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USGS2007

Applying radar technology to migratory bird conservation and management: Strengthening and expanding a collaborative

Executive Summary Understanding the factors affecting migratory bird and bat populations during all three phases of their life cycle—breeding, nonbreeding, and migration—is critical to species conservation planning. This includes the need for information about these species’ responses to natural challenges, as well as information about the effects of human activities and structures. Habitats and other resources critical to migrants during passage and stopover are being destroyed, degraded, and threatened by human activities. Birds and bats are also uniquely susceptible to human use of the airspace. Wind turbines, communication and power transmission towers, and other tall structures, known to cause bird and bat mortality, are being erected or proposed in increasing numbers across the country. In addition, the potential for bird/aircraft collisions poses human safety threats. Management and regulatory agencies, conservation organizations, and industry currently lack the information they need to meet their missions and statutory responsibilities. The biological data available from various radar technologies offer a unique opportunity to learn more about the spatiotemporal distribution patterns, flight characteristics, and habitat use of “aero-fauna.” Recognizing the opportunities presented by radar technologies, the U.S. Geological Survey (USGS), the U.S. Fish and Wildlife Service (USFWS), and university partners collaborated first on individual projects and then in a broader, informal “collaborative” to coordinate their radar-related research and work together to develop the suite of products needed for conservation of birds and bats. Having produced two summary documents (Sojda and others, 2005; Ruth and others, 2005), the next objective was to convene a workshop for researchers, management and regulatory agencies, and other interested parties. The focus of this initial workshop was on strengthening the existing USGS-USFWS-university partnership and expanding the “collaborative” to include new Federal agency partners. The subject matter was centered on discussing available technologies, appropriate applications, management-related needs, and ways to strengthen collaborative research and conservation efforts. The workshop opened with presentations about the history of the “radar collaborative,” a description of the workshop objectives and focuses, and a summary of resource management and regulatory needs. Scientific presentations describing current research projects or subjects followed, given by USGS scientists, as well as scientists from other Federal agencies, academia, conservation and ornithological organizations, and a private contracting firm. Presenters addressed a wide variety of management issues including siting of wind-power facilities, bird/aircraft collisions, effects of hurricanes Katrina and Rita on bird migration, bird use of Conservation Reserve Program land, defining bird migration patterns at a broad regional scale, and associating migrant birds with their stopover habitats. Presentations described a variety of radar technologies including NEXRAD weather surveillance radar, modified mobile marine radar, military tracking radar, pencil beam radar, and dual polarization radar, as well as complementary techniques and analysis methods such as acoustic monitoring, thermal imaging, artificial intelligence, and individual-based modeling. Key issues, themes, and questions identified during the open discussions that followed fell into five main categories: (1) agency needs and challenges; (2) radar technology and applications—technical questions and issues; (3) tools and resources for managers and researchers; (4) standardization of protocols; and (5) collaborative opportunities. Participants identified the following management, regulatory, or business issues facing them which may be addressed with radar technologies: tall structures; wind turbines; identification and protection of key habitats; assessment of management activities; and bird/aircraft strikes. Participants frequently expressed the need for specific information about which radar technologies are best used for answering particular questions. User groups emphasized the importance of clear, defensible scientific information on which they can base their activities. In turn, researchers emphasized their need for clearly defined, specific questions from managers so that they can design and conduct the required research. Discussions about technical issues requiring further research and collaboration included target identity, ground-truthing, linking migrants to habitat, and standardized protocols for applied research. Workshop participants identified and endorsed a series of seven action items that would promote collaboration and begin to address key issues identified at the workshop: Action Item #1 : Establish a working subgroup to address large-scale surveillance radar standardization issues. Action Item #2 : Establish a working subgroup to address small-scale radar standardization issues. Action Item #3 : Bring management and regulatory agencies together to identify the three most important information needs for each key management issue relating to radar technologies. Action Item #4 : Develop Fact Sheet(s) to provide information about radar technology applications to migratory bird and bat conservation issues. Action Item #5 : Create a “radar collaborative” Website to provide information about radar biology applications, contacts, publications, and so forth. Action Item #6 : Formalize and expand the USGS-USFWS “radar collaborative.” Action Item #7 : Advance basic research, such as target identity and validation, which will support and improve our abilities to apply radar technologies to conservation objectives. There was considerable interest in expanding the “radar collaborative” to include those agencies, organizations, and industries represented at the workshop. It was felt that the publication of the workshop proceedings, implementation of action items, and additional future meetings or workshops will be crucial in strengthening the “radar collaborative” effort and promoting the use of these valuable technologies for conserving migratory species.

Open-File Report↗
USGS2014

Status and trends of Caribbean coral reefs: 1970-2012

This it the 9th status report since the Global Coral Reef Monitoring Network (GCRMN) was founded in 1995 was the data arm of the International Coral Reef Initiative (ICRI) to document the ecological condition or corral reefs, strengthen monitoring efforts, and link existing organizations and people working on reefs worldwide. The US Government provided the initial funding to help set up a global network of coral reef workers and has continued to provide core support. Since then, the series of reports have aimed to present the current status of coral reefs of the world or particular regions, the major threats to reefs and their consequences, and any initiative undertaken under the auspices of ICRI or other bodies to arrest or reverse the decline of coral reefs. IUCN assumed responsibility for hosting the global coordination of the GCRMN in 2010 under the scientific direction of Jeremy Jackson with the following objectives: 1. Document quantitatively the global status and trends for corals, macroalgae, sea urchins, and fishes based on available data from individual scientists as well as the peer reviewed scientific literature, monitoring programs, and report. 2. Bring together regional experts in a series of workshops to involve them in data compilation, analysis, and synthesis. 3. Integrate coral reef status and trends with independent environmental, management, and socioeconomic data to better understand the primary factors responsible for coral reef decline, the possible synergies among factors that may further magnify their impacts, and how these stresses may be more effectively alleviated. Work with GCRMN partners to establish simple and practical standardized protocols for future monitoring and assessment. Disseminate information and results to help guide member state policy and actions. The overarching objective is to understand why some reefs are much healthier than others, to identify what kinds of actions have been particularly beneficial or harmful, and to vigorously communicate results in simple and straightforward terms to foster more effective conservation and management. This and subsequent reports will focus on separate biogeographic regions in a stepwise fashion and combine all of the results for a global synthesis in the coming years. We began in the wide Caribbean region because the historical data are so extensive and to refine methods of analysis before moving on to other regions. This report documents quantitative trends for Caribbean reef corals, macroalgae, sea urchins, and fishes based on data from 90 reef locations over the past 43 tears. This is the first report to combine all these disparate kinds of data in a single place to explore how the different major components of coral reef ecosystems interact on a broadly regional oceanic scale. We obtained data from more than 35,000 ecological surveys carried out by 78 principal investigators (PIs) and some 200 colleagues working in 34 countries, states, and territories throughout the wide Caribbean region. We conducted two workshops in Panama and Brisbane, Australia to bring together people who provided the data to assist in data quality control, analysis, and synthesis. The first workshop at the Smithsonian Tropical Research Institute (STRI) in the Republic of Panama 29 April to 5 May, 2012 included scientists from 18 countries and territories to verify and expand the database and to conduct exploratory analyses of status and trends. Preliminary results based on the Panama workshop were presented to the DC Marine Community and Smithsonian Institution Senate of Scientists in May 2012 and at the International Coral Reef Symposium (ICRS) and annual ICRI meeting in Cairns, Australia in July 2012. The second workshop in Brisbane, Australia in December 2012 brought together eight coral reef scientists for more detailed data analysis and organization of results for this report and subsequent publications. Subsequent presentations to solicit comments while the report was being finalized were made in 2013-2014 at the ICRI General meeting in Belize, the biennial meeting of the Association of Island Marine Laboratories in Jamaica, the Panamerican Coral Reef Congress in Merida, Mexico, the annual meeting of he Western Society of Naturalists, and numerous universities in Costa Rica, the USA and Europe. The main body of the report is in two sections. Part I provides an overview of overall status and trends and detailed analyses of the multiple factors responsible for the decline of reef corals throughout the entire wider Caribbean region. The editors are grateful to all the people who have so generously provided data and expertise, but we assume responsibility for the many statements, conclusions and recommendations and final wording of the text. Part II provides a more detailed analysis of the status and trends of coral reef ecosystems in the 32 countries, states, and territories for which we have data. The format includes maps indicating all locations sampled, a detailed table of data sources and sites surveyed, timelines of ecologically important evens, and relevant references. Each of these reports was compiled in consultation with local experts and all those who provided data and advice are listed as authors of each country report.

Report↗
USGS2021

Chapter A6.4. Measurement of pH

The “National Field Manual for the Collection of Water-Quality Data” (NFM) provides guidelines and procedures for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation’s surface-water and groundwater resources. This chapter, NFM A6.4, provides guidance and protocols for the measurement of pH of a water sample, which include the scientific basis of the measurement, selection and maintenance of equipment, calibration, procedures for measurement and reporting, and troubleshooting. It updates and supersedes USGS Techniques of Water-Resources Investigations, book 9, chapter A6.4, version 2.0, by G.F. Ritz and J.A. Collins. The pH of natural waters is routinely measured when water samples are collected, is often measured continually at USGS streamgages, and is a parameter regularly measured during laboratory and field experiments. The field methods for measuring pH described in this chapter are applicable to most natural waters. Before 2017, the NFM chapters were released in the USGS Techniques of Water-Resources Investigations series. Effective in 2018, new and revised NFM chapters are being released in the USGS Techniques and Methods series; this series change does not affect the content and format of the NFM. More information is in the general introduction to the NFM (USGS Techniques and Methods, book 9, chapter A0) at https://doi.org/10.3133/tm9A0 . The authoritative current versions of NFM chapters are available in the USGS Publications Warehouse at https://pubs.er.usgs.gov/ . Comments, questions, and suggestions related to the NFM can be addressed to nfm@usgs.gov .

Techniques and Methods↗
USGS2019

Chapter A6.3. Specific Conductance

The “National Field Manual for the Collection of Water-Quality Data” (NFM) provides guidelines and procedures for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation’s surface-water and groundwater resources. This chapter, NFM A6.3, provides guidance and protocols for the measurement of specific conductance of a water sample, which include the scientific basis of the measurement, selection and maintenance of equipment, calibration, troubleshooting, and procedures for measurement and reporting. It updates and supersedes USGS Techniques of Water-Resources Investigations, book 9, chapter A6.3, version 1.2, by D.B. Radtke, J.V. Davis, and F.D. Wilde. Specific conductance is routinely measured when water samples are collected, is often measured continually at USGS streamgages, and is a parameter regularly measured during laboratory and field experiments. The field method for measuring specific conductance described in this chapter is applicable to most natural waters. Before 2017, the NFM chapters were released in the USGS Techniques of Water-Resources Investigations series. Effective in 2018, new and revised NFM chapters are being released in the USGS Techniques and Methods series; this series change does not affect the content and format of the NFM. More information is in the general introduction to the NFM (USGS Techniques and Methods, book 9, chapter A0) at https://doi.org/10.3133/tm9A0 . The authoritative current versions of NFM chapters are available in the USGS Publications Warehouse at https://pubs.er.usgs.gov. Comments, questions, and suggestions related to the NFM can be addressed to nfm@usgs.gov .

Techniques and Methods↗
USGS2007

Southern California Bight 2003 Regional Monitoring Program: V. water quality

More than $30 million is expended annually on environmental monitoring in the Southern California Bight (SCB), yet only 5% of the Bight is monitored on an ongoing basis. Therefore, environmental managers in the SCB decided to expand their monitoring program and, starting in 1994, decided to conduct periodic regional assessments of ecosystem condition and assess the overall health of the SCB. Sixty-five different organizations collaborated in 2003 to create the third SCB Regional Monitoring Program (Bight '03). Bight '03 was designed to be integrated regional monitoring program that encompasses regulatory, academic, and non-governmental agencies. Bight '03 had three components: Coastal Ecology, Shoreline Microbiology, and Water Quality. This report addresses the purpose, approach, findings, and recommendations from the Water Quality component, which focused on contamination-laden stormwater runoff, in particularly its variability in time and space as well as its short-term ecological impacts. Specifically, the Bight '03 Water Quality component had three primary goals, the first of which was to described the temporal evolution of stormwater plumes produced by the major southern California rivers. Specifically, the study was intended to determine how far offshore the plumes extended, how rapidly they advected, how long before the plumes dispersed and how these properties differed among storms and river systems. The second goal was to describe how the physical properties (e.g., turbidity, temperature, salinity) of the plume related to biogeochemical and ecological properties that are of more direct concern to the water quality management community. Accomplished primarily through ship-based sampling of water quality parameters, this second goal was to describe how far offshore, and for how ;long after the storm, elevated bacterial concentrations, toxicity, and nutrients could be detected. Similar to the fist goal, the study also addressed how these answers differed among storms and river systems. The final goal was to determine whether relationships between environmental indicators derived from coincident satellite remote sensing and in situ data sets are sufficiently robust for remote sensing to become a routine water quality monitoring programs. Remote sensing data potentially provide coastal managers with synoptic near-real time regional information about prevailing ocean conditions and hazards that would complement existing field-based sampling protocols, but only if there is a thorough understanding of how to interpret and utilize the proxy measures, such as ocean color. The understanding of these priorities through Bight '03 sampling is intended to provide the basis for developing more efficient, widespread and coast-effective coastal ocean monitoring techniques. Water quality data were collected across eight major river systems within four geographic regions of southern California. Field measurements included the primary contaminants of interest, i.e., bacterial concentrations, water toxicity, and nutrients, as well as related parameters such as temperatures, salinity, total suspended solids, transmissivity, chlorophyll, and colored dissolved organic material (CDOM) concentrations. For each of the four major regions, i.e., Santa Clara/Ventura Rivers, Ballona Creek/Santa Monica Bay, San Pedro Shelf, and the San Diego, Tijuana Rivers, two stormwater events were sampled for up to three days by ship resulting in 574 water column CTD+ profiles and 705 discrete water samples during 36 ship-days. These data were analyzed in combination with MODIS ocean color satellite remote sensing, buoy meteorological observations, drifters, and HF radar current measurements to evaluate the dispersal patterns, dynamics, and impacts of the freshwater runoff plumes. Based on these data and resulting analyses, the principal conclusions were as follow: - Stormwater runoff turbidity plumes were found to be spatially extensive, covering up to 2500 km 2 within the Southern California Bight nearshore zone, and persisting over the entire duration of the post-storm sampling period (at least 3 days). - The spatial and temporal extent of the portion of the plume with contaminants was far less than that of the turbidity plume, typically representing <10% of its area (30-70% off Tijuana); however, with contaminant impacts generally greatly reduced or absent by the third or fourth day of sampling - Pseudo-nitzschia , a harmful algae that produces domoic acid, was found to be more abundant than previously reported. - Accurately describing stormwater runoff plumes requires a combination of in situ and remote sensing assessment tools, with satellite data providing valuable synoptic information. From these conclusions, the following recommendations are provided: - Future studies designed to describe stormwater plumes should include a combination of ship - and remote sensing-based methods. - CDOM is a good proxy of the freshwater runoff plume and should be added as a standard measurement parameter on water quality instrument packages. - Investigations are needed that assess on a local basis the spatial extent of ecological effects of stormwater plumes early in the storm, ideally accompanied by airborne imagery to provide improved temporal & spatial resolution, to fill in knowledge gaps. The next Bight regional monitoring program should focus on quantifying nutrient loadings and dynamics in association with stormwater runoff and other sources, and characterize their attendant ecosystem impacts such as phytoplankton blooms.

California↗
USGS2019

Sampling across 20 years (1996–2017) reveals loss of diversity and genetic connectivity in the Coachella Valley fringe-toed lizard ( Uma inornata )

The Coachella Valley fringe-toed lizard ( Uma inornata ) is a federally threatened, aeolian sand dune obligate, endemic to the Coachella Valley, California. Historically, U. inornata is thought to have formed a large interconnected metapopulation across the valley, with local dune habitat and population size fluctuations linked to stochastic droughts and flooding. Since the 1950s, aeolian habitat in Coachella Valley has declined by 91–95 percent. What remains is highly fragmented by highways and development in the urban communities of the Coachella Valley, raising concerns that fringe-toed lizard movement and gene flow among remaining habitat fragments is limited or nonexistent. We examined population genetic structure across three sample periods (1996, 2008, and 2017). Over that time, this species has shifted from a panmictic condition (1996) with little or no genetic structure between sites to the current (2017) condition where there are now genetically distinct populations. Two severe droughts (2000–04 and 2012–16) may have accelerated this shift through drought-related population declines and subsequent genetic bottlenecks. Using a combination of microsatellite loci and single nucleotide polymorphisms, we found patterns of decreasing genetic connectivity and diversity over time. These patterns are consistent with reduced fringe-toed lizard movement and gene flow among isolated sand dune systems. Low effective population sizes were recovered in some sites, suggesting genetic drift in smaller and fluctuating populations is likely responsible for loss of genetic diversity. A U.S. Fish and Wildlife Service recovery objective for this species is to maintain genetic diversity; however, evidence of fragmentation suggests that genetic cohesiveness has been altered and that the diversity maintained in individual fragments is lower than in the total metapopulation. Management actions that increase genetic diversity could be implemented, including translocation. We modeled increasing gene flow between 1–10 percent, which showed that allelic richness could increase rapidly if translocated individuals can survive and reproduce. Establishing translocation protocols could help to avoid the high mortality that has occurred with other reptile translocations. Successful translocations could be a useful strategy to replenish lost genetic diversity after bottlenecks and could mitigate the loss of natural gene flow among populations.

California↗
USGS2026

DNA retention in sea lamprey digestive tracts: Insights from controlled feeding experiments

The sea lamprey ( Petromyzon marinus ), a non-native species in the Laurentian Great Lakes, has significantly impacted native fish communities and commercial fisheries, requiring population suppression efforts. While traditional control methods such as lampricides and barriers have reduced sea lamprey population abundance, questions remain regarding sea lamprey dietary composition given the focus of current damage assessments on economically and ecologically important host species. Recent advances in molecular technology offer promising methods of sea lamprey dietary assessment. Specifically, DNA metabarcoding enables species-specific identification of taxonomically diverse prey items from gut and fecal samples, and has proven effective in many taxa, including hematophagous species such as Arctic lamprey ( Lethenteron camtschaticum ) and sea lamprey. However, studies on DNA retention within digestive tracts are limited, particularly given the potential effects of environmental and dietary factors among hematophagous species. We used controlled feeding experiments to understand the effects these factors may have on DNA retention and host detectability within sea lamprey digestive tracts. Additionally, we evaluated the utility of metabarcoding for identifying multiple host species from consecutive feedings. Results indicate that host DNA can be detected up to 30 days post-feeding, with detection probability decreasing with increasing time following feeding. Temperature effects were dependent upon fasting periods, and host-switching trials indicated multiple previous host species could be detected from a single lamprey. Findings provide valuable insights for refining dietary analysis protocols for wild-caught sea lamprey within native and introduced ranges.

Environmental DNA↗
USGS2020

Chapter A6.2. Dissolved oxygen

The “National Field Manual for the Collection of Water-Quality Data” (NFM) provides guidelines and procedures for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation’s surface water and groundwater resources. This chapter, NFM A6.2, provides guidance and protocols for the measurement of dissolved oxygen, which include the scientific basis of the measurement, selection and maintenance of equipment, calibration, troubleshooting, and procedures for measurement and reporting. It updates and supersedes USGS Techniques of Water-Resources Investigations, book 9, chapter A6.2, version 3.0, by Stewart A, Rounds, Franceska D. Wilde, and George F. Ritz. Dissolved oxygen is routinely measured when water samples are collected, is often continually measured at USGS streamgages, and is a parameter regularly measured during laboratory and field experiments. The field method for measuring dissolved oxygen described in this chapter is applicable to most natural waters. Before 2017, the USGS NFM chapters were released in the USGS Techniques of Water-Resources Investigations series. Effective in 2018, new and revised NFM chapters are being released in the USGS Techniques and Methods series; this series change does not affect the content and format of the NFM. More information is in the general introduction to the NFM (USGS Techniques and Methods, book 9, chapter A0—U.S. Geological Survey, 2018) at https://doi.org/10.3133/tm9A0 . The authoritative current versions of NFM chapters are available in the USGS Publications Warehouse at https://pubs.er.usgs.gov . Comments, questions, and suggestions related to the NFM can be addressed to nfm@usgs.gov .

Techniques and Methods↗
USGS2024

Temperature

The “National Field Manual for the Collection of Water-Quality Data” (NFM) provides guidelines and procedures for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation’s surface-water and groundwater resources. This chapter, NFM A6.1, provides guidance and protocols for the measurement of temperature of air, of a surface-water body or in groundwater, which include the scientific basis of the measurement, selection and maintenance of equipment, calibration verification, troubleshooting, and procedures for measurement and reporting. It updates and supersedes USGS Techniques of Water-Resources Investigations, book 9, chapter A6.1, version 2.0, by Franceska D. Wilde. Temperature of air and water is routinely measured when water samples are collected, is often measured continually at USGS streamgages, and is a parameter regularly measured during laboratory and field experiments. The field method for measuring temperature described in this chapter is applicable to air and most natural waters. Before 2017, the NFM chapters were released in the USGS Techniques of Water-Resources Investigations series. Effective in 2018, new and revised NFM chapters are being released in the USGS Techniques and Methods series; this series change does not affect the content and format of the NFM. More information is in the general introduction to the NFM (USGS Techniques and Methods, book 9, chapter A0) at https://doi.org/10.3133/tm9A0 . The authoritative current versions of NFM chapters are available in the USGS Publications Warehouse at https://pubs.usgs.gov/ . Comments, questions, and suggestions related to the NFM can be addressed to nfm@usgs.gov .

Techniques and Methods↗
USGS2013

Salton Sea ecosystem monitoring and assessment plan

The Salton Sea, California’s largest lake, provides essential habitat for several fish and wildlife species and is an important cultural and recreational resource. It has no outlet, and dissolved salts contained in the inflows concentrate in the Salton Sea through evaporation. The salinity of the Salton Sea, which is currently nearly one and a half times the salinity of ocean water, has been increasing as a result of evaporative processes and low freshwater inputs. Further reductions in inflows from water conservation, recycling, and transfers will lower the level of the Salton Sea and accelerate the rate of salinity increases, reduce the suitability of fish and wildlife habitat, and affect air quality by exposing lakebed playa that could generate dust. Legislation enacted in 2003 to implement the Quantification Settlement Agreement (QSA) stated the Legislature’s intent for the State of California to undertake the restoration of the Salton Sea ecosystem. As required by the legislation, the California Resources Agency (now California Natural Resources Agency) produced the Salton Sea Ecosystem Restoration Study and final Programmatic Environmental Impact Report (PEIR; California Resources Agency, 2007) with the stated purpose to “develop a preferred alternative by exploring alternative ways to restore important ecological functions of the Salton Sea that have existed for about 100 years.” A decision regarding a preferred alternative currently resides with the California State Legislature (Legislature), which has yet to take action. As part of efforts to identify an ecosystem restoration program for the Salton Sea, and in anticipation of direction from the Legislature, the California Department of Water Resources (DWR), California Department of Fish and Wildlife (CDFW), U.S. Bureau of Reclamation (Reclamation), and U.S. Geological Survey (USGS) established a team to develop a monitoring and assessment plan (MAP). This plan is the product of that effort. The goal of the MAP is to provide a guide for data collection, analysis, management, and reporting to inform management actions for the Salton Sea ecosystem. Monitoring activities are directed at species and habitats that could be affected by or drive future restoration activities. The MAP is not intended to be a prescriptive document. Rather, it is envisioned to be a flexible, program-level guide that articulates high-level goals and objectives, and establishes broad sideboards within which future project-level investigations and studies will be evaluated and authorized. As such, the MAP, by design, does not, for example, include detailed protocols describing how investigations will be implemented. It is anticipated that detailed study proposals will be prepared as part of an implementation plan that will include such things as specific sampling objectives, sampling schemes, and statistical and spatial limits.

California↗
USGS2005

Submersed Aquatic Vegetation Modeling Output Online

Introduction The ability to predict the distribution of submersed aquatic vegetation in the Upper Mississippi River on the basis of physical or chemical variables is useful to resource managers. Wildlife managers have a keen interest in advanced estimates of food quantity such as American wildcelery (Vallisneria americana) population status to give out more informed advisories to hunters before the fall hunting season. Predictions for distribution of submerged aquatic vegetation beds can potentially increase hunter observance of voluntary avoidance zones where foraging birds are left alone to feed undisturbed. In years when submersed aquatic vegetation is predicted to be scarce in important wildlife habitats, managers can get the message out to hunters well before the hunting season (Jim Nissen, Upper Mississippi River National Wildlife and Fish Refuge, La Crosse District Manager, La Crosse, Wisconsin, personal communication). We developed a statistical model to predict the probability of occurrence of submersed aquatic vegetation in Pool 8 of the Upper Mississippi River on the basis of a few hydrological, physical, and geomorphic variables. Our model takes into consideration flow velocity, wind fetch, bathymetry, growing-season daily water level, and light extinction coefficient in the river (fig. 1) and calculates the probability of submersed aquatic vegetation existence in Pool 8 in individual 5- x 5-m grid cells. The model was calibrated using the data collected in 1998 (516 sites), 1999 (595 sites), and 2000 (649 sites) using a stratified random sampling protocol (Yin and others, 2000b). To validate the model, we chose the data from the Long Term Resource Monitoring Program (LTRMP) transect sampling in backwater areas (Rogers and Owens 1995; Yin and others, 2000a) and ran the model for each 5- x 5-m grid cell in every growing season from 1991 to 2001. We tallied all the cells and came up with an annual average percent frequency of submersed aquatic vegetation occurrence and compared the results with actual LTRMP survey data (fig. 2). Both a paired Student's test (P = 0.4620) and a Wilcoxon's two-sample test (P = 0.4738) did not contradict our null hypothesis that the model prediction and the sampling data are statistically the same. We have not found an effective statistical test to compare model-predicted spatial pattern with aerial photography geographic information, but we are satisfied with the model's outcome on the basis of visual inspection (fig. 3). A unique feature about this model is that a prediction can be made by the end of June each year; therefore, providing wildlife managers an assessment of current year vegetation growth condition 3 to 4 months ahead of the arrival of migrating waterfowl that feed on submersed aquatic vegetation. We are working with the LTRMP partnership to create a mechanism so that model predictions (fig. 4) can be updated annually and the results posted on the LTRMP Web site. Our model underestimated the prevalence of vegetation from 2001 to 2004. We speculate that the summer water level reduction conducted in 2001 and 2002 triggered vegetation responses that are outside the model's domain. Future enhancement of the model will incorporate the summer water level drawdown effects as well as the effects of growth conditions in previous years.

Open-File Report↗
USGS2021

Elk monitoring in Mount Rainier and Olympic National Parks: 2008-2017 synthesis report

In 2008, the U.S. Geological Survey (USGS) began collaborating with the National Park Service (NPS)-North Coast and Cascades Network (NCCN), the Muckleshoot Indian Tribe (MIT), Puyallup Tribe of Indians (PTOI), and Washington Department of Fish and Wildlife (WDFW) to develop a standard survey protocol for monitoring long-term changes in the abundance, distribution, and population composition of elk on key summer ranges within Mount Rainier National Park (MORA) and Olympic National Park (OLYM). In MORA, surveys were conducted in two trend count areas (TCAs) that correspond with primary summer ranges used by the North Rainier Herd, which winters outside the park to the North, and the South Rainier Herd, which winters outside the park primarily to the South. In OLYM, we defined five TCAs including an Olympic Core TCA (hereafter, Core TCA) that encompasses summer ranges on the flanks of Mount Olympus, and four TCAs that encompass other primary summer ranges throughout the park. The standard protocol allows for estimating aerial survey detection biases and adjusting raw survey counts to account for elk that were likely present but not seen during surveys. Previously, we developed a suite of aerial-bias-correction models for use in estimating aerial detection biases and adjusting raw counts of elk in MORA based on sighting conditions related to elk group size, vegetation density, lighting conditions, elk movement, as well as combinations of these and other factors. The models were based on independent sighting records of elk groups by front-seat and back-seat observer pairs in a helicopter, including detection records of some radio-collared elk groups. Here, we analyze results of the first 10 years of elk monitoring in MORA (2008-2017) and 8 years in OLYM (2008-2015). In a previous report covering surveys conducted from 2008-2011, data were not sufficient to model detection biases of aerial surveys conducted in OLYM; hence, analyses of elk population trends were based on counts adjusted for detection biases in MORA, whereas trends in OLYM were based on raw, unadjusted counts (Griffin et al. 2013, Jenkins et al. 2015). Our objectives for the current summary were to: (1) incorporate additional data to update aerial-bias-correction models previously developed for use in MORA to include corrections for aerial detection bias in both MORA and OLYM, (2) examine trends in elk abundance, distribution, and population composition estimates for subalpine summer ranges within MORA and OLYM, and (3) estimate effects of seasonal variation and weather on elk abundance and population composition estimates for subalpine summer ranges in both parks.

Washington↗
USGS2001

Estimating suspended sediment and trace element fluxes in large river basins: Methodological considerations as applied to the NASQAN programme

In 1994, the NASQAN (National Stream Quality Accounting Network) programme was redesigned as a flux-based water-quality monitoring network for the Mississippi, Columbia, Colorado, and Rio Grande Basins. As the new programme represented a departure from the original, new sampling, processing, analytical, and data handling procedures had to be selected/developed to provide data on discharge, suspended sediment concentration, and the concentrations of suspended sediment and dissolved trace elements. Annual suspended sediment fluxes were estimated by summing daily instantaneous fluxes based on predicted suspended sediment concentrations derived from discharge-based log-log regression (rating-curve) models. The models were developed using both historical and current site-specific discharge and suspended sediment concentrations. Errors using this approach typically are less than ?? 10% for the 3-year reporting period; however, the magnitude of the errors increases substantially for temporal spans shorter than 1 year. Total, rather than total-recoverable, suspended sediment-associated trace element concentrations were determined by direct analysis of material dewatered from large-volume whole-water samples. Site-specific intra- and inter-annual suspended sediment-associated chemical variations were less (typically by no more than a factor of two) than those for either discharge or suspended sediment concentrations (usually more than 10-fold). The concentrations, hence the annual fluxes, for suspended sediment-associated phosphorus and organic carbon, determined by direct analyses, were higher than those determined using a more traditional paired, whole-water/filtered-water approach (by factors ranging from 1.5- to 10-fold). This may be important for such issues as eutrophication and coastal productivity. Filtered water-associated (dissolved) trace element concentrations were markedly lower than those determined during the historical NASQAN programme; many were below their respective detection limits. This resulted from the use of clean sampling, processing, and analytical protocols. Hence, the fluxes for filtered water-associated (dissolved) Ag, Pb, Co, V, Be, Sb, and Se, as well as the total (filtered water plus suspended sediment-associated) fluxes for these constituents, could not be estimated.

Hydrological Processes↗
USGS2022

Density surface and excursion sets modeling as an approach to estimating population densities

Effective species management and conservation require knowledge of species distribution and status. We used point-transect distance sampling surveys of the endangered palila ( Loxioides bailleui ), a honeycreeper currently found only on the Island of Hawai'i, USA, to generate robust estimates of total abundance and simultaneously model the distribution, abundance, and spatial correlation of the species as a density surface model (DSM). Point-transect distance sampling is a widely applied method to estimate bird densities accounting for imperfect detection probability. For the DSM we used a generalized additive model framework and soap film smoothers to control the effects of boundary features. This modeling approach allowed us to account for imperfect detection and propagate detection probability uncertainty. We compared the uncertainty in palila abundance estimates using standard point-transect distance sampling to estimates from the DSM. The DSM, accounting for both distance-sampling-derived detection probability variance and the generalized additive model density estimate variance, did not improve population estimator precision; however, it provided insight into the species' distribution, density, and uncertainty. We also applied excursion sets analysis to objectively identify areas where the species occurs in high densities. The 2017 global population of <2,000 individuals was limited to an excursion area of 1,500 ha. Our findings can help management and regulatory agencies by simultaneously mapping a species' distribution and density, improving survey protocols, and providing information important to species conservation.

Hawaii↗
USGS2013

A natural resource condition assessment for Sequoia and Kings Canyon National Parks: Appendix 14: plants of conservation concern

Sequoia and Kings Canyon National Parks are located in the California Floristic Province, which has been named one of world‘s hotspots of endemic biodiversity (Myers et al. 2000). The California Floristic Province is the largest and most important geographic floristic unit in California and extends from the Klamath Mountains of southwestern Oregon to the northwestern portion of Baja California (Hickman 1993). The Sierra Nevada, one of six regions that make up the California Floristic Province, covers nearly 20% of the land in California yet contains over 50% of its flora. Within the Sierra Nevada, the southern Sierra supports more Sierran endemic and rare plant taxa than the central and northern portions of the region (Shevock 1996). Sequoia and Kings Canyon National Parks (SEKI) encompass roughly 20% of the southern Sierra Nevada region. The parks overlap three floristic subregions (central Sierra Nevada High, southern Sierra Nevada High, and southern Sierra Nevada Foothills), and border the Great Basin Floristic Province. The parks support a rich and diverse vascular flora composed of over 1,560 taxa. Of these, 150 taxa are identified as having special status. The term special status is applied here to include taxa that are state or federally listed, rare in California, or at risk because they have a limited distribution. Only one species from these parks is listed under the state or federal Endangered Species Acts ( Carex tompkinsii , Tompkins‘ sedge, is listed as a rare species under the California Endangered Species Act), and one species is under review for federal endangered listing ( Pinus albicaulis , whitebark pine). However, an absence of threatened and endangered species recognized by Endangered Species Acts is not equivalent to an absence of species at risk. There are 83 plant taxa documented as occurring in SEKI that are considered imperiled or vulnerable in the state by the California Department of Fish and Game‘s California Natural Diversity Database (CNDDB 2010a). There are an additional 66 taxa not formally listed by CNDDB that are recognized as having special status because their distribution is restricted to the Sierra Nevada. Special status plants are distributed throughout the two parks and inhabit a wide range of environments along the length of the elevation gradient that characterizes these parks. Ideally, we would assess the condition (status and trends) of each of the taxa on the SEKI special status plant list, documenting current population sizes, demographic rates and demographic trends. We would also hope to quantify the effects of individual stressors on each species based on existing monitoring and research. However, no data are available for most of the species on the special status plant list. For those few species (12 herbaceous species and two tree species) for which we possess some change over time information, the data are not adequate to make a competent assessment. Note that we have not explored the tree demographic information in any detail, as is covered in the NRCA Intact Forest/Five Needle Pines and Sequoia chapters. In general, we are unable to present an ‗integrity‘ metric for special status species in the parks, since the data to quantify the condition of each species in such a manner is not available. In contrast, the park does possess substantial data describing biodiversity in the parks. Therefore, our analysis focuses on describing the distribution and rarity of special status plants within the parks, with a particular focus on assessing the spatial distribution of species richness. We hope that such information will prove useful to park managers in determining which areas in the parks merit the most attention (for example in developing monitoring protocols). We also assess potential vulnerability of special status species to the stressors chosen by the NRCA working group, using both park data and available literature. As a first step, we spent considerable effort updating and refining the criteria for the special status plant list, as this list defines which taxa are considered in our assessment. Observation data of these species was then compiled from all known sources in order to provide a comprehensive view of where special status plants have been documented and, ultimately, to enable the most informed determinations of areas in the parks that potentially support the highest number of rare and endemic taxa. These ‗hot spot‘ analyses are presented by geographic region, vegetation type and elevation. For these and other analyses presented in this report, we place more focus on summarizing findings for the herbaceous and shrub special status taxa than on special status trees. The trees which qualify as special status are the focus of other NRCA chapters, including Giant Sequoia and Intact Forests/Five-needle Pines. We do, however, present their mapped distributions and provide overviews of research related to the special status tree taxa in the Stressors section of this report.

California↗
USGS2026

Advances and applications of Unoccupied Aerial Systems (UAS) research in landscape ecology

Landscape ecologists have long depended on satellite and aerial remote sensing to address questions about landscape pattern and process, structure, and change (Foody 2023 ). Unoccupied aerial systems/vehicles (UAS/UAV, a.k.a. drones) technology is becoming an increasingly popular research tool in environmental sciences allowing scientists to generate low-cost, high-quality, and high-resolution imagery on demand that can be tailored to specific research questions. While satellite data are of a fixed resolution and temporal interval, UAS offer researchers control and flexibility to design studies and collect data at resolutions and scales that provide ecologically relevant information at finer spatial resolutions (e.g., < 30 cm) than what is currently available from satellite platforms (typically > 3m), thus helping capture objects such as individual plant canopies, micro-topography, and individual animals. Unlike satellites with fixed orbits, UAS can be deployed at more optimal temporal frequencies for ecological monitoring. We organized the special collection “Advances and Applications of Unoccupied Aerial Systems (UAS) Research in Landscape Ecology” to showcase the many ways that UAS tools and technologies are currently applied to advance landscape ecological research. When we announced the collection in 2023, only 11 papers published in the journal Landscape Ecology used UAS data, which was a notably small number compared to many other general ecology, environmental science and remote sensing journals. In an attempt to understand why UAS were not more widely used in landscape ecology and provide possible solutions, we published a review article (Villarreal et al. 2025) that identified the challenges, knowledge gaps, and obstacles for the adoption of UAS technologies in landscape ecology research. The main issues we identified include: (1) an abundance of UAS methods papers in the existing literature, with comparatively few studies demonstrating how UAS can be applied to address ecological questions; (2) a perceived scale mismatch between the geographic extent of UAS data collection (local) compared to larger study areas (landscapes) and a need to design robust scaling approaches to connect fine-scale UAS data with broader ecological patterns; and (3) a need for improved integration of UAS data with other commonly used remote sensing datasets including historical high resolution aerial imagery. Additionally, researchers new to UAS remote sensing may be discouraged or overwhelmed by the general lack of scientific consensus and standardized protocols for typical tasks such as data collection, vegetation classification, and change detection, as well as restrictive and/or confusing policy, regulatory, and legal issues surrounding UAS operations (Villarreal et al. 2025).

Landscape Ecology↗
USGS2021

Refining sampling protocols for cavefishes and cave crayfishes to account for environmental variation

Subterranean habitats support a diverse array of organisms and represent imperative habitats in many conservation strategies; however, subterranean habitats are one of the most difficult environments to study. Accounting for variable sampling detection is necessary to properly evaluate conservation options for rare species such as karst and other groundwater organisms. New sampling methods, such as environmental DNA, show promise to improve stygobiont detection; however, sources of sampling bias are poorly understood. Therefore, our objective was to determine factors affecting detection probability of both visual and environmental DNA (eDNA) surveys for cavefishes and cave crayfishes. We sampled 40 sites across the Ozark Highlands ecoregion in Arkansas, Missouri, and Oklahoma, USA using visual and eDNA surveys. We used occupancy modeling to estimate the detection probability of the two taxa using both survey methods under varying environmental conditions. Overall, eDNA sampling resulted in higher detection probability for cavefishes when compared to visual surveys, whereas visual surveys typically had higher detection probability for cave crayfishes. Greater water volume at the time of sampling was related to lower detection using visual surveys for both taxa, but there was no relationship between eDNA detection and water volume. Detection probability of both cavefishes and crayfishes was higher using visual surveys when sampling units were classified by coarse rather than fine substrate, whereas detection of cave crayfishes surveyed using eDNA was higher in coarse substrate environments. Detection of cavefishes and cave crayfishes was higher via eDNA sampling when water was flowing, but similar sampling conditions resulted in lower detection using visual surveys. Our results indicate detection should be considered when sampling stygobionts even if using traditional visual surveys. Environmental DNA is a useful tool; however, the limitations we identified indicate eDNA for these taxa currently are not adequate to replace traditional surveys in subterranean environments.

Arkansas, Missouri, Oklahoma↗
USGS2023

Selenium hazards in the Salton Sea environment—Summary of current knowledge to inform future wetland management

Quaternary marine and continental shales in the western United States are sources of selenium that can be loaded into the aquatic environment through mining, agricultural, and energy production processes. The mobilization of selenium from shales through agricultural irrigation has been recognized since the 1930s; however, discovery of deformities in birds and other wildlife using agricultural habitats during the 1980s spurred studies to determine the extent and effects of the contamination. Through these early studies, researchers determined that biota in the Salton Sea drainage basin was at risk from legacy selenium contamination in the Colorado River watershed. The Salton Sea and its surrounding managed and unmanaged wetlands provide vital inland habitat and trophic support for diverse assemblages of resident and migratory wildlife, and understanding regional selenium hazards for these trust species is a priority for many Federal and State agencies. The modern Salton Sea is a shallow, landlocked saline lake in Riverside and Imperial Counties (not shown) of California that is sustained by irrigation return and perennial river inflow. Changes in water transfer agreements under the 2003 Quantification Settlement Agreement (QSA) have resulted in reduced irrigation flow, declining lake levels, and the evolution of unmanaged wetlands in areas where drains and rivers no longer reach the Salton Sea. These wetlands provide additional habitat for some species of concern, but their potential to increase selenium hazards for trust species is largely unknown. From the 1980s to 2020, efforts to document selenium contamination and effects throughout the region have resulted in a considerable amount of selenium data from the Salton Sea and its surrounding drainage basin; however, no long-term (greater than 20 years), consistent sampling program has been established, and all data have been collected by different entities using a variety of protocols and analytical techniques. This lack of coordination has been previously documented in regional management plans and has led to difficulty in reliably assessing selenium hazards in the Salton Sea environment. This report provides a summary of the available disparate selenium information collected from water, sediment, and biota in the Salton Sea region since the 1980s and to identify data gaps that need to be filled to understand the potential effects of selenium on species of concern, including federally endangered desert pupfish ( Cyprinodon macularius ) and Yuma Ridgway’s Rail ( Rallus obsoletus yumanensis; formerly Yuma Clapper Rail, Rallus longirostris yumanensis ). Available data from the Salton Sea drainage basin show that water from the Colorado River has the lowest selenium concentration of all surface water sources. All other surface water flowing into the Salton Sea has elevated selenium concentrations due to evaporation and evapotranspiration that occurs in agricultural fields and associated water delivery infrastructure or leaching of selenium from irrigated farmland soils. The Salton Sea has lower selenium concentrations because of various biogeochemical processes that recycle selenium into the sediment or volatilize it to the atmosphere; however, these mechanisms are not well defined, and it is not clear if selenium cycling will change in response to possible changes in the oxidation state of the Salton Sea bottom waters as water levels decline. Agricultural drains have the highest average selenium concentrations, but few drains have been sampled since changes in irrigation practices have occurred (due to the 2003 QSA). Groundwater selenium concentrations are variable; some wells south of the Salton Sea have selenium concentrations as high as 300 micrograms per liter (µg/L), whereas selenium concentrations are below detection in other wells. Groundwater and surface-water geothermal discharge zones around the margins of the Salton Sea and in unmanaged wetlands have not been studied in detail, and published selenium measurements are not available for these surface features. Selenium concentrations in the sediment of the Salton Sea drainage basin are highest in wetland particulate organic matter and the Salton Sea lakebed, indicating that removal of selenium from the water to the sediment has been a primary mechanism for keeping selenium concentrations low in the water column. Sediment selenium concentrations in wetlands are lower than in the Salton Sea but higher than inflowing drains and rivers, indicating the lentic wetland sites also may be important sinks for selenium because of biogeochemical processes. Sediment selenium data have not been collected in agricultural drains since changes in irrigation practices occurred (due to the 2003 QSA), and it is unknown if selenium sequestration from the water column has changed in these systems. We divided biological data into broad taxonomic categories, including primary producers, invertebrates, herpetofauna, mammals, fishes, and birds to facilitate evaluation of selenium concentrations and spatiotemporal trends observed in the Salton Sea. Overall, selenium concentrations were substantially greater in algae samples compared to all vascular plant samples combined. Median selenium concentrations in several invertebrate taxa (Chironomidae, Formicidae, Corixidae, Corbiculidae and Nereididae, and Decapoda) exceeded the maximum suggested dietary threshold of 3.0–4.0 micrograms per gram (µg/g) dry weight (dw) for predators consuming invertebrates in aquatic food webs. The greatest number of samples were collected from fish, and selenium distributions among species and locations showed that the range for most samples was lower than the U.S. Environmental Protection Agency selenium criterion for aquatic life (8.5 µg/g dw whole body, 11.3 µg/g dw fillets). The median selenium concentrations for whole body fish were below the selenium criterion in most locations, except for bairdiella ( Bairdiella icistia ) from the Salton Sea and irrigation drains, a few individual tilapia spp. (family Cichlidae, including genera Tilapia, Oreochromis , and their hybrids) from the river and river outlets, and several western mosquitofish ( Gambusia affinis ) and sailfin molly ( Poecilia latipinna ) from irrigation drain outlets. For avian samples combined among years and locations, median selenium concentrations in livers from all families except waders and Ibis (family Threskiornithidae) were higher than levels expected to cause selenium toxicosis (10–20 µg/g dw), and all median egg concentrations were above or near 6.0 μg/g dw, which is a conservative threshold value for reproductive impairment. Most knowledge gaps we identified for water, sediment, and biota were interrelated, and the use of integrated approaches to address knowledge gaps can provide greater insight into the drivers behind selenium hazards. Integrated water, sediment, and biota studies could help identify cost-effective management solutions that serve multiple purposes. A comprehensive analysis of the hydrology, biogeochemistry, and food-web processes in wetlands and other habitats can inform predictive models to identify drivers of selenium bioavailability, uptake from the environment and subsequent trophic transfer, ultimately forming the basis for experimental habitat management manipulations to minimize selenium hazards to wildlife. Furthermore, a comprehensive, long-term sampling and analytical laboratory plan would enable comparison of data among different entities that are sampling at the Salton Sea. Such efforts are well suited to help fill knowledge gaps that preclude understanding of selenium hazards and future management options for biota using Salton Sea habitats, including newly formed wetlands throughout the region. All data compiled for this report are available in two U.S. Geological Survey data releases: Groover and others (2022) for water and sediment samples and De La Cruz and others (2022) for biological samples. The data releases include all publicly available data for selenium concentrations in water, sediment, and biological samples collected in and around the Salton Sea, including the Coachella and Imperial Valleys. The data releases also include previously unpublished data.

California↗