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At least 127 records · Page 7Linked to original sources
USGS2026

Survey protocols drive heterogeneity in occupancy estimates that cannot be standardized using post hoc analyses

Site occupancy models are widely used to estimate species distributions from presence–nondetection data, yet for mobile animals, the true proportion of sites occupied varies in time. Thus, true occupancy and estimates generated from different protocols are affected by temporal characteristics of survey design. Here we tested whether we could standardize occupancy estimates across different sampling protocols with a post hoc statistical test. Using an individual-based movement model of Wood Thrush ( Hylocichla mustelina ), we simulated point count surveys across 3000 populations under 90 spatially and temporally variable sampling protocols. For each simulation, we fit a standard occupancy model, then used minute-level detections to truncate surveys and generate occupancy estimates across increasing survey lengths. We fit asymptotic models to these series to estimate intercepts (instantaneous occupancy) and asymptotes (longer-term occupancy) and evaluated how well they approximated true instantaneous, daily and seasonal occupancy. We were unable to recover instantaneous or seasonal occupancy from any approach. Both standard occupancy models and asymptotic regression (the top-performing asymptotic model) most closely approximated daily occupancy; although asymptotic regression produced slightly less biased estimates, it showed substantially greater variability, resulting in greater overall error. Our results show that post hoc analytical approaches cannot, at present, reliably standardize occupancy estimates across heterogeneous survey designs. Instead, ensuring biologically informative and comparable estimates will depend on standardized survey protocols. Practical implication : Monitoring programs using presence–nondetection data should prioritize consistent survey protocols when estimating occupancy for mobile species, with a focus on daily occupancy as the most attainable and useful metric. Although the highest accuracy and precision were achieved under the most intensive survey protocols, for point counts of Wood Thrush and similar species, four consecutive 15–20 min surveys provide near-optimal precision and can be completed in a single visit, making them well suited for estimating relative occupancy under logistical constraints. Three 20-min surveys spaced ~24 h apart closely approximate daily occupancy while maintaining reasonable precision. Developing similar protocols for other species and survey methods will be critical to ensuring comparable occupancy estimates across space and time.

Ecological Solutions and Evidence↗
USGS2015

Modeling risk of pneumonia epizootics in bighorn sheep

Pneumonia epizootics are a major challenge for management of bighorn sheep ( Ovis canadensis ) affecting persistence of herds, satisfaction of stakeholders, and allocations of resources by management agencies. Risk factors associated with the disease are poorly understood, making pneumonia epizootics hard to predict; such epizootics are thus managed reactively rather than proactively. We developed a model for herds in Montana that identifies risk factors and addresses biological questions about risk. Using Bayesian logistic regression with repeated measures, we found that private land, weed control using domestic sheep or goats, pneumonia history, and herd density were positively associated with risk of pneumonia epizootics in 43 herds that experienced 22 epizootics out of 637 herd-years from 1979–2013. We defined an area of high risk for pathogen exposure as the area of each herd distribution plus a 14.5-km buffer from that boundary. Within this area, the odds of a pneumonia epizootic increased by >1.5 times per additional unit of private land (unit is the standardized % of private land where global  = 25.58% and SD = 14.53%). Odds were >3.3 times greater if domestic sheep or goats were used for weed control in a herd's area of high risk. If a herd or its neighbors within the area of high risk had a history of a pneumonia epizootic, odds of a subsequent pneumonia epizootic were >10 times greater. Risk greatly increased when herds were at high density, with nearly 15 times greater odds of a pneumonia epizootic compared to when herds were at low density. Odds of a pneumonia epizootic also appeared to decrease following increased spring precipitation (odds = 0.41 per unit increase, global  = 100.18% and SD = 26.97%). Risk was not associated with number of federal sheep and goat allotments, proximity to nearest herds of bighorn sheep, ratio of rams to ewes, percentage of average winter precipitation, or whether herds were of native versus mixed or reintroduced origin. We conclude that factors associated with risk of pneumonia epizootics are complex and may not always be from the most obvious sources. The ability to identify high-risk herds will help biologists and managers determine where to focus management efforts and the risk factors that most affect each herd, facilitating more effective, proactive management.

Journal of Wildlife Management↗
USGS2025

Effects of nonmotorized recreation on ungulates in the western United States—A science synthesis to inform National Environmental Policy Act analyses

The U.S. Geological Survey is working with Federal land management agencies to develop a series of science syntheses to support National Environmental Policy Act (NEPA) analyses. This report synthesizes science information about the potential effects of nonmotorized recreation on ungulates in the western United States. We conducted a structured literature search to find published science, data, and analysis methods about the characteristics of nonmotorized recreation, ungulate exposure and response to nonmotorized recreation, and approaches to mitigate negative effects of nonmotorized recreation on ungulates. The sections of the report align with standard elements of the NEPA analysis process. We found that timing, intensity, duration, and spatial distribution of nonmotorized recreation are important factors to understand when assessing effects of recreation on ungulates. Several aspects of ungulate biology, which vary by species, population, and individual, affect ungulate susceptibility to effects from recreation, including diet, migration and movement, and seasonal biology. Techniques for assessing effects include basic spatial analyses based on buffers around trails and recreation sites and more technical analytical methods based on displacement or avoidance of recreation sites. Options for mitigating negative effects of nonmotorized recreation on ungulates include timing and type-of-use restrictions, recreator education, and project design features to avoid human-ungulate conflicts. Public land managers can use this report by incorporating it by reference in NEPA analyses or as a general reference to find literature or identify gaps in the literature about the effects of noise from nonmotorized recreation on ungulates.

Scientific Investigations Report↗
USGS2012

The Mekong Fish Network: expanding the capacity of the people and institutions of the Mekong River Basin to share information and conduct standardized fisheries monitoring

The Mekong River is one of the most biologically diverse rivers in the world, and it supports the most productive freshwater fisheries in the world. Millions of people in the Lower Mekong River Basin (LMB) countries of the Union of Myanmar (Burma), Lao People’s Democratic Republic, the Kingdom of Thailand, the Kingdom of Cambodia, and the Socialist Republic of Vietnam rely on the fisheries of the basin to provide a source of protein. The Mekong Fish Network Workshop was convened in Phnom Penh, Cambodia, in February 2012 to discuss the potential for coordinating fisheries monitoring among nations and the utility of establishing standard methods for short- and long-term monitoring and data sharing throughout the LMB. The concept for this network developed out of a frequently cited need for fisheries researchers in the LMB to share their knowledge with other scientists and decisionmakers. A fish monitoring network could be a valuable forum for researchers to exchange ideas, store data, or access general information regarding fisheries studies in the LMB region. At the workshop, representatives from governments, nongovernmental organizations, and universities, as well as participating foreign technical experts, cited a great need for more international cooperation and technical support among them. Given the limited staff and resources of many institutions in the LMB, the success of the proposed network would depend on whether it could offer tools that would provide benefits to network participants. A potential tool discussed at the workshop was a user-friendly, Web-accessible portal and database that could help streamline data entry and storage at the institutional level, as well as facilitate communication and data sharing among institutions. The workshop provided a consensus to establish pilot standardized data collection and database efforts that will be further reviewed by the workshop participants. Overall, workshop participants agreed that this is the type of support that is greatly needed to answer their most pressing questions and to enable local researchers and resource managers to monitor and sustain the valuable and diverse aquatic life of the Mekong River.

Mekong River↗
USGS2009

Vegetation classification and distribution mapping report: Mesa Verde National Park

The classification and distribution mapping of the vegetation of Mesa Verde National Park (MEVE) and surrounding environment was achieved through a multi-agency effort between 2004 and 2007. The National Park Service’s Southern Colorado Plateau Network facilitated the team that conducted the work, which comprised the U.S. Geological Survey’s Southwest Biological Science Center, Fort Collins Research Center, and Rocky Mountain Geographic Science Center; Northern Arizona University; Prescott College; and NatureServe. The project team described 47 plant communities for MEVE, 34 of which were described from quantitative classification based on f eld-relevé data collected in 1993 and 2004. The team derived 13 additional plant communities from field observations during the photointerpretation phase of the project. The National Vegetation Classification Standard served as a framework for classifying these plant communities to the alliance and association level. Eleven of the 47 plant communities were classified as “park specials;” that is, plant communities with insufficient data to describe them as new alliances or associations. The project team also developed a spatial vegetation map database representing MEVE, with three different map-class schemas: base, group, and management map classes. The base map classes represent the fi nest level of spatial detail. Initial polygons were developed using Definiens Professional (at the time of our use, this software was called eCognition), assisted by interpretation of 1:12,000 true-color digital orthophoto quarter quadrangles (DOQQs). These polygons (base map classes) were labeled using manual photo interpretation of the DOQQs and 1:12,000 true-color aerial photography. Field visits verified interpretation concepts. The vegetation map database includes 46 base map classes, which consist of associations, alliances, and park specials classified with quantitative analysis, additional associations and park specials noted during photointerpretation, and non-vegetated land cover, such as infrastructure, land use, and geological land cover. The base map classes consist of 5,007 polygons in the project area. A field-based accuracy assessment of the base map classes showed overall accuracy to be 43.5%. Seven map classes comprise 89.1% of the park vegetated land cover. The group map classes represent aggregations of the base map classes, approximating the group level of the National Vegetation Classification Standard, version 2 (Federal Geographic Data Committee 2007), and reflecting physiognomy and floristics. Terrestrial ecological systems, as described by NatureServe (Comer et al. 2003), were used as the fi rst approximation of the group level. The project team identified 14 group map classes for this project. The overall accuracy of the group map classes was determined using the same accuracy assessment data as for the base map classes. The overall accuracy of the group representation of vegetation was 80.3%. In consultation with park staff , the team developed management map classes, consisting of park-defined groupings of base map classes intended to represent a balance between maintaining required accuracy and providing a focus on vegetation of particular interest or import to park managers. The 23 management map classes had an overall accuracy of 73.3%. While the main products of this project are the vegetation classification and the vegetation map database, a number of ancillary digital geographic information system and database products were also produced that can be used independently or to augment the main products. These products include shapefiles of the locations of field-collected data and relational databases of field-collected data.

Mesa Verde National Park↗
USGS2020

Supporting the development and use of native plant materials for restoration on the Colorado Plateau (Fiscal Year 19 Report)

A primary focus of the Bureau of Land Management’s (BLM’s) Colorado Plateau Native Plant Program (CPNPP) is to identify and develop appropriate native plant materials (NPMs) for current and future restoration projects. Multiple efforts have characterized the myriad challenges inherent in providing appropriate seed resources to enable effective, widespread restoration and have identified a broad suite of research activities to provide the information necessary to overcome those challenges (e.g., Plant Conservation Alliance 2015; Breed et al. 2018; Winkler et al. 2018). Many of the most complex information needs relate to identifying the appropriate sources of plant species that can successfully establish in dryland environments, like the Colorado Plateau, where low and highly variable precipitation is standard. Providing this information requires synergistic research efforts in which results from earlier investigations inform the design of subsequent investigations. The U.S. Geological Survey Southwest Biological Science Center’s (SBSC’s) research activities in FY19 followed an FY19 Statement of Work to support a research framework that is continually adapting based on the needs of the restoration community and results from previous investigations; the long-term research framework is outlined in the 2019-2023 5-Year Research Strategy (hereafter referred to as the 5-year plan). This research framework provides support for the National Seed Strategy for Rehabilitation and Restoration (Plant Conservation Alliance, 2015), Department of Interior Secretarial Order #3347 (Conservation Stewardship and Outdoor Recreation), and Department of Interior Leadership Priority #1 (Create a conservation stewardship legacy second only to Teddy Roosevelt). Research activities in FY19 centered on landscape genetics, collecting seeds in preparation for experimental common gardens, and planning and trials in support of experimental drought gardens. These activities were supported by three biological technicians, one of which was jointly funded by the Ecological Society of America for six pay periods. Most of the field-related activities, including plant trait measurement, seed/tissue collecting, and GRID (Germination for Restoration Information and Decision-making) experimental treatments at the Canyonlands Research Center near Moab, UT were assigned to these technicians. Contrary to the drought conditions the pervaded the Colorado Plateau in FY18, plentiful spring precipitation resulted in easily-collected plant tissue and seed collections. However, the cool and wet spring delayed the phenology of early blooming species, which caused difficulties for timing seed collecting. Furthermore, seed collecting for late blooming species was difficult because of lower than average monsoon precipitation. While Dr. Rob Massatti was the only scientist supported by the SBSC-CPNPP agreement in FY19, other scientists, including Drs. John Bradford, Seth Munson, Mike Duniway, Sasha Reed, and Daniel Winkler, spent a considerable amount of time providing expert guidance and support for individual projects. Work activities performed in support of each 5-year plan goal are discussed in turn.

Arizona, Colorado, New Mexico, Utah↗
USGS2023

Review and development of best practices for toxicity tests with dreissenid mussels

Since their introduction to North America in the 1980s, research to develop effective control tools for invasive mussels ( Dreissena polymorpha and D. rostriformis bugensis ) has been ongoing across various research institutions using a range of testing methods. Inconsistencies in experimental methods and reporting present challenges for comparing data, repeating experiments, and applying results. The Invasive Mussel Collaborative established the Toxicity Testing Work Group (TTWG) in 2019 to identify “best practices” and guide development of a standard framework for dreissenid mussel toxicity testing protocols. We reviewed the literature related to laboratory-based dreissenid mussel toxicity tests and determined the degree to which standard guidelines have been used and their applicability to dreissenid mussel testing. We extracted detailed methodology from 99 studies from the peer-reviewed and gray literature and conducted a separate analysis for studies using presettlement and postsettlement mussels. We identified specific components of methods and approaches that could be refined or standardized for dreissenid mussels. These components included species identification, collection methods, size/age class distinction, maintenance practices, testing criteria, sample size, response measures, reporting parameters, exposure methods, and mortality criteria. We consulted experts in the field of aquatic toxicology and dreissenid mussel biology on our proposed. The final recommendations contained in the present review are based on published standard guidelines, methods reported in the published and gray literature, and the expertise of TTWG members and an external panel. In addition, our review identifies research needs for dreissenid mussel testing including improved methods for early–life stage testing, comparative data on life stages and between dreissenid mussel species, inclusion of a reference toxicant, and additional testing of nontarget species (i.e., other aquatic organisms). Environ Toxicol Chem 2023;42:1649–1666. © 2023 His Majesty the King in Right of Canada. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. Reproduced with the permission of the Minister of Environment and Climate Change Canada. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Environmental Toxicology and Chemistry↗
USGS2022

Comparison of methods for estimating density and population trends for low-density Asian bears

Populations of bears in Asia are vulnerable to extinction and effective monitoring is critical to measure and direct conservation efforts. Population abundance (local density) or growth (λ ) are the most sensitive metrics to change. We discuss the value in implementing spatially explicit capture-recapture (SCR), the current gold standard for density estimation, and open population SCR (OPSCR) to monitor changes in density over time. We provide guidance for designing studies to provide estimates with sufficient power to detect changes. Because of the wide availability of camera traps and interest in their use, we consider six density estimation methods and their extensions developed for use with camera traps, with specific consideration of assumptions and applications for monitoring Asian bears. We conducted a power analysis to calculate the precision in estimates needed to detect changes in populations with reference to IUCN Red List criteria. We performed a systematic review of empirical studies implementing camera trap abundance estimation methods and considered sample sizes, effort, and model assumptions required to achieve adequate precision for population monitoring. We found SCR and OPSCR, reliant on “marked” individuals, are currently the only methods with enough power to reliably detect even moderate to major (20–80%) declines. Camera trap methods with unmarked individuals rarely achieved precision sufficient to detect even large declines (80–90%), although with some exceptions (e.g., situations with moderate population densities, large number of sampling sites, or inclusion of ancillary local telemetry data. We describe additional estimation options including line transects, direct observations, monitoring age-specific survival and reproductive rates, and hybrid/integrated methodologies that may have potential to work for some Asian bear populations. We conclude monitoring changes in abundance or density is possible for most Asian bear populations but will require collaboration among researchers over broad spatial extents and extensive financial investment to overcome biological and logistical constraints. We strongly encourage practitioners to consider study design and sampling effort required to meet objectives by conducting simulations, power analyses, and assumption checks prior to implementing monitoring efforts, and reporting standardized dispersion measures such as coefficients of variation to allow for assessment of precision. Our guidance is relevant to other low-density and wide-ranging species.

Global Ecology and Conservation↗
USGS2023

Supporting the development and use of native plant materials for restoration on the Colorado Plateau (Fiscal Year 2022 Report)

A primary focus of the Colorado Plateau Native Plant Program (CPNPP) is to identify and develop appropriate native plant materials (NPMs) for current and future restoration projects. Multiple efforts have characterized the myriad challenges inherent in providing appropriate seed resources to enable effective, widespread restoration and have identified a broad suite of research activities to provide the information necessary to overcome those challenges (e.g., Plant Conservation Alliance, 2015; Breed et al., 2018; Winkler et al., 2018; NASEM, 2023). Many of the most complex information needs relate to identifying the appropriate sources of plant species that can successfully establish in dryland environments, like the Colorado Plateau, where low and highly variable precipitation is standard. Providing this information requires synergistic research efforts in which results from earlier investigations inform the design of subsequent investigations. The U.S. Geological Survey (USGS) Southwest Biological Science Center’s (SBSC’s) research activities to support CPNPP in FY22 followed the FY22 Statement of Work to support a research framework that is continually adapting based on the needs of the restoration community and results from previous investigations; the long-term research framework is outlined in the 2019-2023 5-Year Research Strategy (hereafter referred to as the 5-year plan). This research framework provides support for the National Seed Strategy for Rehabilitation and Restoration (Plant Conservation Alliance, 2015), Biden-Harris Administration Executive Order 14008 (Tackling the Climate Crisis at Home and Abroad), and Department of Interior Priority #4 (Working to conserve at least 30% each of our lands and waters by the year 2030). Research activities in FY22 centered on landscape genomics, monitoring common garden and seeding experiments near Vernal and Moab, UT, conducting experimental treatments using the GRID (Germination for Restoration Information and Decision-making) framework, and continuing newer genetics projects to investigate the impact of productions techniques on plant materials and restoration treatments on native plant communities. These activities were supported by two biological science technicians. The effects of the SARS-CoV-2 pandemic were less visible in FY22, allowing SBSC to catch up on backlogged laboratory work. The overall progress of SBSC’s research remains on track with respect to the 5-year plan. While Dr. Rob Massatti was the only scientist supported by the SBSC-CPNPP agreement in FY22, other scientists, including Drs. John Bradford, Seth Munson, Mike Duniway, Sasha Reed, and Daniel Winkler, spent a considerable amount of time providing expertise and support for individual projects. Work activities performed in support of each 5-year plan goal are discussed in turn.

Colorado Plateau↗
USGS2022

Supporting the development and use of native plant materials for restoration on the Colorado Plateau (Fiscal Year 2021 Report)

A primary focus of the Colorado Plateau Native Plant Program (CPNPP) is to identify and develop appropriate native plant materials (NPMs) for current and future restoration projects. Multiple efforts have characterized the myriad challenges inherent in providing appropriate seed resources to enable effective, widespread restoration and have identified a broad suite of research activities to provide the information necessary to overcome those challenges (e.g., Plant Conservation Alliance 2015; Breed et al. 2018; Winkler et al. 2018; McCormick et al. 2021). Many of the most complex information needs relate to identifying the appropriate sources of plant species that can successfully establish in dryland environments, like the Colorado Plateau, where low and highly variable precipitation is standard. Providing this information requires synergistic research efforts in which results from earlier investigations inform the design of subsequent investigations. The U.S. Geological Survey (USGS) Southwest Biological Science Center’s (SBSC’s) research activities to support CPNPP in FY21 followed the FY21 Statement of Work to support a research framework that is continually adapting based on the needs of the restoration community and results from previous investigations; the long-term research framework is outlined in the 2019-2023 5-Year Research Strategy (hereafter referred to as the 5-year plan). This research framework provides support for the National Seed Strategy for Rehabilitation and Restoration (Plant Conservation Alliance 2015), Biden-Harris Administration Executive Order 14008 (Tackling the Climate Crisis at Home and Abroad), and Department of Interior Priority #4 (Working to conserve at least 30% each of our lands and waters by the year 2030). Research activities in FY21 centered on landscape genomics, implementing and monitoring a common garden experiment near Vernal, UT, conducting experimental treatments using the GRID (Germination for Restoration Information and Decision-making) framework, and initiating new genetics projects to investigate the impact of production techniques on plant materials and restoration treatments on native plant communities. These activities were supported by four biological science technicians. The SARS-CoV-2 pandemic delayed some aspects of the FY21 workplan, especially for outside laboratory services. However, goals were largely met, and the overall progress of research remains on track with respect to the 5-year plan. While Dr. Rob Massatti was the only scientist supported by the SBSC-CPNPP agreement in FY21, other scientists, including Drs. John Bradford, Seth Munson, Mike Duniway, Sasha Reed, and Daniel Winkler, spent a considerable amount of time providing expertise and support for individual projects. Work activities performed in support of each 5-year plan goal are discussed in turn. Products resulting from FY21 research activities are reported in Appendix 1.

Arizona, Colorado, New Mexico, Utah↗
USGS2018

Bend-scale geomorphic classification and assessment of the Lower Missouri River from Sioux City, Iowa, to the Mississippi River for application to pallid sturgeon management

Management actions intended to increase growth and survival of pallid sturgeon ( Scaphirhynchus albus ) age-0 larvae on the Lower Missouri River require a comprehensive understanding of the geomorphic habitat template of the river. The study described here had two objectives relating to where channel-reconfiguration projects should be located to optimize effectiveness. The first objective was to develop a bend-scale (that is, at the scale of individual bends, defined as “cross-over to cross-over”) geomorphic classification of the Lower Missouri River to help in the design of monitoring and evaluation of such projects. The second objective was to explore whether geomorphic variables could provide insight into varying capacities of bends to intercept drifting larvae. The bend-scale classification was based on geomorphic and engineering variables for 257 bends from Sioux City, Iowa, to the confluence with the Mississippi River near St. Louis, Missouri. We used k-means clustering to identify groupings of bends that shared the same characteristics. Separate 3-, 4-, and 6-cluster classifications were developed and mapped. The three classifications are nested in a hierarchical structure. We also explored capacities of bends to intercept larvae through evaluation of linear models that predicted persistent sand area or catch per unit effort (CPUE) of age-0 sturgeon as a function of the same geomorphic variables used in the classification. All highly ranked models that predict persistent sand area contained mean channel width and standard deviation of channel width as significant variables. Some top-ranked models also included contributions of channel sinuosity and density of navigation structures. The sand-area prediction models have r-squared values of 0.648–0.674. In contrast, the highest-ranking CPUE models have r-squared values of 0.011–0.170, indicating much more uncertainty for the biological response variable. Whereas the persistent sand model documents that physical processes of transport and accumulation are systematic and predictable, the poor performance of the CPUE models indicate that additional processes will need to be considered to predict biological transport and accumulation.

Iowa, Missouri↗
USGS2025

Estimating occupancy of focal bee species

Current bee monitoring efforts have a limited capacity for understanding factors affecting wild bee population changes, including the effects of management. To improve the effectiveness of wild bee monitoring, we first discuss principles of biological monitoring and provide a framework to design monitoring projects to estimate species occupancy, where occupancy is defined as the probability that a Sampling Unit or site is occupied by the focal species. Monitoring practitioners should first define the desired goal or question of monitoring and secondly select the appropriate state variable for monitoring ( e.g ., species richness, occupancy, abundance). These represent two critical, yet often overlooked, steps in the development of wild bee monitoring projects. As with all forms of demographic monitoring, practitioners who are interested in estimating species occupancy will need to develop a sampling scheme tailored to meet their monitoring objectives. Defining key sampling terms will provide the architecture of their scheme, including the Area of Interest, Sampling Unit, Season, and Replicate Survey. We also highlight data standards, including core data fields that must be collected during Surveys for bee occupancy data and additional, recommended data fields . We illustrate how these monitoring concepts are being applied to the design of a real-world monitoring project for the federally endangered rusty patched bumble bee ( Bombus affinis Cresson). This framework was developed in association with the U.S. National Native Bee Monitoring Network.

Journal of Melittology↗
USGS2003

Seabird tissue archival and monitoring project: Egg collections and analytical results 1999-2002

In 1998, the U.S. Geological Survey Biological Resources Division (USGS-BRD), the U.S. Fish and Wildlife Service (USFWS) Alaska Maritime National Wildlife Refuge (AMNWR), and the National Institute of Standards and Technology (NIST) began the Seabird Tissue Archival and Monitoring Project (STAMP) to collect and cryogenically bank tissues from seabirds in Alaska for future retrospective analysis of anthropogenic contaminants. The approach of STAMP was similar to that of the Alaska Marine Mammal Tissue Archival Project (AMMTAP). AMMTAP was started in 1987 by NIST and the National Oceanic and Atmospheric Administration (NOAA) as part of the Outer Continental Shelf Environmental Assessment Program sponsored by the Minerals Management Service. Presently sponsored by the USGS-BRD, AMMTAP continues its work as part of a larger national program, the Marine Mammal Health and Stranding Response Program. AMMTAP developed carefully designed sampling and specimen banking protocols. Since 1987, AMMTAP has collected tissues from marine mammals taken in Alaska Native subsistence hunts and has cryogenically banked these tissues at the NIST National Biomonitoring Specimen Bank (NBSB). Through its own analytical work and working in partnership with other researchers both within and outside Alaska, AMMTAP has helped to develop a substantial database on contaminants in Alaska marine mammals. In contrast, data and information is limited on contaminants in Alaska seabirds, which are similar to marine mammals in that they feed near the top of the food chain and have the potential for accumulating anthropogenic contaminants. During its early planning stages, STAMP managers identified the seabird egg as the first tissue of choice for study by the project. There is a relatively long history of using bird eggs for environmental monitoring and for investigating the health status of bird populations. Since 1998, protocols for collecting and processing eggs, and cryogenically banking egg samples have been developed by STAMP (see York et al. 2001). Eggs are being collected on an annual basis for several species at nesting colonies throughout Alaska. Aliquots of these egg samples are being analyzed on a regular basis for persistent organic pollutants and mercury. Results of this work have been published in scientific journals (Christopher et al. 2002) and in conference proceedings (Kucklick et al. 2002; Vander Pol et al. 2002a, 2002b). The intent of this report is to provide an up-to-date description of STAMP. The report contains the most recent egg collection inventory, analytical data, preliminary interpretations based on these data, and a discussion of possible future directions of the project.

Report↗
USGS2010

Vegetation classification and distribution mapping report: Canyon de Chelly National Monument

Executive Summary: The classification and distribution mapping of the vegetation of Canyon de Chelly National Monument (CACH) and surrounding environment was accomplished through a multi-agency effort between 2003 and 2007. The National Park Service’s Southern Colorado Plateau Network facilitated the team that conducted the work, which comprised the U.S. Geological Survey’s Southwest Biological Science Center and Fort Collins Science Center, Navajo Natural Heritage Program, Northern Arizona University, and NatureServe. The project team described 48 plant communities for CACH—35 of which were described from quantitative classification based on field-relevé data collected in 2004. Five additional plant communities were based on field relevés collected in a previous study. The team derived four additional plant communities from field observations during the photointerpretation phase of the project, and field documented them during accuracy assessment. The National Vegetation Classification Standard served as a conceptual framework for assigning these plant communities to the alliance and association level. Ten of the 48 plant communities were designated “park specials”, that is, plant communities with insufficient data to describe them as new alliances or associations. The project team also developed a spatial vegetation map database representing CACH, with three different map-class schemas: base, group, and management map classes. The base map classes represented the finest level of spatial detail. Photointerpreters delineated initial polygons through manual interpretation of 2003/2004 1:12,000-scale true color aerial photography supplemented by occasional computer screen digitizing on a mosaic of digitized aerial photos. These polygons were labeled with base map classes during photointerpretation. Field visits verified interpretation concepts. The vegetation map database includes • ? 53 base map classes, which consist of associations and park specials classified with the quantitative analysis • ? additional associations noted during photointerpretation • ? non-vegetated land cover, such as infrastructure, land use, and geological land cover. The base map classes consist of 4,718 polygons in the project area. A field-based accuracy assessment of the base map classes showed the overall accuracy to be 50.8% The group map classes represent aggregations of the base map classes, approximating the group level of the National Vegetation Classification Standard, Version 2 (Federal Geographic Data Committee 2008). Terrestrial ecological systems, as described by NatureServe (Comer et al. 2003), were used as a first approximation of the group level. The project team identified 16 group map classes in this project. The overall accuracy of the group map classes was determined using the same accuracy assessment data as for the base map classes. The overall accuracy of the group representation of vegetation was 79.9%. In consultation with park staff, the team developed management map classes that consisted of park-defined groupings of base map classes and were intended to represent a balance between maintaining required accuracy and providing a focus on vegetation of particular interest or import to park managers. The 28 management map classes have an overall accuracy of 77.1%. While the main products of this project are the vegetation classification and the vegetation map database, a number of ancillary geographic information system and digital database products were also produced that can be used independently, or to augment the main products. These products include shapefiles of the location of field-collected data and relational databases of field-collected data.

Report↗
USGS2001

Detection of bacteria from biological mixtures using immunomagnetic separation combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A rapid method for identifying specific bacteria from complex biological mixtures using immunomagnetic separation coupled to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has been developed. The technique employs commercially available magnetic beads coated with polycolonal antibodies raised against specific bacteria and whole cell analysis by MALDI-MS. A suspension of a bacterial mixture is mixed with the immunomagnetic beads specific for the target microorganism. After a short incubation period (20 mins) the bacteria captured by the beads are washed, resuspended in deionized H2O and directly applied onto a MALDI probe. Liquid suspensions containing bacterial mixtures can be screened within 1 h total analysis time. Positive tests result in the production of a fingerprint mass spectrum primarily consisting of protein biomarkers characteristic of the targeted microorganism. Using this procedure, Salmonella choleraesuis was isolated and detected from standard bacterial mixtures and spiked samples of river water, human urine, and chicken blood. Copyright ?? 2001 John Wiley & Sons, Ltd.

Rapid Communications in Mass Spectrometry↗
USGS2013

Phenology monitoring protocol: Northeast Temperate Network

Phenology is critical to many aspects of human life and nearly all ecological relationships and processes. Recent climate change has already led to widespread changes in phenological patterns across the globe, and more change is inevitable. This protocol has been developed to provide standardized methods for monitoring phenology within the National Park Service (NPS) Northeast Temperate Network (NETN), as part of the NPS Inventory and Monitoring Program (I&M). NETN encompasses the Appalachian National Scenic Trail (APPA), Acadia National Park (ACAD), the Boston Harbor Islands National Recreation Area (BOHA), and 10 national historical parks and national historic sites in the northeastern US. This protocol was developed in collaboration with and relies upon the procedures and infrastructure of the USA National Phenology Network (USA-NPN), including Nature’s Notebook , USA-NPN’s online plant and animal phenology observation program (www.nn.usanpn.org). Organized in 2007, USA-NPN is a nation-wide partnership among federal agencies, schools and universities, citizen volunteers, and others to monitor and understand the influence of seasonal cycles on the nation’s biological resources. The overall goal of NETN’s phenology monitoring program is to determine trends in the phenology of key species in order to assist park managers with the detection and mitigation of the effects of climate change on park resources. An additional programmatic goal is to interest and educate park visitors and staff, as well as a cadre of volunteer monitors.

National Park Service Natural Resource Report↗
USGS2005

Coral disease and health workshop: Coral histopathology II, July 12-14, 2005

The health and continued existence of coral reef ecosystems are threatened by an increasing array of environmental and anthropogenic impacts. Coral disease is one of the prominent causes of increased mortality among reefs globally, particularly in the Caribbean. Although over 40 different coral diseases and syndromes have been reported worldwide, only a few etiological agents have been confirmed; most pathogens remain unknown and the dynamics of disease transmission, pathogenicity and mortality are not understood. Causal relationships have been documented for only a few of the coral diseases, while new syndromes continue to emerge. Extensive field observations by coral biologists have provided substantial documentation of a plethora of new pathologies, but our understanding, however, has been limited to descriptions of gross lesions with names reflecting these observations (e.g., black band, white band, dark spot). To determine etiology, we must equip coral diseases scientists with basic biomedical knowledge and specialized training in areas such as histology, cell biology and pathology. Only through combining descriptive science with mechanistic science and employing the synthesis epizootiology provides will we be able to gain insight into causation and become equipped to handle the pending crisis. One of the critical challenges faced by coral disease researchers is to establish a framework to systematically study coral pathologies drawing from the field of diagnostic medicine and pathology and using generally accepted nomenclature. This process began in April 2004, with a workshop titled Coral Disease and Health Workshop: Developing Diagnostic Criteria co-convened by the Coral Disease and Health Consortium (CDHC), a working group organized under the auspices of the U.S. Coral Reef Task Force, and the International Registry for Coral Pathology (IRCP). The workshop was hosted by the U.S. Geological Survey, National Wildlife Health Center (NWHC) in Madison, Wisconsin and was focused on gross morphology and disease signs observed in the field. A resounding recommendation from the histopathologists participating in the workshop was the urgent need to develop diagnostic criteria that are suitable to move from gross observations to morphological diagnoses based on evaluation of microscopic anatomy. As a continuation of building the foundation and framework for coral disease diagnostics, the CDHC convened the Coral Disease and Health Workshop: Coral Histopathology II in Charleston, South Carolina, July 11-14, 2005. The workshop was hosted by the Department of Pathology and Laboratory Medicine at the Medical University of South Carolina, Charleston, SC which provided expertise, facilities and equipment in support of the workshop. All of the histological slides and related photographs used in the discussions were prepared and supplied by the IRCP. This workshop brought together 15 experts in veterinary and medical pathology and coral biology from national and international research institutes and government laboratories. The mission was to devise a standardized approach to examining microscopic anatomy and pathology of corals and a standardized nomenclature to facilitate accurate descriptions of the microscopic morphology of corals and enhance communication among specialists investigating causes of coral death. 2 The participants of this workshop deliberated for 3 days to refine the nomenclature for gross and microscopic anatomy of corals and systematically described microscopic changes associated with selected coral diseases. The findings and recommendations from the deliberations will be submitted to the research community for peer review. The standardized nomenclature and descriptions produced at this workshop will ultimately be made available to the scientific community through a variety of media including the World Wide Web. An exciting highlight of this meeting was provided by Professor Robert Ogilvie (MUSC Department of Cell Biology and Anatomy) when he introduced participants to a new digital technology that is revolutionizing histology and histopathology in the medical field. The Virtual Slide technology creates digital images of histological tissue sections by computer scanning actual slides in high definition and storing the images for retrieval and viewing. Virtual slides now allow any investigator with access to a computer and the web to view, search, annotate and comment on the same tissue sections in real time. Medical and veterinary slide libraries across the country are being converted into virtual slides to enhance biomedical education, research and diagnosis. The coral health and disease researchers at this workshop deem virtual slides as a significant way to increase capabilities in coral histology and a means for pathology consultations on coral disease cases on a global scale.

NOAA Technical Memorandum↗
USGS1986

Introduction to stream network habitat analysis

Increasing demands on stream resources by a variety of users have resulted in an increased emphasis on studies that evaluate the cumulative effects of basinwide water management programs. Network habitat analysis refers to the evaluation of an entire river basin (or network) by predicting its habitat response to alternative management regimes. The analysis principally focuses on the biological and hydrological components of the riv er basin, which include both micro- and macrohabitat. (The terms micro- and macrohabitat are further defined and discussed later in this document.) Both conceptual and analytic models are frequently used for simplifying and integrating the various components of the basin. The model predictions can be used in developing management recommendations to preserve, restore, or enhance instream fish habitat. A network habitat analysis should begin with a clear and concise statement of the study objectives and a thorough understanding of the institutional setting in which the study results will be applied. This includes the legal, social, and political considerations inherent in any water management setting. The institutional environment may dictate the focus and level of detail required of the study to a far greater extent than the technical considerations. After the study objectives, including species on interest, and institutional setting are collectively defined, the technical aspects should be scoped to determine the spatial and temporal requirements of the analysis. A macro level approach should be taken first to identify critical biological elements and requirements. Next, habitat availability is quantified much as in a "standard" river segment analysis, with the likely incorporation of some macrohabitat components, such as stream temperature. Individual river segments may be aggregated to represent the networkwide habitat response of alternative water management schemes. Things learned about problems caused or opportunities generated may be fed back to the design of new alternatives, which themselves may be similarly tested. One may get as sophisticated an analysis as the decisionmaking process demands. Figure 1 shows a decision point that asks whether the results from the micro- or macrohabitat models display cumulative or synergistic effects. If they do, then network habitat analysis is the appropriate tool. We are left, however, in a difficult bind. We may not know a priori whether the effects are cumulative or synergistic unless some network-type questions are investigated as part of the scoping process. The next several sections raise issues designed to alert the modeler to relevant questions necessary to address this paradox.

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