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At least 55 records · Page 3Linked to original sources
USGS2004

Umbilical scarring in hatchling American alligators

Umbilical scarring is the presence of excess scar tissue deposited between abdominal dermal layers at the site of yolk sac absorption in hatchling American alligators (Alligator mississippiensis). The presence of this dermal condition plays a key evaluatory role in the overall quality and subsequent value for various commercial leather products. Despite the prevalent nature of this condition, currently the industry has no standardized protocols for its quantification. The objectives of this study were to examine the relationship between hatchling weight and age and incidence of umbilical scarring and to develop a quantifiable and reproducible technique to measure this dermal condition in hatchling American alligators. Thirty eggs from each of nine clutches were incubated in two separate incubators at different facilities and hatchling umbilical scarring was measured at 2 and 10 days of age using digital calipers. Umbilical area was calculated by multiplying umbilical length times umbilical width. There was a significant effect of both age and clutch on umbilical area (overall decline of 64%) by 10 days post-hatch. However, only five of the nine clutches utilized expressed a noticeable decline in the size of this dermal condition (range 67-74%). We had hypothesized that larger hatchlings would have larger umbilical areas and a slower rate of improvement in this condition during the first few days post-hatch. The differences in umbilical area and percent decline with age across clutches, however, were not associated with differences in initial hatchling weights. Within clutches and time periods, hatchling weight had no significant effect on the size and/or rate of decline of this condition. ?? 2004 Published by Elsevier B.V.

Aquaculture↗
USGS2013

Native Prairie Adaptive Management: a multi region adaptive approach to invasive plant management on Fish and Wildlife Service owned native prairies

Much of the native prairie managed by the U.S. Fish and Wildlife Service (FWS) in the Prairie Pothole Region (PPR) of the northern Great Plains is extensively invaded by the introduced cool-season grasses, smooth brome ( Bromus inermis ) and Kentucky bluegrass ( Poa pratensis ). Management to suppress these invasive plants has had poor to inconsistent success. The central challenge to managers is selecting appropriate management actions in the face of biological and environmental uncertainties. In partnership with the FWS, the U.S. Geological Survey (USGS) developed an adaptive decision support framework to assist managers in selecting management actions under uncertainty and maximizing learning from management outcomes. This joint partnership is known as the Native Prairie Adaptive Management (NPAM) initiative. The NPAM decision framework is built around practical constraints faced by FWS refuge managers and includes identification of the management objective and strategies, analysis of uncertainty and construction of competing decision models, monitoring, and mechanisms for model feedback and decision selection. Nineteen FWS field stations, spanning four states of the PPR, have participated in the initiative. These FWS cooperators share a common management objective, available management strategies, and biological uncertainties. Though the scope is broad, the initiative interfaces with individual land managers who provide site-specific information and receive updated decision guidance that incorporates understanding gained from the collective experience of all cooperators. We describe the technical components of this approach, how the components integrate and inform each other, how data feedback from individual cooperators serves to reduce uncertainty across the whole region, and how a successful adaptive management project is coordinated and maintained on a large scale. During an initial scoping workshop, FWS cooperators developed a consensus management objective: increase the composition of native grasses and forbs on native sod while minimizing cost. Cooperators agreed that decision guidance should be provided annually and should account for local, real-time vegetation conditions observed on the ground. Over the course of development, two prototypes of the decision framework were considered. The final framework recognized four alternative actions that managers could take in any given year: (1) Graze—targeted use of grazing ungulates to achieve defoliation, (2) Burn—application of prescribed fire as the single form of defoliation, (3) Burn/Graze—a combination treatment, and (4) Rest—no action. The study area included northern mixed-grass and tallgrass prairie. Native vegetation in mixed–grass prairie has a strong cool-season component and thus the dominant native species have a phenology similar to that of smooth brome and Kentucky bluegrass, making management of those species challenging. In contrast, tallgrass prairie has a strong warm-season native component, leading to an existence of cool-season windows, periods of time in the fall and spring when cool‐season invasive grass species are actively growing and vulnerable to damage via select management actions, but warm‐season grass species are not active and are thus less susceptible to damage via the same actions. This dichotomy between prairie types necessitated the development of separate but parallel decision support systems for mixed-grass and tallgrass biomes. Management units are parcels of native prairie that receive a single management treatment at any one time over their entire extent. At any particular time, the vegetation state of each management unit is characterized by the amount of cover of native grasses and forbs and the type of invasive grass that is dominant. In addition, each unit has a defoliation state which reflects the number of years since the last defoliation event and an index to how intensively the unit was managed during the previous 7 years. State-transition models are used to predict the state of a management unit in year t+1 from its state in year t and a prescribed management action that was applied between the two monitoring events. Alternative models are built around key uncertainties that make choice of a management action difficult. Three uncertainties revolve around whether the effect of management actions depends on (1) type of dominant invader, (2) past defoliation history, and (3) level of invasion. Two additional uncertainties are considered when choosing a management action for tallgrass units: (4) the effectiveness of grazing within the cool-season window as a surrogate for burning when smooth brome is the dominant invader, and (5) the differential effect of active management outside the window as compared to rest. Because data on the probability of transitioning from one state to another under the various models were lacking, expert opinion and elicitation were used to parameterize the models. In addition, cooperators participated in elicitation exercises to extract their beliefs regarding the value of having native prairie compared to the cost of achieving it. Quantifying the subjective expression of utility in this way allowed for mathematical representation of the management objective into an objective function. By maximizing the objective function, cumulative utility is maximized, leading to the identification of a sequence of decisions that will achieve the management objective. The NPAM system adopted a vegetation monitoring protocol that was rapid, inexpensive, and familiar to many of the cooperators. The monitoring protocol served three purposes: (1) determining current vegetation and defoliation states of each unit, (2) evaluating progress toward the management objective, and (3) assessing predictive performance of the alternative models. The management year runs from September 1 to August 31. Management can be applied anytime during that period and monitoring takes places from late June to mid-August. Cooperators enter vegetation data and management information into a centralized database by August 25 of each year. Given the current state of the system (vegetation and defoliation states) and the current understanding of the system (or the belief state), identifying the current best management decision is a matter of looking up the combination (that is, system state and belief state) in the appropriate (mixed-grass or tallgrass) optimal decision table. Given complete uncertainty at the outset of decision-making, initial assignment of equal belief weights to each model was believed reasonable. The decisions in the optimal decision table that correspond to the current belief state constitute the current optimal decision policy. By August 31 of each year, individual cooperators are provided with a recommended management action for each of their management units for the upcoming management year. Upon receiving the management recommendations for their units, managers consider the recommendation, along with other relevant information, and at some point during the year one of the management alternatives is carried out. This iterative cycle of making and implementing a management decision, predicting the response, monitoring the outcome, comparing predicted and observed outcomes, updating model weights, and recommending a management action for the next cycle is expected to result in an accumulation of weight on a representative model of system dynamics, thereby increasing understanding needed to effectively manage native prairies. The NPAM system is now entering its second full year of complete operation, and represents one of only a few fully implemented applications of adaptive management within the U.S. Fish and Wildlife Service. NPAM is truly unique in that it originated from the ground up as a result of the leadership and steadfastness of several refuge biologists and managers confronted with a common problem. These biologists recognized that working together across a large landscape presented perhaps the best opportunity for halting and reversing the invasion of native grasslands by non-native cool-season grasses. Importantly, the NPAM system encapsulates the collective thinking and experience of tens if not hundreds of individuals who have battled this vexing problem for much of their careers. The NPAM initiative is rooted in principles of adaptive management, thereby affording the opportunity for grassland managers to pursue management objectives while acquiring information to reduce uncertainty and improve future management. The project introduced a number of technical innovations that will serve as templates for conservation efforts throughout and beyond the U.S. Fish and Wildlife Service. First, NPAM is an on-the-ground implementation of active adaptive management—possibly the first of its kind in conservation management—in which recommended management actions result from a prospective analysis of future learning (Williams, 1996). Second, by the use of dynamic optimization, NPAM demonstrates how decisions can be made that take into account possible future transitions of the system. Third, NPAM demonstrates how models of partial controllability are an effective means of accommodating unpredictable circumstances that cause a manager to follow a different course than was intended. Finally, the database developed for NPAM is an unparalleled system that enables the rapid integration of data from the field for the generation of ‘just-in-time’ management recommendations. In all, NPAM provides an example of how a science-management partnership can be forged to achieve large-scale conservation objectives.

Minnesota;Montana;North Dakota;South Dakota↗
USGS2011

BioData: A national aquatic bioassessment database

BioData is a U.S. Geological Survey (USGS) web-enabled database that for the first time provides for the capture, curation, integration, and delivery of bioassessment data collected by local, regional, and national USGS projects. BioData offers field biologists advanced capabilities for entering, editing, and reviewing the macroinvertebrate, algae, fish, and supporting habitat data from rivers and streams. It offers data archival and curation capabilities that protect and maintain data for the long term. BioData provides the Federal, State, and local governments, as well as the scientific community, resource managers, the private sector, and the public with easy access to tens of thousands of samples collected nationwide from thousands of stream and river sites. BioData also provides the USGS with centralized data storage for delivering data to other systems and applications through automated web services. BioData allows users to combine data sets of known quality from different projects in various locations over time. It provides a nationally aggregated database for users to leverage data from many independent projects that, until now, was not feasible at this scale. For example, from 1991 to 2011, the USGS Idaho Water Science Center collected more than 816 bioassessment samples from 63 sites for the National Water Quality Assessment (NAWQA) Program and more than 477 samples from 39 sites for a cooperative USGS and State of Idaho Statewide Water Quality Network (fig. 1). Using BioData, 20 years of samples collected for both of these projects can be combined for analysis. BioData delivers all of the data using current taxonomic nomenclature, thus relieving users of the difficult and time-consuming task of harmonizing taxonomy among samples collected during different time periods. Fish data are reported using the Integrated Taxonomic Information Service (ITIS) Taxonomic Serial Numbers (TSN's). A simple web-data input interface and self-guided, public data-retrieval web site provides access to bioassessment data. BioData currently accepts data collected using two national protocols: (1) NAWQA and (2) U.S. Environmental Protection Agency (USEPA) National Rivers and Streams Assessment (NRSA). Additional collection protocols are planned for future versions.

Fact Sheet↗
USGS2010

Mount Rainier National Park and Olympic National Park Elk Monitoring Program Annual Report 2010

Fiscal year 2010 was the third year of gathering data needed for protocol development while simultaneously implementing what is expected to be the elk monitoring protocol at Mount Rainier (MORA) and Olympic (OLYM) national parks in the North Coast and Cascades Network (NCCN). Elk monitoring in these large wilderness parks relies on aerial surveys from a helicopter. Summer surveys are planned for both parks and are intended to provide quantitative estimates of abundance, sex and age composition, and distribution of migratory elk in high elevation trend count areas. Spring surveys are planned at Olympic National Park and are intended to provide quantitative estimates of abundance of resident and migratory elk on low-elevation winter ranges within surveyed trend count areas. An unknown number of elk is not detected during surveys. The protocol under development aims to estimate the number of missed elk by applying a model that accounts for detection bias. Detection bias in elk surveys in MORA will be estimated using a double-observer sightability model that was developed based on data from surveys conducted in 2008-2010. The model was developed using elk that were previously equipped with radio collars by cooperating tribes. That model is currently in peer review. At the onset of protocol development in OLYM there were no existing radio- collars on elk. Consequently double-observer sightability models have not yet been developed for elk surveys in OLYM; the majority of the effort in OLYM has been focused on capturing and radio collaring elk to permit the development of sightability models for application in OLYM. As a result, no estimates of abundance or composition are included in this annual report, only raw counts of the numbers of elk seen in surveys. At MORA each of the two trend count areas (North Rainier herd, and South Rainier herd) were surveyed twice. 290 and 380 elk were counted on the two replicates in the North Rainier herd, and 621 and 327 elk counted on the two replicate South Rainier counts. At Olympic National Park, each of three spring trend count areas was surveyed once in March 2010. 27 elk were observed in the South Fork Hoh trend count area, 137 elk were observed in the Hoh trend count area, and 131 elk were observed in the Queets trend count area. In September 2010, 18 elk were captured and fitted with radio collars as part of a contracted animal capture, eradication and tagging of animals (ACETA) operation. These animals will be available to contribute double-observer sightability data in future spring and summer surveys. There were no summer surveys for elk in OLYM in 2010.

Washington↗
USGS2024

Analysis and review of fishery-dependent data for Hawaiian nearshore noncommercial fisheries

Noncommercial, shore-based fisheries provide economic, social, and cultural services to communities throughout the Hawaiian Islands. The State of Hawai‘i Department of Land and Natural Resources (DLNR), Division of Aquatic Resources (DAR) routinely conducts surveys to monitor noncommercial fisheries such that estimates of fishing effort and catch by gear type can be generated and used to implement more sustainable management practices. DAR executes both the Hawai‘i Marine Recreational Fishery Survey (HMRFS), a nationally standardized survey that focuses on intercepting fishers at access points (i.e., boat ramps) across the main Hawaiian Islands, and a set of roving creel surveys on O‘ahu, Maui Nui, and Kaua‘i that observe and intercept fishers at locations along the shoreline outside of those targeted by HMRFS. The latter set of creel surveys were designed to complement HMRFS by expanding its geographic coverage and thus providing a more representative picture of noncommercial fishing in Hawai‘i. Sustainable management priorities set by DAR rely on the availability of statewide, fishery- dependent data. Thus, we collate information from island-based roving creel surveys into a cohesive Statewide Creel Survey Database. Further, we provide preliminary analyses and describe ways that surveys could be streamlined to improve future data collection, analysis, and utility. In so doing, we synthesize the most detailed information to-date about noncommercial shore-based fisheries of Hawai‘i. The unprecedented spatial and temporal coverage of DAR’s dataset reveals the value of their survey efforts over the last decade to address fishery management needs. Our primary objectives, results, and conclusions are summarized below: 1) Integrate DAR roving creel survey data from different islands into a single Statewide Creel Survey Dataset (Chapter II). We describe the collation of creel survey data from O‘ahu, Maui Nui, and Kaua‘i into a statewide dataset. We also offer ways in which these surveys could be streamlined to meet the needs of managers and decision makers. Briefly, these are to create a statewide strategic plan, standardize the execution of standard operating procedures, centralize the creel survey database and associated metadata, and consider using technology that improves the data pipeline, including transitioning from paper-based to electronic systems for data entry and processing. 2) Assess whether the new Statewide Creel Survey Dataset can provide inputs for length-based stock assessments (Chapter III). Only on Maui were interviews conducted with associated catch data. There was reasonably high taxonomic coverage (42 species from 186 interviews with 310 fishers), but low sample sizes for nearly all species precluded the development of length-based stock assessments. We provide summary statistics from the existing data and briefly discuss how technologies could be used to automate analysis of images of noncommercial catch. 3) Analyze the Statewide Creel Survey Dataset for spatial and temporal patterns in fishing effort (Chapter IV): a. Visualizing noncommercial fishing pressure . We found that fishing effort (mean number of fishers observed per survey event at a site) on O'ahu was over three times greater than that recorded during similar surveys conducted on Maui or Kaua'i. We create maps that display the distribution of angling and spearfishing effort around each of the three islands. b. Factors that predict fishing “hotspots” around Maui . Fishing effort on Maui was associated with areas with more wave power and less parking availability. There were half as many fishers in areas with parking lots than in areas with parking on the road shoulder only. c. Changes in fishing effort during the COVID-19 pandemic . There was no change in fishing effort on O‘ahu during the first year of the pandemic, but there was a 20% decline in year 2 and a 33% decline in year 3, both in comparison to pre-pandemic levels. Pre-pandemic creel survey data were unavailable for Maui and Kaua‘i, but fishing effort on these islands also declined as the pandemic progressed at similar or greater rates than those observed on O‘ahu. 4) Quantify potential bias in survey methods by experimentally deriving fisher detection probabilities of shore-based and drone-based surveys (Chapter V): a. Shore-based surveys . We conducted roving creel surveys for four months at three locations around Hilo Bay, designed to emulate and estimate the efficacy of DAR standard operating procedures. There was high agreement between paired observers in counting fishers, leading to near-perfect detection probabilities of both anglers (94%) and spearfishers (97%), but relatively low agreement and detection probabilities of other fishers (throw net, ‘opihi picking, etc.) (52%). b. Drone-based surveys . We used an unmanned aerial vehicle (UAV; operated by DAR staff) to collect imagery of fishers along the Hilo Bay shoreline. We used still images and video clips (with known fishing activity) to build an online survey that was distributed to DAR and HCFRU personnel, asking them to count and categorize resource users as a snorkeler, spearfisher, angler, or other fisher. Only 40.0% of the responses correctly counted and categorized resource users in the image. Anglers were correctly identified and enumerated in 90.0% of the responses, but the correct response rates of the other three user categories ranged from 67.8% – 79.4%. Snorkelers and anglers tended to be undercounted while spearfishers and other fishers were overcounted. 5) Review the potential for incorporating emerging technologies that will improve, augment, and evolve creel survey data collection, especially for spearfishing (Chapter VI). Within the context of monitoring shore-based noncommercial fishing, we review the use of electronic data entry/processing systems with geospatial and image capabilities, field cameras, drones, smart buoys, citizen science apps, data mining social media, artificial intelligence and machine learning. We highlight several of the challenges and considerations when implementing these technologies into creel surveys and provide a synthesis of options that could be used to better estimate spearfishing. The general conclusion of this assessment is that the DAR roving creel survey program is collecting valuable data that supplement the existing HMRFS efforts. However, there are a number of areas that could be improved to make these efforts a more effective tool for decision-making processes in resource management and conservation: 1) Establishment of clear statewide and island objectives for the Statewide Creel Survey Dataset. Currently, data collection efforts are focused towards addressing a very broad purpose – supplementing the HMRFS data collection efforts. However, the results of the preliminary analyses conducted as part of this project suggest that the data could be used to address other areas of need if these objectives were clearly defined. Further, the design of the creel survey would benefit from greater standardization of survey protocols between islands and an effort to define a) the acceptable margins of error associated with the estimates generated by these data and b) the minimum level of change that the surveys would need to detect to be useful to managers. 2) Centralization of data entry, data quality assessment, and data accessibility. Currently, each DAR office manages data entry, checks the data for errors, and is responsible for managing and storing the data. Instituting a centralized data entry system, particularly an online database that can receive survey data from tablets or smartphones running a standardized data collection application would improve efficiency, reduce data entry errors, and accelerate the availability of data to managers. A substantial amount of time and effort from the project described in this report was devoted to checking the dataset for errors. The development and application of data quality assurance protocols would ensure that the data are reliable and available in a timely fashion to support management decisions. 3) Address lingering questions regarding the efficacy of current survey protocols to capture and characterize the spearfishing component of the noncommercial fishery. The results presented in the report suggest that the current creel survey protocols do a good job detecting spearfishers when present but are not capturing sufficient data about their catch or total effort. There are also questions remaining as to whether the survey times and sites are sufficiently capturing the behavior of spearfishers in Hawai‘i. A more thorough assessment – whether through additional research, alteration of survey design, or review of data by representatives of the spearfishing community – would provide insight on how to use the Statewide Creel Survey Database to inform management of spearfishing. 4) Investigate the integration of technological advancements into the creel survey methods. As priorities and needs are developed and formalized, it would be valuable to consider how various technological advancements might enhance and streamline data collection or open new avenues of inquiry.

Hawaii↗
USGS2003

Percentile distributions of median nitrite plus nitrate as nitrogen, total nitrogen, and total phosphorus concentrations in Oklahoma streams, 1973-2001

Nutrients are one of the primary causes of water-quality impairments in streams, lakes, reservoirs, and estuaries in the United States. The U.S. Environmental Protection Agency has developed regional-based nutrient criteria using ecoregions to protect streams in the United States from impairment. However, nutrient criteria were based on nutrient concentrations measured in large aggregated nutrient ecoregions with little relevance to local environmental conditions in states. The Oklahoma Water Resources Board is using a dichotomous process known as Use Support Assessment Protocols to define nutrient criteria in Oklahoma streams. The Oklahoma Water Resources Board is modifying the Use Support Assessment Protocols to reflect nutrient informa-tion and environmental characteristics relevant to Oklahoma streams, while considering nutrient information grouped by geographic regions based on level III ecoregions and state boundaries. Percentile distributions of median nitrite plus nitrate as nitrogen, total nitrogen, and total phosphorous concentrations were calculated from 563 sites in Oklahoma and 4 sites in Arkansas near the Oklahoma and Arkansas border to facilitate development of nutrient criteria for Oklahoma streams. Sites were grouped into four geographic regions and were categorized into eight stream categories by stream slope and stream order. The 50th percentiles of median nitrite plus nitrate as nitrogen, total nitrogen, and total phosphorus concentrations were greater in the Ozark Highland ecoregion and were less in the Ouachita Mountains ecoregion when compared to other geographic areas used to group sites. The 50th percentiles of median concentrations of nitrite plus nitrate as nitrogen, total nitrogen, and total phosphorus were least in first, second, and third order streams. The 50th percentiles of median nitrite plus nitrate as nitrogen, total nitrogen and total phosphorus concentrations in the Ozark Highland and Ouachita Mountains ecoregions were least in first, second, and third order streams with streams slopes greater than 17 feet per mile. Nitrite plus nitrate as nitrogen and total nitrogen criteria determined by the U.S. Environmental Protection Agency for the Ozark Highland ecoregion were less than the 25th percentiles of median nitrite plus nitrate as nitrogen, total nitrogen, and total phosphorus concentrations in the Ozark Highland ecoregion calculated for this report. Nitrite plus nitrate as nitrogen and total nitrogen criteria developed by the U.S. Environmental Protection Agency for the Ouachita Mountains ecoregion were similar to the 25th percentiles of median nitrite plus nitrate as nitrogen and total nitrogen concentrations in the Ouachita Mountains ecoregion calculated for this report. Nitrate as nitrogen and total phosphorus concentrations currently (2002) used in the Use Support Assessment Protocols for Oklahoma were greater than the 75th percentiles of median nitrite plus nitrate as nitrogen and total phosphorus concentrations calculated for this report.

Oklahoma↗
USGS2018

Monitoring wadeable stream habitat conditions in Southeast Coast Network parks: Protocol narrative

The Southeast Coast Network (SECN) has initiated a monitoring effort to assess habitat conditions in wadeable streams at national parks, recreation areas, battlefields, and monuments in Alabama, Georgia, and South Carolina. This monitoring effort includes Chattahoochee River National Recreation Area, Kennesaw Mountain National Battlefield Park, Congaree National Park, Horseshoe Bend National Military Park, and Ocmulgee National Monument. Stream habitat monitoring was implemented in 2016, and focuses specifically on providing relevant data to assess the physical condition of Piedmont and upper Coastal Plain streams with respect to aquatic and riparian habitats and how these habitats may be changing over time. The habitat assessment methods proposed in this protocol rely on standard data collection methods and standard operating procedures currently in use by the U.S. Geological Survey, U.S. Environmental Protection Agency, and U.S. Forest Service that have been modified to better meet the needs of National Park Service (NPS) managers. The Southeast Coast Network’s wadeable stream protocol was developed to begin a monitoring program that will provide insight into the status of, and trends in, stream and riparian habitat conditions. The number of reaches surveyed at each park is dependent on the spatial extent of the park and the total number of wadeable streams that are present within park boundaries. Regardless of the size of the park and the number of reaches that are to be monitored, selected reaches (1) are representative of the processes influencing the streams in each park; (2) can address current and anticipated management concerns, and (3) offer the most utility for future complementary studies.

Natural Resource Report↗
USGS2006

Remote sensing for grassland management in the arid Southwest

We surveyed a group of rangeland managers in the Southwest about vegetation monitoring needs on grassland. Based on their responses, the objective of the RANGES (Rangeland Analysis Utilizing Geospatial Information Science) project was defined to be the accurate conversion of remotely sensed data (satellite imagery) to quantitative estimates of total (green and senescent) standing cover and biomass on grasslands and semidesert grasslands. Although remote sensing has been used to estimate green vegetation cover, in arid grasslands herbaceous vegetation is senescent much of the year and is not detected by current remote sensing techniques. We developed a ground truth protocol compatible with both range management requirements and Landsat's 30 m resolution imagery. The resulting ground-truth data were then used to develop image processing algorithms that quantified total herbaceous vegetation cover, height, and biomass. Cover was calculated based on a newly developed Soil Adjusted Total Vegetation Index (SATVI), and height and biomass were estimated based on reflectance in the near infrared (NIR) band. Comparison of the remotely sensed estimates with independent ground measurements produced r2 values of 0.80, 0.85, and 0.77 and Nash Sutcliffe values of 0.78, 0.70, and 0.77 for the cover, plant height, and biomass, respectively. The approach for estimating plant height and biomass did not work for sites where forbs comprised more than 30% of total vegetative cover. The ground reconnaissance protocol and image processing techniques together offer land managers accurate and timely methods for monitoring extensive grasslands. The time-consuming requirement to collect concurrent data in the field for each image implies a need to share the high fixed costs of processing an image across multiple users to reduce the costs for individual rangeland managers.

Rangeland Ecology and Management↗
USGS2007

Monitoring Ground-Water Quality in Coastal Ecosystems

INTRODUCTION The Cape Cod National Seashore (CACO) extends along more than 70 km of Atlantic Ocean open-beach coastline and includes three large saltwater bays - Wellfleet Harbor, Nauset Marsh, and Pleasant Bay (fig. 1). CACO encompasses about 18,000 ha of uplands, lakes, wetlands, and tidal lands (Godfrey and others, 1999) including most habitats typical of the sandy coast in National seashores and parks extending southward from Massachusetts to Florida. In 1995, CACO was selected by the National Park Service (NPS) as a prototype park typifying the Atlantic and Gulf Coast biogeographic region for long-term coastal ecosystem monitoring. The U.S. Geological Survey (USGS) is currently (2007) assisting the NPS in the development of protocols for a Long-Term Coastal Ecosystem Monitoring Program at the CACO in Massachusetts. The overall purpose of the monitoring program is to characterize both natural and human-induced change in the biological resources of the CACO, over a time scale of decades, in the context of a changing global ecosystem.

Open-File Report↗
USGS1998

The Wisconsin Frog and Toad Survey: Update and 1984-97 trends [abstract]

The Wisconsin Frog and Toad Survey (WFTS) is a volunteer-based, roadside auditory count that began in 1981. It's protocols were recently modified for continent-wide use by the North American Amphibian Monitoring Plan (NAAMP). In 1997 we initiated a study to compare data collected by the WFTS and NAAMP protocols, in order to guide WFTS transition from its current methodology to one more compatible with NAAMP, without losing the use of data collected since 1981. In this paper we present results from the first year of this study, along with results from analyses of WFTS data, including distributional maps, 1984-97 population trends, phenological information, and progress on a new web page.

Book chapter↗
USGS2015

Assessment of general health of fishes collected at selected sites in the Great Lakes Basin In 2012

During the past decade, there has been a substantive increase in the detection of “emerging contaminants”, defined as a new substance, chemical, or metabolite in the environment; or a legacy substance with a newly expanded distribution, altered release, or a newly recognized effect (such as endocrine disruption). Emerging contaminants include substances such as biogenic hormones (human and animal), brominated flame retardants, pharmaceuticals, personal care products, plasticizers, current use pesticides, detergents, and nanoparticles. These contaminants are frequently not regulated or inadequately regulated by state or Federal water quality programs. Information about the toxicity of these substances to fish and wildlife resources is generally limited, compared to more highly regulated contaminants, and some classes have been shown to cause affects (for example feminization of male fish, immunomodulation) that are not evaluated via traditional toxicity testing protocols. As a result, these compounds may pose a substantial, but currently poorly documented threat to aquatic ecosystems. Failure to identify and understand the impacts of these emerging contaminants on fish and wildlife resources may result in deleterious impacts to Great Lakes resources that can result in adverse ecological, economic and recreational consequences. The U. S. Fish and Wildlife Service received funding through the Great Lakes Restoration Initiative (GLRI) for an Early Warning Program to detect and identify emerging contaminants and to evaluate the effects of these contaminants on fish and wildlife. The U.S. Geological Survey (WV Cooperative Fish and Wildlife Research Unit and National Fish Health Research Laboratory, Leetown Science Center) developed and implemented a biological effects monitoring protocol to assist in this program. Fish collections and measurements of biomarkers of exposure in Fall 2010 and Spring 2011 occurred at individual sites within select Areas of Concern (AOCs). They provided an assessment of the utility of the suite of biomarkers and also identified sites for more in-depth analyses. Selected areas are characterized as areas with known emerging contaminants, sensitive or listed species, areas downstream from municipal wastewater discharges or receiving waters for industrial facilities, and/or areas susceptible to agricultural or urban contamination, or harbors or ports. The results of the 2010- 2011 studies were summarized in Blazer et al. 2014 a, b, c; Braham et al. in review and Blazer et al. in review.

Great Lakes↗
USGS2019

Use of set blanks in reporting pesticide results at the U.S. Geological Survey National Water Quality Laboratory, 2001-15

Executive Summary Background .—Pesticide results from the U.S. Geological Survey (USGS) National Water Quality Laboratory (NWQL) are used for water-quality assessments by many agencies and organizations. The USGS is committed to providing data of the highest possible quality to the consumers of its data. A cooperator’s inquiries about specific pesticide detections in water revealed potential laboratory contamination issues for some results. Consequently, the USGS conducted an extensive evaluation of potential low-level contamination related to processing or analysis of water-quality samples at NWQL for 21 pesticide compounds of interest to the cooperator. This is the most comprehensive study of NWQL pesticide quality-control (QC) results to date. Purpose and scope .—The purpose of this study was to document protocols used by the NWQL to censor pesticide results and to determine the effects of laboratory contamination—as determined from detections in laboratory set blanks—on pesticide detections in groundwater and surface-water samples. More than 30,000 pesticide results from 113 selected batches of samples (2 percent or less of total batches) analyzed by the NWQL during the 15 years from 2001 to 2015 were reviewed. All laboratory results from the selected batches, including results from environmental (surface water and groundwater) and QC (set-blank, blind-blank, and blind-spike) samples, were evaluated. The study includes results for 21 pesticide compounds analyzed in groundwater and surface-water samples collected across the United States. Eleven pesticide compounds were analyzed by a gas chromatography/mass spectrometry method and 10 compounds by a liquid chromatography/mass spectrometry method. Objectives and methods .—The objectives of this study were to (1) determine the characteristics of laboratory contamination over time, (2) compare distributions of pesticide results in set blanks with distributions in environmental samples, (3) evaluate the potential for false-positive and false-negative reporting of results, and (4) evaluate the effects of reevaluating historical pesticide results using 2017 compound identification protocols on detections of pesticides in groundwater and surface-water samples. The 113 instrument batches selected for this study contained detections of one or more of the 21 pesticide compounds in set blanks or were among those batches with the highest pesticide detection frequencies in set blanks. As a result, the dataset for this study was targeted toward pesticides and batches with laboratory contamination. The objectives were addressed by statistically comparing environmental and set-blank results; computing moving averages of set-blank detection frequencies to identify periods of episodic contamination; and using summary statistics, tabular summaries, and graphical approaches, such as time-series plots and cumulative distribution functions. Results .— Objective 1 : Laboratory contamination, as determined by pesticide detections in set blanks, was found in 13 percent of set-blank results from the 113 targeted batches included in this study (as compared to 6 percent of set-blank results from all 7,620 batches analyzed during the study period). It is estimated that 92 percent of the laboratory contamination during the study period was episodic, meaning that it occurred during discrete periods of time. All 21 of the targeted pesticide compounds had periods of episodic contamination, with most episodes ranging in duration from about 1 to 8 months. The remaining 8 percent of laboratory contamination was random or from a known source (deterministic). Objective 2 : For some compounds, graphs of cumulative distribution functions of the entire distributions of set-blank and environmental samples overlap, suggesting that there is no difference in the distributions of the two types of samples. However, time-series graphs show that detections in set blanks often occur at different times (sometimes separated by years) than detections in environmental samples, indicating clear differences in those distributions, and indicating the importance of evaluating the timing of detections in all sample types. For most compounds detected in set-blank and environmental samples, detection frequencies were significantly greater in set blanks than in groundwater or surface-water samples ( p <0.05). There are several explanations for this finding, including that the 113 batches of samples chosen for this study targeted batches with detections in set blanks or that detections in set-blank samples were historically determined with less stringent identification criteria than for environmental samples (groundwater and surface-water samples). Objective 3 : The false-positive and false-negative rates from blind samples submitted during the study period by the USGS Quality Systems Branch generally were less than 1 and 5 percent, respectively, for the 21 pesticides. The only compound with a false-positive rate greater than 1 percent was flumetsulam (2.6 percent), indicating that there is a higher likelihood of flumetsulam being reported as a detection when it is not present in an environmental sample compared with the reporting of other compounds. Objective 4 : Altogether, for data in targeted batches, NWQL would have reported 0.1 percent of results from groundwater samples and 1.4 percent of results from surface-water samples differently if 2017 identification protocols were applied to historical pesticide results. In most of these cases, detections observed in historical results would change to nondetections. The small percentages of changes that would occur if historical data were reevaluated indicate that historical protocols used by the NWQL to identify detections in environmental samples were robust and produced results that are predominantly consistent with current [2017] practices. Conclusions .—The NWQL produces high-quality pesticide results at environmentally relevant concentrations. NWQL identification protocols and censoring practices are largely effective at minimizing the reporting of false-positive and false-negative results. Laboratory contamination, when it occurred, tended to occur in episodes; thus, evaluating the timing and magnitude of detections in set blanks relative to detections in environmental samples was determined to be an important consideration for analysis of environmental results. Because NWQL censoring practices do not address all types and occurrences of laboratory contamination, options for additional censoring practices are provided for data users with more specific or stringent data-quality objectives. The methods used to analyze the 21 compounds for this report can similarly be applied to all 173 pesticide compounds that were analyzed by the NWQL during the same time period. This study also has helped to identify potential improvements in reporting USGS data, such as conducting more frequent review of set-blank datasets.

Scientific Investigations Report↗
USGS2012

St. Petersburg Coastal and Marine Science Center's Core Archive Portal

This Web site contains information on rock cores archived at the U.S. Geological Survey (USGS) St. Petersburg Coastal and Marine Science Center (SPCMSC). Archived cores consist of 3- to 4-inch-diameter coral cores, 1- to 2-inch-diameter rock cores, and a few unlabeled loose coral and rock samples. This document - and specifically the archive Web site portal - is intended to be a 'living' document that will be updated continually as additional cores are collected and archived. This document may also contain future references and links to a catalog of sediment cores. Sediment cores will include vibracores, pushcores, and other loose sediment samples collected for research purposes. This document will: (1) serve as a database for locating core material currently archived at the USGS SPCMSC facility; (2) provide a protocol for entry of new core material into the archive system; and, (3) set the procedures necessary for checking out core material for scientific purposes. Core material may be loaned to other governmental agencies, academia, or non-governmental organizations at the discretion of the USGS SPCMSC curator.

Data Series↗
USGS2017

Evolutionary dynamics of an expressed MHC class IIβ locus in the Ranidae (Anura) uncovered by genome walking and high-throughput amplicon sequencing

The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and disease resistance. Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class IIβ chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a range of anuran taxa.

Developmental and Comparative Immunology↗
USGS2015

The U.S. Geological Survey Geologic Collections Management System (GCMS)—A master catalog and collections management plan for U.S. Geological Survey geologic samples and sample collections

**Updated guidance is available in USGS Instructional Memorandum CSS 2019-01 .** Abstract The U.S. Geological Survey (USGS) is widely recognized in the earth science community as possessing extensive collections of earth materials collected by research personnel over the course of its history. In 2006, a Geologic Collections Inventory was conducted within the USGS Geology Discipline to determine the extent and nature of its sample collections, and in 2008, a working group was convened by the USGS National Geologic and Geophysical Data Preservation Program to examine ways in which these collections could be coordinated, cataloged, and made available to researchers both inside and outside the USGS. The charge to this working group was to evaluate the proposition of creating a Geologic Collections Management System (GCMS), a centralized database that would (1) identify all existing USGS geologic collections, regardless of size, (2) create a virtual link among the collections, and (3) provide a way for scientists and other researchers to obtain access to the samples and data in which they are interested. Additionally, the group was instructed to develop criteria for evaluating current collections and to establish an operating plan and set of standard practices for handling, identifying, and managing future sample collections. Policies and procedures promoted by the GCMS would be based on extant best practices established by the National Science Foundation and the Smithsonian Institution. The resulting report—USGS Circular 1410, “The U.S. Geological Survey Geologic Collections Management System (GCMS): A Master Catalog and Collections Management Plan for U.S. Geological Survey Geologic Samples and Sample Collections”—has been developed for sample repositories to be a guide to establishing common practices in the collection, retention, and disposal of geologic research materials throughout the USGS. While constructing this report, the GCMS’s potential customers and their needs were considered. Two critical definitions have been clarified: a repository is a facility for the long-term management of geologic collections, and a collection is a set of specimens that have been brought together on the basis of some common characteristic. Required sample metadata for newly collected samples, as well as for older collections, were also stipulated and are listed and explained in this report. Several basic policies are also recommended by the GCMS in order to standardize operations among the physical repositories where collections are currently housed. The GCMS Collection Management Plan provides a set of protocols and templates for the management of scientific collections, including access, storage, transfer, and disposal of physical geologic samples and data. This plan is flexible to allow each repository to adapt the practices best suited to its collections. The general consideration for implementation of the GCMS is that all active USGS geologic sample repositories will form the core of GCMS and that participating science centers will develop procedures based on proposed GCMS methodologies. The GCMS is a collective resource for the entire USGS community and the users who discover the geologic materials kept in these repositories and seek to access them.

Circular↗
USGS2004

Review of Results and Recommendations from the GCMRC 2000-2003 Remote-Sensing Initiative for Monitoring Environmental Resources Within the Colorado River Ecosystem

In mid-2000, the Grand Canyon Monitoring and Research Center (GCMRC) began a remote-sensing initiative to evaluate all remote-sensing technologies and methods that had potential for providing improved data (capability) for its various programs that monitor the Colorado River ecosystem (CRE). The primary objective of the initiative was to determine the most cost-effective data collection protocols for GCMRC programs that (1) provide the accuracies required for currently measured parameters, (2) provide additional parameters for ecological monitoring, (3) reduce environmental impact by being less invasive than current methods, and (4) expand geographic extent of current ground approaches. The initial phase of the remote-sensing initiative determined the types of sampling parameters and their required accuracies for monitoring. This information was used to determine the most appropriate sensors for evaluation. The initiative evaluated 25 different data collections over a three-year period; many more remote-sensing instruments were considered, but were not evaluated because they could not meet the basic requirements on spatial resolution, wavelength, positional accuracy, or elevation accuracy. It was hoped that the evaluations would lead to a minimum set of technologies that would satisfy many program requirements. The results from all of our evaluations are reviewed in this report and are briefly summarized in this report.

Open-File Report↗
USGS2008

Winter bird population studies and project prairie birds for surveying grassland birds

We compared 2 survey methods for assessing winter bird communities in temperate grasslands: Winter Bird Population Study surveys are area-searches that have long been used in a variety of habitats whereas Project Prairie Bird surveys employ active-flushing techniques on strip-transects and are intended for use in grasslands. We used both methods to survey birds on 14 herbaceous reforested sites and 9 coastal pine savannas during winter and compared resultant estimates of species richness and relative abundance. These techniques did not yield similar estimates of avian populations. We found Winter Bird Population Studies consistently produced higher estimates of species richness, whereas Project Prairie Birds produced higher estimates of avian abundance for some species. When it is important to identify all species within the winter bird community, Winter Bird Population Studies should be the survey method of choice. If estimates of the abundance of relatively secretive grassland bird species are desired, the use of Project Prairie Birds protocols is warranted. However, we suggest that both survey techniques, as currently employed, are deficient and recommend distance- based survey methods that provide species-specific estimates of detection probabilities be incorporated into these survey methods.

Southeastern Naturalist↗
USGS2014

Reach-scale comparison of habitat and mollusk assemblages for select sites in the Clinch River with regional context

Several hypotheses, including habitat degradation and variation in fluvial geomorphology, have been posed to explain extreme spatial and temporal variation in Clinch River mollusk assemblages. We examined associations between mollusk assemblage metrics (richness, abundance, recruitment) and physical habitat (geomorphology, streambed composition, fish habitat, and riparian condition) at 10 sites selected to represent the range of current assemblage condition in the Clinch River. We compared similar geomorphological units among reaches, employing semi-quantitative and quantitative protocols to characterize mollusk assemblages and a mix of visual assessments and empirical measurements to characterize physical habitat. We found little to no evidence that current assemblage condition was associated with 54 analyzed habitat metrics. When compared to other sites in the Upper Tennessee River Basin (UTRB) that once supported or currently support mollusk assemblages, Clinch River sites were more similar to each other, representing a narrower range of conditions than observed across the larger geographic extent of the UTRB. A post-hoc analysis suggested stream size and average boundary shear stress at bankfull stage may have historically limited species richness in the UTRB (p < 0.001). Associations between mollusk assemblages and physical habitat in the UTRB and Clinch River currently appear obscured by other factors limiting richness, abundance, and recruitment.

Tennessee, Virginia↗