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Picornaviruses and reoviruses of fishes

The number of fish viruses isolated in cell culture or observed by electron microscopy continues to increase rapidly. Until recently, most viruses that were isolated from finfish and characterized were found to be members of the Rhabdoviridae, Iridoviridae, or Herpesviridae (Wolf and Mann 1980). In a comprehensive review of fish viruses published in 1984, there were no picornaviruses and only two reoviruses listed (Wolf 1984). The expansion of aquaculture into the rearing of new species at high density in different geographic areas, and the use of improved methods of detection that include newly developed cell lines and increased sampling effort, have led to the discovery of fish viruses representing nearly all families of animal viruses. Among the newest additions, are a member of the family Picornaviridae and several new viruses that belong within the Reoviridae.

Book chapter

Social and biological perspectives to investigate and address illegal shooting of raptors

Humans have shot raptors for centuries. However, in many countries these actions have been illegal since the mid-twentieth century. Despite this history, there is not a comprehensive understanding of the characteristics of this activity, its frequency, and why it occurs. We used literature review and principles drawn from ecology, sociology, and criminology to understand this problem. First, we review literature on raptor shooting globally to explore documented motivations for shooting and we describe the history of raptor shooting in the United States of America (USA). Then, to illustrate the contemporary frequency and geographic breadth of the shooting of raptors, we systematically compile records from scientific and media reports from across the USA. Finally, we outline a transdisciplinary framework to meet the challenge of understanding and managing illegal shooting of raptors. Our framework encompasses six best practices: (1) understand the biology of the problem, (2) build professional networks and partnerships, (3) leverage engagement and public support, (4) apply insights from study of human-wildlife interactions, (5) draw lessons from criminology, and (6) use implementation science to evaluate outcomes. We illustrate application of these best practices with a case study from an Illegal Shooting Working Group recently formed in Boise, Idaho, USA. There is growing recognition that illegal shooting of raptors is a pressing conservation challenge. Solving this challenge can be facilitated by inclusion of information from multiple fields of study; the approach we outline provides one potential mechanism to address this issue.

Global Ecology and Conservation

Existing evidence on the effects of climate variability and climate change on ungulates in North America: A systematic map

Background Climate is an important driver of ungulate life-histories, population dynamics, and migratory behaviors. Climate conditions can directly impact ungulates via changes in the costs of thermoregulation and locomotion, or indirectly, via changes in habitat and forage availability, predation, and species interactions. Many studies have documented the effects of climate variability and climate change on North America’s ungulates, recording impacts to population demographics, physiology, foraging behavior, migratory patterns, and more. However, ungulate responses are not uniform and vary by species and geography. Here, we present a systematic map describing the abundance and distribution of evidence on the effects of climate variability and climate change on native ungulates in North America. Methods We searched for all evidence documenting or projecting how climate variability and climate change affect the 15 ungulate species native to the U.S., Canada, Mexico, and Greenland. We searched Web of Science, Scopus, and the websites of 62 wildlife management agencies to identify relevant academic and grey literature. We screened English-language documents for inclusion at both the title and abstract and full-text levels. Data from all articles that passed full-text review were extracted and coded in a database. We identified knowledge clusters and gaps related to the species, locations, climate variables, and outcome variables measured in the literature. Review findings We identified a total of 674 relevant articles published from 1947 until September 2020. Caribou ( Rangifer tarandus ), elk ( Cervus canadensis ), and white-tailed deer ( Odocoileus virginianus ) were the most frequently studied species. Geographically, more research has been conducted in the western U.S. and western Canada, though a notable concentration of research is also located in the Great Lakes region. Nearly 75% more articles examined the effects of precipitation on ungulates compared to temperature, with variables related to snow being the most commonly measured climate variables. Most studies examined the effects of climate on ungulate population demographics, habitat and forage, and physiology and condition, with far fewer examining the effects on disturbances, migratory behavior, and seasonal range and corridor habitat. Conclusions The effects of climate change, and its interactions with stressors such as land-use change, predation, and disease, is of increasing concern to wildlife managers. With its broad scope, this systematic map can help ungulate managers identify relevant climate impacts and prepare for future changes to the populations they manage. Decisions regarding population control measures, supplemental feeding, translocation, and the application of habitat treatments are just some of the management decisions that can be informed by an improved understanding of climate impacts. This systematic map also identified several gaps in the literature that would benefit from additional research, including climate effects on ungulate migratory patterns, on species that are relatively understudied yet known to be sensitive to changes in climate, such as pronghorn ( Antilocapra americana ) and mountain goats ( Oreamnos americanus ), and on ungulates in the eastern U.S. and Mexico.

Environmental Evidence

Reports and maps of the Military Geology Unit, 1942-1975

Included here are reports and maps which were prepared in the Military Geology Unit of the U. S. Geological Survey from 1942 through 1975. In addition to the references prepared primarily for military use and listed here, more than 200 reports of more general geologic interest were prepared for publication as Survey bulletins and professional papers and in outside journals. These reports are listed in "Publications of the Geological Survey" and other bibliographies. Military Geology reports generally include basic subjects such as rock types, soils, water resources, landforms and vegetation, as well as interpretive subjects such as suitability of terrain for cross-country movement and for construction of roads and airfields in areas throughout the world. Reports on specific areas range from generalized texts with small scab maps derived from published sources to detailed texts with large-scale maps commonly based on photo-interpretation and, especially for Alaska and western Pacific islands, involving field mapping. Other reports treat topics of interest in military geology without reference to specific areas. A number of reports covering the moon include the first photogeologic map of the near side. Authors are cited for some kinds of reports; however, many intelligence reports were published anonymously. Most of the reports were prepared by teams made up mainly of geologists but commonly including soils scientists, botanists, climatologists and geographers. Nearly all the soil scientists and climatologists were members of the World Soil Geography Unit, Soil Survey, Soil Conservation Service, U. S. Department of Agriculture. Manuscripts from this Unit were passed through a common review and other processing, as were the manuscripts originating in the Military Geology office, to be issued under the aegis of the latter. In some instances where it has not been possible to list all authors, names of project supervisors are given. File copies of many of the Military Geology reports prepared since 1975 are kept in the Special Geologic Studies Group, U.S. Geological Survey, National Center, Reston, and may be examined there by appropriately cleared persons. Additionally, copies of many of the unclassified studies are in the U.S. Geological Survey Library. Some of the older reports are in the files of the Terrain Analysis Center, Fort Belvoir, Virginia, and other offices within the Corps of Engineers. Most of the reports are out of print and many of the other studies are no longer available.

Open-File Report

Natural resource inventory and monitoring for Ulaan Taiga Specially Protected Areas—An assessment of needs and opportunities in northern Mongolia

Between 1997 and 2011, Mongolia established three specially protected areas in the north-central part of the country to protect various high-value resources. These areas are jointly referred to as the Ulaan Taiga Specially Protected Areas. In accordance with the goals of the draft general management plan, this report identifies options for initiating an inventory and monitoring program for the three protected areas. Together, the three areas comprise over 1.5 million hectares of mountainous terrain west of Lake Hovsgol and bordering the Darkhad Valley. The area supports numerous rare ungulates, endangered fish, and over 40 species of threatened plants. Illegal mining, illegal logging, and poaching pose the most immediate threats to resources. As a first step, a review of published literature would inform natural resource management at the Ulaan Taiga Specially Protected Areas because it would inform other inventories. Vegetation classification and mapping also would inform other inventory efforts because the process incorporates geographic analysis to identify environmental gradients, fine-scale sampling that captures species composition and structure, and landscape-scale results that represent the variety and extent of habitats for various organisms. Mapping using satellite imagery reduces the cost per hectare. Following a determination of existing knowledge, field surveys of vertebrates and vascular plants would serve to build species lists and fill in gaps in existing knowledge. For abiotic resources, a focus on monitoring air quality, evaluating and monitoring water quality, and assembling and storing weather data would provide information for correlating resource response status with changing environmental conditions. Finally, we identify datasets that, if incorporated into a geographic information system, would inform resource management. They include political boundaries, infrastructure, topography, surficial geology, hydrology, fire history, and soils. In terms of tracking high-value resources, vegetation monitoring at the plot scale would provide a basis for detecting change in such characteristics as plant species composition, vegetation structure, and productivity that are associated with landscape-scale factors such as climate change or biotic interactions. Continued population monitoring of rare ungulates, particularly argali or wild sheep ( Ovis ammon ), would provide information on how populations are responding to natural and anthropogenic stressors. Siberian taimen ( Hucho taimen ) also is an important monitoring target given ongoing threats of poaching and climate change.

Ulaan Taiga Specially Protected Areas

Map showing potential metal-mine drainage hazards in Colorado, based on mineral-deposit geology

This map, compiled by the U.S. Geological Survey (USGS) in cooperation with the Colorado Geological Survey (CGS) and the U. S. Bureau of Land Management (BLM), shows potential mine-drainage hazards that may exist in Colorado metal-mining districts, as indicated by the geologic characteristics of the mineral deposits that occur in the respective districts. It was designed to demonstrate how geologic and geochemical information can be used on a regional scale to help assess the potential for mining-related and natural drainage problems in mining districts, unmined mineralized areas, and surrounding watersheds. The map also provides information on the distribution of different mineral deposit types across Colorado. A GIS (Geographic Information System) format was used to integrate geologic, geochemical, water-quality, climate, landuse, and ecological data from diverse sources. Likely mine-drainage signatures were defined for each mining district based on: (1) a review of the geologic characteristics of the mining district, including mineralogy, trace-element content, host-rock lithology, and wallrock alteration, and; (2) results of site specific studies on the geologic controls on mine-drainage composition.

Colorado

Euryhalinity in an evolutionary context

This chapter focuses on the evolutionary importance and taxonomic distribution of euryhalinity. Euryhalinity refers to broad halotolerance and broad halohabitat distribution. Salinity exposure experiments have demonstrated that species vary tenfold in their range of tolerable salinity levels, primarily because of differences in upper limits. Halotolerance breadth varies with the species&rsquo; evolutionary history, as represented by its ordinal classification, and with the species&rsquo; halohabitat. Freshwater and seawater species tolerate brackish water; their empirically-determined fundamental haloniche is broader than their realized haloniche, as revealed by the halohabitats they occupy. With respect to halohabitat distribution, a minority of species (<10%) are euryhaline. Habitat-euryhalinity is prevalent among basal actinopterygian fishes, is largely absent from orders arising from intermediate nodes, and reappears in the most derived taxa. There is pronounced family-level variability in the tendency to be halohabitat-euryhaline, which may have arisen during a burst of diversification following the Cretaceous-Palaeogene extinction. Low prevalence notwithstanding, euryhaline species are potent sources of evolutionary diversity. Euryhalinity is regarded as a key innovation trait whose evolution enables exploitation of new adaptive zone, triggering cladogenesis. We review phylogenetically-informed studies that demonstrate freshwater species diversifying from euryhaline ancestors through processes such as landlocking. These studies indicate that some euryhaline taxa are particularly susceptible to changes in halohabitat and subsequent diversification, and some geographic regions have been hotspots for transitions to freshwater. Comparative studies on mechanisms among multiple taxa and at multiple levels of biological integration are needed to clarify evolutionary pathways to, and from, euryhalinity.

Book chapter

Advancing barrier island habitat mapping using landscape position information

Barrier islands are dynamic ecosystems that change gradually from coastal processes, including currents and tides, and rapidly from episodic events, such as storms. These islands provide many important ecosystem services, including storm protection and erosion control to the mainland, habitat for fish and wildlife, and tourism. Habitat maps, developed by scientists, provide a critical tool for monitoring changes to these dynamic ecosystems. Barrier island monitoring often requires custom habitat maps due to several factors, including island size and the classification of unique geomorphology-based habitats, such as beach, dune, and barrier flats. In this study, we reviewed barrier-island-specific habitat mapping efforts and highlighted common habitat class types, source data, and mapping approaches. We also developed a framework for mapping geomorphology-based barrier island habitats using a rule-based, geographic object-based image analysis approach, which included the use of field data, tide data, high-resolution orthophotography, and lidar data. This framework integrates several barrier island mapping advancements with regard to the use of landscape position information for automated dune extraction and the use of Monte Carlo analyses for the treatment of elevation uncertainty for elevation-dependent habitats. Specifically, we used the uncertainty analyses to refine automated dune delineation based on elevation relative to extreme storm water levels and to increase the accuracy of intertidal and supratidal/upland habitat delineation. We found that dune extraction results were enhanced when elevation relative to storm water levels and visual interpretation were also applied. This framework could also be applied to beach–dune systems found along a mainland.

Alabama

Land use change and effects on water quality and ecosystem health in the Lake Tahoe basin, Nevada and California: year-1 progress

As part of the requirements for the Geographic Research and Applications Prospectus grants, this Open-File Report is the second of two that resulted from the first year of the project. The first Open-File Report (OFR 01-418) introduced the project, reviewed the existing body of literature, and outlined the research approach. This document will present an update of the research approach and offer some preliminary results from multiple efforts, specifically, the production of historical digital orthophoto quadrangles, the development of the land use/land cover (LULC) classification system, the development of a temporal transportation layer, the classification of anthropogenic cover types from the IKONOS imagery, a preliminary evaluation of landscape ecology metrics (quantification of spatial and temporal patterns of ecosystem structure and function with appropriate indices) and their utility in comparing two LULC systems, and a new initiative in community-based science and facilitation.

Open-File Report

Shallow landslide hazard map of Seattle, Washington

Landslides, particularly debris flows, have long been a significant cause of damage and destruction to people and property in the Puget Sound region. Following the years of 1996 and 1997, the Federal Emergency Management Agency designated Seattle as a &ldquo;Project Impact&rdquo; city with the goal of encouraging the city to become more disaster resistant to landslides and other natural hazards. A major recommendation of the Project Impact council was that the city and the U.S. Geological Survey collaborate to produce a landslide hazard map. An exceptional data set archived by the city containing more than 100 yr of landslide data from severe storm events allowed comparison of actual landslide locations with those predicted by slope-stability modeling. We used an infinite-slope analysis, which models slope segments as rigid friction blocks, to estimate the susceptibility of slopes to debris flows, which are water-laden slurries that can form from shallow failures of soil and weathered bedrock and can travel at high velocities down steep slopes. Data used for the analysis consisted of a digital slope map derived from recent light detection and ranging (LiDAR) imagery of Seattle, recent digital geologic mapping of the city, and shear-strength test data for the geologic units found in the surrounding area. The combination of these data layers within a geographic information system (GIS) platform allowed us to create a shallow landslide hazard map for Seattle.

Washington

The south Florida environment: A region under stress

This report provides an overview of the environmental setting in South Florida and serves as review and framework for developing U.S. Geological Survey programs in the region. The report describes the predevelopment and the current (present-day) environmental conditions in South Florida with emphasis on the quantity and quality of water. The geographical area covered is the southern one-half of the State and includes the South Florida National Water-Quality Assessment study area and adjacent coastal waters. This study area covers about 19,500 square miles and is the watershed of the larger regional ecosystem. The regional ecosystem includes the coastal waters between Charlotte Harbor on the Gulf of Mexico and the St. Lucie River on the Atlantic Ocean and the lands that drain into these waters.

Florida

Mycoplasmosis and upper respiratory tract disease of tortoises: a review and update

Tortoise mycoplasmosis is one of the most extensively characterized infectious diseases of chelonians. A 1989 outbreak of upper respiratory tract disease (URTD) in free-ranging Agassiz's desert tortoises ( Gopherus agassizii ) brought together an investigative team of researchers, diagnosticians, pathologists, immunologists and clinicians from multiple institutions and agencies. Electron microscopic studies of affected tortoises revealed a microorganism in close association with the nasal mucosa that subsequently was identified as a new species, Mycoplasma agassizii . Over the next 24 years, a second causative agent, Mycoplasma testudineum , was discovered, the geographic distribution and host range of tortoise mycoplasmosis were expanded, diagnostic tests were developed and refined for antibody and pathogen detection, transmission studies confirmed the pathogenicity of the original M. agassizii isolate, clinical (and subclinical) disease and laboratory abnormalities were characterized, many extrinsic and predisposing factors were found to play a role in morbidity and mortality associated with mycoplasmal infection, and social behavior was implicated in disease transmission. The translation of scientific research into management decisions has sometimes led to undesirable outcomes, such as euthanasia of clinically healthy tortoises. In this article, we review and assess current research on tortoise mycoplasmosis, arguably the most important chronic infectious disease of wild and captive North American and European tortoises, and update the implications for management and conservation of tortoises in the wild.

The Veterinary Journal

Response of the North American monsoon to regional changes in ocean surface temperature

The North American monsoon (NAM), an onshore wind shift occurring between July and September, has evolved in character during the Holocene largely due to changes in Northern Hemisphere insolation. Published paleoproxy and modeling studies suggest that prior to ∼8000 cal years BP, the NAM affected a broader region than today, extending westward into the Mojave Desert of California. Holocene proxy SST records from the Gulf of California (GoC) and the adjacent Pacific provide constraints for this changing NAM climatology. Prior to ∼8000 cal years BP, lower GoC SSTs would not have fueled northward surges of tropical moisture up the GoC, which presently contribute most of the monsoon precipitation to the western NAM region. During the early Holocene, the North Pacific High was further north and SSTs in the California Current off Baja California were warmer, allowing monsoonal moisture flow from the subtropical Pacific to take a more direct, northwesterly trajectory into an expanded area of the southwestern U.S. west of 114°W. A new upwelling record off southwest Baja California reveals that enhanced upwelling in the California Current beginning at ∼7500 cal year BP may have triggered a change in NAM climatology, focusing the geographic expression of NAM in the southwest USA into its modern core region east of ∼114°W, in Arizona and New Mexico. Holocene proxy precipitation records from the southwestern U.S. and northwestern Mexico, including lakes, vegetation/pollen, and caves are reviewed and found to be largely supportive of this hypothesis of changing Holocene NAM climatology.

Arizona;Colorado;New Mexico;Texas;Utah

Conserving climate-change refugia: Insights from research and practice

As the impacts of anthropogenic climate change increase, conservation of climate-change refugia has become a key strategy for effective environmental stewardship. Over the last 5 years, the field of climate-change refugia conservation has made exciting advances, shifting from concepts and theory to refugia mapping and implementation. However, few studies have advanced to action on the ground; while 84% of studies identified and mapped refugia, only 4% involved implementing management action. Moreover, taxonomic and geographic gaps remain, with most studies focused on terrestrial plants and vertebrates in Europe and North America. Here, we outline impediments to implementation following the steps of the Climate-Change Refugia Conservation Cycle. Based on a systematic literature review, we elucidate advances and obstacles with examples from a diversity of systems and sectors from across the world and highlight emerging work bridging the gap between research and implementation.

Conservation Science and Practice

Climate, environment, and disturbance history govern resilience of western North American Forests

Before the advent of intensive forest management and fire suppression, western North American forests exhibited a naturally occurring resistance and resilience to wildfires and other disturbances. Resilience, which encompasses resistance, reflects the amount of disruption an ecosystem can withstand before its structure or organization qualitatively shift to a different basin of attraction. In fire-maintained forests, resilience to disturbance events arose primarily from vegetation pattern-disturbance process interactions at several levels of organization. Using evidence from 15 ecoregions, spanning forests from Canada to Mexico, we review the properties of forests that reinforced qualities of resilience and resistance. We show examples of multi-level landscape resilience, of feedbacks within and among levels, and how conditions have changed under climatic and management influences. We highlight geographic similarities and important differences in the structure and organization of historical landscapes, their forest types, and in the conditions that have changed resilience and resistance to abrupt or large-scale disruptions. We discuss the role of the regional climate in episodically or abruptly reorganizing plant and animal biogeography and forest resilience and resistance to disturbances. We give clear examples of these changes and suggest that managing for resilient forests is a construct that strongly depends on scale and human social values. It involves human communities actively working with the ecosystems they depend on, and the processes that shape them, to adapt landscapes, species, and human communities to climate change while maintaining core ecosystem processes and services. Finally, it compels us to embrace management approaches that incorporate ongoing disturbances and anticipated effects of climatic changes, and to support dynamically shifting patchworks of forest and non-forest. Doing so could make these shifting forest conditions and wildfire regimes less disruptive to individuals and society.

western North America

Environmental Contaminants and Terrestrial Vertebrates: Effects on Populations, Communities, and Ecosystems

The desire of resource managers, risk assessors, and the general public to better understand the consequences of environmental contamination has produced a strong and growing need for information on the effects of contaminants on populations and groups of species, and over moderate to large areas of land or water. However, the problems associated with research involving populations and groups of species or large and complex geographic areas, especially in terrestrial environments, are well known within the scientific community. With the previous thoughts in mind, an interactive symposium was held at the University of Maryland in October 1998. The purpose of the symposium was to review and critically evaluate our understanding of the effects of contaminants on terrestrial vertebrates at levels of organization above that of the individual. Invited background and technical presentations provided a common baseline of information for symposium participants. Discussion groups were then asked to critically evaluate the topics of two technical sessions. Several presentations of recent or ongoing research provided participants with examples of current approaches to assessments of the effects of contaminants on terrestrial vertebrates at the population or higher level of organization. The book consists of 10 chapters written by presenters at the symposium and three chapters conveying the reports of discussion group.

SETAC Special Publications Series.

Coastal wetlands of Chesapeake Bay

Wetlands are prominent landscapes throughout North America. The general characteristics of wetlands are controversial, thus there has not been a systematic assessment of different types of wetlands in different parts of North America, or a compendium of the threats to their conservation. Wetland Habitats of North America adopts a geographic and habitat approach, in which experts familiar with wetlands from across North America provide analyses and syntheses of their particular region of study. Addressing a broad audience of students, scientists, engineers, environmental managers, and policy makers, this book reviews recent, scientifically rigorous literature directly relevant to understanding, managing, protecting, and restoring wetland ecosystems of North America.

Book chapter