule set used by Knight et al. (1995) to differentiate unique family groups is currently under development. Once complete, we intend to use it to verify the accuracy of the rules using known bears and their telemetry locations in test runs. We hope to have this work complete by summer 2004. The grizzly bear recovery plan (USFWS 1993) established mortality quotas at 4% of the minimum population estimate derived from female with COY data and no more than 30% of the 4% (1.2%) could be female bears. Simulation modeling (Harris 1984) established sustainable mortality at around 6% of the population. We used the latest information on reproduction and survival to estimate population trajectory in the same simulation model originally used by Harris. A Wildlife Monograph has been drafted and submitted for consideration as a publication. We anticipate final word sometime during winter 2005. Our project addressing the potential application of stable isotopes and trace elements to quantify consumption rates of whitebark pine ( Pinus albicaulis ) and cutthroat trout ( Oncorhynchus clarki ) by grizzly bears was completed. Our manuscript on consumption rates of whitebark pine has been published (Canadian Journal of Zoology 81:763-770). A copy can be found on the Interagency Grizzly Bear Study Team (IGBST) website http://www.nrmsc.usgs.gov/research/igbst-home.htm. The manuscript on fish consumption is in final review and should be published in 2004. We began a new study in Grand Teton National Park evaluating habitat use both temporally and spatially between grizzly and black ( Ursus americanus ) bears. We will employ a new form of Global Positioning System (GPS) technology that incorporates a spread spectrum communication system. Spread spectrum allows for transfer of stored GPS locations from the collar to a remote receiving station. We tested 2 collars during the fall of 2003 and provide a summary of the results. We will attempt to deploy several of these collars during the 2004 field season. The annual reports of the IGBST summarize annual data collection. Because additional information can be obtained after publication, data summaries are subject to change. For that reason, data analyses and summaries presented in this report supersede all previously published data. The study area and sampling techniques are reported by Blanchard (1985), Mattson et al. (1991a), and Haroldson et al. (1998).

Montana

The humane capture, handling, and disposition of migratory birds

The purpose of this document is to provide guidance on the humane capture, handling, and care of migratory birds trapped for any purpose. It is intended for wildlife managers, regulatory personnel, and individuals that handle or authorize handling of live-captured migratory birds. The U.S. Fish and Wildlife Service – Migratory Bird Program (USFWS), the U.S. Geological Survey Bird Banding Laboratory (BBL), and U.S. Department of Agriculture Animal Plant Health Inspection Service Wildlife Services (WS) collaboratively prepared this document.

Final Report

Land-cover change in the Ozark Highlands, 1973-2000

Led by the Geographic Analysis and Monitoring Program of the U.S. Geological Survey (USGS) in collaboration with the U.S. Environmental Protection Agency (EPA) and the National Aeronautics and Space Administration (NASA), the Land-Cover Trends Project was initiated in 1999 and aims to document the types, geographic distributions, and rates of land-cover change on a region by region basis for the conterminous United States, and to determine some of the key drivers and consequences of the change (Loveland and others, 2002). For 1973, 1980, 1986, 1992, and 2000 land-cover maps derived from the Landsat series are classified by visual interpretation, inspection of historical aerial photography and ground survey, into 11 land-cover classes. The classes are defined to capture land cover that is discernable in Landsat data. A stratified probability-based sampling methodology undertaken within the 84 Omernik Level III Ecoregions (Omernik, 1987) was used to locate the blocks, with 9 to 48 blocks per ecoregion. The sampling was designed to enable a statistically robust 'scaling up' of the sample-classification data to estimate areal land-cover change within each ecoregion (Loveland and others, 2002; Stehman and others, 2005). At the time of writing, approximately 90 percent of the 84 conterminous United States ecoregions have been processed by the Land-Cover Trends Project. Results from these completed ecoregions illustrate that across the conterminous United States there is no single profile of land-cover/land-use change, rather, there are varying pulses affected by clusters of change agents (Loveland and others, 2002). Land-Cover Trends Project results for the conterminous United States to-date are being used for collaborative environmental change research with partners such as; the National Science Foundation, the National Oceanic and Atmospheric Administration, and the U.S. Fish and Wildlife Service. The strategy has also been adapted for use in a NASA global deforestation initiative, and elements of the project design are being used in the North American Carbon Program's assessment of forest disturbance.

Open-File Report

Wolf depredation on livestock in Minnesota

Depredation by wolves (Canis lupus) on cattle, sheep, and other livestock in Minnesota currently is a minor problem except to a few individual farmers. Indices to the seriousness of the problem are available only from recent years, so historical trends cannot be detected. From 1976 through 1980 the number of farms in the wolf range suffering verified losses to wolves ranged from 9 to 19 (mean of x = 13) per year out of about 12,230. From 1977 through 1980, the highest cattle losses claimed by farmers were 0.45 per 1,000 cattle available in 1979; the highest sheep losses claimed were 1.18 per 1,000 available in 1980. Many claims of losses (especially of calves) are based on missing animals, and few wolves are involved in the verified losses. Most losses occur in summer when livestock are released to graze in open and wooded pasture. Herd management practices, such as calving in forested or brushy pastures and disposal of carcasses in or near pastures, are responsible for many instances of wolf depredation. Failure to distinguish wolves from coyotes (Canis latrans) has contributed to an exaggerated view of the importance of wolves as livestock predators. Recently the number of wolves killed in depredation control has declined, whereas the number of livestock killed has remained fairly stable. Results of the U.S. Fish and Wildlife Service's depredation- control program in 1979 and 1980 suggest that highly restricted trapping, coupled with other management methods, has potential for reducing both livestock losses and the number of wolves that need to be killed.

Resource Publication

Habitat Suitability Index Models: Yellow perch

A review and synthesis of existing information were used to develop riverine and lacustrine habitat models for yellow perch (Perca flavescens). The models are scaled to produce an index of habitat suitability between 0 (unsuitable habitat) to 1 (optimally suitable habitat) for riverine, lacustrine, and palustrine habitat in the 48 contiguous United States. Habitat Suitability Indexes (HSI's) are designed for use with the Habitat Evaluation Procedures developed by the U.S. Fish and Wildlife Service. Also included are discussions of Suitability Index (SI) curves as used in the Instream Flow Incremental Methodology (IFIM) and SI curves available for an IFIM analysis of yellow perch habitat.

FWS/OBS

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

Ecology of Greater Sage-Grouse in the Bi-State Planning Area Final Report, September 2007

Conservation efforts for greater sage-grouse (Centrocercus urophasianus), hereafter sage-grouse, are underway across the range of this species. Over 70 local working groups have been established and are implementing on-the-ground sage-grouse oriented conservation projects. Early on in this process, the California Department of Fish and Game (CDFG) recognized the need to join in these efforts and received funding from the U.S. Fish and Wildlife Service (USFWS) under the Candidate Species Conservation Program to help develop a species conservation plan for sage-grouse in the Mono County area. This conservation plan covers portions of Alpine, Mono, and Inyo counties in California and Douglas, Esmeralda, Lyon, and Mineral counties in Nevada. A concurrent effort underway through the Nevada Governor's Sage-grouse Conservation Team established Local Area Working Groups across Nevada and eastern California. The Mono County populations of sage-grouse were encompassed by the Bi-State Local Planning Area, which was comprised of six population management units (PMUs). The state agencies from California (CDFG) and Nevada (Nevada Department of Wildlife; NDOW) responsible for the management of sage-grouse agreed to utilize the process that had begun with the Nevada Governor's Team in order to develop local plans for conservation planning and implementation. Resources from the USFWS were applied to several objectives in support of the development of the Bi-State Local Area Sage-grouse Conservation Plan through a grant to the U.S. Geological Survey (USGS). Objectives included: (1) participate in the development of the Bi-State Conservation Plan, (2) compile and synthesize existing sage-grouse data, (3) document seasonal movements of sage-grouse, (4) identify habitats critical to sage-grouse, (5) determine survival rates and identify causal factors of mortality, (6) determine nest success and brood success of sage-grouse, and (7) identify sage-grouse lek sites. Progress reports completed in 2004 and 2005 addressed each of the specific objectives and this final report focuses on the biological information gathered in support of local conservation efforts. Participation in the development of the Bi-State Local Area Conservation Plan was accomplished on multiple scales. Beginning in the fall of 2002, USGS personnel began participating in meetings of local stakeholders involved in the development of a sage-grouse conservation plan for the Bi-State planning area. This included attendance at numerous local PMU group meetings and field trips as well as participating on the technical advisory committee (TAC) for the Bi-State group. Whenever appropriate, ongoing results and findings regarding sage-grouse ecology in the local area were incorporated into these working group meetings. In addition, the USGS partnered with CDFG to help reorganize one of the local PMU groups (South Mono) and edited that portion of the Bi-State plan. The USGS also worked closely with CDFG to draft a description of the state of knowledge for sage-grouse genetic information for inclusion in the Bi-State Conservation Plan. The first edition of the Bi-State Conservation Plan for Greater Sage-Grouse was completed in June 2004 (Bi-State Sage-grouse Conservation Team 2004). This report is organized primarily by PMU to facilitate the incorporation of these research findings into the individual PMU plans that compose the Bi-State plan. Information presented in this report was derived from over 7,000 radio-telemetry locations obtained on 145 individual sage-grouse during a three year period (2003-2005). In addition, we collected detailed vegetation measurements at over 590 habitat sampling plots within the study area including canopy cover, shrubs, forbs, and grasses diversity. Vegetation data collection focused on sage-grouse nests, and brood-use areas. Additionally we collected data at random sites to examine sage-grouse habitat relationships within the study area. The majori

Open-File Report

Spatial and temporal variation in marine birds in the north Gulf of Alaska: The value of marine bird monitoring within Gulf Watch Alaska

Birds offer useful insights into marine ecosystems. Marine birds are responsive to spatial and temporal variation in the environment, that often originates with fluctuations in oceanographic and climatic drivers and permeates up through food webs to conspicuous top predators such as seabirds (Coyle and Pinchuk 2005, Speckman et al. 2005, Gonzales-Solis et al. 2009, Cushing et al., this report). In that way, marine birds are excellent assimilators, samplers, and indicators of the status of marine environments (Montevecchi 1993, Piatt et al. 2007b, Zador et al. 2013). Marine bird responses to dynamic marine ecosystems can be detected in a variety of metrics, including abundance, distribution, and productivity. For example, in the northern Gulf of Alaska (GOA), decadal-scale variation in oceanographic conditions has been associated with dramatic shifts in prey composition and abundance (Anderson and Piatt 1999). In turn, these shifts were more closely correlated with changes in abundance of fish-eating birds of Prince William Sound (PWS), such as pigeon guillemots (Golet et al. 2002) and marbled and Kittlitz’s murrelets (Kuletz et al. 2011a, 2011b), than in the abundance of species that primarily consume plankton or benthic prey (Agler et al. 1999, Cushing et al., this report). Birds also are responsive to anthropogenic influences in marine environments, including commercial fishing, contamination, introduction of non-native species, coastal development, offshore resource extraction, and vessel traffic. A major anthropogenic perturbation in the northern GOA was the 1989 Exxon Valdez oil spill, in which marine birds suffered high immediate mortality (Piatt and Ford 1996). Additionally, several species showed long-term evidence of declines in the oiled areas of PWS (Lance et al. 2001), as well as impacts to reproductive success years later (Golet et al. 2002). However, the degree of direct impact and vulnerability to chronic injury, which was related to exposure to lingering oil, varied widely among species (see Esler et al., this report). Research and monitoring directed at documenting the timelines and mechanisms of wildlife recovery following the Exxon Valdez oil spill led to an unprecedented understanding of oil spill effects on marine birds, as well as previously unknown information about marine bird ecology in the northern GOA. Quantifying effects of anthropogenic influences requires an understanding of variation in marine bird abundance, distribution, and productivity, in relation to naturally occurring dynamics in marine environments continued marine bird work as part of Gulf Watch Alaska will facilitate this. In addition to their value as indicators of marine conditions and anthropogenic influences, marine birds are protected under the Migratory Bird Treaty Act and are managed by the U.S. Fish and Wildlife Service (USFWS). Marine birds have high societal value from a wide variety of interests (e.g., tourism, bird watching, hunting, mythology), and are an important source of subsistence foods in Alaska (Naves and Braem 2014). Because of the conservation interest in marine birds, as well as their value for indicating the status of marine ecosystems, monitoring of marine birds is an important component of many ocean monitoring programs, including Gulf Watch Alaska.

Alaska

Science support for evaluating natural recovery of polychlorinated biphenyl concentrations in fish from Crab Orchard Lake, Crab Orchard National Wildlife Refuge, Illinois

Introduction Crab Orchard Lake in southern Illinois is one of the largest and most popular recreational lakes in the state. Construction of the nearly 7,000-acre reservoir in the late 1930s created employment opportunities through the Works Progress Administration, and the lake itself was intended to supply water, control flooding, and provide recreational opportunities for local communities (Stall, 1954). In 1942, the Department of War appropriated or purchased more than 20,000 acres of land around Crab Orchard Lake and constructed the Illinois Ordnance Plant, which manufactured bombs and anti-tank mines during World War II. After the war, an Act of Congress transferred the property to the U.S. Department of the Interior. Crab Orchard National Wildlife Refuge was established on August 5, 1947, for the joint purposes of wildlife conservation, agriculture, recreation, and industry. Production of explosives continued, but new industries also moved onsite. More than 200 tenants have held leases with Crab Orchard National Wildlife Refuge and have operated a variety of manufacturing plants (electrical components, plated metal parts, ink, machined parts, painted products, and boats) on-site. Soils, water, and sediments in several areas of the refuge were contaminated with hazardous substances from handling and disposal methods that are no longer acceptable environmental practice (for example, direct discharge to surface water, use of unlined landfills). Polychlorinated biphenyl (PCB) contamination at the refuge was identified in the 1970s, and a PCB-based fish-consumption advisory has been in effect since 1988 for Crab Orchard Lake. The present advisory covers common carp ( Cyprinus carpio ) and channel catfish ( Ictalurus punctatus ); see Illinois Department of Public Health (2017). Some of the most contaminated areas of the refuge were actively remediated, and natural ecosystem recovery processes are expected to further reduce residual PCB concentrations in the lake. The U.S. Fish and Wildlife Service sought technical support to understand environmental drivers of current (2017) PCB residues in fish tissue and patterns in PCB residues through time to inform the fish-consumption advisory for Crab Orchard Lake. This project is planned in two phases (Tasks 1 and 2); the first phase is included in this report. Task 1, reported here, includes a review of existing literature and a brief overview focused on environmental and biochemical/physiological processes that drive PCB residues in fish tissue. This review specifically targets processes that are relevant for freshwater lacustrine environments such as those at Crab Orchard Lake. In addition to discussions of environmental fate, metabolism, and accumulation of PCBs, this review includes a brief scientifically based explanation of approaches used to establish fish-consumption advisories. A planned second task (Task 2) will include a compilation and summary of existing data on PCB residues in fish tissue samples from Crab Orchard Lake. This summary will also place Crab Orchard Lake data in a broader geographic context through a comparison with fish data from other Midwestern lakes. When Task 1 and Task 2 are complete, resource managers will have (a) a synthesis of existing literature that characterizes the processes influencing the fate of residual PCBs remaining in systems such as Crab Orchard Lake, (b) a summary of natural PCB attenuation processes for use in risk communication with the public, and (c) a summary of existing data on PCBs in fish tissues from Crab Orchard Lake, including exploratory plots of tissue residues through time. Overall, this project will provide data to help resource managers better understand the ecological and public health consequences of residual PCBs in Crab Orchard Lake.

Illinois

Recent scientific contributions by the U.S. Geological Survey in the San Francisco Bay and Sacramento–San Joaquin Delta Estuary

Introduction The San Francisco Bay and Sacramento–San Joaquin Delta Estuary (hereafter, Bay-Delta) is the largest estuary on the West Coast of the United States. The Bay-Delta covers more than 1,600 square miles and drains a watershed of more than 75,000 square miles, which is greater than 40 percent of California. The region surrounding the Bay-Delta is home to about 10 million people, and its habitats (fig. 1) support more than 800 plant and animal species. The waterways of the Bay-Delta are the central hub of California’s extensive freshwater delivery system, supplying water to more than 27 million Californians and 4 million acres of farmland in the Central Valley. The U.S. Geological Survey (USGS) is the primary science agency of the U.S. Department of the Interior, providing a broad range of Earth, water, biological, and mapping data and expertise to inform natural resource management across the country. This fact sheet focuses on research conducted by the USGS in the Bay-Delta region, mostly within the past 5 years. The fact sheet is organized across five major themes: water flow and water quality, fish and wildlife, wetland restoration, invasive species, and hazards. In each of these areas, the USGS works closely with Federal, State, and local agencies; academia; and non-governmental organizations to provide objective, evidence-based science. The data and knowledge gained from USGS research and monitoring are publicly available and are routinely used by agencies, including the U.S. Bureau of Reclamation, U.S. Army Corps of Engineers, U.S. Fish and Wildlife Service, California Department of Water Resources, California Department of Fish and Wildlife, California State Water Resources Control Board, Delta Stewardship Council, and many additional organizations and stakeholders to inform management of the Bay-Delta region and its resources.

California

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

Habitat Suitability Index Models: Rainbow trout

A review and synthesis of existing information were used to develop riverine and lacustrine habitat models for rainbow trout (Salmo gairdneri), a freshwater species. The models are scaled to produce an index of habitat suitability between 0 (unsuitable habitat) to 1 (optimally suitable habitat) for freshwater areas of the continental United States. Other habitat suitability models found in the literature are also included. Habitat suitability indexes (HSI's) are designed for use with the habitat evaluation procedures developed by the U.S. Fish and Wildlife Service. Also included are discussions of Suitability Index (SI) curves as used in the Instream Flow Incremental Methodology (IFIM) and SI curves available for an IFIM analysis of Fallfish habitat.

FWS/OBS