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Observer-free experimental evaluation of habitat and distance effects on the detection of anuran and bird vocalizations

Acoustic surveys of vocalizing animals are conducted to determine density, distribution, and diversity. Acoustic surveys are traditionally performed by human listeners, but automated recording devices (ARD) are becoming increasingly popular. Signal strength decays, or attenuates, with increasing distance between source and receiver and some habitat types may differentially increase attenuation beyond the effects of distance alone. These combined effects are rarely accounted for in acoustic monitoring programs. We evaluated the performance of three playback devices and three ARD models using the calls of six anurans, six birds, and four pure tones. Based on these evaluations, we determined the optimal playback and recording devices. Using these optimal devices, we broadcast and recorded vocalizations in five habitat types along 1,000 m transects. We used generalized linear models to test for effects of habitat, distance, species, environmental, and landscape variables. We predicted detection probabilities for each vocalization, in each habitat type, from 0 to 1,000 m. Among playback devices, only a remote predator caller simulated vocalizations consistently. Differences of ~10 dB were observed among ARDs. For all species, we found differences in detectability between open and closed canopy habitats. We observed large differences in predicted detection probability among species in each habitat type, as well as along 1,000 m transects. Increases in temperature, barometric pressure, and wind speed significantly decreased detection probability. However, aside from differences among species, habitat, and distance, topography impeding a line‐of‐sight between sound source and receiver had the greatest negative influence on detections. Our results suggest researchers should model the effects of habitat, distance, and frequency on detection probability when performing acoustic surveys. To optimize survey design, we recommend pilot measurements among varying habitats.

Ecology and Evolution↗

Disturbance refugia within mosaics of forest fire, drought, and insect outbreaks

Disturbance refugia – locations that experience less severe or frequent disturbances than the surrounding landscape – provide a framework to highlight not only where and why these biological legacies persist as adjacent areas change but also the value of those legacies in sustaining biodiversity. Recent studies of disturbance refugia in forest ecosystems have focused primarily on fire, with a growing recognition of important applications to land management. Given the wide range of disturbance processes in forests, developing a broader understanding of disturbance refugia is important for scientists and land managers, particularly in the context of anthropogenic climate change. We illustrate the framework of disturbance refugia through the individual and interactive effects of three prominent forest disturbance agents: fire, drought, and insect outbreaks. We provide examples of disturbance refugia and related applications to natural resource management in western North America, demonstrate methods for characterizing refugia, identify research priorities, and discuss why a more comprehensive definition of disturbance refugia is relevant to conservation globally.

Frontiers in Ecology and the Environment↗

Incremental evolution of modeling a prognosis for polar bears in a rapidly changing Arctic

Updating predictions of the response of high-profile, at-risk species to climate change and anthropogenic stressors is vital for informing effective conservation action. Here, we review two prior generations of Bayesian network probability models predicting changes in global polar bear ( Ursus maritimus ) population status, and provide a contemporary update based on recent research findings and sea-ice projections by newer climate models. We compare predictions of polar bear population response from all 3 models among four circumpolar Arctic ecoregions, using sea ice projections based on three IPCC greenhouse gas emissions scenarios (SSP2.6, 4.5, 8.5). Consistent with the previous two model generations, polar bears will continue to experience increasing probability of declining or greatly declining populations throughout the 21st century, varying by emission scenario. Populations within the Polar Basin Divergent Ice Ecoregion have the highest predicted probability of declines, but predictions were slightly less dire relative to the previous model generation. Most of the influence, denoted by model sensitivity analysis, is from expected degradation and loss of sea ice and reduced access to marine prey. The lack of terrestrial prey adequate to substitute for loss of access to marine prey, as well as human-caused bear morality associated with hunting and defense of life and property encountered when polar bears are increasingly forced ashore also contributed to predicted declines. Although some tidewater glacial fjords and other localized onshore resources may provide local refugia, their benefit is transient. Our findings continue to inform priorities for inventory, monitoring, and research needs, and suggest that similar updates to models of other at-risk species can capitalize on the comparison framework we present here.

Ecological Indicators↗

Understanding predator-prey-competitor dynamics between Lower Missouri River Macrhybopsis and Scaphirhynchus using a population—bioenergetics model ensemble

The pallid sturgeon Scaphirhynchus albus is a long-lived, endangered fish in the Missouri River. Individuals become piscivorous as adults, so recruitment from stocking or reproduction could reduce populations of prey, including Macrhybopsis chubs. We constructed an individual- and age-based, multi-species, predator-prey-competitor model (IAMP) to represent the benthic community (sturgeons, chubs, and chironomids) of the Lower Missouri River (LMR) to explore scenarios of potential predator-prey-competitor dynamics. Our simulations suggest that chubs alone are unlikely able to support a level of LMR pallid sturgeon similar to historical or current populations. These simulations also suggest that adult pallid sturgeon may need to shift to non-chub prey fish to achieve the greater sizes observed in the Upper Missouri River. When annual hydrologic regimes were included, we found a negative relationship between chub relative abundance and previous year 30-day minimum flows. Inclusion of temporal environmental variability made it clear that large chub populations may be necessary to support LMR pallid sturgeon. When full stochasticity was included in the IAMP, chub population sizes needed to increase further to ensure continued reproduction and recruitment of both chubs and pallid sturgeon. These results support the hypothesis that the pallid sturgeon population in the Lower Missouri River may be food-limited. However, the full extent of this limitation and the management changes needed to address this will require more research on the biology and population dynamics of this fish community, on pallid sturgeon interactions with prey species, and on how sympatric species may be affected during the pallid sturgeon recovery process.

Colorado, Kansas, Minnesota, Missouri, Montana, Ne↗

Woodland salamander responses to a shelterwood harvest-prescribed burn silvicultural treatment within Appalachian mixed-oak forests

Forest management practices that mimic natural canopy disturbances, including prescribed fire and timber harvests, may reduce competition and facilitate establishment of favorable vegetative species within various ecosystems. Fire suppression in the central Appalachian region for almost a century has contributed to a transition from oak-dominated to more mesophytic, fire-intolerant forest communities. Prescribed fire coupled with timber removal is currently implemented to aid in oak regeneration and establishment but responses of woodland salamanders to this complex silvicultural system is poorly documented. The purpose of our research was to determine how woodland salamanders respond to shelterwood harvests following successive burns in a central Appalachian mixed-oak forest. Woodland salamanders were surveyed using coverboard arrays in May, July, and August–September 2011 and 2012. Surveys were conducted within fenced shelterwood-burn (prescribed fires, shelterwood harvest, and fencing to prevent white-tailed deer [Odocoileus virginianus] herbivory), shelterwood-burn (prescribed fires and shelterwood harvest), and control plots. Relative abundance was modeled in relation to habitat variables measured within treatments for mountain dusky salamanders (Desmognathus ochrophaeus), slimy salamanders (Plethodon glutinosus), and eastern red-backed salamanders (Plethodon cinereus). Mountain dusky salamander relative abundance was positively associated with canopy cover and there were significantly more individuals within controls than either shelterwood-burn or fenced shelterwood-burn treatments. Conversely, habitat variables associated with slimy salamanders and eastern red-backed salamanders did not differ among treatments. Salamander age-class structure within controls did not differ from shelterwood-burn or fenced shelterwood-burn treatments for any species. Overall, the woodland salamander assemblage remained relatively intact throughout the shelterwoodburn silvicultural treatment compared to previous research within the same study area that examined pre-harvest fire effects. However, because of the multi-faceted complexities of this specific silvicultural system, continued research is warranted that evaluates long-term, additive impacts on woodland salamanders within managed central Appalachian deciduous forests.

West Virginia↗

Bridging the gap between spatial modeling and management of invasive annual grasses in the imperiled sagebrush biome

Invasions of native plant communities by non-native species present major challenges for ecosystem management and conservation. Invasive annual grasses such as cheatgrass, medusahead, and ventenata are pervasive and continue to expand their distributions across imperiled sagebrush-steppe communities of the western United States. These invasive grasses alter native plant communities, ecosystem function, and fire regimes, threatening sagebrush ecosystem persistence. Spatial data describing the distribution and abundance of invasive species are often used by resource managers to identify, target, and determine needed interventions. However, there are challenges associated with translating these datasets into management actions. We conducted a review of available spatial products to assess advances in, and barriers to, applying contemporary model-based maps to support rangeland management. We found dozens of regional data products describing cheatgrass or annual herbaceous cover and few maps describing ventenata or medusahead. Over the past decade, IAG spatial data increased in spatial and temporal resolution and increasingly used response variables that indicate the severity of infestation such as percent cover. Despite improvements, use of such data is limited by the time required to find, compare, understand, and translate model-based maps into management strategy. There is also a need for products with higher spatial resolution and accuracy. In collaboration with a multipartner stakeholder group, we identified key considerations that guide selection of IAG spatial data products for use by land managers and other users. On the basis of these considerations, we discuss issues that contribute to a research-implementation gap between users and product developers and suggest future directions for improved development of management-ready spatial products.

Rangeland Ecology & Management↗

Satellite and airborne remote sensing of gross primary productivity in boreal Alaskan lakes

In terrestrial and marine ecosystems, remote sensing has been used to estimate gross primary productivity (GPP) for decades, but few applications exist for shallow freshwater ecosystems.Here we show field-based GPP correlates with satellite and airborne lake color across a range of optically and limnologically diverse lakes in interior Alaska. A strong relationship between in situ GPP derived from stable oxygen isotopes (δ 18 O) and space-based lake color from satellites (e.g. Landsat-8, Sentinel-2 and CubeSats) and airborne imagery (AVIRIS-NG) demonstrates the potential power of this technique for improving spatial and temporal monitoring of lake GPP when coupled with additional field validation measurements across different systems. In shallow waters clear enough for sunlight to reach lake bottoms, both submerged vegetation (macrophytes and algae) and phytoplankton likely contribute to GPP. The stable isotopes and remotely sensed shallow lake color used here integrate both components. These results demonstrate the utility of lake color as a feasible means for mapping lake GPP from remote sensing. This novel methodology estimates GPP from remote sensing in shallow lakes by combining field measurements of oxygen isotopes with airborne, satellite and CubeSat imagery. This use of lake color for providing insight into ecological processes of shallow lakes is recommended, especially for remote arctic and boreal landscapes.

Alaska↗

Predation on native sculpin by exotic brown trout exceeds that by native cutthroat trout within a mountain watershed (Logan, UT, USA)

We explored potential negative effects of exotic brown trout ( Salmo trutta ) on native sculpin ( Cottus sp.) on the Logan River, Utah, USA by (i) examining factors most strongly correlated with sculpin abundance (e.g., abiotic conditions or piscivory?), (ii) contrasting the extent of brown trout predation on sculpin with that by native cutthroat trout ( Oncorhynchus clarkii utah ) and (iii) estimating the number of sculpin consumed by brown trout along an elevational gradient using bioenergetics. Abundance of sculpin across reaches showed a strong ( r ≥ 0.40) and significant ( P < 0.05) correlation with physical variables describing width (positive) and gradient (negative), but not with abundance of piscivorous brown trout or cutthroat trout. In mainstem reaches containing sculpin, we found fish in 0% of age‐1, 10% of age‐2 and 33% of age‐3 and older brown trout diets. Approximately 81% of fish consumed by brown trout were sculpin. Despite a similar length–gape relationship for native cutthroat trout, we found only two fish (one sculpin and one unknown) in the diets of native cutthroat trout similar in size to age‐3 brown trout. Based on bioenergetics, we estimate that an average large (> 260 mm) brown trout consumes as many as 34 sculpin per year. Nevertheless, results suggest that sculpin abundance in this system is controlled by abiotic factors and not brown trout predation. Additional research is needed to better understand how piscivory influences brown trout invasion success, including in‐stream experiments exploring trophic dynamics and interactions between brown trout and native prey under different environmental conditions.

Utah↗

Density-dependent and environmental influences on juvenile walleye Sander vitreus (Mitchill) survivorship in northern Wisconsin lakes

Walleye, Sander vitreus (Mitchill), natural recruitment has declined in northern Wisconsin lakes over time. Age-0 and age-1 walleye relative abundance (catch per unit effort; CPE) data from northern Wisconsin (1986–2019) were used to test for abiotic (i.e. lake characteristics and temperature variables) and biotic (age-0 and age-1 CPE) factors influencing age-0 to age-1 walleye mortality. Age-0 to age-1 walleye mortality was elevated at high age-0 CPE and variable at low age-0 CPE, which indicated strong density-dependence. Environmental factors such as spawning and ontogenetic phenology (climate change and ice-off dates), trophic mismatches, and metabolic and consumptive demand influenced age-0 to age-1 walleye mortality less strongly. Elevated age-0 to age-1 walleye mortality at low age-0 CPE supports previous findings of depensatory recruitment dynamics in northern Wisconsin walleye populations. Additional research is needed to address elevated juvenile walleye mortality at low adult stock sizes and/or with declining natural recruitment to inform management decisions.

Wisconsin↗

Conservation of marine birds of northern North America: Papers from the international symposium held at the Seattle Hyatt House, Seattle, Washington, 13-15 May 1975

The international symposium "Conservation of Marine Birds of Northern North America" was convened because of a growing awareness that not all was well with our marine birds. The symposium provided a forum for scientists, governmental administrators, conservationists, and laypeople to discuss the diverse topics and issues that we must all understand if we are to act both responsively and responsibly to assure that marine birds will not be lost through our neglect. The symposium was cosponsored by the Natural Resources Council of America, National Audubon Society, National Wildlife Federation, and the U.S. Department of the Interior, Fish and Wildlife Service; additional support was provided by the Canadian Wildlife Service, the International Association of Game, Fish, and Conservation Commissioners, the Pacific Seabird Group, the Sierra Club, the Smithsonian Institution, the Wildlife Management Institute, and the Wildlife Society. Persons interested and knowledgeable in the many and varied aspects of marine bird conservation were invited to participate in this symposium. There were 139 registered and several score of unregistered participants in attendance. Major topics treated were: (1) socioeconomic considerations and conservation of marine birds; (2) the marine environment of birds; (3) status of marine bird populations on land and sea; (4) the biology and ecology of marine birds in the North; (5) conflicts between the conservation of marine birds and uses of other resources; (6) programs and authorities related to the conservation of marine birds; and (7) conservation of marine birds in other lands.

Wildlife Research Report↗

Cape Romain partnership for coastal protection

This final report summarizes activities, outcomes, and lessons learned from a 3-year project titled “Climate Change Adaptation for Coastal National Wildlife Refuges” with the Cape Romain National Wildlife Refuge (NWR) and local partners in the surrounding South Carolina Lowcountry. The Lowcountry is classified as the 10-county area encompassing the coastal plain of South Carolina (this report specifically focuses on Berkeley, Charleston, and Georgetown Counties). The goals of this work, sponsored by the U.S. Geological Survey’s Southeast Climate Adaptation Science Center (SECASC), were to foster active engagement with stakeholders; to develop a comprehensive definition of adaptation problems faced by agencies, organizations, and individuals near the Cape Romain NWR that accounts for global change, local values, knowledge and perceptions; and to encourage social learning and building of effective networks and trust across South Carolina Lowcountry organizations and individuals. Although project scoping began at the scale of the Atlantic seaboard, by engaging with NWRs from Massachusetts to Florida, participating refuge personnel eventually selected the Cape Romain NWR to serve as a case study for testing our goals. The Cape Romain Partnership for Coastal Conservation was established to address global change impacts at a regional level and includes representation from Federal and State resource agencies, local conservation nongovernmental organizations, and organizations representing underserved community interests. Research topics, originating from discussions with Cape Romain Partnership for Coastal Conservation members, focused on quantifying key drivers of change including localized sea-level rise (SLR) predictions, estimates of coastal hurricane inundation as amplified by SLR, and urban growth trends and forecasts. These key drivers provided a foundation to engage stakeholders in planning exercises to begin a process of collective understanding and collaborative decision making. The goal of this process was to develop collective strategies of adaptation to enhance community and ecosystem resilience in the South Carolina Lowcountry. South Carolina’s Lowcountry is experiencing rapid environmental and social transformation because of SLR rates approaching twice the global average, chronic tidal flooding and catastrophic storm surges, erosion and loss of habitats that provide essential services to wildlife and humans, and increasing social polarization fueled by aggressive low-density urban growth and other forms of land conversion. To support characterizations of plausible future scenarios, we used available or, in some cases, developed new models to project future conditions of key environmental and social-economic drivers. Because of the imprecision of mean global SLR projections, the SECASC commissioned a climatological study to account for local conditions and multiple representative concentration pathways to project a tailored distribution of future sea levels. These projections were matched to SLR scenarios provided by existing models to anticipate the range of future coastal habitat changes in the South Carolina Lowcountry. SLR scenarios were also incorporated into existing storm-surge models, which do not account for alternate baseline sea levels, to project the local effects of future hurricanes. To evaluate the extent and effects of population growth and urban expansion, we relied on an existing urban-growth model to map the spatial distribution of land-conversion probabilities, the total area of which is predicted to increase twofold to threefold over the next 60 years. In addition to this simplified model, an econometric model is in development to account for nonlinear feedback dynamics in land value, land use, and ecosystem service production. Although not yet completed, the goals of this model are to produce more-detailed projections of growth dynamics and to allow predictions of development patterns resulting from alternate land-use planning policies and incentives. Collaborative planning for an uncertain future requires more than providing decision makers with information on future physical and ecological conditions; developing effective and consensual strategies must also integrate sociological values, multiple cultural perspectives, and an understanding of human behavior. To support broad stakeholder engagement in integrative approaches to adaptation planning, emphasis was placed on the importance of considering differences in how individuals perceive their environment and create meaning. Because cultural frameworks form the basis for perceptions and, ultimately, the behaviors of individuals and institutions, we describe a model of human behavior and how it can be used to understand the effect of cultural complexity and variation in perception on choices, behavioral change, and long-term maintenance of behaviors. We consider a model commonly used in the field of behavioral health that accommodates variation in human perception when describing stages of behavior and the dynamics of behavioral change. Tailoring communication and engagement activities to targeted stakeholders is likely to benefit from increased understanding of behavioral change processes. The complex nature of this problem limited the usefulness of a traditional decision-analytic approach, we explored alternative methods for engagement, collaborative learning and decision making. Recognizing that project partners and Lowcountry stakeholders may be at different stages of preparedness and interest level for modifying behavior as a function of global change, we facilitated a scenario-planning exercise to familiarize partners with this well-established approach for communicating the opportunities and threats arising under alternative, plausible futures. We developed narratives for four alternative South Carolina Lowcountry scenarios to be used in later strategic planning that focus on quantitative trends for three primary drivers with high impact and high uncertainty: manifestations of climate change, social-political shifts at a global level, and forces of local value and power structures. This scenario-planning exercise underscored the complex relation between the temporospatial scale of the production of ecological goods and services and the institutional scale at which they are managed. We then guided the partners through an assessment of the relevant strengths and weaknesses of the Cape Romain Partnership for Coastal Protection, using the threats and opportunities characterized by each scenario to understand how the partnership might respond when attempting to meet conservation and societal objectives. The partnership identified key strengths including partnership experience, outreach and technical capacities, a substantial conservation land base, and high social cohesion in the South Carolina Lowcountry. Limited communication expertise, institutional inertia, and insufficient staffing and funding were recognized as important weaknesses across the partnership. By examining and scoring combinations of internal strengths and weaknesses and external threats and opportunities, the partnership developed sets of prioritized strategies to consider in the context of a given scenario. Although we had insufficient time to examine all scenarios in detail, the intent was to identify a portfolio of strategic actions to address threats and opportunities represented in multiple plausible futures. Top-ranking strategies encompassed a range of actions that focused on strengthening the conservation community and communicating the benefits of nature (that is, ecosystem services) to leveraging partnerships to expand land protection. This report also details the methods and preliminary results of several models developed or applied in support of this project. Two parcel-selection algorithms were used to evaluate anticipated habitat changes and patterns of urban growth to guide decisions on optimal conservation reserve design to protect habitat communities. One approach used a widely available planning software (MARXAN) to maximize conservation benefits near the Cape Romain NWR, whereas the other approach was a novel application of economic theory to account for uncertainty in future conditions and for the risks of unanticipated habitat loss. This latter model applies modern portfolio theory to estimate the risk of investing in any portfolio of land parcels (that is, candidate “reserves”) under climate-change uncertainty by quantifying the variation and spatial correlation of conservation benefits derived from each portfolio. We expanded the range of actions beyond simply whether or not to invest in a set of land parcels, an approach commonly used in spatial conservation planning, to also include consideration of divestment from currently protected lands. Such refinements allow for better accounting of system dynamics and can evaluate the benefits of flexible conservation tools such as rolling easements. Model results were conditional on a decision maker’s risk tolerance but highlighted general strategies of land conservation to increase future habitat representation beyond what is expected under the current protected land base. We built models that may help inform coastal planning by estimating salinity dynamics and the performance of oyster reef restoration efforts to predict the combined effects of global change and management of freshwater flows on coastal habitats and the processes that contribute to their resilience. These models can support restoration decisions by evaluating the expected benefits of site locations for shoreline protection and fisheries production. Lastly, we developed a spatially explicit economic model that predicts feedback dynamics among land value, land-use change, and effects on ecosystem service provision to explore zoning policies and incentives on urban growth and ecosystem services. We summarize these efforts with insights and considerations for the Cape Romain Partnership for Coastal Protection to continue to engage stakeholders in effective adaptation planning. First, notions of place attachment (referred to as sense of place), and the role of culture in social discourse are increasingly being used to understand the complex interactions between society and the environment and how societies respond and adapt to climate change. Sense of place was a unifying theme whenever the future of the South Carolina Lowcountry was discussed. The contribution of the South Carolina Lowcountry’s environmental wealth, rich cultural heritage, and quality of life to sense of place has important implications for how adaptation planning might best be pursued. More community-based governance of the commons (in other words, natural and cultural resources held in common), in which broad stakeholder participation and power sharing are key elements, is considered important. This devolution of governance is characterized by polycentric institutions and self-organizing social networks that promote a local culture of knowledge sharing, problem solving, and learning. These so-called bridging organizations (or individuals) often provide the leadership necessary to bring together potentially disparate Government agencies and institutions, private organizations, and individuals in a collective process of problem solving. Our observations also suggest that the conservation community in the South Carolina Lowcountry views its activities as integral to the broader governance of social-ecological systems, in which responses to the forces of global change are mediated through culture, economics, and politics. Rather than directly competing with other interests, the South Carolina Lowcountry conservation community seems to embrace an interpretation of conservation in which the fundamental objective is the quality of human life rather than environmental protection. Fundamental to the types of governance reforms described above is the notion of coproduction, in which experts and users collaborate to develop a shared body of knowledge. In this approach, scientists work with stakeholders to help frame questions, design research, and collect and analyze data. Such sustained collaborations are increasingly believed to be an effective way to produce useable (or actionable) science. The emphasis on social learning, leveraging strong social networks, coordinating and deliberating among diverse stakeholders, and applying principles of adaptive management is an essential contribution to adaptive capacity. The diverse and robust set of scientific approaches, methods to help stakeholders collaborate in effective and goal-driven planning processes, and decision tools resulting from this project hopefully will assist Cape Romain NWR and its partners prepare for climatic, ecological, and social changes over the coming decades.

South Carolina↗

Biomedical and veterinary science can increase our understanding of coral disease

A balanced approach to coral disease investigation is critical for understanding the global decline of corals. Such an approach should involve the proper use of biomedical concepts, tools, and terminology to address confusion and promote clarity in the coral disease literature. Investigating disease in corals should follow a logical series of steps including identification of disease, systematic morphologic descriptions of lesions at the gross and cellular levels, measurement of health indices, and experiments to understand disease pathogenesis and the complex interactions between host, pathogen, and the environment. This model for disease investigation is widely accepted in the medical, veterinary and invertebrate pathology disciplines. We present standard biomedical rationale behind the detection, description, and naming of diseases and offer examples of the application of Koch's postulates to elucidate the etiology of some infectious diseases. Basic epidemiologic concepts are introduced to help investigators think systematically about the cause(s) of complex diseases. A major goal of disease investigation in corals and other organisms is to gather data that will enable the establishment of standardized case definitions to distinguish among diseases. Concepts and facts amassed from empirical studies over the centuries by medical and veterinary pathologists have standardized disease investigation and are invaluable to coral researchers because of the robust comparisons they enable; examples of these are given throughout this paper. Arguments over whether coral diseases are caused by primary versus opportunistic pathogens reflect the lack of data available to prove or refute such hypotheses and emphasize the need for coral disease investigations that focus on: characterizing the normal microbiota and physiology of the healthy host; defining ecological interactions within the microbial community associated with the host; and investigating host immunity, host-agent interactions, pathology, pathogenesis, and factors that promote the pathogenicity of the causative agent(s) of disease.

Journal of Experimental Marine Biology and Ecology↗

FishStan: Hierarchical Bayesian models for fisheries

Fisheries managers and ecologists use statistical models to estimate population-level relations and demographic rates (e.g., length-maturity curves, growth curves, and mortality rates). These relations and rates provide insight into populations and inputs for other models. For example, growth curves may vary across lakes showing fish populations differ due to management actions or underlying environmental conditions. A fisheries manager could use this information to set lake-specific harvest limits or an ecologist could use this information to test scientific hypotheses about fish populations. The above example also demonstrates how populations exist within hierarchical structures where sub-populations may be nested within a meta-population. More generally, these hierarchical structures may be both biological (e.g., different lakes or river pools) and statistical (e.g., correlated error structures). Currently, limited options exist for fitting these hierarchical models and people seeking to use them often must program their own implementations. Furthermore, many fisheries managers and researchers may not have Bayesian programming skills, but many can use interactive languages such as R. Additionally, programs such as JAGS often require long run times (e.g., hours if not days) to fit hierarchical models and programs such as Stan can be more difficult to program because it is a compiled language. We created fishStan to share hierarchical models for fisheries and ecology in an easy-to-use R package.

Journal of Open Source Software↗

Contaminants in urban waters—Science capabilities of the U.S. Geological Survey

Streams and estuaries with urban watersheds commonly exhibit increased streamflow and decreased base flow; diminished stream-channel stability; excessive amounts of contaminants such as pesticides, metals, industrial and municipal waste, and combustion products; and alterations to biotic community structure. Collectively, these detrimental effects have been termed the “urban-stream syndrome.” Water-resource managers seek to lessen the effects on receiving water bodies of new urban development and remediate the effects in areas of existing urbanization. Similarly, the scientific community has produced extensive research on these topics, with researchers from the U.S. Geological Survey (USGS) leading many studies of urban streams and the processes responsible for the urban-stream syndrome. Increasingly, USGS studies are evaluating the effects of management and restoration activities to better understand how urban waters respond to the implementation of management practices. The USGS has expertise in collecting and interpreting data for many physical, chemical, and ecological processes in urban waters and, thus, provides holistic assessments to inform managers of urban water resources.

Fact Sheet↗

Ecological Investigations of the Federally Endangered Shivwits Milk-Vetch (Astragalus ampullarioides)--2006 Annual Report

Astragalus ampullarioides (Welsh) Welsh, the Shivwits milk-vetch, is an herbaceous perennial legume that was listed as federally endangered in September 2001. Known populations of this edaphic endemic species are restricted to Washington County, Utah, with the majority of occurrences found on gently sloping outcrops of the Triassic Petrified Forest Member of the Chinle Formation at the edge of the Mojave Desert. At the time of listing in 2001, surveys estimated a total of 1000 individuals for the species. In April-May 2006, surveys estimated approximately 4205 individuals distributed among six populations. Of the total number of individuals estimated in spring 2006, over 75 percent were distributed among three subpopulations in Zion National Park and approximately 60 percent occurred at a single 0.3-ha site in the Park. In addition to small population sizes and limited geographic distributions, the species is threatened to varying degrees by urbanization, livestock grazing, off-road vehicle use, and invasive exotic plants. In April 2006, the U.S. Geological Survey (USGS) initiated ecological investigations of the Shivwits milk-vetch to support conservation management and recovery of the species by the National Park Service (NPS; Zion National Park), the U.S. Fish and Wildlife Service (USFWS), the Bureau of Land Management (BLM), the Shivwits Band of the Paiute Tribe, and other cooperators such as The Nature Conservancy of Utah (TNC). To date, funding for this research has been provided by the Southwest Biological Science Center of the USGS Biological Resources Discipline, the USGS-NPS Park-Oriented Biological Support Project, and the Earth Surface Dynamics Program of the USGS Geologic Discipline. Additional logistical support has been provided by the Bureau of Land Management, Grand Staircase-Escalante National Monument. General objectives of this research are (1) to develop a better understanding of species-environment relations to support habitat modelling, future surveys for additional recovery populations, and potential efforts to establish new recovery populations; and (2) to evaluate effects of invasive exotic plants on habitat conditions and measures of milk-vetch performance. Specific objectives are to: Describe the distribution and abundance of milk-vetch populations and associated invasive exotic plant species within and outside of Zion National Park (Zion NP) in relation to geologic / geomorphic setting, soil properties, and plant community composition. In a field setting in Zion NP, conduct experiments to evaluate effects of invasive exotic plants on reproductive output and seedling establishment of A. ampullarioides across a gradient of exotic species biomass. Conduct greenhouse studies and analyze soils to evaluate effects of invasive exotic plants on soil biological properties (including mycorrhizal inocculation potential) that affect cycling and plant uptake of essential mineral nutrients. Based on environmental characteristics of known population locations, use Geographic Information System (GIS) tools to prepare a predictive habitat model that can be used to guide future surveys and efforts to evaluate sites for reintroduction efforts. This report describes 2006 progress and future plans for achieving these four objectives.

Open-File Report↗

Structured decision making and optimal bird monitoring in the northern Gulf of Mexico

The avian conservation community struggles to design and implement large scale, long-term coordinated bird monitoring programs within the northern Gulf of Mexico due to the complexity of the conservation enterprise in the region; this complexity arises from the diverse stakeholders, multiple jurisdictions, complex ecological processes, myriad habitats, and over 500 species of birds using the region for at least some part of their annual cycle. In addition, long-term monitoring over large spatial scales is difficult because of the need for monitoring data to both (1) evaluate management and restoration outcomes, and (2) provide reliable information about the status and trends of bird populations over time. To address these challenges, the Gulf of Mexico Avian Monitoring Network developed a problem statement: “How can a cost-effective monitoring strategy for the Gulf Coast bird community and ecosystem be developed that evaluates ongoing conservation activities and chronic and acute threats; maximizes learning; and is flexible and holistic enough to detect novel ecological threats and evaluate new and emerging conservation activities?” A structured decision-making framework was then used to articulate and quantify stakeholder values related to the problem statement. One use of the stakeholder values was to develop a regional, strategic plan for bird monitoring, which is presented elsewhere. A formal and complete decision support tool for conservation investments in monitoring and research guided by the stakeholder values is presented in this report. The technical aspects of the stakeholder value model and a portfolio analysis that could be used to guide decision making when allocating resources for monitoring activities is described. Whereas the decision analysis presented here could be useful to any decision maker faced with difficult choices about resource allocation, it is designed for decision makers who request monitoring study proposals and then determine which combination of proposals to fund. The portfolio decision support tool is designed to help funding agencies and organizations identify resource allocation strategies to maximize stated objectives. To begin the decision analysis, an objectives hierarchy and quantitative performance metrics from the values of the Gulf of Mexico bird conservation community were created by a panel of regional stakeholders. Each fundamental objective and sub-objective in the hierarchy is composed of several performance metrics. To test the decision support tool, the authors evaluated a combination of monitoring study proposals written for the region and simulated proposals. Each proposal was scored against the performance metrics and used multi-attribute utility theory to combine the multiple objectives into a measure of total monitoring benefit. The total monitoring benefit and costs of each proposal were then used in a constrained optimization routine to identify optimal monitoring portfolios, that is, a combination of activities that maximizes monitoring benefits while meeting cost and other constraints of interest to stakeholders. A graphical solution based on the concept of Pareto efficiency, which is useful in situations when cost constraints and exact budgets are not known, is also provided. Finally, an evaluation of the sensitivity of the decision-making framework to the weights assigned to objectives by stakeholders is included. This decision support tool allows decision makers to identify an optimal suite of monitoring proposals with a transparent portfolio analysis that includes user-defined constraints (such as costs).

Alabama, Florida, Louisiana, Mississippi, Texas↗

Natural resource condition assessment: Olympic National Park

The Natural Resource Assessment Program aims to document condition and trends of selected park resources while identifying emerging issues and information needs. This information is intended to serve as a platform for natural resource managers to use in developing future resource stewardship priorities and planning. Olympic National Park (OLYM) on Washington’s Olympic Peninsula protects remarkable examples of several Pacific Northwestern ecosystems, including the glacier-capped Olympic Mountains, oldgrowth temperate rainforests, pristine river systems, and wild Pacific coastline and islands. The park provides habitat for numerous plants and animals, including at least 16 animal and eight plant taxa endemic to the Olympic Peninsula. The park’s lakes and rivers support over 70 stocks of Pacific salmonids and 29 native freshwater fish species. The rocky intertidal community is one of the most complex and diverse shorelines in the United States. Although we conducted in-depth assessments on a limited number of resources, the general condition of several other physical and biological components of OLYM ecosystems is described in Chapter 2, along with an overview of park history and ecology. In Chapter 3, we describe how we chose our focal resources and measures, as well as our protocol for conducting the assessment. In Chapter 4, we provide a detailed assessment of each resource, with a summary of condition and trends. In Chapter 5, we further interpret and discuss the implications of each focal resource status, highlighting future areas for monitoring and research. We summarize the general findings from our assessments below.

Washington↗

Effects of flow diversion on Snake Creek and its riparian cottonwood forest, Great Basin National Park

Snake Creek flows east from the southern Snake Range in Nevada over complex lithology before leaving Great Basin National Park. The river travels over a section of karst limestone where some surface water naturally recharges the groundwater flow system. In 1961 a water diversion pipeline was constructed by downstream water users to transport surface water through the groundwater recharge zone to reduce potential water losses. The diversion pipeline dewaters a 5-km reach for most of the year by transporting water past the recharge zone then returning it to the channel downstream. Snake Creek was incorporated into the newly established Great Basin National Park in 1986, and today park managers and visitors are concerned that the diversion has destabilized Snake Creek’s riparian ecosystem in this arid region where it has high ecological value. The objectives of this study were to 1) document riparian cottonwood forest conditions in the pipeline-dewatered (DW) reach, 2) evaluate Snake Creek water availability and whether it can support a healthy riparian ecosystem, and 3) determine if dewatering has shifted the fluvial system into an unnatural and poorly functioning state. We pursued these ecohydrological study objectives in 11 research investigations of Snake Creek’s DW reach and nearby reference reaches. The research investigations analyzed: 1) riparian forest condition, tree age, growth, and death; 2) tree ring chronologies through time and space; 3) hydroclimatic drivers of tree growth; 4) stable carbon isotopes extracted from tree rings; 5) cottonwood ecophysiology related to water transport and water stress; 6) historical aerial photography; 7) stand-level riparian forest production; 8) groundwater availability as related to surface water and plant rooting zones; 9) near-surface geophysics using electrical resistivity imaging; 10) channel and valley geomorphology; and 11) in-channel wood jams caused by fallen trees. Integrating these diverse research topics provided a full perspective of historical and modern conditions along Snake Creek. We found that modern hydrological conditions in Snake Creek’s DW reach could not maintain the drought-sensitive ecosystem. The riparian cottonwoods ( Populus angustifolia and P. angustifolia x P. trichocarpa ) have experienced significant dieback. Tree mortality was 2.4 times higher in the DW reach than in reference reaches, and surviving trees supported only 60% of the live canopy compared to trees in reference reaches. Changes in the DW reach forest began in the 1960s and became more severe during the last two decades. Stable carbon isotope ratios and branch dieback analyses both demonstrated initial forest adjustments related to water stress beginning in the early 1960s. Tree ring width chronologies indicated two periods of growth decline in the DW relative to control reaches. The first decline in the 1960s represented an immediate adjustment to the modified flow regime, and the second decline in the 2000s demonstrated reduced resilience to atmospheric drought. Aerial photos and stand-level forest production calculations indicated that substantial riparian forest decline occurred in the 1990s–2010s in the DW reach compared to reference reaches. Stable carbon isotope ratios and leaf water potentials revealed that trees in the DW reach experienced greater drought stress than those in reference reaches. Monitoring wells and electrical resistivity surveys both showed riparian water tables to be largely supported by in-channel surface water flow, indicating that the flow diversion removed water that recharges alluvial groundwater and sustains riparian plants. Areas of widespread tree mortality in the DW reach also corresponded to a larger and more unstable channel with a high instream wood load from fallen trees. Modern conditions of Snake Creek in the DW reach robustly suggest that dewatering the river and its associated riparian corridor adversely affected the riparian ecosystem. The degraded condition is likely to persist and intensify unless water is returned to the channel. As we documented during the wet 1980s and the scientific literature suggest, a partial recovery of the riparian ecosystem is likely possible with restored flows.

Nevada↗