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At least 91 records · Page 5Linked to original sources
USGS2012

The Cottonwood Lake study area, a long-term wetland ecosystem monitoring site

The Cottonwood Lake study area is one of only three long-term wetland ecosystem monitoring sites in the prairie pothole region of North America; the other two are Orchid Meadows in South Dakota and St. Denis in Saskatchewan. Of the three, Cottonwood Lake has, by far, the longest continuous data-collection record. Research was initiated at the study area in 1966, and intensive investigations of the hydrology, chemistry, and biology of prairie pothole wetlands continue at the site today. This fact sheet describes the study area, provides an overview of wetland ecology research that has been conducted at the site in the past, and provides an introduction to current work being conducted at the study area by USGS scientists.

North Dakota↗
USGS2018

A method to detect discontinuities in census data

The distribution of pattern across scales has predictive power in the analysis of complex systems. Discontinuity approaches remain a fruitful avenue of research in the quest for quantitative measures of resilience because discontinuity analysis provides an objective means of identifying scales in complex systems and facilitates delineation of hierarchical patterns in processes, structure, and resources. However, current discontinuity methods have been considered too subjective, too complicated and opaque, or have become computationally obsolete; given the ubiquity of discontinuities in ecological and other complex systems, a simple and transparent method for detection is needed. In this study, we present a method to detect discontinuities in census data based on resampling of a neutral model and provide the R code used to run the analyses. This method has the potential for advancing basic and applied ecological research.

Ecology and Evolution↗
USGS2018

New global high-resolution centerlines dataset of selected river systems

We present the first high resolution (1:20,000) river centerlines shapefiles from 50 large rivers across the world. Rivers were selected based on the criteria of having more than 1000 km length and which have been reported to have a significant contribution to global fishery production. Since large rivers often span multiple countries, the degree of changes (i.e., anthropogenic or climate derived) varies from region to region. These high-resolution layers were developed to enable researchers to delineate accurate river length, from headwaters regions to their delta and assess or visualize the ongoing changes more accurately in these river systems. Further, these polylines could be used in coordination with satellite derived environmental or landscape variables for ecological research (e.g. predicting biodiversity, estimating biomass).

Data in Brief↗
USGS2021

Research to inform Caltrans best management practices for reptile and amphibian road crossings

In October of 2014, the U.S. Geological Survey (USGS) began a 5-year project to conduct research to inform Best Management Practices (BMPs) for amphibian and reptile crossing and barrier systems in California. To inform future conservation and transportation planning, this project involved identification of species at highest risk of negative road impacts, creation of geodatabase and spatial mapping tools that crosswalk with California Essential Habitat Connectivity Planning, and field research to address information gaps in the efficacy of reptile and amphibian passage and barrier systems. Per the agreement with California Department of Transportation (Caltrans; agreement 65A0553), this project was part of a broader collaborative effort between the Western Transportation Institute (WTI) of Montana State University and USGS Western Ecological Research Center (WERC). As part of this broader project, WTI conducted a worldwide literature review and gap analysis and produced the BMP manual for herpetofauna in California. WTI and USGS were contracted separately although we worked closely together throughout this broader effort and each brought particular expertise to the project. WTI has expertise in highways, the attributes of the highway environment, and has broad international experience with road ecology and herpetofauna connectivity systems worldwide. USGS WERC has expertise with California amphibian and reptile species and their ecology, study design and implementation, as well as expertise in landscape connectivity and road ecology.

California↗
USGS2022

Natives bite back! Are Burmese pythons beginning to encounter the resilience of the Everglades Ecosystem?

Burmese pythons ( Python bivittatus ) is a large, invasive reptile known in Florida for its devastating impacts on native species in the Greater Everglades Ecosystem. Several organizations and individuals are taking action to research and/or remove the snakes, including the U.S. Geological Survey (USGS). Since 2018, scientists from USGS’s Fort Collins Science Center have been working closely with the National Park Service (NPS) in Big Cypress National Preserve to use radiotelemetry and track Burmese pythons for various ecological research project and management (enabled by invaluable partnerships with the University of Florida and Zoo Miami). Over those years, we have encountered some incidental, but intriguing findings.

Florida↗
USGS2022

Errors in aerial survey count data: Identifying pitfalls and solutions

Accurate estimates of animal abundance are essential for guiding effective management, and poor survey data can produce misleading inferences. Aerial surveys are an efficient survey platform, capable of collecting wildlife data across large spatial extents in short timeframes. However, these surveys can yield unreliable data if not carefully executed. Despite a long history of aerial survey use in ecological research, problems common to aerial surveys have not yet been adequately resolved. Through an extensive review of the aerial survey literature over the last 50 years, we evaluated how common problems encountered in the data (including nondetection, counting error, and species misidentification) can manifest, the potential difficulties conferred, and the history of how these challenges have been addressed. Additionally, we used a double-observer case study focused on waterbird data collected via aerial surveys and an online group (flock) counting quiz to explore the potential extent of each challenge and possible resolutions. We found that nearly three quarters of the aerial survey methodology literature focused on accounting for nondetection errors, while issues of counting error and misidentification were less commonly addressed. Through our case study, we demonstrated how these challenges can prove problematic by detailing the extent and magnitude of potential errors. Using our online quiz, we showed that aerial observers typically undercount group size and that the magnitude of counting errors increases with group size. Our results illustrate how each issue can act to bias inferences, highlighting the importance of considering individual methods for mitigating potential problems separately during survey design and analysis. We synthesized the information gained from our analyses to evaluate strategies for overcoming the challenges of using aerial survey data to estimate wildlife abundance, such as digital data collection methods, pooling species records by family, and ordinal modeling using binned data. Recognizing conditions that can lead to data collection errors and having reasonable solutions for addressing errors can allow researchers to allocate resources effectively to mitigate the most significant challenges for obtaining reliable aerial survey data.

Alabama, Florida, Louisiana, Mississippi, Texas↗
USGS2018

Winter feeding of elk in the Greater Yellowstone Ecosystem and its effects on disease dynamics

Providing food to wildlife during periods when natural food is limited results in aggregations that may facilitate disease transmission. This is exemplified in western Wyoming where institutional feeding over the past century has aimed to mitigate wildlife–livestock conflict and minimize winter mortality of elk ( Cervus canadensis ). Here we review research across 23 winter feedgrounds where the most studied disease is brucellosis, caused by the bacterium Brucella abortus . Traditional veterinary practices (vaccination, test-and-slaughter) have thus far been unable to control this disease in elk, which can spill over to cattle. Current disease-reduction efforts are being guided by ecological research on elk movement and density, reproduction, stress, co-infections and scavengers. Given the right tools, feedgrounds could provide opportunities for adaptive management of brucellosis through regular animal testing and population-level manipulations. Our analyses of several such manipulations highlight the value of a research–management partnership guided by hypothesis testing, despite the constraints of the sociopolitical environment. However, brucellosis is now spreading in unfed elk herds, while other diseases (e.g. chronic wasting disease) are of increasing concern at feedgrounds. Therefore experimental closures of feedgrounds, reduced feeding and lower elk populations merit consideration.

Wyoming↗
USGS2019

Selecting ecological models using multi-objective optimization

Choices in ecological research and natural resource management require balancing multiple, often competing objectives. Examples include maximizing species persistence in a wildlife conservation context, while minimizing cost, or balancing opposing stakeholder objectives when managing wildlife populations. Multiple-objective optimization (MOO) provides a unifying framework for solving multiple objective problems. Model selection is a critical component of ecological inference and prediction and requires balancing the competing objectives of model fit and model complexity. The tradeoff between model fit and model complexity provides a basis for describing the model-selection problem within the MOO framework. We discuss MOO and two strategies for solving the MOO problem; modeling preferences pre-optimization and post-optimization. Most conventional model selection methods can be formulated as solutions of MOO problems via specification of pre-optimization preferences. We reconcile model selection within the MOO framework. We also consider model selection using post-optimization specification of preferences. That is, by first identifying Pareto optimal solutions, and then selecting among them. We demonstrate concepts with an ecological application of model selection using avian species richness data in the continental United States.

Ecological Modelling↗
USGS2017

Integrating count and detection–nondetection data to model population dynamics

There is increasing need for methods that integrate multiple data types into a single analytical framework as the spatial and temporal scale of ecological research expands. Current work on this topic primarily focuses on combining capture–recapture data from marked individuals with other data types into integrated population models. Yet, studies of species distributions and trends often rely on data from unmarked individuals across broad scales where local abundance and environmental variables may vary. We present a modeling framework for integrating detection–nondetection and count data into a single analysis to estimate population dynamics, abundance, and individual detection probabilities during sampling. Our dynamic population model assumes that site-specific abundance can change over time according to survival of individuals and gains through reproduction and immigration. The observation process for each data type is modeled by assuming that every individual present at a site has an equal probability of being detected during sampling processes. We examine our modeling approach through a series of simulations illustrating the relative value of count vs. detection–nondetection data under a variety of parameter values and survey configurations. We also provide an empirical example of the model by combining long-term detection–nondetection data (1995–2014) with newly collected count data (2015–2016) from a growing population of Barred Owl ( Strix varia ) in the Pacific Northwest to examine the factors influencing population abundance over time. Our model provides a foundation for incorporating unmarked data within a single framework, even in cases where sampling processes yield different detection probabilities. This approach will be useful for survey design and to researchers interested in incorporating historical or citizen science data into analyses focused on understanding how demographic rates drive population abundance.

Ecology↗
USGS2021

The spatial-temporal relationship of blue-winged teal to domestic poultry: Movement state modeling of a highly mobile avian influenza host

1. Migratory waterfowl facilitate long distance dispersal of zoonotic pathogens and are increasingly recognized as contributing to the geographic spread of avian influenza viruses (AIV). AIV are globally distributed and have the potential to produce highly contagious poultry disease, economically impact both large-scale and backyard poultry producers, and raise the specter of epidemics and pandemics in human populations. 2. Because migratory waterfowl behavior varies across multiple spatial and temporal scales, the timing and distribution of wild bird AIV introductions to poultry are also heterogeneous in time and space. To help reduce economic impacts to the poultry industry and enable poultry producers to better anticipate when and where poultry outbreaks may occur, it is critically important to consider the movement ecology of the waterfowl species transporting and transmitting AIV. 3. We used telemetry for a geographically widespread and common AIV host, blue-winged teal ( Spatula discors ; BWTE), to model reservoir host movement states with respect to backyard and commercial poultry facilities in the United States. Our modeling framework enabled us to estimate wild bird proximity to poultry facilities while concurrently assessing the influence of poultry facilities on BWTE movement state transition. Our primary objective was to estimate the likelihood of duck and poultry overlap by estimating when and where BWTE were geographically closest to poultry. 4. Synthesis and applications . Migratory waterfowl facilitate dispersal of the avian influenza viruses that cause highly contagious poultry disease. Movement analysis of blue-winged teal indicates that spatio-temporal overlap between wild birds and poultry facilities varies by season, the poultry type produced (e.g., turkey, chicken), and if the facility is a commercial or backyard operation. These findings are broadly applicable to disease ecology research and can be applied by poultry producers to improve bio-security, enhance poultry management, and prioritize disease surveillance efforts.

Journal of Applied Ecology↗
USGS2023

U.S. Geological Survey science to support wildlife disease management

Introduction The U.S. Geological Survey (USGS) serves a principal role in conducting wildlife disease outbreak investigations, surveillance, and ecological research to support management of diseases in free-ranging native wildlife. Approximately 60 percent of emerging human infectious diseases such as COVID-19, are zoonotic, meaning they are transmitted between animals and humans and 70 percent of these diseases originate in wildlife (Jones and others, 2008). The effects of emerging wildlife diseases are global and profound, often resulting in economic and agricultural impacts, declines in wildlife populations, and ecological disturbances.

Fact Sheet↗
USGS2011

Rapid diagnosis of avian influenza virus in wild birds: Use of a portable rRT-PCR and freeze-dried reagents in the field

Wild birds have been implicated in the spread of highly pathogenic avian influenza (HPAI) of the H5N1 subtype, prompting surveillance along migratory flyways. Sampling of wild birds for avian influenza virus (AIV) is often conducted in remote regions, but results are often delayed because of the need to transport samples to a laboratory equipped for molecular testing. Real-time reverse transcriptase polymerase chain reaction (rRT-PCR) is a molecular technique that offers one of the most accurate and sensitive methods for diagnosis of AIV. The previously strict lab protocols needed for rRT-PCR are now being adapted for the field. Development of freeze-dried (lyophilized) reagents that do not require cold chain, with sensitivity at the level of wet reagents has brought on-site remote testing to a practical goal. Here we present a method for the rapid diagnosis of AIV in wild birds using an rRT-PCR unit (Ruggedized Advanced Pathogen Identification Device or RAPID, Idaho Technologies, Salt Lake City, UT) that employs lyophilized reagents (Influenza A Target 1 Taqman; ASAY-ASY-0109, Idaho Technologies). The reagents contain all of the necessary components for testing at appropriate concentrations in a single tube: primers, probes, enzymes, buffers and internal positive controls, eliminating errors associated with improper storage or handling of wet reagents. The portable unit performs a screen for Influenza A by targeting the matrix gene and yields results in 2-3 hours. Genetic subtyping is also possible with H5 and H7 primer sets that target the hemagglutinin gene. The system is suitable for use on cloacal and oropharyngeal samples collected from wild birds, as demonstrated here on the migratory shorebird species, the western sandpiper (Calidrus mauri) captured in Northern California. Animal handling followed protocols approved by the Animal Care and Use Committee of the U.S. Geological Survey Western Ecological Research Center and permits of the U.S. Geological Survey Bird Banding Laboratory. The primary advantage of this technique is to expedite diagnosis of wild birds, increasing the chances of containing an outbreak in a remote location. On-site diagnosis would also prove useful for identifying and studying infected individuals in wild populations. The opportunity to collect information on host biology (immunological and physiological response to infection) and spatial ecology (migratory performance of infected birds) will provide insights into the extent to which wild birds can act as vectors for AIV over long distances.

Journal of Visualized Experiments↗
USGS2000

Ecotoxicology of Amphibians and Reptiles

For many years, ecological research on amphibians and reptiles has lagged behind that of other vertebrates such as fishes, birds, and mammals, despite the known importance of these animals in their environments. The lack of study has been particularly acute in the he area of ecotoxicology where the number of published scientific papers is a fraction of that found for the other vertebrate classes. Recently, scientists have become aware of severe crises among amphibian populations, including unexplained and sudden extinctions, worldwide declines, and hideous malformations. In many of these instances, contaminants have been listed as probable contributors. Data on the effects of contaminants on reptiles are so depauperate that even the most elementary interpretations are difficult. This state-of-the-science review and synthesis of amphibian and reptile ecotoxicology demonstrates the inter-relationships among distribution, ecology, physiology, and contaminant exposure, and interprets these topics as they pertain to comparative toxicity, population declines, malformations, and risk assessment . In this way, the book identifies and serves as a basis for the most pressing research needs in the coming years. The editors have invited 27 other internationally respected experts to examine the state of existing data in specific areas, interpret it in light of current problems, and identify research gaps and needs. Through its emphasis on recent research, extensive reviews and synthesis, Ecotoxicology of Amphibians and Reptiles will remain a definitive reference work well into the new century.

SETAC Technical Publications Series.↗
USGS2012

Matrix population models from 20 studies of perennial plant populations

Demographic transition matrices are one of the most commonly applied population models for both basic and applied ecological research. The relatively simple framework of these models and simple, easily interpretable summary statistics they produce have prompted the wide use of these models across an exceptionally broad range of taxa. Here, we provide annual transition matrices and observed stage structures/population sizes for 20 perennial plant species which have been the focal species for long-term demographic monitoring. These data were assembled as part of the "Testing Matrix Models" working group through the National Center for Ecological Analysis and Synthesis (NCEAS). In sum, these data represent 82 populations with >460 total population-years of data. It is our hope that making these data available will help promote and improve our ability to monitor and understand plant population dynamics.

Ecology↗
USGS2013

ʻŌhiʻa Lehua rainforest: born among Hawaiian volcanoes, evolved in isolation: the story of a dynamic ecosystem with relevance to forests worldwide

In the early 1970s, a multidisciplinary team of forest biologists began a study of Hawaiian ecosystems under the International Biological Program (IBP). Research focus was on the intact native ecosystems in and around Hawai'i Volcanoes National Park, in particular the ʻŌhiʻa Lehua rainforest. Patches of dead ʻŌhiʻa stands had been reported from the windward slopes of Mauna Loa and Mauna Kea. Subsequent air photo analyses by a team of US and Hawai'i State foresters discovered rapidly spreading ʻŌhiʻa dieback, also called ʻŌhiʻa forest decline. A killer disease was suspected to destroy the Hawaiian rain forest in the next 15-25 years. Ecological research continued with a focus on the dynamics of the Hawaiian rainforest. This book explains what really happened and why the ʻŌhiʻa rainforest survived in tact as everyone can witness today.

Hawai'i↗
USGS2017

Culturally induced range infilling of eastern redcedar: a problem in ecology, an ecological problem, or both?

The philosopher John Passmore distinguished between (1) “problems in ecology,” or what we might call problems in scientific understanding of ecological change, and (2) “ecological problems,” or what we might call problems faced by societies due to ecological change. The spread of eastern redcedar ( Juniperus virginiana ) and conversion of the central and southern Great Plains of North America to juniper woodland might be categorized as a problem in ecology, an ecological problem, or both. Here, we integrate and apply two interdisciplinary approaches to problem-solving—social-ecological systems thinking and ecocriticism—to understand the role of human culture in recognizing, driving, and responding to cedar’s changing geographic distribution. We interpret the spread of cedar as a process of culturally induced range infilling due to the ongoing social-ecological impacts of colonization, analyze poetic literary texts to clarify the concepts that have so far informed different cultural values related to cedar, and explore the usefulness of diverse interdisciplinary collaborations and knowledge for addressing social-ecological challenges like cedar spread in the midst of rapidly unfolding global change. Our examination suggests that it is not only possible, but preferable, to address cedar spread as both a scientific and a social problem. Great Plains landscapes are teetering between grassland and woodland, and contemporary human societies both influence and choose how to cope with transitions between these ecological states. We echo previous studies in suggesting that human cultural values about stability and disturbance, especially cultural concepts of fire, will be primary driving factors in determining future trajectories of change on the Great Plains. Although invasion-based descriptors of cedar spread may be useful in ecological research and management, language based on the value of restraint could provide a common vocabulary for effective cross-disciplinary and interdisciplinary communication about the relationship between culture and cedar, as well as an ethical framework for cross-cultural communication, decision-making, and management.

Ecology and Society↗
USGS2017

Seventy-five years of vegetation treatments on public rangelands in the Great Basin of North America

On the Ground Land treatments occurring over millions of hectares of public rangelands in the Great Basin over the last 75 years represent one of the largest vegetation manipulation and restoration efforts in the world. The ability to use legacy data from land treatments in adaptive management and ecological research has improved with the creation of the Land Treatment Digital Library (LTDL), a spatially explicit database of land treatments conducted by the U.S. Bureau of Land Management. The LTDL contains information on over 9,000 confirmed land treatments in the Great Basin, composed of seedings (58%), vegetation control treatments (24%), and other types of vegetation or soil manipulations (18%). The potential application of land treatment legacy data for adaptive management or as natural experiments for retrospective analyses of effects of land management actions on physical, hydrologic, and ecologic patterns and processes is considerable and just beginning to be realized.

California, Idaho, Nevada, Oregon, Utah↗
USGS2019

Sampling and analysis frameworks for inference in ecology

1. Reliable statistical inference is central to ecological research, much of which seeks to estimate population attributes and their interactions. The issue of sampling design and its relationship to inference has become increasingly important due to rapid proliferation of modeling methodology (line transect modeling, capture-recapture, estimation of occurrence, model selection procedures, hierarchical modeling) and new sampling approaches (adaptive sampling, other specialized designs). It is important for ecologists using these advanced methods to be aware of how the linkages between sample selection and data analysis can potentially affect inference. 2. We examine design-based and model-based inference frameworks for ecological data collected randomly, purposively, or opportunistically. We elucidate differences in the probability structures for data arising from these frameworks, clarify the assumptions that underlie them, and demonstrate their differences. 3. Design-based inference builds on a probability structure inherited from randomized data collection, whereas model-based inference relies on an assumed stochastic model of the data. By itself, a design-based approach is of limited value for inferences about causal hypotheses. In contrast, model-based inference is dependent on a conditionality principle that can seldom be shown to be met for an ecological system. We describe the conditions under which one can safely ignore sampling design in model-based analysis, along with inferential implications if these conditions are not met. The special case of opportunistic sampling is discussed. 4. We present a combined framework that takes advantage of both approaches to inference, and provides a robust methodology that can deal with the modeling of sampling problems such as nondetection and misclassification, as well as the exploration of causal hypotheses. The combined framework can be useful for identifying optimal sampling strategies. 5. Each approach to inference has its strengths and weaknesses, and practitioners should be aware of these in order to tailor designs and analyses to specific questions. We use the approaches and their underlying rationales to provide guidelines for choosing designs and estimators for reliable inference.

Methods in Ecology and Evolution↗