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At least 865 records · Page 48Linked to original sources
USGS2003

Use of retrospective data to assess ecotoxicological monitoring needs for terrestrial vertebrates residing in Atlantic coast estuaries

The “Contaminant Exposure and Effects–Terrestrial Vertebrates” (CEE-TV) database contains 4,336 records of ecotoxicological information for free-ranging amphibians, reptiles, birds, and mammals residing in Atlantic and Florida Gulf coast estuaries and their drainages. To identify spatial data gaps, those CEE-TV records for which the specific study location were known ( n =2,740) were combined with watershed and wildlife management unit boundaries using Geographic Information Systems software. The US Environmental Protection Agency's Index of Watershed Indicators (IWI), which classifies watersheds based on water quality and their vulnerability to pollution, was used to prioritize these data gaps. Of 136 watersheds in the study area, 15 that are classified by the IWI as having water quality problems or high vulnerability to pollution lacked terrestrial vertebrate ecotoxicological monitoring or research in the past decade. Older studies within some of these watersheds documented high levels of contaminants in wildlife tissues. Of 90 National Wildlife Refuge units, 42 without current data fall within watersheds of concern. Of 40 National Park units larger than 1 km 2 , 17 without current data fall within watersheds of concern. Issues encountered in this analysis highlighted the need for spatially and temporally replicated field monitoring programs that utilize random sampling. Without data from such studies, it will be difficult to perform unbiased assessments of regional trends in contaminant exposure and effects in terrestrial vertebrates.

Ecotoxicology↗
USGS2006

Influence of alternative silviculture on small mammals

HIGHLIGHT: A variety of harvest methods promote diversity within forests while still generating income. For example, recent studies have shown that when dead wood is left on the forest floor during harvest, biodiversity increases. A new Cooperative Forest Ecosystem Research (CFER) program fact sheet summarizes how small mammals respond to dead wood in forests that are harvested with alternative methods. CFER is developing a series of fact sheets about responses to changes in young western Oregon forests. The fact sheets are designed to help resource managers balance management needs, including timber and wildlife. The USGS provides a primary source of financial support for CFER, a consortium of federal and state partners conducting research in support of the Northwest Forest Plan.

Fact Sheet↗
USGS2022

Wind River subbasin restoration: Annual Report of U.S. Geological Survey activities January 2020 through December 2020

We sampled juvenile wild Steelhead Trout Oncorhynchus mykiss in headwater streams of the Wind River, WA, to characterize population attributes and investigate life-history metrics, particularly migratory patterns, and early life-stage survival. We used passive integrated transponder (PIT) tagging and a series of instream PIT-tag interrogation systems (PTISs) to track juveniles and adults. The Wind River subbasin is considered a wild Steelhead refuge by Washington Department of Fish and Wildlife (WDFW). No hatchery Steelhead Trout have been released in the Wind River subbasin since 1997, and hatchery adults are estimated at less than one percent of spawners in most years. Over twenty years of Steelhead Trout status and trend monitoring and research in the subbasin is contributing to understanding of population response to numerous restoration actions in the subbasin, including removal of Hemlock Dam from Trout Creek in 2009, which had an outdated adult ladder and contributed to increased water temperatures reducing performance of juvenile Steelhead Trout. Data from our study, and companion work by Washington Department of Fish and Wildlife, are contributing to Bonneville Power Administration’s (BPA) Research, Monitoring, and Evaluation (RM&E) Program Strategy of Fish Population Status Monitoring (https://www.cbfish.org/ProgramStrategy.mvc/Index). Specifically, this work addresses the substrategies of 1) Assessing the Status and Trends of Diversity of Natural Origin Fish Populations and Uncertainties Research regarding differing life histories of a wild Steelhead Trout population, 2) Assessing the Status and Trend of Adult Natural Origin Fish Populations, and 3) Monitoring and Evaluating the Effectiveness of Tributary Habitat Actions Relative to Environmental, Physical, or Biological Performance Objectives. During summer and fall 2020, we PIT-tagged 1,415 Steelhead parr (age-0 and age-1) in the Trout Creek and upper Wind River watersheds. Recaptures and detections of PIT-tagged Steelhead Trout parr happened through repeat headwater sampling, smolt trap operations, and instream PTISs and Columbia River PIT-tag detection infrastructure. Throughout the year, we maintained a series of six instream PTISs to monitor movement of tagged Steelhead Trout parr, smolts, and adults, providing data to population assessments, and life-cycle research and modeling. Detection data from PIT-tagged adult Steelhead Trout at PTISs allow assessment of adult escapement to tributary watersheds within the Wind River subbasin. Adult Steelhead Trout detection efficiency estimates at our primary PTIS in Trout Creek have been greater than 92 percent during eight of the past nine years and have exceeded 90% at our primary PTIS in the Wind River the past three years. Adult escapement estimates to tributary watersheds are helping evaluate the efficacy of the 2009 removal of Hemlock Dam from rkm 2.0 of Trout Creek. The dam had potential negative effects on Steelhead Trout populations in Trout Creek due to hydrologic impairment, increased temperatures, and adult passage issues. Hemlock Dam was laddered for adult passage, but not to modern standards, which likely resulted in avoidance by some adult Steelhead Trout. We continue to improve our PTISs in the Wind River subbasin. The improvements in siting and addition of grid power to the upper Wind River PTIS (site code WRU, rkm 27.6) during 2016 and 2017, and the addition of the Mine Reach site (site code MIN, rkm 36.0) have much improved PIT-tagged fish monitoring in the upper Wind River watershed. The paired PTIS design in the upper Wind River watershed (sites WRU and MIN), matches that in the Trout Creek watershed (sites TRC and TC4) and will allow comparisons of Steelhead Trout population metrics between the two watersheds as response to Hemlock Dam removal continues and future restoration efforts occur in Trout Creek. We installed two new PTISs during 2020. Both were installed downstream of our primary interrogation sites on Trout Creek and in the mainstem Wind River. We hope the two new sites will provide interrogations information that will allow us to better estimate detection efficiencies of downstream moving juvenile Steelhead Trout at the primary interrogation sites. The additional interrogations will be particularly important for those fish tagged with 9-mm PIT tags as less information from downstream locations is available from them. These sites and other status and trend data will allow evaluation of further planned restoration within the watershed, particularly that proposed for the headwaters of Trout Creek. Detections at the instream PTISs have demonstrated trends of age-0 and age-1 parr emigration from natal areas during summer and fall, in addition to the expected movement of parr and smolts in spring. We have estimated that from 15 to 51% of parr tagged as age-0 fish in headwater areas make downstream migrations at age 1 for additional rearing during both spring and fall. We have estimated that up to 27% of Steelhead Trout parr, tagged as age-1 fish, make downstream migrations during fall. These findings raise questions about where parr most successfully rear and whether migrations are density or habitat quality driven. Broader monitoring programs would give a more comprehensive understanding of juvenile Steelhead Trout production and rearing and productivity contribution. Repeat sampling at consistent locations in the subbasin has enabled assessment of juvenile Steelhead Trout growth patterns. Growth rates (relative change in weight) of age-0 PITtagged parr during summer were similar across the subbasin but lower for age-1 parr in the Trout Creek watershed than the upper Wind River watershed. Yearly relative growth for parr tagged at age-0 is similar across the subbasin. Non-native Brook Trout Salvelinus confluentus are present in the subbasin, chiefly the Trout Creek watershed, and repeat sampling has allowed us to index their prevalence. Mean percent-of-catch that is Brook Trout, at four sample sites in Trout Creek, has declined from the period 1998 – 2003 to the period 2011 – 2020. Percent-of-catch and number of Brook Trout at the Trout Creek sites from 2011 through 2020 declined, though both metrics increased in 2018. Evaluation and planning of restoration efforts are critical to ensure efficient use of resources. Assessing Steelhead Trout life history variation in the Wind River subbasin will inform research and tracking of many populations and help inform habitat restoration and water allocation planning. Movement of Steelhead Trout parr from natal areas to other rearing areas raises questions regarding juvenile abundance, origin, and habitat use within watersheds. Improved PTISs and focused PIT tagging of age-0 and age-1 Steelhead Trout parr allow investigation of such questions. Increasingly detailed viable salmonid population information, such as that provided by PIT-tagging and instream PTIS networks like those in the Wind River can provide data to inform fisheries policy and management and understand life-history strategies and limiting factors. Such efforts also provide assessment of long-term effects of habitat restoration actions such as the removal of Hemlock Dam on Trout Creek, and the proposed Stage-0 restoration effort for upper Trout Creek, which would be a large-scale effort to reset sections of stream within their floodplain, restoring connectivity and interaction with surrounding landscape.

Washington↗
USGS2021

A decision tool to identify population management strategies for common ravens and other avian predators

Some avian species have developed the capacity to leverage resource subsidies associated with human manipulated landscapes to increase population densities in habitats with naturally low carrying capacities. Elevated corvid densities and new territory establishment have led to an unsustainable increase in depredation pressure on sympatric native wildlife prey populations as well as in crop damage. Yet, subsidized predator removal programs aimed at reducing densities are likely most effective longer-term when conducted in tandem with subsidy control, habitat management, and robust assessment monitoring programs. We developed decision support software that leverages stage structured Lefkovitch population matrices to compare and identify treatment strategies that reduce subsidized avian predator densities most efficiently, in terms of limiting both cost and take levels. The StallPOPd (Version 4; available at https://doi.org/10.7298/sk2e-0c38.4) software enables managers to enter the area of their management stratum and the demographic properties (vital rates) of target bird population(s) of interest to evaluate strategies to decrease or curtail further population growth. Strategies explicitly include the reduction in fertility (i.e., eggs hatched) and/or the culling of hatchlings, non-breeders and/or breeders, but implicitly comprise reduction in survival or reproduction through subsidy denial. We illustrate the utilities of the software with examples using common ravens ( Corvus corax; ravens) in the Mojave Desert of California, USA. Unfortunately, the survival and reproduction effects of each unit of a particular subsidy in that system have remained elusive, though this is the priority of current research. Because the software leverages a life history representation that is known to characterize hundreds of wildlife species in addition to ravens, the work expands the suite of tools available to wildlife managers and agricultural industry specialists to abate bird damage and impacts on sensitive wildlife in habitats with persistent human subsidies.

Human-Wildlife Interactions↗
USGS2023

Selenium hazards in the Salton Sea environment—Summary of current knowledge to inform future wetland management

Quaternary marine and continental shales in the western United States are sources of selenium that can be loaded into the aquatic environment through mining, agricultural, and energy production processes. The mobilization of selenium from shales through agricultural irrigation has been recognized since the 1930s; however, discovery of deformities in birds and other wildlife using agricultural habitats during the 1980s spurred studies to determine the extent and effects of the contamination. Through these early studies, researchers determined that biota in the Salton Sea drainage basin was at risk from legacy selenium contamination in the Colorado River watershed. The Salton Sea and its surrounding managed and unmanaged wetlands provide vital inland habitat and trophic support for diverse assemblages of resident and migratory wildlife, and understanding regional selenium hazards for these trust species is a priority for many Federal and State agencies. The modern Salton Sea is a shallow, landlocked saline lake in Riverside and Imperial Counties (not shown) of California that is sustained by irrigation return and perennial river inflow. Changes in water transfer agreements under the 2003 Quantification Settlement Agreement (QSA) have resulted in reduced irrigation flow, declining lake levels, and the evolution of unmanaged wetlands in areas where drains and rivers no longer reach the Salton Sea. These wetlands provide additional habitat for some species of concern, but their potential to increase selenium hazards for trust species is largely unknown. From the 1980s to 2020, efforts to document selenium contamination and effects throughout the region have resulted in a considerable amount of selenium data from the Salton Sea and its surrounding drainage basin; however, no long-term (greater than 20 years), consistent sampling program has been established, and all data have been collected by different entities using a variety of protocols and analytical techniques. This lack of coordination has been previously documented in regional management plans and has led to difficulty in reliably assessing selenium hazards in the Salton Sea environment. This report provides a summary of the available disparate selenium information collected from water, sediment, and biota in the Salton Sea region since the 1980s and to identify data gaps that need to be filled to understand the potential effects of selenium on species of concern, including federally endangered desert pupfish ( Cyprinodon macularius ) and Yuma Ridgway’s Rail ( Rallus obsoletus yumanensis; formerly Yuma Clapper Rail, Rallus longirostris yumanensis ). Available data from the Salton Sea drainage basin show that water from the Colorado River has the lowest selenium concentration of all surface water sources. All other surface water flowing into the Salton Sea has elevated selenium concentrations due to evaporation and evapotranspiration that occurs in agricultural fields and associated water delivery infrastructure or leaching of selenium from irrigated farmland soils. The Salton Sea has lower selenium concentrations because of various biogeochemical processes that recycle selenium into the sediment or volatilize it to the atmosphere; however, these mechanisms are not well defined, and it is not clear if selenium cycling will change in response to possible changes in the oxidation state of the Salton Sea bottom waters as water levels decline. Agricultural drains have the highest average selenium concentrations, but few drains have been sampled since changes in irrigation practices have occurred (due to the 2003 QSA). Groundwater selenium concentrations are variable; some wells south of the Salton Sea have selenium concentrations as high as 300 micrograms per liter (µg/L), whereas selenium concentrations are below detection in other wells. Groundwater and surface-water geothermal discharge zones around the margins of the Salton Sea and in unmanaged wetlands have not been studied in detail, and published selenium measurements are not available for these surface features. Selenium concentrations in the sediment of the Salton Sea drainage basin are highest in wetland particulate organic matter and the Salton Sea lakebed, indicating that removal of selenium from the water to the sediment has been a primary mechanism for keeping selenium concentrations low in the water column. Sediment selenium concentrations in wetlands are lower than in the Salton Sea but higher than inflowing drains and rivers, indicating the lentic wetland sites also may be important sinks for selenium because of biogeochemical processes. Sediment selenium data have not been collected in agricultural drains since changes in irrigation practices occurred (due to the 2003 QSA), and it is unknown if selenium sequestration from the water column has changed in these systems. We divided biological data into broad taxonomic categories, including primary producers, invertebrates, herpetofauna, mammals, fishes, and birds to facilitate evaluation of selenium concentrations and spatiotemporal trends observed in the Salton Sea. Overall, selenium concentrations were substantially greater in algae samples compared to all vascular plant samples combined. Median selenium concentrations in several invertebrate taxa (Chironomidae, Formicidae, Corixidae, Corbiculidae and Nereididae, and Decapoda) exceeded the maximum suggested dietary threshold of 3.0–4.0 micrograms per gram (µg/g) dry weight (dw) for predators consuming invertebrates in aquatic food webs. The greatest number of samples were collected from fish, and selenium distributions among species and locations showed that the range for most samples was lower than the U.S. Environmental Protection Agency selenium criterion for aquatic life (8.5 µg/g dw whole body, 11.3 µg/g dw fillets). The median selenium concentrations for whole body fish were below the selenium criterion in most locations, except for bairdiella ( Bairdiella icistia ) from the Salton Sea and irrigation drains, a few individual tilapia spp. (family Cichlidae, including genera Tilapia, Oreochromis , and their hybrids) from the river and river outlets, and several western mosquitofish ( Gambusia affinis ) and sailfin molly ( Poecilia latipinna ) from irrigation drain outlets. For avian samples combined among years and locations, median selenium concentrations in livers from all families except waders and Ibis (family Threskiornithidae) were higher than levels expected to cause selenium toxicosis (10–20 µg/g dw), and all median egg concentrations were above or near 6.0 μg/g dw, which is a conservative threshold value for reproductive impairment. Most knowledge gaps we identified for water, sediment, and biota were interrelated, and the use of integrated approaches to address knowledge gaps can provide greater insight into the drivers behind selenium hazards. Integrated water, sediment, and biota studies could help identify cost-effective management solutions that serve multiple purposes. A comprehensive analysis of the hydrology, biogeochemistry, and food-web processes in wetlands and other habitats can inform predictive models to identify drivers of selenium bioavailability, uptake from the environment and subsequent trophic transfer, ultimately forming the basis for experimental habitat management manipulations to minimize selenium hazards to wildlife. Furthermore, a comprehensive, long-term sampling and analytical laboratory plan would enable comparison of data among different entities that are sampling at the Salton Sea. Such efforts are well suited to help fill knowledge gaps that preclude understanding of selenium hazards and future management options for biota using Salton Sea habitats, including newly formed wetlands throughout the region. All data compiled for this report are available in two U.S. Geological Survey data releases: Groover and others (2022) for water and sediment samples and De La Cruz and others (2022) for biological samples. The data releases include all publicly available data for selenium concentrations in water, sediment, and biological samples collected in and around the Salton Sea, including the Coachella and Imperial Valleys. The data releases also include previously unpublished data.

California↗
USGS2006

The Amphibian Research and Monitoring Initiative (ARMI): 5-year report

The Amphibian Research and Monitoring Initiative (ARMI) is an innovative, multidisciplinary program that began in 2000 in response to a congressional directive for the Department of the Interior to address the issue of amphibian declines in the United States. ARMI’s formulation was cross-disciplinary, integrating U.S. Geological Survey scientists from Biology, Water, and Geography to develop a course of action (Corn and others, 2005a). The result has been an effective program with diverse, yet complementary, expertise. ARMI’s approach to research and monitoring is multiscale. Detailed investigations focus on a few species at selected local sites throughout the country; monitoring addresses a larger number of species over broader areas (typically, National Parks and National Wildlife Refuges); and inventories to document species occurrence are conducted more extensively across the landscape. Where monitoring is conducted, the emphasis is on an ability to draw statistically defensible conclusions about the status of amphibians. To achieve this objective, ARMI has instituted a monitoring response variable that has nationwide applicability. At research sites, ARMI focuses on studying species/environment interactions, determining causes of observed declines, and developing new techniques to sample populations and analyze data. Results from activities at all scales are provided to scientists, land managers, and policymakers, as appropriate. The ARMI program and the scientists involved contribute significantly to understanding amphibian declines at local, regional, national, and international levels. Within National Parks and National Wildlife Refuges, findings help land managers make decisions applicable to amphibian conservation. For example, the National Park Service (NPS) selected amphibians as a vital sign for several of their monitoring networks, and ARMI scientists provide information and assistance in developing monitoring methods for this NPS effort. At the national level, ARMI has had major exposure at a variety of meetings, including a dedicated symposium at the 2004 joint meetings of the Herpetologists’ League, the American Society of Ichthyologists and Herpetologists, and the Society for the Study of Amphibians and Reptiles. Several principal investigators have brought international exposure to ARMI through venues such as the World Congress of Herpetology in South Africa in 2005 (invited presentation by Dr. Gary Fellers), the Global Amphibian Summit, sponsored by the International Union for Conservation of Nature (IUCN) and Wildlife Conservation International, in Washington, D.C., 2005 (invited participation by Dr. P.S. Corn), and a special issue of the international herpetological journal Alytes focused on ARMI in 2004 (edited by Dr. C.K. Dodd, Jr.). ARMI research and monitoring efforts have addressed at least 7 of the 21 Threatened and Endangered Species listed by the U.S. Fish and Wildlife Service (California red-legged frog [Rana draytonii], Chiricahua leopard frog [R. chiricahuensis], arroyo toad [Bufo californicus], dusky gopher frog [Rana sevosa], mountain yellow-legged frog [R. muscosa], flatwoods salamander [Ambystoma cingulatum], and the golden coqui [Eleutherodactylus jasperi]), and 9 additional species of concern recognized by the IUCN. ARMI investigations have addressed time-sensitive research, such as emerging infectious diseases and effects on amphibians related to natural disasters like wildfire, hurricanes, and debris flows, and the effects of more constant, environmental change, like urban expansion, road development, and the use of pesticides. Over the last 5 years, ARMI has partnered with an extensive list of government, academic, and private entities. These partnerships have been fruitful and have assisted ARMI in developing new field protocols and analytic tools, in using and refining emerging technologies to improve accuracy and efficiency of data handling, in conducting amphibian disease, malformation, and environmental effects research, and in implementing a network of monitoring and research sites. Accomplishments from these endeavors include more than 40 publications on amphibian status and trends, nearly 100 publications on amphibian ecology and causes of declines, and over 30 methodological publications. Several databases have emerged as a result of ARMI and its partnerships; one, a digital atlas of ranges for all U.S. amphibian species, was used by the IUCN to display amphibian distribution maps in the Global Amphibian Assessment Project. Given the scope of ARMI and the panoply of projects, findings have had implications for policy. Investigations that demonstrate amphibian declines or illuminate causes of declines provide valuable information about habitat management, environmental effects, mechanisms for the spread of disease, and human/amphibian interfaces. This information has been made available to land managers, scientists, educators, Congress and other policymakers, and the public. The support afforded ARMI by Congress has been influential in the program’s development and success. The value of ARMI’s efforts will continue to increase as we are able to extend our studies spatially and temporally to answer critical questions with more confidence. We are using ARMI’s resources efficiently and continuing to develop innovative mechanisms for leveraging resources for maximum effectiveness during challenging financial times. This report is a 5-year retrospective of the structure, methodology, progress, and contributions to the broader scientific community that have resulted from this national USGS program. We evaluate ARMI’s success to date, with regard to the challenges faced by the program and the strengths that have emerged. We chart objectives for the next 5 years that build on current accomplishments, highlight areas meriting further research, and direct efforts to overcome existing weaknesses.

Scientific Investigations Report↗
USGS2019

Estimating occurrence, prevalence, and detection of amphibian pathogens: Insights from occupancy models

Understanding the distribution of pathogens across landscapes and their prevalence within host populations is a common aim of wildlife managers. Despite the need for unbiased estimates of pathogen occurrence and prevalence for planning effective management interventions, many researchers fail to account for imperfect pathogen detection. Instead raw data are often reported, which may lead to ineffective, or even detrimental, management actions. We illustrate the utility of occupancy models for generating unbiased estimates of disease parameters by 1) providing a written tutorial describing how to fit these models in Program PRESENCE and 2) presenting a case study with the pathogen ranavirus. We analyzed ranavirus detection data from a wildlife refuge (Maryland, US) using occupancy modeling, which yields unbiased estimates of pathogen occurrence and prevalence. We found ranavirus prevalence was underestimated by up to 30% if imperfect pathogen detection was ignored. The unbiased estimate of ranavirus prevalence in larval wood frog ( Lithobates sylvaticus ; 0.73) populations was higher than in larval spotted salamander ( Ambystoma maculatum ; 0.56) populations. In addition, the odds of detecting ranavirus in tail samples were 6.7 times higher than detecting ranavirus in liver samples. Therefore, tail samples presented a nonlethal sampling method for ranavirus that may be able to detect early (nonsystemic) infections.

Maryland↗
USGS1988

Air pollution and wildlife toxicology: An overlooked problem

Since the 1880s, there have been repeated reports worldwide of toxic effects to wildlife from air pollution . Incidents in North America were recorded as early as the 1920s and as recently as last year. The effects have ranged from death and injury to increased incidence of infectious diseases, and they are the result of exposure to both gaseous and particulate emissions. Compared with other threats to wildlife , for instance, pesticides, the toxicological relationship between air pollution and effects in wildlife is not well understood. Our limited understanding is based primarily on reports of symptoms observed in the field and on information extrapolated from studies in livestock and laboratory animals. Few controlled wildlife studies, such as those that have evaluated pesticide effects, have been conducted. Current air quality standards cannot be assumed to protect wildlife from the effects of air pollution . This article reviews the current state of knowledge of air pollution and wildlife toxicology and the continuing threat air pollution presents to wildlife . The available information on reported effects of gaseous and particulate pollutants (i.e., sulfur dioxide, hydrogen sulfide, oxidants, arsenic, cadmium, fluoride, lead and selenium) on terrestrial wildlife , along with similar toxicological data for domestic animals, is summarized. Information on the toxic effects, tolerance levels, pathways of contamination, and risks to wildlife from air pollution is given, and gaps in knowledge are pointed out. Areas where research is needed are identified. Copyright © 1988 SETAC

Environmental Toxicology and Chemistry↗
USGS2016

Measuring the relationship between sportfishing trip expenditures and anglers’ species preferences

We examined the relationship between fishing trip expenditures and anglers’ species preferences from a survey of Oklahoma resident anglers conducted in 2014. Understanding patterns in fishing trip expenditures is important because a significant share of state wildlife agency revenue comes from taxes on purchases of fishing equipment. Presently, there is little research that addresses the question of how spending levels vary within groups of sportspersons, including anglers. We used regression analysis to identify a relationship between trip spending and several preference variables, and included controls for other characteristics of fishing trips, such as location, party size, and duration. We received 780 surveys for a response rate of 26%, but only 506 were useable due to missing data or nonfishing responses. Average trip expenditures were approximately US$140, regardless of species preferences, but anglers who preferred to fish for trout and black bass tended to spend more than those who preferred to fish for catfish and panfish. These results were even more pronounced when location was considered, those who last fished at lakes spending more than those who fished at rivers or ponds. The results underscore the differences in spending among anglers with different preferred species and fishing locations.

North American Journal of Fisheries Management↗
USGS2020

Multi‐species occupancy models: Review, roadmap, and recommendations

Recent technological and methodological advances have revolutionized wildlife monitoring. Although most biodiversity monitoring initiatives are geared towards focal species of conservation concern, researchers are increasingly studying entire communities, specifically the spatiotemporal drivers of community size and structure and interactions among species. This has resulted in the emergence of multi‐species occupancy models (MSOMs) as a promising and efficient approach for the study of community ecology. Given the potential of MSOMs for conservation and management action, it is critical to know whether study design and model assumptions are consistent with inference objectives. This is especially true for studies that are designed for a focal species but can give insights about a community. Here, we review the recent literature on MSOMs, identify areas of improvement in the multi‐species study workflow, and provide a reference model for best practices for focal species and community monitoring study design. We reviewed 92 studies published between 2009 and early 2018, spanning 27 countries and a variety of taxa. There is a consistent under‐reporting of details that are central to determining the adequacy of designs for generating data that can be used to make inferences about community‐level patterns of occupancy, including the spatial and temporal extent, types of detectors used, covariates considered, and choice of field methods and statistical tools. This reporting bias could consequently result in skewed estimates, affecting conservation actions and management plans. On the other hand, comprehensive reporting is likely to help researchers working on MSOMs assess the robustness of inferences, in addition to making strides in terms of reproducibility and reusability of data. We use our literature review to inform a roadmap with best practices for MSOM studies, from simulations to design considerations and reporting, for the collection of new data as well as those involving existing datasets.

Ecography↗
USGS2014

BatTool: an R package with GUI for assessing the effect of White-nose syndrome and other take events on Myotis spp. of bats

Background: Myotis species of bats such as the Indiana Bat and Little Brown Bat are facing population declines because of White-nose syndrome (WNS). These species also face threats from anthropogenic activities such as wind energy development. Population models may be used to provide insights into threats facing these species. We developed a population model, BatTool, as an R package to help decision makers and natural resource managers examine factors influencing the dynamics of these species. The R package includes two components: 1) a deterministic and stochastic model that are accessible from the command line and 2) a graphical user interface (GUI). Results: BatTool is an R package allowing natural resource managers and decision makers to understand Myotis spp. population dynamics. Through the use of a GUI, the model allows users to understand how WNS and other take events may affect the population. The results are saved both graphically and as data files. Additionally, R-savvy users may access the population functions through the command line and reuse the code as part of future research. This R package could also be used as part of a population dynamics or wildlife management course. Conclusions: BatTool provides access to a Myotis spp. population model. This tool can help natural resource managers and decision makers with the Endangered Species Act deliberations for these species and with issuing take permits as part of regulatory decision making. The tool is available online as part of this publication.

Source Code for Biology and Medicine↗
USGS2014

Water-quality modeling of Klamath Straits Drain recirculation, a Klamath River wetland, and 2011 conditions for the Link River to Keno Dam reach of the Klamath River, Oregon

The upper Klamath River and adjacent Lost River are interconnected basins in south-central Oregon and northern California. Both basins have impaired water quality with Total Maximum Daily Loads (TMDLs) in progress or approved. In cooperation with the Bureau of Reclamation, the U.S. Geological Survey (USGS) and Watercourse Engineering, Inc., have conducted modeling and research to inform management of these basins for multiple purposes, including agriculture, endangered species protection, wildlife refuges, and adjacent and downstream water users. A water-quality and hydrodynamic model (CE-QUAL-W2) of the Link River to Keno Dam reach of the Klamath River for 2006–09 is one of the tools used in this work. The model can simulate stage, flow, water velocity, ice cover, water temperature, specific conductance, suspended sediment, nutrients, organic matter in bed sediment and the water column, three algal groups, three macrophyte groups, dissolved oxygen, and pH. This report documents two model scenarios and a test of the existing model applied to year 2011, which had exceptional water quality. The first scenario examined the water-quality effects of recirculating Klamath Straits Drain flows into the Ady Canal, to conserve water and to decrease flows from the Klamath Straits Drain to the Klamath River. The second scenario explicitly incorporated a 2.73×10 6 m 2 (675 acre) off-channel connected wetland into the CE-QUAL-W2 framework, with the wetland operating from May 1 through October 31. The wetland represented a managed treatment feature to decrease organic matter loads and process nutrients. Finally, the summer of 2011 showed substantially higher dissolved-oxygen concentrations in the Link-Keno reach than in other recent years, so the Link-Keno model (originally developed for 2006–09) was run with 2011 data as a test of model parameters and rates and to develop insights regarding the reasons for the improved water-quality conditions.

Oregon↗
USGS2019

U.S. Geological Survey science for the Wyoming Landscape Conservation Initiative—2017 annual report

The Wyoming Landscape Conservation Initiative (WLCI) was established in 2008 to address the scientific and conservation questions associated with land use changes because of energy development and other factors in southwest Wyoming. Over the past decade, partners from U.S. Geological Survey (USGS), State and Federal land management agencies, universities, and the public have collaborated to implement a long-term (defined here as more than 10 years), science-based program that assesses and enhances the quality and quantity of wildlife habitats in this region while facilitating responsible development. The USGS Science Team completes scientific research and develops tools that inform and support WLCI partner planning, decision making, and on-the-ground management actions. In fiscal year 2017, USGS published 18 products (including peer-reviewed journal articles, USGS series publications, and data releases), prepared an additional 7 products for publication, and presented 14 talks or posters at professional scientific meetings in addition to numerous informal presentations to WLCI partners at meetings and workshops. In this report, we summarize the science themes that describe USGS science for the WLCI and highlight work completed in fiscal year 2017 for each science theme. We also provide information on how USGS science is being used by land managers to better achieve habitat conservation objectives.

Wyoming↗
USGS2019

Monitoring breeding and survival of ring-necked pheasant (Phasianus colchicus) in the Sacramento Valley, Sacramento-San Joaquin River Delta, and Klamath Basin, northern California—Five-year summary, 2013–17

The U.S. Geological Survey Western Ecological Research Center, Pheasants Forever, Mandeville Island Duck Club, and the California Department of Fish and Wildlife collaborated in a reconnaissance study to monitor populations of ring-necked pheasant ( Phasianus colchicus ) using radio-telemetry in the Sacramento Valley, Sacramento-San Joaquin River Delta, and Klamath Basin of northern California. The purpose of this study was to provide agencies and private landowners with a framework of decision-support tools to help manage pheasant populations in California. During winter, spring, and autumn of 2013–17, we radio- or Global Positioning System-marked 227 female pheasant across six study sites. Data collection was focused on investigating nest-site and brood-rearing habitat selection, examining avian predator composition, and estimating population vital rates to improve our understanding of pheasant population dynamics and to identify factors that may contribute to decreases in pheasant populations in California. The cumulative annual adult survival probability across all sites during 2013–17 was 27.6 percent (95-percent confidence interval [CI], 21.9–33.6), and the cumulative nest and brood survival probabilities were 34.5 percent (95-percent CI, 27.0–42.2) and 54.2 percent (95-percent CI, 43.7–63.5), respectively. Evidence from microhabitat surveys completed at nest-sites, brood locations, and random locations suggested that marked female pheasant tended to select increasing vertical cover and residual vegetation cover and tended to avoid areas of increasing bare ground cover regardless of life-history stage. However, females at nest-sites selected increasing grass cover and height, whereas brood-rearing females tended to select increasing forb cover and height. Only perennial grass cover and perennial grass height were shown to have a positive influence on nest survival, which suggests that increasing perennial grass cover in areas occupied by pheasant may increase nest survival. Analysis of environmental factors linked to vital rate information are ongoing and will continue with investigations at increased spatial scales (that is, macro-habitat) to develop integrated population models that can incorporate abundance estimates from crow count data with vital rates from telemetry data. This report includes results from 5 years of data collection and should be interpreted with caution, as these findings are preliminary.

California↗
USGS2011

Geospatial characteristics of Florida's coastal and offshore environments: Distribution of important habitats for coastal and offshore biological resources and offshore sand resources

The Geospatial Characteristics GeoPDF of Florida's Coastal and Offshore Environments is a comprehensive collection of geospatial data describing the political boundaries and natural resources of Florida. This interactive map provides spatial information on bathymetry, sand resources, and locations of important habitats (for example, Essential Fish Habitats (EFH), nesting areas, strandings) for marine invertebrates, fish, reptiles, birds, and marine mammals. The map should be useful to coastal resource managers and others interested in marine habitats and submerged obstructions of Florida's coastal region. In particular, as oil and gas explorations continue to expand, the map can be used to explore information regarding sensitive areas and resources in the State of Florida. Users of this geospatial database will have access to synthesized information in a variety of scientific disciplines concerning Florida's coastal zone. This powerful tool provides a one-stop assembly of data that can be tailored to fit the needs of many natural resource managers. The map was originally developed to assist the Bureau of Ocean Energy Management, Regulation, and Enforcement (BOEMRE) and coastal resources managers with planning beach restoration projects. The BOEMRE uses a systematic approach in planning the development of submerged lands of the Continental Shelf seaward of Florida's territorial waters. Such development could affect the environment. BOEMRE is required to ascertain the existing physical, biological, and socioeconomic conditions of the submerged lands and estimate the impact of developing these lands. Data sources included the National Oceanic and Atmospheric Administration, BOEMRE, Florida Department of Environmental Protection, Florida Geographic Data Library, Florida Fish and Wildlife Conservation Commission, Florida Natural Areas Inventory, and the State of Florida, Bureau of Archeological Research. Federal Geographic Data Committee (FGDC) compliant metadata are provided as attached xml files for all geographic information system (GIS) layers.

Florida↗
USGS2011

Geospatial characteristics of Florida's coastal and offshore environments: Coastal habitats, artificial reefs, wrecks, dumping grounds, harbor obstructions and offshore sand resources

The Geospatial Characteristics GeoPDF of Florida's Coastal and Offshore Environments is a comprehensive collection of geospatial data describing the political boundaries and natural resources of Florida. This interactive map provides spatial information on bathymetry, sand resources, coastal habitats, artificial reefs, shipwrecks, dumping grounds, and harbor obstructions. The map should be useful to coastal resource managers and others interested in marine habitats and submerged obstructions of Florida's coastal region. In particular, as oil and gas explorations continue to expand, the map may be used to explore information regarding sensitive areas and resources in the State of Florida. Users of this geospatial database will have access to synthesized information in a variety of scientific disciplines concerning Florida's coastal zone. This powerful tool provides a one-stop assembly of data that can be tailored to fit the needs of many natural resource managers. The map was originally developed to assist the Bureau of Ocean Energy Management, Regulation, and Enforcement (BOEMRE) and coastal resources managers with planning beach restoration projects. The BOEMRE uses a systematic approach in planning the development of submerged lands of the Continental Shelf seaward of Florida's territorial waters. Such development could affect the environment. BOEMRE is required to ascertain the existing physical, biological, and socioeconomic conditions of the submerged lands and estimate the impact of developing these lands. Data sources included the National Oceanic and Atmospheric Administration, BOEMRE, Florida Department of Environmental Protection, Florida Geographic Data Library, Florida Fish and Wildlife Conservation Commission, Florida Natural Areas Inventory, and the State of Florida, Bureau of Archeological Research. Federal Geographic Data Committee (FGDC) compliant metadata are provided as attached xml files for all geographic information system (GIS) layers.

Florida↗