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Wildlife mortality investigation and disease research: contributions of the USGS National Wildlife Health Center to endangered species management and recovery

The U.S. Geological Survey—National Wildlife Health Center (NWHC) provides diagnostic services, technical assistance, applied research, and training to federal, state, territorial, and local government agencies and Native American tribes on wildlife diseases and wildlife health issues throughout the United States and its territories, commonwealth, and freely associated states. Since 1975, >16,000 carcasses and specimens from vertebrate species listed under the Endangered Species Act have been submitted to NWHC for determination of causes of morbidity or mortality or assessment of health/disease status. Results from diagnostic investigations, analyses of the diagnostic database, technical assistance and consultation, field investigation of epizootics, and wildlife disease research by NWHC wildlife disease specialists have contributed importantly to the management and recovery of listed species.

EcoHealth

Contributions to Industrial-Minerals Research

Contributions to Industrial-Minerals Research, an ongoing series of U.S. Geological Survey (USGS) Bulletin chapters, presents research strategies, results, and updates of investigations of industrial minerals by USGS scientists and cooperators. Industrial minerals are defined as valuable nonmetallic, nonfuel geologic materials, generally rocks or minerals, used in a wide range of construction and industrial applications-for example, sand, gravel, and crushed rock used as aggregate for construction; limestone used for cement; phosphate for fertilizers and insecticides; and diatomite used for filtration, fillers, and abrasives. The term also comprises some processed materials, such as cement and metallic compounds with major utilization in nonmetallic forms. For example, titanium is commonly grouped with industrial minerals because more than 90 percent of it is sold and utilized in the form of the oxide (TiO2) rather than as Ti metal. Other metals and metallic compounds commonly grouped with industrial minerals include Mn, Cr, Fe oxides, and rare-earth elements (REEs).

Bulletin

Contribution of research to management and recovery of the roseate tern: review of a twelve-year project

The Northwest Atlantic population of the Roseate Tern (Sterna dougallii) is largely confined to a small breeding area along the northeast coast of the USA between 40? and 42?N. This population was listed as endangered in the USA in 1987 because it was dangerously concentrated into a few breeding sites (85% on two islands in the 1980s). The nesting population in the area from Long Island, New York to Cape Cod, Massachusetts has been studied intensively since 1987, in conjunction with a program of management of the breeding colonies. This paper summarizes the results of the research program and discusses the extent to which it has contributed to effective management. The regional population now numbers about 4,000 breeding pairs and has been increasing slowly since 1987, except between 1991 and 1992 when it declined by about 17%. This decline was probably caused by Hurricane `Bob' in August 1991. Roseate Terns have specialized foraging habits and are concentrated into a small number of foraging areas near the nesting colonies. The historically important breeding sites were taken over by large gulls between 1930 and 1972. Many of the terns moved to less suitable sites near the mainland, where they are subject to predation by mainland-based predators. Despite this, Roseate Terns breed with high success at many sites. The sex-ratio is skewed towards females; about 12% of nests are attended by female-female pairs. The annual adult survival rate (0.83) is unusually low for a seabird. Most mortality occurs away from the breeding grounds, but the winter quarters remained unknown until one roost site was found in Brazil in 1995-1997. A major management goal has been to restore former colony-sites by eliminating nesting gulls, but the success of some of these projects has been questionable because they may have attracted birds to sites with higher levels of predation. Although the research has yielded important information about the biology and demography of the species, it has taken longer than expected to obtain and analyze data from multiple sites on this long-lived species. Most work has been carried out at breeding sites: critical studies on feeding ecology and winter ecology have been hampered by insufficient funding and the paucity of self-motivated biologists. Hence, the program has not yet provided all the keys to restoring the population.

Waterbirds

An Automated Cropland Classification Algorithm (ACCA) for Tajikistan by combining Landsat, MODIS, and secondary data

The overarching goal of this research was to develop and demonstrate an automated Cropland Classification Algorithm (ACCA) that will rapidly, routinely, and accurately classify agricultural cropland extent, areas, and characteristics (e.g., irrigated vs. rainfed) over large areas such as a country or a region through combination of multi-sensor remote sensing and secondary data. In this research, a rule-based ACCA was conceptualized, developed, and demonstrated for the country of Tajikistan using mega file data cubes (MFDCs) involving data from Landsat Global Land Survey (GLS), Landsat Enhanced Thematic Mapper Plus (ETM+) 30 m, Moderate Resolution Imaging Spectroradiometer (MODIS) 250 m time-series, a suite of secondary data (e.g., elevation, slope, precipitation, temperature), and in situ data. First, the process involved producing an accurate reference (or truth) cropland layer (TCL), consisting of cropland extent, areas, and irrigated vs. rainfed cropland areas, for the entire country of Tajikistan based on MFDC of year 2005 (MFDC2005). The methods involved in producing TCL included using ISOCLASS clustering, Tasseled Cap bi-spectral plots, spectro-temporal characteristics from MODIS 250 m monthly normalized difference vegetation index (NDVI) maximum value composites (MVC) time-series, and textural characteristics of higher resolution imagery. The TCL statistics accurately matched with the national statistics of Tajikistan for irrigated and rainfed croplands, where about 70% of croplands were irrigated and the rest rainfed. Second, a rule-based ACCA was developed to replicate the TCL accurately (∼80% producer’s and user’s accuracies or within 20% quantity disagreement involving about 10 million Landsat 30 m sized cropland pixels of Tajikistan). Development of ACCA was an iterative process involving series of rules that are coded, refined, tweaked, and re-coded till ACCA derived croplands (ACLs) match accurately with TCLs. Third, the ACCA derived cropland layers of Tajikistan were produced for year 2005 (ACL2005), same year as the year used for developing ACCA, using MFDC2005. Fourth, TCL for year 2010 (TCL2010), an independent year, was produced using MFDC2010 using the same methods and approaches as the one used to produce TCL2005. Fifth, the ACCA was applied on MFDC2010 to derive ACL2010. The ACLs were then compared with TCLs (ACL2005 vs. TCL2005 and ACL2010 vs. TCL2010). The resulting accuracies and errors from error matrices involving about 152 million Landsat (30 m) pixels of the country of Tajikistan (of which about 10 million Landsat size, 30 m, cropland pixels) showed an overall accuracy of 99.6% (k hat = 0.97) for ACL2005 vs. TCL2005. For the 3 classes (irrigated, rainfed, and others) mapped in ACL2005, the producer’s accuracy was >86.4% and users accuracy was >93.6%. For ACL2010 vs. TCL2010, the error matrix showed an overall accuracy on 96.2% (k hat = 0.96). For the 3 classes (irrigated, rainfed, and others) mapped in ACL2010, the producer’s and user’s accuracies for the irrigated areas were ≥82.9%. Any intermixing was overwhelmingly between irrigated and rainfed croplands, indicating that croplands (irrigated plus rainfed areas) as well as irrigated areas were mapped with high levels of accuracies (∼90% or higher) even for the independent year. The ACL2005 and ACL2010, each, were produced using ACCA algorithm in ∼30 min using a Dell Precision desktop T7400 computer for the entire country of Tajikistan once the MFDCs for the years were ready. The ACCA algorithm for Tajikistan is made available through US Geological Survey’s ScienceBase: http://www.sciencebase.gov/catalog/folder/4f79f1b7e4b0009bd827f548 or at: https://powellcenter.usgs.gov/globalcroplandwater/content/models-algorithms . The research contributes to the efforts of global food security through research on global croplands and their water use (e.g., https://powellcenter.usgs.gov/globalcroplandwater/ ). The above results clearly demonstrated the ability of a rule-based ACCA to rapidly and accurately produce cropland data layer year after year (hindcast, nowcast, forecast) for the country it was developed using MFDCs that consist of combining multiple sensor data and secondary data. It needs to be noted that the ACCA is applicable to the area (e.g., country, region) for which it is developed. In this case, ACCA is applicable for the Country of Tajikistan to hindcast, nowcast, and forecast agricultural cropland extent, areas, and irrigated vs. rainfed. The same fundamental concept of ACCA applies to other areas of the World where ACCA codes need to be modified to suite the area/region of interest. ACCA can also be expanded to compute other crop characteristics such as crop types, cropping intensities, and phenologies.

Remote Sensing

Global research priorities for sea turtles: Informing management and conservation in the 21st century

Over the past 3 decades, the status of sea turtles and the need for their protection to aid population recovery have increasingly captured the interest of government agencies, non-governmental organisations (NGOs) and the general public worldwide. This interest has been matched by increased research attention, focusing on a wide variety of topics relating to sea turtle biology and ecology, together with the interrelations of sea turtles with the physical and natural environments. Although sea turtles have been better studied than most other marine fauna, management actions and their evaluation are often hindered by the lack of data on turtle biology, human–turtle interactions, turtle population status and threats. In an effort to inform effective sea turtle conservation a list of priority research questions was assembled based on the opinions of 35 sea turtle researchers from 13 nations working in fields related to turtle biology and/or conservation. The combined experience of the contributing researchers spanned the globe as well as many relevant disciplines involved in conservation research. An initial list of more than 200 questions gathered from respondents was condensed into 20 metaquestions and classified under 5 categories: reproductive biology, biogeography, population ecology, threats and conservation strategies.

Endangered Species Research

In memoriam - William Toshio (Tosh) Yasutake, 1922-2016

William Toshio (Tosh) Yasutake, 1922-2016 passed away peacefully at home on December 12, 2016, at the age of 94. He is survived by Fumi, his wife of 66 years, as well as four children and six grandchildren. With his death, the fish health community has lost an outstanding scientist as well as a kind, unassuming, and wonderful human being. Tosh was born on June 10, 1922, in Seattle, Washington, to Jack and Hide Yasutake. He was in his first year of studies at the University of Washington when Pearl Harbor was attacked by Imperial Japan on December 7, 1941. Following the attack, Tosh and his family (father, mother, sister, and two brothers) were among the 110,000–120,000 people of Japanese ancestry who were forced from their homes on the Pacific coast and incarcerated in internment camps in the interior. In June 1942, Tosh enlisted in the U.S. Army, serving as an unarmed combat medic in the famed 442nd Regimental Combat Team, the most decorated unit for its size and length of service in the history of American warfare. Wounded in October 1944 during the Vosges Mountains campaign near Bruyères, France, Tosh was evacuated and missed the ensuing battle to rescue the “Lost Battalion,” at which his replacement was killed. Tosh returned to action in Italy in February 1945 and served until the end of the war in Europe, earning both a Purple Heart and a Bronze Star for bravery. In October 2010, the Congressional Gold Medal was awarded to the 442nd Regimental Combat Team, and in 2012 the surviving members were made chevaliers of the French Légion d’Honneur for actions contributing to the liberation of France in World War II. After the war, Tosh returned to the University of Washington on the GI Bill and received a B.S. degree in zoology in 1951. In 1953 he began his research career at the U.S. Fish and Wildlife Service’s Western Fish Nutrition Laboratory at Cook, Washington, where he conducted pioneering research on nutritional fish diseases with John Halver. Tosh was one of the first to recognize hepatomas in hatchery-reared Rainbow Trout and helped to trace the disease to an aflatoxin produced by the mold Aspergillus flavis , which grew during the storage of ingredients for fish diets. In 1960, he transferred to the Western Fisheries Research Center (WFRC) in Seattle (then called the Western Fish Disease Laboratory) to start a fish pathology diagnostic laboratory. There he described the histopathology of diseases of economically important fishes, identified etiologic agents, and worked with hatchery biologists to improve the health, quality, and survival of salmonids released from federal and state hatcheries. Tosh was instrumental in recognizing that the viruses of Oregon sockeye disease and Chinook Salmon virus disease were one entity and in giving the disease its present name: infectious hematopoietic necrosis. In recognition of his pioneering research, Tosh was awarded a doctorate in fish pathology by the University of Tokyo in 1980, the first American to have been so honored. In 1983, he published his classic textbook The Microscopic Anatomy of Salmonids: An Atlas , which quickly became a standard reference work in fish pathology and is still in wide use today. For his outstanding career achievements, in 1987 Tosh received the S. F. Snieszko Distinguished Service Award, the highest honor bestowed by the American Fisheries Society’s Fish Health Section (AFS–FHS). Tosh retired in 1988 but continued his research at the WFRC as a senior scientist emeritus, providing technical assistance to federal and state agencies and to the aquaculture industry worldwide. His culminating project was to digitize his lifetime collection of photomicrographs and prepare an atlas, “Histopathology of Selected Parasitic Salmonid Diseases: A Color Atlas,” that is now posted on the Web sites of the WFRC and the AFS–FHS. Although his presence will be sorely missed, his research contributions have become part of the foundation of today’s knowledge of fisheries biology and have assured him a place in history.

Journal of Aquatic Animal Health

Exploring the dynamic interactions between the Southern San Andreas Fault and a normal fault under the Salton Sea

We investigate the dynamic interactions between the Southern San Andreas Fault (SSAF) and a proximal normal fault (NF) beneath the Salton Sea in southern California. The NF, positioned near the SSAF terminus at Bombay Beach, exhibits 11–15 displacement events across 14 stratigraphic sequences, with a range of 0.2–1.4 m of vertical offset since ∼2–3 ka. Notably, four of these events may align temporally with SSAF earthquakes, raising questions about the possible interplay between the two faults. Utilizing dynamic rupture models, we analyze the coseismic interactions between the SSAF and NF, addressing under what conditions the SSAF induces slip on the NF. Our findings reveal that a suite of SSAF ruptures, particularly those propagating from north to south, can trigger slip on the normal fault and replicate observed vertical offsets. If the SSAF extends beneath the Salton Sea, earthquakes originating south of the NF intersection are less likely to trigger normal fault slip, although we cannot exclude this possibility. Some SSAF ruptures do not trigger discernible slip on the NF, rendering such events undetectable in the stratigraphic record. Our research contributes toward discussions regarding the seismic hazard in southern California, shedding light on the interplay between the SSAF and NF.

California

Controls on the geochemical evolution of Prairie Pothole Region lakes and wetlands over decadal time scales

One hundred sixty-seven Prairie Pothole lakes, ponds and wetlands (largely lakes) previously analyzed chemically during the late 1960’s and early to mid-1970’s were resampled and reanalyzed in 2011–2012. The two sampling periods differed climatically. The earlier sampling took place during normal to slightly dry conditions, whereas the latter occurred during and immediately following exceptionally wet conditions. As reported previously in Mushet et al. ( 2015 ), the dominant effect was expansion of the area of these lakes and dilution of their major ions. However, within that context, there were significant differences in the evolutionary pathways of major ions. To establish these pathways, we employed the inverse modeling computer code NetpathXL. This code takes the initial and final lake composition and, using mass balance constrained by the composition of diluting waters, and input and output of phases, calculates plausible geochemical evolution pathways. Despite the fact that in most cases major ions decreased, a subset of the lakes had an increase in SO 4 2− . This distinction is significant because SO 4 2− is the dominant anion in a majority of Prairie Pothole Region wetlands and lakes. For lakes with decreasing SO 4 2− , the proportion of original lake water required for mass balance was subordinate to rainwater and/or overland flow. In contrast, lakes with increasing SO 4 2− between the two sampling episodes tended to be dominated by original lake water. This suite of lakes tended to be smaller and have lower initial SO 4 2− concentrations such that inputs of sulfur from dissolution of the minerals gypsum or pyrite had a significant impact on the final sulfur concentration given the lower dilution factors. Thus, our study provides context for how Prairie Pothole Region water bodies evolve geochemically as climate changes. Because wetland geochemistry in turn controls the ecology of these water bodies, this research contributes to the prediction of the impact of climate change on this important complex of ecosystems.

North Dakota

Deaf, deafblind, and hard of hearing university student experiences with earthquake early warning in the United States: Evaluating language planning and technology access

The growing literature on deaf and hard of hearing (DHH+) populations and disasters demonstrates that emergency communication (including alerts) is not reaching global DHH + individuals with dangerous impacts for morbidity and mortality. This is the first research study in the U.S. to qualitatively explore the experiences of DHH + persons with earthquake early warning (EEW) through group-based dialogue sessions. The study investigates eight DHH + university students'past earthquake experiences, access to EEW alerts, and perceptions of ShakeAlert Ⓡ , an EEW system for detecting earthquakes and alerting residents of California, Oregon, and Washington. Findings highlight key gaps in disaster alert usability within four thematic areas: lack of messaging in participants' language(s), unclear alert messaging, deficient message delivery mechanisms for deafblind persons, and insufficient access to earthquake information and training that leads to dependence on informal information networks. Weaknesses identified in these four themes reduce DHH + trust in EEW systems and compromise the capacity of alert recipients to take swift protective action or to mentally prepare before shaking starts. The study also underscores structural factors such as insufficient linguistic representation in disaster language planning and technology design, which ignores the linguistic and sensory access needs of DHH + individuals. Building on disaster language planning frameworks, we recommend involving DHH + populations to co-develop EEW alerts. By centering DHH + perspectives, this research contributes to ongoing efforts to ensure that EEW systems reach everyone.

California

OpenCLC: An open-source software tool for similarity assessment of linear hydrographic features

The National Hydrography Dataset (NHD) is a foundational geospatial data source in the United States that enables extensive and diverse environmental research and supports decision-making in numerous contexts. However, the NHD requires regular validation and update given possible inconsistent initial collection and hydrographic changes. Furthermore, systems or tools that use NHD data must manage regular updates that occur within the high-resolution version of the NHD (NHD HR). This research contributes to filling this gap by establishing an open-source software tool named OpenCLC, which automatically identifies matching and mismatching line features between two sets of hydrographic flowlines. Aside from identifying differences among two version of NHD lines, results can be applied to improve the quality of NHD HR content. OpenCLC significantly outperforms the best available commercial off-the-shelf software in computational scalability, and it is made widely available as part of the CyberGIS Toolkit to benefit broad environmental and geospatial science communities.

SoftwareX

Comparing three approaches of evapotranspiration estimation in mixed urban vegetation; field-based, remote sensing-based and observational-based methods

Despite being the driest inhabited continent, Australia has one of the highest per capita water consumptions in the world. In addition, instead of having fit-for-purpose water supplies (using different qualities of water for different applications), highly treated drinking water is used for nearly all of Australia’s urban water supply needs, including landscape irrigation. The water requirement of urban landscapes, and particularly urban parklands, is of growing concern. The estimation of ET and subsequently plant water requirements in urban vegetation needs to consider the heterogeneity of plants, soils, water and climate characteristics. Accurate estimation of evapotranspiration (ET), which is the main component of a plant’s water requirement, in urban parks is highly desirable because this water maintains the health of green infrastructure and this in turn provides essential ecosystem services. This research contributes to a broader effort to establish sustainable irrigation practices within the Adelaide Parklands in Adelaide, South Australia.

Remote Sensing

A real-time fish detection system for partially dewatered fish to support selective fish passage

Recent advances in fish transportation technologies and deep machine learning-based fish classification have created an opportunity for real-time, autonomous fish sorting through a selective passage mechanism. This research presents a case study of a novel application that utilizes deep machine learning to detect partially dewatered fish exiting an Archimedes Screw Fish Lift (ASFL). A MobileNet SSD model was trained on images of partially dewatered fish volitionally passing through an ASFL. Then, this model was integrated with a network video recorder to monitor video from the ASFL. Additional models were also trained using images from a similar fish scanning device to test the feasibility of this approach for fish classification. Open source software and edge computing design principles were employed to ensure that the system is capable of fast data processing. The findings from this research demonstrate that such a system integrated with an ASFL can support real-time fish detection. This research contributes to the goal of automated data collection in a selective fish passage system and presents a viable path towards realizing optical fish sorting.

Michigan

Using climate information for fuels management

Climate has come to the forefront of wildfire discussions in recent years as research contributes to the general understanding of how climate influences fuels availability to burn, the occurrence of severe fire weather conditions and other wildfire parameters. This understanding has crossed over into wildfire management applications through the creation of tools like climate forecasts for wildfire and drought indices, which are now widely used in wildfire suppression and mitigation planning. The overall question is how can climate information help fire managers meet management objectives? Climate underlies weather. For example, a number of days could be generally wet, but that may occur in the context of a two-year overall drought. Knowing the baseline climate is not only critical to preventing escaped prescribed fires, but also how it may affect fire behavior, fire effects and whether or not fire managers will meet their fuels management objectives. Thus, for fire managers to use prescribed and WFU fire safely and effectively, and to minimize the number of escaped fires and conversions to suppression, they need to understand how current climate conditions will impact the use of fire. One example is the need to use prescribed fire under set “burn windows”. Since meteorological conditions vary considerably from year to year for a given day, fire managers will be more successful in utilizing burn windows effectively if they understand those climate thresholds conducive to an increased number of safe burn windows, and are able to predict and take advantage of those burn windows. While climate and wildfire has been studied extensively, climate and fire use has not. The initial goal of this project was to assess how climate impacts prescribed fire use in a more general sense. After a preliminary informal survey in the spring of 2003, we determined that 1) there is insufficient data (less than 10 years) to conduct empirical correlative studies similar to those of the relationships between climate and wildfire (e.g., Swetnam and Betancourt 1990), and 2) prescribed fire policy has many regulations that potentially inhibited the use of climate information for decision-making. It was also determined that because fire use is a human decision, it would be more informative to ask fire managers themselves how climate impacts fire use through their decision-making processes, and whether or not they use climate information for prescribed fire. The first task for this project was to complete a regional survey of prescribed fire managers in California and Nevada. During the second phase of the project, additional prescribed fire managers were surveyed across the country. During the third year a second survey of WFU managers was completed. The goals of these inquiries were to determine: 1) If fire managers use climate information for fuels management; 2) The perspective fire managers have towards climate affecting fuels management; 3) Determine any obstacles that make it difficult to use climate information for fuels management; and 4) Determine climate information managers need to help them make better decisions for fire use.

Climate Ecosystem Fire Applications

Wind River watershed restoration: Annual Report April 2004 - March 2005

During 2004, researchers from U.S. Geological Survey’s Columbia River Research Laboratory (USGS-CRRL) collected temperature, flow, and habitat data to characterize physical habitat condition and variation within and among tributaries and mainstem sections in the Wind River subbasin. Juvenile salmonid population surveys were conducted within select study areas throughout the subbasin. We expanded our survey coverage of the mainstem Wind River to a reach in the vicinity of Carson National Fish Hatchery to assess effects of non-indigenous Chinook on native steelhead. These efforts add to a database of habitat and fish data collected in the Wind River since 1996. This research contributes to the Wind River Restoration Project, which includes active stream habitat restoration and monitoring of adult and juvenile steelhead populations.

Washington

Landsat still contributing to environmental research

Landsat data have enabled continuous global monitoring of both human-caused and other land cover disturbances since 1972. Recently degraded performance and intermittent service of the Landsat 7 and Landsat 5 sensors, respectively, have raised concerns about the condition of global Earth observation programs. However, Landsat imagery is still useful for landscape change detection and this capability should continue into the foreseeable future.

Trends in Ecology and Evolution

Biases in the literature on direct wildlife mortality from energy development

Comparing environmental impacts of different energy sources can inform energy investments and environmental conservation. Direct wildlife mortality from energy development receives substantial public and scientific attention, but it is unclear whether rigorous comparisons of mortality among energy sources are possible. To address this question, we compared availability of mortality studies among energy sources, wildlife groups, and regions, and assessed comparability of mortality indicators measured. Whereas wind and hydropower have received substantial mortality research exceeding their proportional contributions to global energy production, coal, oil and gas, and bioenergy have received fewer studies and are underrepresented relative to their contributions. Furthermore, research is biased toward birds and fish and North America and Europe, and there are inconsistencies among energy sources and limited replication of most indicators measured. These results indicate that rigorous comparisons of direct wildlife mortality among energy sources are not currently possible and highlight research needs for improving understanding of energy's environmental impacts.

BioScience

Distinct pathways to stakeholder use versus academic contribution in climate adaptation research

Challenges facing societies around the globe as they plan for and adapt to climate change are so large that usable, research-driven recommendations to inform management actions are urgently needed. We sought to understand factors that influence the variation of academic contribution and use of collaborative research on climate change. We surveyed researchers ( n = 31), program-leaders ( n = 5), and stakeholders ( n = 81) from projects supported by a federally funded network across the United States. Our results suggest that peer-reviewed publications do not lead to use, but frequency of meetings with stakeholders significantly increased use. Overall, the factors needed for projects to have high degrees of academic contributions are distinct from those needed to be useful to stakeholders. Furthermore, leadership perceptions of use of projects were significantly different from users. Our quantitative results can inform future requests for proposals and better enable researchers using collaborative approaches to conduct science that is more often used by stakeholders.

Conservation Letters