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USGS2023

Evaluating management alternatives for Wyoming elk feedgrounds in consideration of chronic wasting disease

Executive Summary The authors used decision and modeling analyses to evaluate management alternatives for a decision on whether to permit Cervus canadensis (elk) feeding on two sites on Bridger-Teton National Forest, Dell Creek and Forest Park. Supplemental feeding of elk could increase the transmission of chronic wasting disease (CWD) locally and disease spread regionally, potentially impacting elk populations over time with wider implications for Odocoileus hemionus (mule deer) and Odocoileus virginianus (white-tailed deer) populations and hunting, tourism, and regional revenue. Supplemental feeding is thought to improve overwinter elk survival and reduce the commingling of elk with cattle during months when brucellosis transmission risk is highest. We worked with the U.S. Department of Agriculture Forest Service to identify their fundamental objectives and associated performance metrics related to this feedground decision. We then developed disease and habitat selection models to quantify the effect of four management alternatives on select performance metrics. The four alternatives were to continue to permit feeding, phaseout permits to feed in three years, permit feeding on an emergency basis, or stop permitting feeding. In this report, we present methods and summarized results on disease and habitat selection models and summaries of other performance metrics analyzed by BIO-WEST, Inc. and Cirrus Ecological Solutions as part of an Environmental Impact Statement. Data from Wyoming Game and Fish Department (WGFD) supported the assumption that supplemental elk feeding allows for larger elk populations in a region. We documented that herd units (HU) without feedgrounds had 23 percent lower densities of elk per area of winter range when compared against HUs with feedgrounds, after accounting for differences in sightability of elk during counts on and off feedgrounds. Thus, throughout our analyses, we assumed feedground closures would reduce elk carrying capacity resulting in an average decline of previously fed elk population segments by 23 percent (5th and 95th percentiles = [11 percent, 35 percent]) by year 20. Most of that decline occurred within the first few years after a feedground ceases to operate. We used a panel of CWD experts to help estimate CWD trans-mission in fed and unfed elk population segments. In aggregate, the expert panel estimated that median values of direct and indirect transmission of CWD are expected to be 1.9 and 4 times higher, respectively, in fed elk populations compared to unfed elk. We used these disease transmission estimates in combination with local elk demographic rates and carrying capacity estimates to project disease and population dynamics. In year 20, we predicted CWD prevalence would increase to 42 percent (5th and 95th percentiles = [29 percent, 55 percent]), and 13 percent (5th and 95th percentiles = [4 percent, 26 percent]) on average for fed and unfed elk population segments, respectively, given a starting prevalence of 1.6 percent. The prevalence estimates for the unfed elk population segments are in the range of previous observations of CWD in elk in the western United States. The average CWD prevalence from 2016 to 2018 in the unfed elk population of Wind Cave National Park in South Dakota was 18 percent overall but up to 30 percent in some regions (Sargeant and others, 2021). Meanwhile, CWD prevalence in the Iron Mountain and Laramie Peak elk herds in Wyoming from 2016 to 2018 was 14 percent and 7 percent, respectively, despite being present since at least 2002 (Wyoming Game and Fish Department, 2020b). From 2016 to 2020, elk that were fed at Dell Creek and Forest Park constituted on average 12–20 percent of the total elk on their respective HUs. As a result, the differences between management alternatives are modest when considering the closure of only one feedground on a HU. The no feeding alternative for Forest Park resulted in a CWD prevalence of 17 percent (SD = 7 percent) in the Afton HU compared to 20 percent (SD = 7 percent) with continued feeding by year 20. In the Upper Green River HU, no feeding on Dell Creek resulted in a CWD prevalence of 27 percent (SD = 6 percent) compared to 30 percent (SD = 5 percent) with continued feeding. In terms of disease-associated mortality, we predicted the closure of Forest Park and Dell Creek feedgrounds would reduce the total number of CWD mortalities by 9 percent in the Upper Green River HU and 26 percent in the Afton HU during the 20-year timespan. Our spatial analyses predicted that management alternative effects vary by HU as a function of private property and other wildlife winter ranges proximity relative to feedground location. The predicted number of elk abortions on private land, as a proxy for brucellosis risk to cattle, may increase by 8–21 percent in the absence of feeding at Dell Creek and Forest Park. Eight feedgrounds are located on Bridger-Teton National Forest, all of which have permits that have expired or will expire prior to 2028. In addition, WGFD could change their management of feedgrounds given new information; therefore, we also assessed the cumulative effects of continued feeding, phaseout, and no feeding management alternatives across five HUs south of Jackson, Wyoming (Afton HU, Fall Creek HU, Piney HU, Pinedale HU, and Upper Green River HU). These five HUs ranged from about 41 to 85 percent of the elk herd using feedgrounds, which corresponded to a CWD prevalence at year 20 of 23–34 percent if all feedgrounds in those five HUs remained open relative to 12 to 14 percent if all feedgrounds were closed. We predicted feedground closures may result in immediate reductions in population size relative to alternatives that continue feeding (for example, continued feeding and emergency feeding alternatives); however, over longer periods of time, CWD-associated mortality leads to larger population reductions. The no feeding alternative resulted in higher elk population sizes compared to the continued feeding alternative after about 10 years of implementation. Delayed action under a phaseout alternative resulted in increasing the CWD prevalence to 20 percent relative to 12 to 14 percent, on average, without feeding on HUs with a large population of fed elk such as the Upper Green River HU. Summarizing our cumulative results across all five of the analyzed HUs, we predicted continued feeding will lead to fewer elk by year 20 (mean = 8,300, standard deviation [SD] = 740) compared to no feeding at U.S. Department of Agri-culture Forest Service sites (10,700, SD = 890). The closure of all feedgrounds was projected to result in the largest elk populations at year 20 (12,500, SD = 980). No feeding at all sites also resulted in the largest cumulative harvest of 57,700 (SD = 2,600) compared to 51,100 (SD = 3,800) for continued feeding at all current feedground sites on the five HUs. Continued feeding also resulted in the lowest brucellosis costs to producers ($194,600, SD = $11,500) compared to no feeding on all feedgrounds ($243,000, SD = $13,700). Assuming moderate reductions in hunter interest because of increasing CWD prevalence in elk, we predicted that no feeding resulted in regional revenues generated by hunting activities of $190 million (SD = $10 million) compared to $173 million (SD = $10 million) for continued feeding over the 20-year timeframe. Recent CWD detections in mule deer and elk in Grand Teton National Park has elevated the importance of the cur-rent decision on whether, and how, to permit elk feeding on Dell Creek and Forest Park and the management of the other feedgrounds. Aggressive male harvest has slowed, but not stopped, the increasing prevalence of CWD in mule deer (Conner and others, 2021). It is unclear whether harvest management can be an effective tool to slow the spread of CWD in elk. There are also no effective treatments or vaccines for CWD, and it is unlikely that any will be developed that can be easily deployed in the near future. Thus, reducing artificial aggregations is one of the few management approaches suggested by the Western Association of Fish and Wildlife Agencies (Almberg and others, 2017). Future surveillance and monitoring can be designed to resolve uncertainties that can improve future decision-making. If feedgrounds close, research could quantify elk population reductions in the absence of feeding, the redistribution of fed elk to other places, or the consequences of elk movement on private property. If feedgrounds remain open, research could assess how rapidly CWD spreads in artificial aggregations of elk; however, surveillance programs would need to be designed with sufficient power to detect initial changes of CWD prevalence. Delaying action on feedground management was projected to be costly. Results of the phaseout alternative relative to the no feeding alternative suggested a 3-year delay was enough for substantial long-term changes in CWD prevalence. The long-term persistence of infectious CWD prions in the environment suggests that feedground management decisions may have long-lasting consequences. Our results indicated tradeoffs in the ability of a management agency to achieve all their objectives, and all management alternatives resulted in significant reductions in elk population size. This report contains the foundational elements for formal decision analysis methods, which can be implemented to help decision makers transparently evaluate the consequences of decision alternatives and identify the set of actions that best achieve agency and stakeholder priorities.

Wyoming↗

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↗

USGS2015

Habitat influences distribution of chronic wasting disease in white-tailed deer

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy that was first detected in 1967 in a captive research facility in Colorado. In the northeastern United States, CWD was first confirmed in white-tailed deer ( Odocoileus virginianus ) in 2005. Because CWD is a new and emerging disease with a spatial distribution that had yet to be assessed in the Northeast, we examined demographic, environmental, and spatial effects to determine how each related to this spatial distribution. The objectives of our study were to identify environmental and spatial effects that best described the spatial distribution of CWD in free-ranging white-tailed deer and identify areas that support deer that are at risk for CWD infection in the Northeast. We used Bayesian hierarchical modeling that incorporated demographic covariates, such as sex and age, along with environmental covariates, which included elevation, slope, riparian corridor, percent clay, and 3 landscapes (i.e., developed, forested, open). The model with the most support contained landscape covariates and spatial effects that represented clustering of CWD in adjacent grid cells. Forested landscapes had the strongest relationship with the distribution of CWD, with increased risk of CWD occurring in areas that had lesser amounts of forest. Our results will assist resource managers in understanding the spatial distribution of CWD within the study area, and in surrounding areas where CWD has yet to be found. Efficiency of disease surveillance and containment efforts can be improved by allocating resources used for surveillance in areas with deer populations that are at greatest risk for infection.

Journal of Wildlife Management↗

USGS2020

Black abalone surveys at Naval Base Ventura County, San Nicolas Island, California: 2019, annual report

The U.S. Geological Survey Western Ecological Research Center’s Santa Cruz Field Station, Santa Cruz, California, has been funded by the U.S. Navy to continue monitoring a suite of intertidal black abalone sites at San Nicolas Island, California. The nine rocky intertidal sites were established in 1980 by Glenn VanBlaricom (then of the U.S. Fish and Wildlife Service) to study the potential impact of translocated sea otters on the intertidal black abalone population at the island. The sites were monitored from 1981 to 1997, usually annually or semi-annually. Monitoring resumed in 2001, and regular annual monitoring cycles have been conducted at the sites since then. The study sites became particularly important, from a management perspective, after a virulent disease decimated black abalone populations throughout southern California beginning in the mid-1980s. The disease, withering syndrome, was first observed on San Nicolas Island in 1992 and during the next few years reduced the population there by approximately 99 percent. The species was subsequently listed as endangered under the Endangered Species Act in 2009. The subject of this report is the 2019 monitoring cycle of the sites and how the current status fits into the long-term data at San Nicolas Island. Since 2001, the monitored population has increased nearly tenfold to approximately 8.7 percent of the pre-disease level. This increase has resulted from generally higher levels of recruitment than seen in the first two decades of monitoring, punctuated by a few high recruitment events. Most of the population growth has been at two of the nine sites (sites 7 and 8). This pattern continued in 2019 with increasing numbers at sites 7 and 8 and the highest number of abalone counted and measured island-wide since 1996. However, counts declined at six of the sites during the last year and the increases in counts at sites 7 and 8 barely offset these losses. Recruitment rates have fallen since a peak in 2017 but 2019 continued to show some additional recruitment. The distance between adjacent black abalone, a metric relevant to potential reproduction, has decreased substantially since it was first consistently measured in 2005. Although sand burial can have devastating localized consequences to black abalone, the sand cover data we collected was not sufficient to suggest an obvious temporal or site-based pattern to sedimentation, and there is no indication that this was a factor in any of the declines recorded in 2019. Continued monitoring of these sites can provide island biologists with species trends to aid in adaptive management of the resource.

California↗

USGS2025

Challenges and opportunities in mitigating sarcoptic mange in wild South American camelids

Vicuñas ( Vicugna vicugna ) and guanacos ( Lama guanicoe ) are the two species of wild South American camelids whose distributions range from Peru to northern Argentina and southern Peru to southern Argentina, respectively. Listed as critically endangered in the 1960s due to poaching, vicuña numbers had been gradually recovering; however, new concerns about population stability have arisen with recent observations of sarcoptic mange outbreaks in this species. Sarcoptic mange is an infectious skin disease caused by the microscopic burrowing mite, Sarcoptes scabiei , which infects nearly 150 mammalian species globally, including guanaco and vicuña. Wild camelid populations across Argentina, Bolivia, Chile, and Peru have been affected by sarcoptic mange, with the most severe outbreaks resulting in localized extirpation. Population declines have conservation and economic implications, as many local communities harvest vicuña and guanaco fiber for profit. We review the current literature on sarcoptic mange in wild camelids from Argentina, Bolivia, Chile, and Peru to establish a current state of knowledge on spatial prevalence, management, and therapeutics, and identify existing knowledge gaps. Critical next steps include 1) implementation of effective management strategies that limit the transmission of sarcoptic mange, 2) standardization of data collected during community capture (i.e., chaccu) events, 3) assessing the potential role of community captures in mite transmission, and 4) evaluation of treatment options and best practices for implementation. Further, there is a need for capacity building to improve disease diagnostics and surveillance in wild camelids. A multisectoral collaboration between governmental authorities, communities, academic institutions, and national and international organizations focusing on wild South American camelid conservation could contribute to building actions aimed at preventing future outbreaks and mitigating the current burden of sarcoptic mange disease.

Journal of Wildlife Management↗

USGS1983

Neoplasms identified in free-flying birds

Nine neoplasms were identified in carcasses of free-flying wild birds received at the National Wildlife Health Laboratory; gross and microscopic descriptions are reported herein. The prevalence of neoplasia in captive and free-flying birds is discussed, and lesions in the present cases are compared with those previously described in mammals and birds.

Avian Diseases↗

USGS2024

Using mobile acoustic monitoring and false-positive N-mixture models to estimate bat abundance and population trends

Estimating the abundance of unmarked animal populations from acoustic data is challenging due to the inability to identify individuals and the need to adjust for observation biases including detectability (false negatives), species misclassification (false positives), and sampling exposure. Acoustic surveys conducted along mobile transects were designed to avoid counting individuals more than once, where raw counts are commonly treated as an index of abundance. More recently, false-positive abundance models have been developed to estimate abundance while accounting for imperfect detection and misclassification. We adapted these methods to model summertime abundance and trends of three species of bats at multiple spatial scales using acoustic recordings collected along mobile transects by partners of the North American Bat Monitoring Program (NABat) from 2012 to 2020. This multiscale modeling spanned individual transect routes, larger NABat grid cells (10 km × 10 km), and across the entire extent of modeled species ranges. We estimated relationships between species abundances and a suite of abiotic and biotic predictors (landcover types, climatological variables, physiographic diversity, building density, and the impacts of white-nose syndrome [WNS]) and found varying levels of support between species. We present clear evidence of substantial declines in populations of tricolored bats ( Perimyotis subflavus ) and little brown bats ( Myotis lucifugus ), declines that corresponded in space and time with the progression of WNS, a devastating disease of hibernating bats. In contrast, our analysis revealed that similar population-wide declines probably have not occurred in big brown bats ( Eptesicus fuscus ), a species known to be less affected by WNS. This study provides the first abundance-based species distribution predictions and population trends for bats in their summer ranges in North America. These models will probably be applicable to assessing wildlife populations in other monitoring programs where acoustic data are used or where false-negative and false-positive detections are present. Finally, our abundance framework (as a spatial point pattern process) can serve as a foundation from which more sophisticated integrated species distribution models that incorporate additional streams of monitoring data (e.g., stationary acoustics, captures) can be developed for North American bats.

Ecological Monographs↗

USGS2025

Status and trends of forest bird populations at Hakalau Forest National Wildlife Refuge, 1987–2024

Since 1985, the Hakalau Forest Unit of the Big Island National Wildlife Refuge Complex (hereafter, Hakalau) has protected the largest endemic forest bird diversity in the State of Hawaii. This includes three endangered and one threatened species and their habitats. Hakalau’s vast area (155 km2), mostly high elevation (>1500 m) montane forest, provides refuge from avian malaria (Plasmodium relictum) vectored by introduced southern house mosquitoes (Culex quinquefasciatus). However, increases in the seasonal temperatures optimal for disease carrying mosquitoes associated with climate change have coincided with recent downward trends of native species in the closed forest area of the refuge (1450–1750 m), where disease is most likely to occur. Therefore, to inform refuge management with the most updated information on these populations and their trends, we analyzed forest bird survey data collected using point transect distance sampling with new survey data from 2021–2024. We stratified our analysis across management units, including the open forest and pasture since 1987, and the closed forest since 1999, and across four elevation ranges (<1500, 1500–1700, 1700–1900, and >1900 m) since 1999. We used distance sampling to estimate species- and strata-specific abundances and applied log-linear regression to detect trends across the timeseries. We found a continuation of previous trends, wherein most native forest birds declined in the closed forest strata (mostly below 1700 m) and increased in the highest elevation and pasture strata. Patterns were highly species-specific for the three lower elevations and open forest strata. ‘Apapane (Himatione sanguinea) and warbling white-eye (Zosterops japonicus), the most abundant native and introduced bird species, respectively, increased in nearly all strata. ‘I‘iwi (Drepanis coccinea) and Hawai‘i ‘amakihi (Chlorodrepanis virens virens), also common, decreased in closed forest, were stable in open forest, and increased in pasture. Both species were generally stable or increasing across all elevation bands, except Hawaiʻi ʻamakihi decreased in the below 1500 m and the 1500–1700 m elevation bands. All three of the federally endangered forest bird species declined in closed forest. Hawai‘i ‘ākepa (Loxops coccineus) also declined in the open forest and 1700–1900 m band and was the only species to decline overall. ‘Akiapōlā‘au (Hemignathus wilsoni) declined in closed forest but increased overall. ‘Alawī (Loxops mana, also known as Hawai‘i creeper) also decreased in the closed forest, but was stable to increasing in most strata and remained stable overall. Hawaiʻi ʻelepaio (Chasiempis sandwichensis) declined in closed forest, was stable in open forest and most elevation strata, and increased in pasture. ʻŌmaʻo (Myadestes obscurus) was stable in open and closed forest and at middle elevations and increased in the pasture. Introduced red-billedleiothrix (Leiothrix lutea) declined in closed forest, was stable in the open forest and at most elevations, and increased in the pasture. Coinciding with these changes, seasonal conditions for vector occurrence have continued to lengthen in the lower elevation strata through 2024, while Hakalau’s outplanting efforts continued to increase forest cover in the pasture, suggesting that disease-free habitat may have decreased in the closed forest and increased in the pasture. The declines in the closed forest and mixture of trends in the open forest and middle elevations bands suggest emigration into the higher elevation strata from lower elevation strata, and that possible threats have suppressed forest birds even at elevations >1500 m.

Hawaii↗

USGS2005

Comparison of individual and pooled sampling methods for detecting bacterial pathogens of fish

Examination of finfish populations for viral and bacterial pathogens is an important component of fish disease control programs worldwide. Two methods are commonly used for collecting tissue samples for bacteriological culture, the currently accepted standards for detection of bacterial fish pathogens. The method specified in the Office International des Epizooties Manual of Diagnostic Tests for Aquatic Animals permits combining renal and splenic tissues from as many as 5 fish into pooled samples. The American Fisheries Society (AFS) Blue Book/US Fish and Wildlife Service (USFWS) Inspection Manual specifies the use of a bacteriological loop for collecting samples from the kidney of individual fish. An alternative would be to more fully utilize the pooled samples taken for virology. If implemented, this approach would provide substantial savings in labor and materials. To compare the relative performance of the AFS/USFWS method and this alternative approach, cultures of Yersinia ruckeri were used to establish low-level infections in groups of rainbow trout (Oncorhynchus mykiss) that were sampled by both methods. Yersinia ruckeri was cultured from 22 of 37 groups by at least 1 method. The loop method yielded 18 positive groups, with 1 group positive in the loop samples but negative in the pooled samples. The pooled samples produced 21 positive groups, with 4 groups positive in the pooled samples but negative in the loop samples. There was statistically significant agreement (Spearman coefficient 0.80, P < 0.001) in the relative ability of the 2 sampling methods to permit detection of low-level bacterial infections of rainbow trout.

Journal of Veterinary Diagnostic Investigation↗

USGS2017

Guidance documents: Continued support to improve operations of fish hatcheries and field sites to reduce the impact or prevent establishment of New Zealand Mudsnails and other invasive mollusks

This project tested and revised a risk assessment/management tool authored by Moffitt and Stockton designed to provide hatchery biologists and others a structure to measure risk and provide tools to control, prevent or eliminate invasive New Zealand mudsnails (NZMS) and other invasive mollusks in fish hatcheries and hatchery operations. The document has two parts: the risk assessment tool, and an appendix that summarizes options for control or management. The framework of the guidance document for risk assessment/hatchery tool combines approaches used by the Hazard Analysis and Critical Control Points (HACCP) process with those developed by the Commission for Environmental Cooperation (CEC), of Canada, Mexico, and the United States, in the Tri-National Risk Assessment Guidelines for Aquatic Alien Invasive Species. The framework approach for this attached first document assesses risk potential with two activities: probability of infestation and consequences of infestation. Each activity is treated equally to determine the risk potential. These two activities are divided into seven basic elements that utilize scientific, technical, and other relevant information in the process of the risk assessment. To determine the probability of infestation four steps are used that have scores reported or determined and averaged. This assessment follows a familiar HACCP process to assess pathways of entry, entry potential, colonization potential, spread potential. The economic, environmental and social consequences are considered as economic impact, environmental impact, and social and cultural influences. To test this document, the Principal Investigator worked to identify interested hatchery managers through contacts at regional aquaculture meetings, fish health meetings, and through the network of invasive species managers and scientists participating in the Western Regional Panel on Aquatic Nuisance Species and the 100th Meridian Initiative's Columbia River Basin Team, and the Western New Zealand Mudsnail Conference in Seattle. Targeted hatchery workshops were conducted with staff at Dworshak National Fish Hatchery Complex (ID), Similkameen Pond, Oroville WA, and Ringold Springs State Hatchery (WA). As a result of communications with hatchery staff, invasive species managers, and on site assessments of hatchery facilities, the document was modified and enhanced. Additional resources were added to keep it up to date. The result is a more simplified tool that can lead hatchery or management personnel through the process of risk assessment and provide an introduction to the risk management and communication process. In addition to the typical HACCP processes, this tool adds steps to rate and consider uncertainty and the weight of evidence regarding options and monitoring results . Uncertainty of outcome exists in most tools that can be used to control or prevent NZMS or other invasive mollusks from infesting an area. In additional this document emphasizes that specific control tools and plans must be tailored to each specific setting to consider the economic, environmental and social influences. From the testing and evaluation process, there was a strong recognition that a number of control and prevention tools previously suggested and reported in the literature from laboratory and small scale trials may not be compatible with regional and national regulations, economic constraints, social or cultural constraints, engineering or water chemistry characteristics of each facility. The options for control are summarized in the second document, Review of Control Measures for Hatcheries Infested with NZMS (Appendix A) that provides sources for additional resources and specific tools, and guidance regarding the feasibility and success of each approach. This tool also emphasizes that management plans need to be adaptive and incorporate oversight from professionals familiar with measuring risks of fish diseases, and treatments (e.g. the fish health practitioners and water quality and effluent management teams). Finally, with such a team, the adaptive management approach must be ongoing, and become a regular component of hatchery operations. Although it was the intent that this two part document would be included as part of the revised National Management and Control Plan for the NZMS proposed by the U.S. Fish and Wildlife Service (USFWS) and others, it is provided as a stand-alone document.

Cooperator Science Series↗

USGS2015

Context-dependent survival, fecundity and predicted population-level consequences of brucellosis in African buffalo

Chronic infections may have negative impacts on wildlife populations, yet their effects are difficult to detect in the absence of long-term population monitoring. Brucella abortus , the bacteria responsible for bovine brucellosis, causes chronic infections and abortions in wild and domestic ungulates, but its impact on population dynamics is not well understood. We report infection patterns and fitness correlates of bovine brucellosis in African buffalo based on (1) 7 years of cross-sectional disease surveys and (2) a 4-year longitudinal study in Kruger National Park (KNP), South Africa. We then used a matrix population model to translate these observed patterns into predicted population-level effects. Annual brucellosis seroprevalence ranged from 8·7% (95% CI = 1·8–15·6) to 47·6% (95% CI = 35·1–60·1) increased with age until adulthood (>6) and varied by location within KNP. Animals were on average in worse condition after testing positive for brucellosis ( F = −5·074, P < 0·0001), and infection was associated with a 2·0 (95% CI = 1·1–3·7) fold increase in mortality (χ 2 = 2·039, P = 0·036). Buffalo in low body condition were associated with lower reproductive success ( F = 2·683, P = 0·034), but there was no association between brucellosis and pregnancy or being observed with a calf. For the range of body condition scores observed in the population, the model-predicted growth rate was λ = 1·11 (95% CI = 1·02–1·21) in herds without brucellosis and λ = 1·00 (95% CI = 0·85–1·16) when brucellosis seroprevalence was 30%. Our results suggest that brucellosis infection can potentially result in reduced population growth rates, but because these effects varied with demographic and environmental conditions, they may remain unseen without intensive, longitudinal monitoring.

Kruger National Park↗

USGS2019

Evaluating community-level response to management actions across a diverse Hawaiian forest bird community

Although species‐specific approaches are necessary to understand the dynamics of individual species composing a community, they do not offer a framework for making optimal management decisions at the community level. Here, we present a simple framework for comparing the response of entire communities to multiple management scenarios. Our approach uses a weighted average of standardized species‐specific responses to produce a single integrative measure of the community response and employs mixed‐effect linear models to quantify the increase in the community response due to each management action, or combination of actions. We demonstrate our approach with a simulation study assessing the potential benefits of multiple management actions on the avian community of Hakalau Forest National Wildlife Refuge, Hawaiʻi, which is composed of eight native species with conservation status varying from endangered to least concern. Management actions considered included a reduction of avian malaria transmission risk, reducing rat predation, and increasing forest habitat. We used three different prioritization (weighting) schemes to assess whether the response to management actions differed along a conservation gradient (from endangered to least concern). We also investigated whether future changes in disease distribution as a result of climate change will alter the relationship between management practices and community response. Our community‐level analysis produced three important insights, highlighting the need to consider the response from multiple species to changing threats and management actions. First, increasing the amount of habitat always had the greatest positive impact on the avian community, regardless of the weighting scheme. Second, the community response to management was different under current vs. future conditions, with increased benefit in the future when disease risks were higher. Third, the response to management varied along the conservation gradient. Reducing malaria transmission risk in 2100 had the greatest benefit to endangered species, while increasing forest habitat had the greatest benefit to “least concern” species. However, reducing rat predation appeared to benefit a subset of species based on ecological factors unrelated to rarity, such as nest accessibility. Our approach is widely applicable using experimental, observational, or simulation‐based data, allowing managers to consider the response of all species while weighting their priority levels.

Hawaii↗

USGS2015

Laboratory investigations of African Pouched Rats ( Cricetomys gambianus ) as a potential reservoir host species for Monkeypox Virus

Monkeypox is a zoonotic disease endemic to central and western Africa, where it is a major public health concern. Although Monkeypox virus (MPXV) and monkeypox disease in humans have been well characterized, little is known about its natural history, or its maintenance in animal populations of sylvatic reservoir(s). In 2003, several species of rodents imported from Ghana were involved in a monkeypox outbreak in the United States with individuals of three African rodent genera ( Cricetomys , Graphiurus , Funisciurus ) shown to be infected with MPXV. Here, we examine the course of MPXV infection in Cricetomys gambianus (pouched Gambian rats) and this rodent species’ competence as a host for the virus. We obtained ten Gambian rats from an introduced colony in Grassy Key, Florida and infected eight of these via scarification with a challenge dose of 4X10 4 plaque forming units (pfu) from either of the two primary clades of MPXV: Congo Basin (C-MPXV: n = 4) or West African (W-MPXV: n = 4); an additional 2 animals served as PBS controls. Viral shedding and the effect of infection on activity and physiological aspects of the animals were measured. MPXV challenged animals had significantly higher core body temperatures, reduced activity and increased weight loss than PBS controls. Viable virus was found in samples taken from animals in both experimental groups (C-MPXV and W-MPXV) between 3 and 27 days post infection (p.i.) (up to 1X10 8 pfu/ml), with viral DNA found until day 56 p.i. The results from this work show that Cricetomys gambianus (and by inference, probably the closely related species, Cricetomys emini ) can be infected with MPXV and shed viable virus particles; thus suggesting that these animals may be involved in the maintenance of MPXV in wildlife mammalian populations. More research is needed to elucidate the epidemiology of MPXV and the role of Gambian rats and other species.

PLoS Neglected Tropical Diseases↗

USGS2024

Forest bird populations at the Big Island National Wildlife Refuge Complex, Hawai'i

E ndemic Hawaiian forest birds have experienced dramatic population declines. The Big Island National Wildlife Refuge Complex (Refuge Complex) was established for the conservation of endangered forest birds and their habitats. Surveys have been conducted at two units of the Refuge Complex to monitor forest bird populations and their response to management actions. We analyzed survey data from 1987 to 2019 at the Hakalau Forest Unit (HFU) and from 1995 to 2019 at the Kona Forest Unit (KFU). We analyzed three strata at HFU: open-forest, closed-forest, and afforested-pasture, and two strata at KFU: upper (>1,524 m elevation) and lower (<1,524 m). In all years, ‘i‘iwi Vestiaria coccinea , ‘apapane Himatione sanguinea , and Hawai'i ‘amakihi Chlorodrepanis virens virens were the most abundant species at HFU. Three endangered forest bird species, Hawai'i ‘ākepa Loxops coccineus , ‘alawī Loxops mana (also known as Hawai'i creeper) and ‘akiapōlā‘au Hemignathus wilsoni , had much lower densities. The most abundant species at KFU was ‘apapane, followed by Hawai'i ‘amakihi at much lower densities. We found a continuation of several trends observed in previous analyses at HFU up to 2012, with most species’ trends upward in afforested-pasture stratum, stable in the open-forest stratum, and downward in the closed-forest stratum. However, more species were showing downward trends in all three strata during the most recent decade. Results were mixed at KFU, with most species’ trends downward in the upper stratum and upward in the lower stratum. Populations of endangered species were either locally extirpated at KFU or in numbers too low to reliably estimate population abundance. The Refuge Complex is important for conservation of forest birds on Hawai'i Island. Our results show that HFU supports the majority of three endangered forest bird species. Threats to forest birds at the Refuge Complex appear to be having a negative impact. These threats include habitat loss, disease, feral ungulates, and nonnative predators. Continuing and enhancing management actions, such as forest restoration and removal of invasive species, could help mitigate these impacts and allow the Refuge Complex to remain a key site for forest bird conservation in Hawai'i.

Hawaii↗

USGS2025

Evaluation of SARS-CoV-2 antibody detection methods for wild Cervidae

Wildlife surveillance programs often use serological data to monitor exposure to pathogens. Diagnostic sensitivity and specificity of a serological assay quantify the true positive and negative rates of the diagnostic assay, respectively. However, an assay’s accuracy can be affected by wild animals’ pathogen exposure history and quality of the sample collected, requiring separate estimates of an assay’s detection ability for wild-sampled animals where an animal’s true disease status is unknown (referred to hereafter as sampling sensitivity and specificity). We assessed the sampling sensitivity and specificity of a Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) surrogate virus neutralization test (sVNT) and conventional virus neutralization tests (cVNT) to detect antibodies for ancestral and Omicron B.1.1.529 variants of SARS-CoV-2 in wild white-tailed deer ( Odocoileus virginianus ) and mule deer ( Odocoileus hemionus ). We studied the influence of sample collection method using paired blood samples collected in serum separator tubes and on Nobuto strips from the same animal. Mean estimates of sampling sensitivity and specificity ranged from 0.21–0.95 and 0.94–1.00, respectively, varying by sample collection method, host species, and SARS-CoV-2 variant targeted by the assay. Broadly, sampling sensitivity was estimated to be higher for 1) sera collected in tubes, 2) detecting pre-Omicron SARS-CoV-2 variants, and 3) sVNT relative to cVNT assays. Sampling specificity tended to be high for all tests. We augmented our study with SARS-CoV-2 spike protein sequences derived from sampling locations and times coincident with white-tailed deer captures, finding common amino acid mutations relative to the sVNT Omicron antigen variant. The mutations may indicate that the SARS-CoV-2 variants circulating in cervids from 2021 through 2024 may be better adapted to cervid hosts and more closely related to variants that circulated in humans prior to Omicron variants. We conclude our study with an inter-test comparison of sVNT results, revealing that 40 % inhibition is an optimal threshold for test positivity when testing deer sera for responses to Omicron variant B.1.1.529, compared to the 30 % inhibition recommended for ancestral variants.

Colorado, Illinois, Minnesota, New York, Pennsylva↗

USGS2019

Artificial intelligence and avian influenza: Using machine learning to enhance active surveillance for avian influenza viruses

Influenza A viruses are one of the most significant viral groups globally with substantial impacts on human, domestic animal and wildlife health. Wild birds are the natural reservoirs for these viruses, and active surveillance within wild bird populations provides critical information about viral evolution forming the basis of risk assessments and countermeasure development. Unfortunately, active surveillance programs are often resource‐intensive, and thus, enhancing programs for increased efficiency is paramount. Machine learning, a branch of artificial intelligence applications, provides statistical learning procedures that can be used to gain novel insights into disease surveillance systems. We use a form of machine learning, gradient boosted trees, to estimate the probability of isolating avian influenza viruses (AIV) from wild bird samples collected during surveillance for AIVs from 2006 to 2011 in the United States. We examined several predictive features including age, sex, bird type, geographic location and matrix gene rRT‐PCR results. Our final model had high predictive power and only included geographic location and rRT‐PCR results as important predictors. The highest predicted viral isolation probability was for samples collected from the north‐central states and the south‐eastern region of Alaska. Lower rRT‐PCR Ct‐values are associated with increased likelihood of AIV isolation, and the model estimated 16% probability of isolating AIV from samples declared negative (i.e., ≥35 Ct‐value) using the rRT‐PCR screening test and standard protocols. Our model can be used to prioritize previously collected samples for isolation and rapidly evaluate AIV surveillance designs to maximize the probability of viral isolation given limited resources and laboratory capacity.

Transboundary and Emerging Diseases↗

USGS2021

Understanding mast seeding for conservation and land management

Masting, the intermittent and synchronous production of large seed crops, can have profound consequences for plant populations and the food webs that are built on their seeds. For centuries, people have recorded mast crops because of their importance in managing wildlife populations. In the past 30 years, we have begun to recognize the importance of masting in conserving and managing many other aspects of the environment: promoting the regeneration of forests following fire or other disturbance, conserving rare plants, conscientiously developing the use of edible seeds as non-timber forest products, coping with the consequences of extinctions on seed dispersal, reducing the impacts of plant invasions with biological control, suppressing zoonotic diseases and preventing depredation of endemic fauna. We summarize current instances and future possibilities of a broad set of applications of masting. By exploring in detail several case studies, we develop new perspectives on how solutions to pressing conservation and land management problems may benefit by better understanding the dynamics of seed production. A lesson common to these examples is that masting can be used to time management, and often, to do this effectively, we need models that explicitly forecast masting and the dynamics of seed-eating animals into the near-term future.

Philosophical Transactions of the Royal Society B:↗

USGS1989

Lead poisoning: The invisible disease

Lead poisoning is an intoxication resulting from absorption of hazardous levels of lead into body tissues. Lead pellets from shot shells, when ingested, are the most common source of lead poisoning in migratory birds. Other far less common sources include lead fishing sinkers, mine wastes, paint pigments, bullets, and other lead objects that are swallowed.

Fish and Wildlife Leaflet↗