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At least 1,531 records · Page 85Linked to original sources
USGS2012

Enterococci in the environment

Enterococci are common, commensal members of gut communities in mammals and birds, yet they are also opportunistic pathogens that cause millions of human and animal infections annually. Because they are shed in human and animal feces, are readily culturable, and predict human health risks from exposure to polluted recreational waters, they are used as surrogates for waterborne pathogens and as fecal indicator bacteria (FIB) in research and in water quality testing throughout the world. Evidence from several decades of research demonstrates, however, that enterococci may be present in high densities in the absence of obvious fecal sources and that environmental reservoirs of these FIB are important sources and sinks, with the potential to impact water quality. This review focuses on the distribution and microbial ecology of enterococci in environmental (secondary) habitats, including the effect of environmental stressors; an outline of their known and apparent sources, sinks, and fluxes; and an overview of the use of enterococci as FIB. Finally, the significance of emerging methodologies, such as microbial source tracking (MST) and empirical predictive models, as tools in water quality monitoring is addressed. The mounting evidence for widespread extraenteric sources and reservoirs of enterococci demonstrates the versatility of the genus Enterococcus and argues for the necessity of a better understanding of their ecology in natural environments, as well as their roles as opportunistic pathogens and indicators of human pathogens.

Microbiology and Molecular Biology Reviews↗
USGS2024

Benthic community metrics track hydrologically stressed mangrove systems

Mangrove restoration efforts have increased in order to help combat their decline globally. While restoration efforts often focus on planting seedlings, underlying chronic issues, including disrupted hydrological regimes, can hinder restoration success. While improving hydrology may be more cost-effective and have higher success rates than planting seedlings alone, hydrological restoration success in this form is poorly understood. Restoration assessments can employ a functional equivalency approach, comparing restoration areas over time with natural, reference forests in order to quantify the relative effectiveness of different restoration approaches. Here, we employ the use of baseline community ecology metrics along with stable isotopes to track changes in the community and trophic structure and enable time estimates for establishing mangrove functional equivalency. We examined a mangrove system impacted by road construction and recently targeted for hydrological restoration within the Rookery Bay National Estuarine Research Reserve, Florida, USA. Samples were collected along a gradient of degradation, from a heavily degraded zone, with mostly dead trees, to a transition zone, with a high number of saplings, to a full canopy zone, with mature trees, and into a reference zone with dense, mature mangrove trees. The transition, full canopy, and reference zones were dominated by annelids, gastropods, isopods, and fiddler crabs. Diversity was lower in the dead zone; these taxa were enriched in 13 C relative to those found in all the other zones, indicating a shift in the dominant carbon source from mangrove detritus (reference zone) to algae (dead zone). Community-wide isotope niche metrics also distinguished zones, likely reflecting dominant primary food resources (baseline organic matter) present. Our results suggest that stable isotope niche metrics provide a useful tool for tracking mangrove degradation gradients. These baseline data provide critical information on the ecosystem functioning in mangrove habitats following hydrological restoration.

Florida↗
USGS2025

The Grouse & Grazing Project: Effects of cattle grazing on demographic traits of greater sage-grouse

Greater sage-grouse (Centrocercus urophasianus) were once widespread within sagebrush -grassland ecosystems of western North America, but populations have declined since the mid-1960s. Though sage-grouse were not listed as threatened or endangered under the Endangered Species Act (ESA), when examined in 2015, they remain a species of interest and concern. Roughly half of the sage-grouse’s remaining habitat is on federal land, most of it managed by the Bureau of Land Management (BLM) and the U.S. Forest Service (USFS). Livestock grazing is the most extensive land use within sage-grouse habitat and the effects of livestock grazing on sage-grouse are often debated. The extensive decade-long research project summarized in this report was initiated to provide rigorous experimental research to inform the debate regarding the relationship between livestock grazing and sage-grouse. In 2012, the Idaho Grouse & Grazing Project was started with several partners including the University of Idaho, BLM, Idaho Department of Fish and Game (IDFG), and other partners to evaluate the effects of cattle grazing on sage-grouse vital rates. Many additional supporters have provided resources to this research effort including the Public Lands Council, Idaho Cattle Association, Idaho Governor’s Office of Species Conservation, Western Association of Fish & Wildlife Agencies, U.S. Fish and Wildlife Service, USFS, and numerous grazing associations and ranchers in Idaho. This 10-year research project was a scientifically rigorous and replicated experiment, occurring across five study sites in Idaho. This document is intended to provide a summary of the findings of this unprecedented study. Annual reports are available on the project’s website: https://idahogrousegrazing.org and scientific papers are being prepared and submitted to journals. The project focused on the influence of spring cattle grazing on sage-grouse vital rates across five study sites in Idaho including 21 BLM grazing pastures. From 2014-2023, we captured 1,343 grouse, documented the fate of 1,285 nests, and tracked 399 broods. Vegetation was characterized at 4,777 plots and grazing utilization levels were recorded at >30,000 locations. Because insects are an important food source for sage-grouse hens and their chicks, insect biomass and diversity were also examined in this study. We collected arthropods in 12,151 pitfall samples and 6,217 sweep-net samples across 786 plots within our five study sites. At each study site, three or four grazing treatments were implemented after two years of pre-treatment field investigations. These controlled cattle grazing treatments included spring-grazing in even years, spring-grazing in odd years, spring-and-fall grazing in alternating years, and a no grazing (or rested) control. Once grazing treatments were implemented at a study site, we measured sage-grouse demographic traits for 4-8 years post-treatment. Stocking rate (grazing intensity) was assessed across pastures each year and was influenced by vegetation communities, topography, and water sources. Grazed pastures exhibited lower grass cover and height compared to the no grazing pastures, and the extent of this difference varied based on annual precipitation levels. Rested pastures maintained higher grass cover and grass height, but the differences in habitat structure did not consistently translate to differences in sage-grouse demographic traits. Apparent nesting success varied annually and by site, ranging from 24% to 44% over the study period. Like some other studies, results from this research show that successful (i.e., hatched) sage-grouse nests have taller grass heights than failed nests. The average grass height surrounding successful nests in grazed pastures was shorter than that surrounding successful nests in non-grazed (i.e., rested) pastures. It is well documented that grazing reduces grass height, and these observations have led to widely held assumptions that livestock grazing reduces grass height which negatively affects sage-grouse nesting habitat. At the pasture scale, this study has found that sage-grouse nesting success is no greater in pastures that were rested for 4-8 years than those currently or recently grazed. This study gives no indication that removing cattle from pastures affected nesting success. We found some evidence that nest density varied among the grazing treatments, but we did not see compelling evidence of increases in density of nesting hens following cessation of grazing in the no grazing treatments. Brood survival varied by site and year but showed no strong effect of grazing treatment. Climatic conditions, particularly drought in 2021, had a greater effect on brood survival than grazing metrics. We also found no differences in hen survival among the grazing treatments. Results of this study suggest that hens nesting in spring and fall grazed pastures had similar or even slightly higher brood survival than hens in the rested pastures or the spring grazed pastures. Arthropod biomass and species diversity varied among our study sites and the differences between grazed and rested pastures also varied among study sites. Average biomass and diversity of arthropods was higher in the spring grazed pastures on two of three sites examined but higher in the rested pastures on the other site examined. Some taxa of arthropods were more abundant in grazed pastures while other taxa were more abundant in rested pastures. For example, Carabidae (Ground Beetles) and Formicidae (Ants) had higher biomass in grazed pastures, while Tenebrionidae (Darkling Beetles) and Acrididae (Grasshoppers) had higher biomass in non-grazed pastures. Results indicate that grazing effects on arthropod biomass and arthropod diversity are study site-dependent, suggesting a need to better quantify the most important prey taxa for sage-grouse chicks and to better control for other factors that influence arthropod abundance. Based on results of this research, livestock grazing, when properly managed, does not appear to negatively impact sage-grouse nest survival or brood success. This study provides critical insights for land managers balancing livestock production with sage-grouse conservation, supporting adaptive grazing strategies that maintain both economic and ecological objectives.

Idaho↗
USGS2000

Ecotoxicology of wild mammals

An international group of 32 scientists has critically reviewed the scientific literature on exposure and effects of environmental contaminants in wild mammals. Although the absolute number of toxicological studies in domesticated and wild mammals eclipses that for birds, a detailed examination of scientific publications and databases reveal that information for 'wild' birds is actually greater than that for 'wild' mammals. Of the various taxa of mammals, ecotoxicological data is most noticeably lacking for marsupials and monotremes. In contrast, rodents (comprising 43% of all mammal species) have been studied extensively, despite evidence of their tolerance to some organochlorine compounds, rodenticides, and even radionuclides. Mammalian species at greatest risk of exposure include those that consume a high percentage of their body weight on a daily basis (e.g., shrews, moles and bats). Aquatic mammals tend to bioaccumulate tremendous burdens of lipophilic contaminants, although storage in their fat depots may actually limit toxicity. Carnivores appear to be more sensitive to adverse effects of environmental contaminants than herbivores. Remarkably few of the thousands of compounds manufactured worldwide have been toxicologically evaluated in wild mammals, and concentrations of even fewer have been monitored in tissues. Overarching research needs include: development of new exposure/effects models and better methods for estimation of species sensitivities; generation of comparative data on contaminant bioavailability, sublethal responses and detoxication mechanisms; enhanced understanding of pesticide, industrial contaminant and metal interactions; identification of endocrine disruptive contaminants and their overall ecological significance; and finally, estimating the relative contribution of environmental contamination as a factor affecting wild mammal populations.

Society of Environmental Toxicology and Chemistry,↗
USGS2000

Protection of fish spawning habitat for the conservation of warm-temperature reef-fish fisheries of shelf-edge reefs of Florida

We mapped and briefly describe the surficial geology of selected examples of shelf-edge reefs (50–120 m deep) of the southeastern United States, which are apparently derived from ancient Pleistocene shorelines and are intermittently distributed throughout the region. These reefs are ecologically significant because they support a diverse array of fish and invertebrate species, and they are the only aggregation spawning sites of gag ( Mycteroperca microlepis ), scamp ( M. phenax ), and other economically important reef fish. Our studies on the east Florida shelf in the Experimental Oculina Research Reserve show that extensive damage to the habitat-structuring coral Oculina varicosa has occurred in the past, apparently from trawling and dredging activities of the 1970s and later. On damaged or destroyed Oculina habitat, reef-fish abundance and diversity are low, whereas on intact habitat, reef-fish diversity is relatively high compared to historical diversity on the same site. The abundance and biomass of the economically important reef fish was much higher in the past than it is now, and spawning aggregations of gag and scamp have been lost or greatly reduced in size. On the west Florida shelf, fishers have concentrated on shelf-edge habitats for over 100 yrs, but fishing intensity increased dramatically in the 1980s. Those reefs are characterized by low abundance of economically important species. The degree and extent of habitat damage there is unknown. We recommend marine fishery reserves to protect habitat and for use in experimentally examining the potential production of unfished communities.

Florida↗
USGS2000

Protection of fish spawning habitat for the conservation of warm temperate reef fish fisheries of shelf-edge reefs of Florida

We mapped and briefly describe the surficial geology of selected examples of shelf-edge reefs (50–120 m deep) of the southeastern United States, which are apparently derived from ancient Pleistocene shorelines and are intermittently distributed throughout the region. These reefs are ecologically significant because they support a diverse array of fish and invertebrate species, and they are the only aggregation spawning sites of gag ( Mycteroperca microlepis ), scamp ( M. phenax ), and other economically important reef fish. Our studies on the east Florida shelf in the Experimental Oculina Research Reserve show that extensive damage to the habitat-structuring coral Oculina varicosa has occurred in the past, apparently from trawling and dredging activities of the 1970s and later. On damaged or destroyed Oculina habitat, reef-fish abundance and diversity are low, whereas on intact habitat, reef-fish diversity is relatively high compared to historical diversity on the same site. The abundance and biomass of the economically important reef fish was much higher in the past than it is now, and spawning aggregations of gag and scamp have been lost or greatly reduced in size. On the west Florida shelf, fishers have concentrated on shelf-edge habitats for over 100 yrs, but fishing intensity increased dramatically in the 1980s. Those reefs are characterized by low abundance of economically important species. The degree and extent of habitat damage there is unknown. We recommend marine fishery reserves to protect habitat and for use in experimentally examining the potential production of unfished communities.

Florida↗
USGS2023

Effects of sucker gigging on fish populations in Oklahoma scenic rivers

Suckers (Catostomidae) are ecologically important, and some support popular fisheries, despite not being considered ‘sport fish’ in most states. Gigging suckers is a popular and culturally significant pastime in the Ozark Highlands, but little is known about the effect of gigging harvest on population dynamics of suckers. Therefore, research is needed to determine safe levels of sucker harvest that ensure sustainability of sucker gigging and protect overall ecosystem function. The objectives of this study were to: 1) determine the spatial distribution of common sucker species during spawning season (when sucker gigging is most effective), 2) determine the population size, age structure , and total mortality rate for common sucker species, and 3) model the effects of different harvest rates on sucker populations to determine the harvest rate at which growth overfishing and recruitment overfishing begin. Suckers were sampled using electrofishing, modified fyke netting, gillnetting, hoop netting, and seining and marked with passive integrated transponder (PIT) tags to provide information about population size, demographics, and coarse-scale movement patterns. A subset of fish sampled using the above gears and additional fish collected during gigging tournaments in 2017-2019 and 2021-2022 (no tournament was held in 2020) were used for age analyses. Tournament data collected prior to the initiation of this project were obtained from the state agency. Data from gigging tournaments indicated Golden Redhorse Moxostoma erythrurum, Black Redhorse M. duquesnei, White Sucker Catostomus commersonii, and Spotted Sucker Minytrema melanops were vulnerable to gigging harvest. Selection by giggers for larger individuals was apparent for all species except Golden Redhorse in 2019. Spotted Suckers constituted most fish harvested, but the proportion of each species harvested still varied among years. A total of 943 fish were aged from samples obtained from 2017 to 2022 and results from subsequent analyses indicated a high degree of variation in growth rates within and among species. Over 4,700 suckers were tagged with PIT tags and over 400 recaptures of these tagged fish were made since autumn 2018. Preliminary analyses indicate survival was consistent across samples and species, and detection rates varied by sampling event (3-month periods). Our most likely top multistrata model suggested that a large portion of fish within the upper Spavinaw, lower Spavinaw, and reservoir sections remain in these locations year-round (means: 0.46 – 0.67). Despite this, transition probabilities are still high for movement from upper Spavinaw to lower Spavinaw (mean: 0.32) and from lower Spavinaw to upper Spavinaw (mean: 0.38). Likewise, transition probabilities were high for movement from lower Spavinaw to the reservoir (mean: 0.15) and from the reservoir to lower Spavinaw (mean: 0.32). Transition probabilities between upper Spavinaw and the reservoir were low in both directions (means < 0.01). Population sizes, growth trajectories and length-weight relationships varied among species. Preliminary harvest models suggest species-specific regulation may be scientifically appropriate; however, it may be difficult for giggers to identify species while gigging. Based on our model results, there appears to be little risk of recruitment or growth overfishing for any species at current exploitation levels.

Oklahoma↗
USGS1974

New concepts regarding the production of waterfowl and other game birds in areas of diversified agriculture

Many concepts regarding breeding ecology of waterfowl and the influences of environmental factors on annual production have changed in the past 20 years. These influences are especially pronounced in the prairie region of central North America where agriculture becomes more intensive each year. The principal task assigned to this Research Center when established in 1965 was to determine the relative impact of these influences on production and to identify those facets of breeding biology, nesting habitat requirements and other factors that may be altered to increase production on lands dedicated for this purpose. A corollary objective was to develop methods for enhancing production of waterfowl and other ground-nesting birds on private lands in agricultural areas. Some of the highlights of our findings to date, together with the results from current work of others, provide new information on waterfowl that indicates: (1) homing instincts are not as specific as indicated by earlier workers, (2) there are differences in pioneering between species, sexes and age classes, (3) strength and duration of pair bonds vary by species and age classes, (4) territorial tolerances for most species are greater than previously indicated, (5) there is differential productivity by age classes in some species, (6) there has been a gradual decline in nesting success in the prairie region the past 30 years, (7) adverse influences of intensive agriculture are increasing, (8) mammalian predation is an important factor, (9) high quality, secure nesting habitat and a complex of wetland types are the essential components of an optimum production unit, (10) the size and shape of blocks of nesting cover are important management considerations, (11) overharvest of local breeding populations is becoming a serious problem in some areas. Each of these subjects is discussed as related to research objectives and current management problems. Recommendations are presented for obtaining maximum production of waterfowl and other game birds on public and private lands in agricultural areas.

Book chapter↗
USGS2017

A synthesis of thresholds for focal species along the U.S. Atlantic and Gulf Coasts: A review of research and applications

The impacts from climate change are increasing the possibility of vulnerable coastal species and habitats crossing critical thresholds that could spur rapid and possibly irreversible changes. For species of high conservation concern, improved knowledge of quantitative thresholds could greatly improve management. To meet this need, we synthesized information pertaining to biological responses as tipping points to sea level rise (SLR) and coastal storms for 45 fish, wildlife, and plant species along the U.S. Atlantic and Gulf Coasts and Caribbean through a literature review and expert elicitation. Although these species were selected based on their ecological, economic, and cultural importance, just over half (56%, n = 25) have quantitative threshold data currently available that can be used to assess the effects of SLR and storms during some aspect of their life history. Birds, reptiles, and plants represent the best studied coastal species. Thirteen of the species (29%) are projected to lose at least 50% of their population or habitat (e.g., foraging, nesting, spawning, or resting habitat) in some areas with a 0.5 m or greater rise in sea levels by 2100. Two species (a bird and reptile) may gain habitat from projected SLR and be resilient to future impacts. Numeric thresholds were not available for the remaining 20 species we searched for. Coastal fishes, mammals, and amphibians were among the groups representing a major information gap in this field of research. In addition, quantitative threshold responses to coastal storms were scarce for all taxa. While vulnerability assessments and qualitative research related to the impacts of SLR and storms on coastal species and habitats are increasing, work that incorporates quantitative thresholds as response and impact metrics remains limited. Additional monitoring, modeling, and research that provides multiple quantitative thresholds across species' life stages and/or latitudinal gradients is ideal to support robust coastal management and decision-making across spatio-temporal scales in the face of climate change.

Ocean and Coastal Management↗
USGS2002

Ecological dynamics of wetlands at Lisbon Bottom, Big Muddy National Fish and Wildlife Refuge, Missouri

The study documented the interaction between hydrology and the biological dynamics within a single spring season at Lisbon Bottom in 1999. The study goal was to provide information necessary for resource managers to develop management strategies for this and other units of the Big Muddy National Fish and Wildlife Refuge. Researchers studied the hydrology, limnology, and biological dynamics of zooplankton, macroinvertebrates, fish and waterbird communities. Lisbon Bottom is one of several parcels of 1993 flood-damaged land that was purchased from willing sellers by the U.S. Fish and Wildlife Service as part of the Big Muddy National Fish and Wildlife Refuge. Lisbon Bottom is a loop bend in the river near Glasgow in Howard County, Missouri between approximately river mile (RM) 213 to RM 219. Flooding at Lisbon in 1993 and 1995 breeched local levees and created a diverse wetland complex.

Missouri↗
USGS1996

Developing a temporal database of urban development for the Baltimore/Washington region

The U.S. Geological Survey (USGS), the University of Maryland Baltimore County (UMBC), and the U.S. Bureau of the Census are working together as a multiagency, multidisciplinary team in developing a temporal database that documents the growth of the Baltimore-Washington metropolitan region. This database consists of urban development, principal transportation, shoreline, and population density change. The urban development theme, considered a primary data layer in the study of urban land transformation resulting from human impact on the land, is the focus of this paper. The Baltimore-Washington Spatial Dynamics and Human Impacts Study builds on earlier research efforts that mapped urban land use change for the San Francisco Bay area (Acevedo and Bell, 1994; Bell and others, 1995; Kirtland and others, 1994). In developing a temporal database (Acevedo and others, in press), the team participants hope to provide data that can be used to study patterns of urban growth; assess ecological, environmental, and climatic impacts of urban change; and model and predict future urbanization patterns and impacts (Clarke and others, 1996). Both the San Francisco and Baltimore-Washington regions were selected because of the rapid urban growth and resulting impacts on their ecosystems. The Chesapeake Bay region in particular has undergone extensive environmental agitation due to the hydrologic problems that have arisen from the increase in impermeable surfaces and structures, that is buildings and pavement that physically cover the soil. Because of the inability of water to percolate into the ground, little purification occurs by filtration. Water runs over paved surfaces and quickly washes high levels of toxins directly into the water system. Toxins like gasoline, oil, and fertilizer have dramatically affected the local streams, rivers, and the bay. ABSTRACT The U.S. Geological Survey, the University of Maryland Baltimore County, and the U.S. Bureau of the Census are developing a temporal database to study urban development in the Baltimore-Washington region. The primary data layer, the extent of urban or built-up areas, was compiled using a geographic information system and historical maps, remotely sensed data, digital land use data, and census information from a variety of sources. Urban land use change has been documented by the Baltimore-Washington Spatial Dynamics & Human Impact Study Team for the last 200 years. The methods, definitions, and collection criteria used to define urban or built-up areas were developed by a multi-disciplinary team that also ensures consistency in collection techniques and documentation methods for subsequent application in other regions. Animation techniques were used to visualize the database and to document the evolution of the region's urban landscape. The database is an important tool to urban and regional planners, ecologists, and global change researchers for measuring trends in urban sprawl, analyzing patterns of water pollution, understanding the impacts of development on ecosystems, and developing predictive modeling techniques to better forecast areas of urban growth. This paper describes the techniques used to map the extent of urban areas for Phase I and does not discuss Phase II in detail because the work is still in progress. In this study, urban development is defined as areas of intensive use, with much of the land covered by structures. The built-up areas are characterized by the existence of a systematic street pattern, and the relative concentration of buildings and associated intensive use areas, such as parking lots. Using this definition, urban development does not refer to political boundaries and may include incorporated or unincorporated areas as well as military reservations. ABSTRACT The U.S. Geological Survey, the University of Maryland Baltimore County, and the U.S. Bureau of the Census are developing a temporal database to study urban development in the Baltimore-Washington region. The primary data layer, the extent of urban or built-up areas, was compiled using a geographic information system and historical maps, remotely sensed data, digital land use data, and census information from a variety of sources. Urban land use change has been documented by the Baltimore-Washington Spatial Dynamics & Human Impact Study Team for the last 200 years. The methods, definitions, and collection criteria used to define urban or built-up areas were developed by a multi-disciplinary team that also ensures consistency in collection techniques and documentation methods for subsequent application in other regions. Animation techniques were used to visualize the database and to document the evolution of the region's urban landscape. The database is an important tool to urban and regional planners, ecologists, and global change researchers for measuring trends in urban sprawl, analyzing patterns of water pollution, understanding the impacts of development on ecosystems, and developing predictive modeling techniques to better forecast areas of urban growth. To build the urban component of the temporal database, a multidisciplinary team was assembled and a phased approach initiated. Expanding on procedures developed for the San Francisco Regional Study (Bell and others, 1995), the team developed data definitions, a classification scheme, compilation criteria, mapping specifications, guidelines for source materials, and metadata specifications to support development of a logically consistent dataset. Extensive documentation procedures were established to ensure consistency in data collection, and for subsequent application to other regions. Phase II was the implementation of the regional mapping effort. ABSTRACT The U.S. Geological Survey, the University of Maryland Baltimore County, and the U.S. Bureau of the Census are developing a temporal database to study urban development in the Baltimore-Washington region. The primary data layer, the extent of urban or built-up areas, was compiled using a geographic information system and historical maps, remotely sensed data, digital land use data, and census information from a variety of sources. Urban land use change has been documented by the Baltimore-Washington Spatial Dynamics & Human Impact Study Team for the last 200 years. The methods, definitions, and collection criteria used to define urban or built-up areas were developed by a multi-disciplinary team that also ensures consistency in collection techniques and documentation methods for subsequent application in other regions. Animation techniques were used to visualize the database and to document the evolution of the region's urban landscape. The database is an important tool to urban and regional planners, ecologists, and global change researchers for measuring trends in urban sprawl, analyzing patterns of water pollution, understanding the impacts of development on ecosystems, and developing predictive modeling techniques to better forecast areas of urban growth. The study area for Phase I consisted of an approximate area of 15- by 15-minute segment centered around the city of Baltimore (fig. 1). Phase I was used as a prototype for the technique development and integration that the multiagency collaborative effort would require. The regional study, Phase II, encompassed a 2-degree square centered on Washington, D.C. With more than 7 million people spread across 39 counties, the Baltimore-Washington region is one the Nation's fastest growing metropolitan areas. The two cities are rapidly merging into one.

Maryland↗
USGS2016

Uncertainty in biological monitoring: a framework for data collection and analysis to account for multiple sources of sampling bias

Biological monitoring programmes are increasingly relying upon large volumes of citizen-science data to improve the scope and spatial coverage of information, challenging the scientific community to develop design and model-based approaches to improve inference. Recent statistical models in ecology have been developed to accommodate false-negative errors, although current work points to false-positive errors as equally important sources of bias. This is of particular concern for the success of any monitoring programme given that rates as small as 3% could lead to the overestimation of the occurrence of rare events by as much as 50%, and even small false-positive rates can severely bias estimates of occurrence dynamics. We present an integrated, computationally efficient Bayesian hierarchical model to correct for false-positive and false-negative errors in detection/non-detection data. Our model combines independent, auxiliary data sources with field observations to improve the estimation of false-positive rates, when a subset of field observations cannot be validated a posteriori or assumed as perfect. We evaluated the performance of the model across a range of occurrence rates, false-positive and false-negative errors, and quantity of auxiliary data. The model performed well under all simulated scenarios, and we were able to identify critical auxiliary data characteristics which resulted in improved inference. We applied our false-positive model to a large-scale, citizen-science monitoring programme for anurans in the north-eastern United States, using auxiliary data from an experiment designed to estimate false-positive error rates. Not correcting for false-positive rates resulted in biased estimates of occupancy in 4 of the 10 anuran species we analysed, leading to an overestimation of the average number of occupied survey routes by as much as 70%. The framework we present for data collection and analysis is able to efficiently provide reliable inference for occurrence patterns using data from a citizen-science monitoring programme. However, our approach is applicable to data generated by any type of research and monitoring programme, independent of skill level or scale, when effort is placed on obtaining auxiliary information on false-positive rates.

Methods in Ecology and Evolution↗
USGS2011

Recent and historic drivers of landscape change in the Everglades ridge, slough, and Tree Island mosaic

More than half of the original Everglades extent formed a patterned peat mosaic of elevated ridges, lower and more open sloughs, and tree islands aligned parallel to the dominant flow direction. This ecologically important landscape structure remained in a dynamic equilibrium for millennia prior to rapid degradation over the past century in response to human manipulation of the hydrologic system. Restoration of the patterned landscape structure is one of the primary objectives of the Everglades restoration effort. Recent research has revealed that three main drivers regulated feedbacks that initiated and maintained landscape structure: the spatial and temporal distribution of surface water depths, surface and subsurface flow, and phosphorus supply. Causes of recent degradation include but are not limited to perturbations to these historically important controls; shifts in mineral and sulfate supply may have also contributed to degradation. Restoring predrainage hydrologic conditions will likely preserve remaining landscape pattern structure, provided a sufficient supply of surface water with low nutrient and low total dissolved solids content exists to maintain a rainfall-driven water chemistry. However, because of hysteresis in landscape evolution trajectories, restoration of areas with a fully degraded landscape could require additional human intervention.

Critical Reviews in Environmental Science and Tech↗
USGS2024

The potential for species distribution models to distinguish source populations from sinks

1. While species distribution models (SDM) are frequently used to predict species occurrences to help inform conservation management, there is limited evidence evaluating whether habitat suitability can reliably predict intrinsic growth rates or distinguish source from sink populations. Filling this knowledge gap is critical for conservation science, as applications of SDMs for management purposes ultimately depend on these typically unobserved population or metapopulation dynamics. 2. Using regression, we associate previously published population level estimates of intrinsic growth and abundance derived from a Bayesian analysis of mark-recapture data for 17 bird species found in the contiguous United States with SDM habitat suitability estimates fitted here to opportunistic data for these same species. We then use AUC to measure how well SDMs can distinguish populations categorized as sources and sinks, depending on their intrinsic growth rates estimated from the mark-recapture data. We built SDMs using two different approaches, boosted regression trees (BRT) and Generalized Linear Models (GLM), and compared their predictive performance. Each SDM was built with presence points obtained from eBird and 10 environmental variables previously selected to model intrinsic growth rates and abundance for these species. 3. We show that SDMs built with opportunistic data are poor predictors of species demography in general; both BRT and GLM explained very little spatial variation of intrinsic growth rate and population abundance (median R2 across 17 species was close to 0.1 for both SDM methods). SDMs do, however, estimate higher suitability for source populations as compared to sinks. Out of 13 species which had both source and sink populations, both BRT and GLM had AUC values greater than 0.7 for 7 species when discriminating between sources and sinks. 4. Habitat suitability have the potential to be a useful measure to indicate a population’s ability to sustain itself as a source population, however more research on a diverse set of taxa is essential to fully explore this potential. This interpretation of habitat suitability can be particularly useful for conservation practice, and identification of explicit cases of when and how SDMs fail to match population demography can be informative for advancing ecological theory.

Journal of Animal Ecology↗
USGS2011

An evaluation of the science needs to inform decisions on Outer Continental Shelf energy development in the Chukchi and Beaufort Seas, Alaska

The U. S. Geological Survey (USGS) was asked to conduct an initial, independent evaluation of the science needs that would inform the Administration's consideration of the right places and the right ways in which to develop oil and gas resources in the Arctic Outer Continental Shelf (OCS), particularly focused on the Beaufort and Chukchi Seas. Oil and gas potential is significant in Arctic Alaska. Beyond petroleum potential, this region supports unique fish and wildlife resources and ecosystems, and indigenous people who rely on these resources for subsistence. This report summarizes key existing scientific information and provides initial guidance of what new and (or) continued research could inform decision making. This report is presented in a series of topical chapters and various appendixes each written by a subset of the USGS OCS Team based on their areas of expertise. Three chapters (Chapters 2, 3, and 4) provide foundational information on geology; ecology and subsistence; and climate settings important to understanding the conditions pertinent to development in the Arctic OCS. These chapters are followed by three chapters that examine the scientific understanding, science gaps, and science sufficiency questions regarding oil-spill risk, response, and impact (Chapter 5), marine mammals and anthropogenic noise (Chapter 6), and cumulative impacts (Chapter 7). Lessons learned from the 1989 Exxon Valdez Oil Spill are included to identify valuable "pre-positioned" science and scientific approaches to improved response and reduced uncertainty in damage assessment and restoration efforts (appendix D). An appendix on Structured Decision Making (appendix C) is included to illustrate the value of such tools that go beyond, but incorporate, science in looking at what can/should be done about policy and implementation of Arctic development. The report provides a series of findings and recommendations for consideration developed during the independent examination of science gaps and sufficiency. These recommendations are important for understanding what the USGS discovered in the course of this study and to help inform and improve decision making.

Circular↗
USGS2025

Shallow geologic framework of the Mississippi Sound and the potential for sediment resources

The Mississippi Sound, an estuarine environment located between the mainland and barrier islands bordering the northern Gulf of America (formerly the Gulf of Mexico), serves as a vital ecosystem for the States of Mississippi and Alabama. Spanning approximately 100 kilometers from east to west and covering 1,400 square kilometers, the sound is home to marine industry and ports, and its shallow and brackish waters sustain a diverse array of marine life. Barrier islands along the southern edge of the sound separate the microtidal estuary from the Gulf of America. This protection from gulf wave action mediates current flow within the sound, resulting in predominantly fine-grained sediment deposition along the seafloor. This study, conducted by the U.S. Geological Survey in cooperation with the U.S. Army Corps of Engineers, provides insight on fluvial and tidal processes spanning the past 5,000 years. The report synthesizes existing research to provide a comprehensive overview of the sound geology, from Pleistocene origins to present-day morphology, and utilizes high-resolution single channel seismic profiles and sediment data to identify and map sedimentary deposits and morphologic features at and below the seafloor. Despite its ecological significance, the Mississippi Sound faces environmental challenges, including water-quality issues, habitat degradation, storm-induced erosion, and the ongoing threats of sea-level rise and environmental changes. This study uses the present-day understanding of the sound's geology to inform coastal management decisions, hazard assessment, and potential mineral resources.

Louisiana, Mississippi↗
USGS2019

Back from the brink: Sustainable management of the Lake Erie walleye fishery

This chapter describes management actions implemented after a large-scale population decline of the Walleye Sander vitreus population in Lake Erie, one of the Laurentian Great Lakes in North America. Intensive fishery exploitation during the 1950s combined with declining water quality conditions collapsed the Walleye stock during the early 1960s. The fishery persisted at low levels until 1970 when the fishery was closed (1970–1972) due to elevated mercury concentrations in Walleye tissue. Lake Erie fishery managers at the time recognized the need for a coordinated, multi-agency approach to protect this ecologically, economically, and socially important resource. The harvest ban was lifted in 1973 when mercury levels dropped below advisory levels. In 1976, an interagency management framework was established, which relied on a coordinated, science-based management philosophy consisting of estimating safe harvest levels, performing applied research, and conducting annual population assessments. The population rebounded during the 1980s in response to improving environmental conditions, regulated harvest, and a series of strong recruitment events. Declines in harvest and population size were again observed during the late 1990s and mid-2000s, likely due to variation in natural processes controlling recruitment, and fishery managers enacted harvest practices during this period to promote long-term sustainability. Today, Lake Erie Walleyes support one of the largest self-sustaining freshwater fisheries in North America. Throughout the years, Lake Erie managers have iteratively adopted changes to their population assessment model and altered harvest policies to avoid future fishery and population collapses. More than 40 years later, Lake Erie continues to support commercial and recreational fisheries lake wide. Lessons learned from the stock recovery and subsequent coordinated management for fishery sustainability include the importance of conducting routine population assessments, using science-based research to address key uncertainties, adopting modern stock assessment approaches, incorporating stakeholder input into the quota setting process, and addressing environmental concerns collaboratively at the lake level.

Book chapter↗
USGS2018

DEEP SEARCH: Deep sea exploration to advance research on coral/canyon/cold seep habitats

Launched in August 2017, Deep Sea Exploration to Advance Research on Coral/Canyon/Cold seep Habitats (DEEP SEARCH) is a multiyear, multi-agency study to characterize the deep-sea ecosystems of the US Mid- and South Atlantic (Figure 1). The study is funded through an interagency partnership between NOAA, the Bureau of Ocean Energy Management (BOEM), and the US Geological Survey, and it is sponsored by the National Oceanographic Partnership Program. DEEP SEARCH will spend four and a half years (from 2017 to 2021) researching the habitats of the US Atlantic to better understand the distribution of sensitive seafloor communities to inform potential offshore energy development and other deep-sea management needs.

Oceanography↗