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USGS2004

Population dynamics of the California Spotted Owl (Strix occidentalis occidentalis): a meta-analysis

We conducted a meta-analysis to provide a current assessment of the population characteristics of California Spotted Owls (Strix occidentalis occidentalis) resident on four study areas in the Sierra Nevada and one study area in southern California. Our meta-analysis followed rigorous a priori analysis protocols, which we derived through extensive discussion during a week-long analysis workshop. Because there is great interest in the owl?s population status, we used state-of-the-art analytical methods to obtain results as precise as possible. Our meta-analysis included data from five California study areas located on the Lassen National Forest (1990-2000), Eldorado National Forest (1986-2000), Sierra National Forest (1990-2000), Sequoia and Kings Canyon national parks (1990-2000), and San Bernardino National Forest (1987-1998). Four of the five study areas spanned the length of the Sierra Nevada, whereas the fifth study area encompassed the San Bernardino Mountains in southern California. Study areas ranged in size from 343 km2 (Sequoia and Kings Canyon) to 2,200 km (Lassen). All studies were designed to use capture-recapture methods and analysis. We used survival in a meta-analysis because field methods were very similar among studies. However, we did not use reproduction in a meta-analysis because it was not clear if variation among individual study-area protocols used to assess reproductive output of owls would confound results. Thus, we analyzed fecundity only by individual study area. We examined population trend using the reparameterized Jolly-Seber capture-recapture estimator (8t) We did not estimate juvenile survival rates because of estimation problems and potential bias because of juvenile emigration from study areas. We used mark-recapture estimators under an information theoretic framework to assess apparent survival rates of adult owls. The pooled estimate for adult apparent survival for the five study areas was 0.833, which was lower than pooled adult survival rates (0.850) from 15 Northern Spotted Owl (S. o. caurina) studies. Estimates of survival from the best model on the Lassen (N = 0.829, 95% confidence intervals [CI = 0.798 to 0.857), Eldorado (N = 0.815, 95% CI = 0.772 to 0.851), Sierra (N = 0.818, 95% CI = 0.781 to 0.850), and San Bernardino (N = 0.813, 95% CI = 0.782 to 0.841) were not different. However, the Sequoia and Kings Canyon population had a higher survival rate (N = 0.877, 95% CI = 0.842 to 0.905) than the other study areas. Management history and forest structure (e.g. presence of giant sequoia [Sequoiadendron giganteum]) on the Sequoia and Kings Canyon study area differed from all other study areas. There appears to be little or no evidence for temporal variation in adult apparent survival on any of the study areas. Although we did not directly compare fecundity estimates were highly variable among years within all study areas (CV of temporal process variation = 0.672-0.817). Estimates for fecundity among the study populations were Lassen (b = 0.336, SE = 0.083), Eldorado (b = 0.409, SE = 0.087), Sierra (b = 0.284, SE = 0.073), Sequoia and Kings Canyon (b = 0.289, SE = 0.074), and San Bernardino (b = 0.362, SE = 0.038). During most years, the Sierra Nevada populations showed either moderate or poor fecundity. However, 1992 appeared to be an exceptional reproductive year for owls in the Sierra Nevada. In contrast, the San Bernardino population had less variable reproduction (CV of temporal process variation = 0.217), but experienced neither the exceptional reproduction of 1992 nor the extremely poor years that characterized all of the Sierra Nevada study areas. Because fecundity may be influenced by weather patterns, it was possible that the different weather patterns between southern California and the Sierra Nevada accounted for that difference. Except for Eldorado, all estimates for 8t, were <1.0, but none was different from 8 = 1.0 given the 95% confidence i

Ornithological Monographs↗

USGS2015

Biodegradability of dissolved organic carbon in permafrost soils and aquatic systems: a meta-analysis

As Arctic regions warm and frozen soils thaw, the large organic carbon pool stored in permafrost becomes increasingly vulnerable to decomposition or transport. The transfer of newly mobilized carbon to the atmosphere and its potential influence upon climate change will largely depend on the degradability of carbon delivered to aquatic ecosystems. Dissolved organic carbon (DOC) is a key regulator of aquatic metabolism, yet knowledge of the mechanistic controls on DOC biodegradability is currently poor due to a scarcity of long-term data sets, limited spatial coverage of available data, and methodological diversity. Here, we performed parallel biodegradable DOC (BDOC) experiments at six Arctic sites (16 experiments) using a standardized incubation protocol to examine the effect of methodological differences commonly used in the literature. We also synthesized results from 14 aquatic and soil leachate BDOC studies from across the circum-arctic permafrost region to examine pan-arctic trends in BDOC. An increasing extent of permafrost across the landscape resulted in higher DOC losses in both soil and aquatic systems. We hypothesize that the unique composition of (yedoma) permafrost-derived DOC combined with limited prior microbial processing due to low soil temperature and relatively short flow path lengths and transport times, contributed to a higher overall terrestrial and freshwater DOC loss. Additionally, we found that the fraction of BDOC decreased moving down the fluvial network in continuous permafrost regions, i.e. from streams to large rivers, suggesting that highly biodegradable DOC is lost in headwater streams. We also observed a seasonal (January–December) decrease in BDOC in large streams and rivers, but saw no apparent change in smaller streams or soil leachates. We attribute this seasonal change to a combination of factors including shifts in carbon source, changing DOC residence time related to increasing thaw-depth, increasing water temperatures later in the summer, as well as decreasing hydrologic connectivity between soils and surface water as the thaw season progresses. Our results suggest that future climate warming-induced shifts of continuous permafrost into discontinuous permafrost regions could affect the degradation potential of thaw-released DOC, the amount of BDOC, as well as its variability throughout the Arctic summer. We lastly recommend a standardized BDOC protocol to facilitate the comparison of future work and improve our knowledge of processing and transport of DOC in a changing Arctic.

Biogeosciences↗

USGS2023

A pilot biodiversity inventory and monitoring protocol in support of coastal adaptation projects in tidal and nearshore subtidal habitats of Boston Harbor Islands

The Boston Harbor Islands National Recreation Area (BOHA) is at high risk to the impacts of sealevel rise (SLR) and erosion from coastal storms. In June 2021, the National Trust for Historic Preservation listed the islands as one of America’s 11 Most Endangered Historic Places due to climate change. BOHA partners have been working to find climate adaptive solutions to protect and sustain critical ecological and cultural resources on the islands. A range of coastal adaptation efforts are currently under consideration including increased shoreline armoring and nature-based adaptation solutions. Any action taken in the coastal zone will require an assessment of environmental and ecological communities that could potentially be impacted by disturbance caused by restoration or adaptation projects. The primary goals of the initial phase of this project were to: 1) synthesize occurrence and distribution records of biodiversity living in and using mixed coarse substrate habitats of the intertidal zone of the Boston Harbor Islands; and 2) identify and compile potential methods to develop a standard and repeatable monitoring protocol to track changes (natural or anthropogenic) in intertidal biodiversity over time and across locations; and 3) conduct preliminary site scoping of target islands to identify locations for collecting new baseline data. A biodiversity inventory list was compiled, showing a total of 451 unique species were observed in BOHA between 1861-2020. Of this list, 55 species (invertebrates: 47; algae: 8) were considered nonindigenous species; a watchlist was also developed to help BOHA partners identify potential future invaders that could colonize and impact intertidal communities due to ongoing climate change or disturbance events. Native species observed in BOHA were evaluated using existing conservation frameworks and climate vulnerability information to prioritize species at greatest risk from anthropogenic and environmental stressors for future actions. Lastly, site scoping activities during 2021 identified three types of sites for future intertidal monitoring initiatives: (1) sites with relatively high biodiversity and foundational species, (2) erosional sites near cultural areas of importance to NPS, and (3) sites with generic (common across islands) biodiversity. Overall results are anticipated to help the NPS and BOHA partners identify a suite of species and sites for future monitoring given anticipated adaptation projects and ongoing changes due to SLR, coastal storms and other stressors.

Massachusetts↗

USGS2019

Study design and methods for a wetland condition assessment on U.S. Fish and Wildlife Service fee-title lands in the Prairie Pothole Region of North Dakota, South Dakota, and Montana, USA

The U.S. Fish and Wildlife Service (FWS) manages wetlands and grasslands for wildlife habitat throughout the central North American Prairie Pothole Region (PPR). PPR wetlands, or potholes, are widely recognized as critical habitats for North American migratory waterfowl, waterbirds, and other wildlife. Potholes also provide other ecosystem services such as carbon sequestration, flood mitigation, filtration of pollutants, groundwater recharge, nutrient retention, and recreational opportunities. Wetland condition assessments have been completed nationally at coarse scales, but focused, regionwide assessments of the biological condition of potholes managed by the FWS are lacking. Therefore, FWS personnel require information pertaining to the biological condition and status of wetlands on FWS fee-title lands in the PPR to support management, restoration, and acquisition efforts. The biological condition of wetlands typically is reflected by their plant communities, and these communities correspond to past and current management and anthropogenic disturbances; thus, plant communities are a suitable surrogate of wetland condition. This report describes the study design, selection of sample sites, and field survey methods for a wetland condition assessment for FWS fee-title lands in the PPR of North Dakota, South Dakota, and Montana. Various spatial databases were gathered (for example, National Wetlands Inventory) to identify and assess potholes on FWS fee-title lands and to facilitate the selection of study sites. A spatially balanced, site-selection process resulted in the inclusion of 125 temporarily and 125 seasonally ponded potholes distributed across the area of interest; the first 100 for each classification were considered the primary study sites, whereas the remaining 25 were considered an oversample to replace those deemed not appropriate for sampling by field crews. Study sites were within native prairie and reseeded grasslands on FWS National Wildlife Refuges and Waterfowl Production Areas and are distributed among the primary physiographic subregions of the PPR: the Glaciated Plains, Missouri Coteau, and Prairie Coteau; a small number of sites also are within the Lake Agassiz Plain and Turtle Mountains. Site assessment protocols, vegetation survey methods, data analyses, and condition categories (for example, poor, good, very good) for the wetland assessment are based on the North Dakota Rapid Assessment Method and an Index of Plant Community Integrity developed for potholes. Results of the wetland condition assessment will aid FWS staff in assessing past and current management and help to identify priority areas for future management and acquisition.

North Dakota, South Dakota, Montana↗

USGS2002

Research plan for lands administered by the U.S. Department of the Interior in the Interior Columbia Basin and Snake River Plateau

This document presents a long-term research strategy designed to address current and future research needs for management of Department of the Interior-administered ecosystems in the Intermountain West. Although the research plan was developed in the context of the Interior Columbia Basin Ecosystem Management Project, the plan addresses many high-priority issues facing land managers throughout the Intermountain West. These issues pose management challenges that may be addressed with applied research both currently and in upcoming decades. Possessing a particular focus on semiarid ecosystems, the plan is a collection of research questions under five categories of research emphases: 1) restoration; 2) rangeland health; 3) aquatic-terrestrial connections; 4) development of monitoring and evaluation protocols; and 5) species and habitats at risk. The goal of the research strategy is to provide ideas for integrating emerging scientific understanding into future management in order to restore and maintain long-term ecosystem health and ecological integrity; provide consistent management direction over broad spatial and temporal scales; emphasize adaptive management over the long term; restore and maintain habitats for plant and animal species; and support economic and social needs of people, without compromising the above goals. Research questions are prioritized into three categories based on the immediacy of their need, feasibility of addressing the question rigorously under varying funding budgets, and magnitude of risk posed by not addressing the issue. The research strategy is intended to support and integrate with existing management efforts and strategies. As such, it melds observational studies with experimental manipulation, treating management actions as experiments whenever feasible. The research strategy focuses on disturbance processes and events that have been the primary drivers of change, to provide a predictive model for future changes. These drivers include fire, nonnative plants, herbivory, roads and associated human influences, and climate change. Whereas management in the western United States has striven to move from an inefficient species-based approach to a habitat-based approach, the plan focuses on ecosystem function and ecological processes as critical measures of habitat response. Because of the large amount and contiguity of public lands in the western United States, the region presents both a compelling opportunity to implement landscape-level science and a challenge to underst

Information and Technology Report↗

USGS2001

The use of forward looking infrared to locate bird carcasses in agricultural areas

Helicopter-mounted Forward Looking Infrared has mainly been used for large animal censuses. I examined the use of this instrument in locating bird carcasses in agricultural fields to improve current carcass searching techniques. Mallard (Arias platyrhynchos) and northern bobwhite quail (Colinus virginianus) carcasses were measured with an infrared thermometer immediately following death and for 5 consecutive nights to determine the optimal time for detection. Preliminary flights were conducted to design a protocol that was used in test flights. Bird species (mallard versus quail) and cover type (bare ground versus short grass) were compared in the flights. Carcasses were recovered with the aid of Global Positioning Systems. Carcasses remained above ambient ground temperatures for all or part of night 1. Quail carcass temperatures decreased faster than mallard carcasses. In warmer weather, carcass temperatures increased 3-5 nights following death. In colder weather, carcasses were 1-2 C cooler than the ground after the first night. Mallard and quail carcasses were both detected on bare ground and short grass cover types with Forward Looking Infrared. The carcass recovery rates were 40% arid 30% on bare ground and short grass, respectively. There were no significant differences in detection for species or cover type. In warmer weather, carcasses could be detected for several hours following death and again 3-5 nights after death. Carcasses may be detected as objects cooler than the ground in colder weather. Forward Looking Infrared was successful in detecting mallard and quail carcasses. Further research should evaluate improved mapping techniques to enhance carcass recovery.

Book↗

USGS2003

Effect of analytical conditions in wavelength dispersive electron microprobe analysis on the measurement of strontium-to-calcium (Sr/Ca) ratios in otoliths of anadromous salmonids

The use of strontium-to-calcium (Sr/Ca) ratios in otoliths is becoming a standard method to describe life history type and the chronology of migrations between freshwater and seawater habitats in teleosts (e.g. Kalish, 1990; Radtke et al., 1990; Secor, 1992; Rieman et al., 1994; Radtke, 1995; Limburg, 1995; Tzeng et al. 1997; Volk et al., 2000; Zimmerman, 2000; Zimmerman and Reeves, 2000, 2002). This method provides critical information concerning the relationship and ecology of species exhibiting phenotypic variation in migratory behavior (Kalish, 1990; Secor, 1999). Methods and procedures, however, vary among laboratories because a standard method or protocol for measurement of Sr in otoliths does not exist. In this note, we examine the variations in analytical conditions in an effort to increase precision of Sr/Ca measurements. From these findings we argue that precision can be maximized with higher beam current (although there is specimen damage) than previously recommended by Gunn et al. (1992).

Fishery Bulletin↗

USGS2018

Brook Floater rapid assessment monitoring protocol

The Brook Floater ( Alasmidonta varicosa ) is a small (<100 mm), stream dwelling freshwater mussel (Family: Unionidae) from Atlantic Slope drainages in the eastern U.S. (Nedeau 2008). Brook Floater have dramatically contracted in distribution over recent decades, and there is limited evidence of recruitment in most locations, despite minimal effort to document population status (Wicklow et al., 2017). Brook Floater is listed as a Species of Greatest Conservation Need (SGCN) throughout its range in the United States (state-listed as imperiled or critically imperiled in all 15 states), has been extirpated from two states (Rhode Island and Delaware) and was recently petitioned for Federal listing in 2011 (Wicklow et al. 2017). Currently, there is a U.S. Fish and Wildlife (USFWS) Species Status Assessment underway to determine if federal listing under the Endangered Species Act is warranted. Brook Floater is also listed as a species of special concern in Canada, the northern extent of its range. In 2016, a state wildlife grant was awarded to develop range-wide conservation initiatives and strategies, including the development of rapid assessment and long-term monitoring techniques, in addition to developing conservation strategies to improve its probability of persistence in the future. The purpose of this protocol is to describe and facilitate a rapid approach to estimating Brook Floater occupancy to better understand the factors that influence Brook Floater distribution. Occupancy estimation approaches allow for estimation of species occupancy (; percent area occupied) within some scale of interest (for our purposes, the watershed), while simultaneously estimating species detection probability (p; the probability of finding an organism, if present). Occupancy estimation has been used with many wildlife taxa and is essential for understanding the presence or absence of wildlife in a particular area while accounting for imperfect detection (i.e., p<1; MacKenzie et al. 2004, Shea et al. 2013, Wisniewski et al. 2013, Pandolfo et al. 2016, MacKenzie 2016). This approach does not rely on existing information about species presence or absence to select sites. Occupancy estimation operates on a robust probabilistic framework of randomly selected sites to infer what proportion of sites are occupied. Occupancy estimation also incorporates imperfect detection (p <1; i.e., animals are cryptic and elusive; observers have varying experience searching, etc.; MacKenzie et al. 2003). For example, two mussel species that occupy a site might have two very different detection histories, as determined by revisiting a site and using the same methods on repeated visits to find both species. See hypothetical results here: Visits 1 2 3 4 5 Mussel species A 1 1 1 0 1 Mussel species B 0 0 0 1 0 (1 = detected, 0=not detected) Both of these mussel species occupy this site, yet Mussel A was detected in 4 out of 5 visits (high p) and Mussel B was detected in 1 out of 5 visits (low p) with the methods used to survey this site. Covariates may explain differences in detection between species or visits. Organisms may be: 1) present and not observed, 2) present and unavailable for capture (i.e., buried in sediment), or 3) not present at the site. Occupancy estimation uses repeated visits of randomly selected sites to build species detection histories (i.e., 1, 0, 1) to simultaneously estimate occupancy () and p. Typically, repeated visits are discrete sampling events and are more time consuming because each site requires >3 separate visits. In our rapid assessment protocol, we use multiple independent observers searching longitudinal lanes to estimate detection in a single site visit as opposed to multiple discrete visits. Below are hypothetical results of occupancy by observer: Independent Observers 1 2 3 4 5 Mussel species A 1 1 0 1 1 Mussel species B 1 0 0 1 0 (1 = detected, 0=not detected) Objectives: The objectives of this rapid assessment survey approach are to guide collection of data that can be used to: A. Estimate the occupancy of Brook Floater within watersheds. B. Estimate the effects of reach- and watershed-scale habitat features on Brook Floater occurrence. C. Understand how survey covariates (e.g., surveyor experience) influence detection of Brook Floater. While this protocol explicitly targets collection of Brook Floater, it is likely that the methods can be adapted for occupancy surveys of other stream-dwelling freshwater mussel species.

Cooperator Science Series↗

USGS2026

Resources to inform the 2026 Colorado Climate Preparedness Roadmap: Compound hazards and associated public health implications

Changing environmental conditions are increasing the frequency and severity of extreme weather and environmental hazards, including heat waves, wildfires, drought, reduced water quality, and degraded air quality from ozone (O3) and fine particulate matter pollution (AghaKouchak et al., 2020; Bolinger et al., 2024; Colorado Health Institute, 2023a; Fann et al., 2015; IPCC, 2023a; Nagamoto et al., 2024; Nolte et al., 2018, 2021; Zscheischler et al., 2020). Strong scientific evidence indicates that climate change will increase risks to public health and safety throughout the 21st century, particularly through compound climate events (AghaKouchak et al., 2020; Cascio, 2018; Childs et al., 2022; Ebi, 2025; IPCC, 2023a, 2023b; Ma et al., 2024; Marlier et al., 2026; National Academy of Medicine, 2025; Reid et al., 2016; Reid & Maestas, 2019; Simpson et al., 2023; van den Hurk et al., 2023; Volckens, 2024; Zscheischler et al., 2018, 2020). Compound hazards, which are co-occurring or sequential hazards such as heat waves occurring alongside drought, wildfire, and poor air quality from smoke, can amplify public health risks beyond the effects of individual hazards alone (Marlier et al., 2026; Zscheischler et al., 2020). In Colorado, compound climate events with clear implications for public health are already evident (see “Core definitions” section for additional context on compound climate events). Recent statewide assessments have documented increasing heat waves, drought, and wildfires linked to rising temperatures, while emerging data show that climate change is reversing decades of air quality improvements through increased O3 and fine particulate matter pollution due to wildfire, and increased aerosolized topsoil (i.e., dust) due to drought (Bolinger et al., 2024; Childs et al., 2022; Fann et al., 2015; Ghanbari et al., 2023; Larsen et al., 2022; Nolte et al., 2018, 2021; Volckens, 2024). These environmental shifts are associated with increases in eye and kidney-health related concerns, heat-related illness, exacerbations of asthma and other respiratory conditions, increased risk of infectious disease, cardiovascular stress, and mental health impacts, with disparities in risk for children, older adults, outdoor workers, and communities with existing health and economic vulnerabilities (Baraghoshi et al., 2023; Butler-Dawson et al., 2026; Cascio, 2018; Cleland et al., 2022; Colorado Health Institute, 2023a; Grover et al., 2024; Lee et al., 2023; Ma et al., 2024; Macaluso et al., 2024; Marlier et al., 2026; National Academy of Medicine, 2025; Patnaik et al., 2024; Peters et al., 2019; Reid et al., 2016; Reid & Maestas, 2019). The state is actively pursuing strategies to mitigate the risks of these compound climate events on the public, including expanding climate and health surveillance, strengthening early-warning systems and public communication around smoke and air quality, and developing integrated policy agendas that link climate mitigation, adaptation, and health equity (CDPHE, 2025; Colorado Health Institute, 2023b; Zemaitis & Bailey, 2024). For example, state and partner organizations have articulated cross-sector goals to prepare for health impacts related to extreme heat, wildfires, flooding, drought, declines in water quality, and poor air quality, including updating workplace safety protocols, enhancing community-based resilience, adapting clinical care assessments to include climate-related stressors, and improving access to mental and behavioral health services following climate-related disasters (Colorado Health Institute, 2023b; CDPHE, 2025; Zemaitis & Bailey, 2024). To better prepare for current risks and make informed decisions, more information is needed, including methods to analyze historical and projected conditions in near real time, characterize interactions among compound hazards, and translate climate and air quality science into actionable guidance for public health agencies, health care systems, and communities across Colorado (Ebi, 2025; Marlier et al., 2026; National Academy of Medicine, 2025; Simpson et al., 2023; Zscheischler et al., 2018). For this report, we focus on extreme heat and outdoor air quality (ozone [O3] and fine particulate matter [PM2.5]) as the main compound hazards causing compound climate events, given that 1) the state of Colorado has experienced poor air quality for some time, 2) these climate events are affecting large population numbers, and 3) there is capacity to consider and respond to these climate-driven events.

Colorado↗

USGS1994

A survey protocol for the Southwestern Willow Flycatcher (Empidonax traillii extimus)

The southwestern willow flycatcher ( Empidonax traillii extimus ) is a riparian obligate neotropical migrant, nesting in cottonwood-willow associations and structurally similar riparian vegetation associations. The southwestern willow flycatcher has declined through the twentieth century, primarily due to a number of factors, including loss and fragmentation of riparian habitat, brood parasitism by brown-headed cowbirds ( Molothrus ater ), invasion of riparian habitat by the exotic tamarisk ( Tamarix sp.), and predation (Hunter et al. 1987), Unitt 1987, Hunter et al. 1988, Whitfield 1990, Harris 1991, Rosenberg et al. 1991). In 1991 the U.S. Fish and Wildlife Service (USFWS) designated the southwestern willow flycatcher as a candidate category 1 species (USFWS 1991), indicating that the USFWS had sufficient information to support listing under the Endangered Species Act of 1973, as amended (Act), but that a proposal to list was precluded by other listing actions of higher priority. In July 1993, the USFWS proposed to list E. t. extimus as an endangered species and to designate critical habitat under the Act (USFWS 1993). The states of Arizona, New Mexico, and California comprise most of the southwestern willow flycatcher's historic and current range. Each of these states lists the species as endangered [Arizona Game and Fish Department (AGFD) 1988, New Mexico Department of Game and Fish (NMDGF) 1988, California Department of Game and Fish 1991]. Because of the precarious status of the southwestern willow flycatcher (Unitt 1987, USFWS 1993), there is a need to identify as many remaining breeding locations as possible. This survey protocol was developed to facilitate and standardize breeding surveys, and is based primarily on extensive 1992 and 1993 field surveys. It was developed at the request of the Arizona Partners in flight, and organization of Federal and State agencies, nongovernmental organizations, and individuals. This protocol is intended to be useful throughout the range of the southwestern willow flycatcher. The authors welcome any suggestions on refining this protocol.

Report↗

USGS2022

Multi-decadal sandbar response to flow management downstream from a large dam—The Glen Canyon Dam on the Colorado River in Marble and Grand Canyons, Arizona

Sandbars are an important resource in the Colorado River corridor in Marble and Grand Canyons, Arizona, downstream from Glen Canyon Dam. Sandbars provide aquatic and riparian habitat and are used as campsites by river runners and hikers. The study area is the Colorado River between Glen Canyon Dam and Diamond Creek, which is about 388 kilometers (241 miles) downstream from the dam. Closure of Glen Canyon Dam in 1963 and subsequent flow regulation reduced the sediment supply, limited the magnitude and frequency of floods, and increased the magnitude of baseflows. The result has been widespread erosion of sandbars and expansion of native and non-native vegetation on previously bare sand deposits in this debris-fan dominated canyon river. This study reports on the on-going long-term measurement program of Northern Arizona University, initiated in 1990 with the Bureau of Reclamation, and now also with the U.S. Geological Survey’s Grand Canyon Monitoring and Research Center. We report on all sandbar measurements made between 1990 and 2020 to demonstrate the multi-decadal response of the sandbar monitoring sites resulting from flow regulation by Glen Canyon Dam. Because only one study site is located in Glen Canyon, the 25 kilometer (15.5 miles) reach just below Glen Canyon Dam, analyses of sandbar response are only made for the next two canyon segments in the down-river direction, Marble Canyon (388 kilometers [99 miles]) and Grand Canyon (265 kilometers [165 miles]), respectively, where the majority of study sites are located. We show that a majority of monitoring sites increased in volume during a period of frequent controlled floods intended to rebuild sandbars. In the period from 2004 to 2020, which included seven controlled floods, a median discharge of 350 cubic meters per second (m 3 /s), and greater than average tributary sand inputs in more than half of the years, net deposition occurred at 86 percent of long-term monitoring sites. This period was preceded by a period of net erosion (1990–2003) when there was one controlled flood greater than the nominal powerplant capacity of 940 m 3 /s. During this period the median discharge from Glen Canyon Dam was 376 m 3 /s and greater than average sand inputs occurred in only 36 percent of those years. At the end of the monitoring period in 2020, 61 percent of the study sites measured since 1990 underwent a net increase in sand volume. For the entire 31-year period, these trends were statistically significant for all six sandbar types studied, indicating that increased frequency of controlled flooding maintained sandbar volume at the majority of sites monitored. These floods, also referred to as high-flow experiments (HFEs), are part of a decision-making protocol approved in 2012 for coordinating dam releases timed to occur following large sand inputs to the Colorado River by a major tributary. These findings are based on digital elevation models (DEMs) derived from approximately (~)1,800 repeat surveys of sandbar and channel bed topography made annually, or more frequently, at the 45 long-term monitoring sites, of which 31 have been monitored since 1990 and 14 were added between 1990 and 2008. This large collection of monitoring sites comprises just 7 to 9 percent of all sandbars in Marble and Grand Canyons, respectively. Nevertheless, when compared with measurements of a larger sample, these sites provide consistent characterization of average sandbar response, despite the local variability in channel and debris fan geometry. We use sand volume and normalized sand volume for tracking geomorphic changes of sandbars, because these metrics are sensitive to both changes in sandbar area and sandbar elevation. Based on checkpoint comparisons and repeat measurements, DEM elevation uncertainty was determined to be ±0.05 meter (m) and this uncertainty was used in a spatially uniform estimate of volume uncertainty. We find that the magnitudes of the topographic changes were substantially greater than the measurement uncertainty. Sandbars of similar type throughout both Marble and Grand Canyons have responded similarly during the period of the HFE protocol, despite variations in sand supply and longitudinal extent of those inputs. It should be noted that tributary-supplied sand to Glen Canyon is negligible, much of the riverbed is now armored with cobbles, and the channel bed degradation is irreversible in the current flow and sediment supply regime. Because all these HFEs have been conducted during periods of sediment enrichment, other factors such as vegetation and geomorphic setting are likely the primary causes of variation among the monitoring sites. A larger percentage of the sandbar population, predominantly located in narrow reaches where stage changes are greater, is composed of sandbar types that remain dynamic and consistently aggrade during HFEs. In contrast, wide reaches of the river corridor where stage change is not as great are characterized by sandbars that have been stabilized by vegetation and progressive aggradation during floods. In the former case, a majority of sandbars are likely to remain dynamic, requiring continued use of HFEs to achieve desired management goals. In the latter case, HFEs can do no better than replace the sediment eroded during normal dam operation between high-flow events, as they become less effective because of a diminishing amount of accommodation space available for deposition. Long-term sandbar trajectory and the continued effectiveness of HFEs are related to the differential vegetation establishment at each bar type. Future sandbar monitoring may need to consider the effects of riparian vegetation removal.

Arizona↗

USGS2014

Long Term Resource Monitoring Program procedures: fish monitoring

This manual constitutes the second revision of the U.S. Army Corps of Engineers’ Upper Mississippi River Restoration-Environmental Management Program (UMRR-EMP) Long Term Resource Monitoring Program (LTRMP) element Fish Procedures Manual. The original (1988) manual merged and expanded on ideas and recommendations related to Upper Mississippi River fish sampling presented in several early documents. The first revision to the manual was made in 1995 reflecting important protocol changes, such as the adoption of a stratified random sampling design. The 1995 procedures manual has been an important document through the years and has been cited in many reports and scientific manuscripts. The resulting data collected by the LTRMP fish component represent the largest dataset on fish within the Upper Mississippi River System (UMRS) with more than 44,000 collections of approximately 5.7 million fish. The goal of this revision of the procedures manual is to document changes in LTRMP fish sampling procedures since 1995. Refinements to sampling methods become necessary as monitoring programs mature. Possible refinements are identified through field experiences (e.g., sampling techniques and safety protocols), data analysis (e.g., planned and studied gear efficiencies and reallocations of effort), and technological advances (e.g., electronic data entry). Other changes may be required because of financial necessity (i.e., unplanned effort reductions). This version of the LTRMP fish monitoring manual describes the most current (2014) procedures of the LTRMP fish component.

Illinois;Iowa;Minnesota;Montana;Wisconsin↗

USGS2018

Global Modern Charcoal Dataset (GMCD): A tool for exploring proxy-fire linkages and spatial patterns of biomass burning

Progresses in reconstructing Earth's history of biomass burning has motivated the development of a modern charcoal dataset covering the last decades through a community-based initiative called the Global Modern Charcoal Dataset (GMCD). As the frequency, intensity and spatial scale of fires are predicted to increase regionally and globally in conjunction with changing climate, anthropogenic activities and land-use patterns, there is an increasing need to further understand, calibrate and interrogate recent and past fire regimes as related to changing fire emissions and changing carbon sources and sinks. Discussions at the PAGES Global Paleofire Working Group workshop 2015, including paleoecologists, numerical modelers, statisticians, paleoclimatologists, archeologists, and anthropologists, identified an urgent need for an open, standardized, quality-controlled and globally representative dataset of modern sedimentary charcoal and other sediment-based fire proxies. This dataset fits into a gap between metrics of biomass burning indicators, current fire regimes and land cover, and carbon emissions inventories. The dataset will enable the calibration of paleofire data with other modern datasets including: data of satellite derived fire occurrence, vegetation patterns and species diversity, land cover change, and a range of sources capturing biochemical cycling. Standardized protocols are presented for collecting and analyzing sediment-based fire proxies, including charcoal, levoglucosan, black carbon, and soot. The GMCD will provide a publicly-accessible repository of modern fire sediment surface samples in all terrestrial ecosystems. Sample collection and contributions to the dataset will be solicited from lacustrine, peat, marine, glacial, or other sediments, from a wide variety of ecosystems and geographic locations .

Quaternary International↗

USGS2014

Climate change and plant community composition in national parks of the southwestern US: forecasting regional, long-term effects to meet management needs

The National Park Service (NPS) faces tremendous management challenges in the future as climates alter the abundance and distribution of plant species. These challenges will be especially daunting in the southwestern U.S., where large increases in aridity are forecasted. The expected reduction in water availability will negatively affect plant growth and may result in shifts of plant community composition. Synthesis of climate and plant vital sign data from National Park Service Inventory and Monitoring (I&M) networks is essential to provide park managers with important insights into contemporary climate responses and a sound basis to forecast likely future changes at species, community, and ecosystem scales. We describe a collaboration between the U.S. Geological Survey (USGS) and NPS in which we have conducted regional cross-site assessments across the Sonoran and Chihuahuan Deserts to understand plant species responses to past climate and forecast future plant community composition. We also determined whether a widely-implemented vegetation monitoring protocol in these deserts is suitable to track long-term vegetation changes caused by climate and other factors. Our results from these analyses are intended to help natural resource managers identify and prepare for changes in plant cover and community composition and evaluate the efficacy of current monitoring programs.

Arizona, New Mexico, Texas↗

USGS2011

Comparative evaluation of molecular diagnostic tests for Nucleospora salmonis and prevalence in migrating juvenile salmonids from the Snake River, USA

Nucleospora salmonis is an intranuclear microsporidian that primarily infects lymphoblast cells and contributes to chronic lymphoblastosis and a leukemia-like condition in a range of salmonid species. The primary goal of this study was to evaluate the prevalence of N. salmonis in out-migrating juvenile hatchery and wild Chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss from the Snake River in the U.S. Pacific Northwest. To achieve this goal, we first addressed the following concerns about current molecular diagnostic tests for N. salmonis : (1) nonspecific amplification patterns by the published nested polymerase chain reaction (nPCR) test, (2) incomplete validation of the published quantitative PCR (qPCR) test, and (3) whether N. salmonis can be detected reliably from nonlethal samples. Here, we present an optimized nPCR protocol that eliminates nonspecific amplification. During validation of the published qPCR test, our laboratory developed a second qPCR test that targeted a different gene sequence and used different probe chemistry for comparison purposes. We simultaneously evaluated the two different qPCR tests for N. salmonis and found that both assays were highly specific, sensitive, and repeatable. The nPCR and qPCR tests had good overall concordance when DNA samples derived from both apparently healthy and clinically diseased hatchery rainbow trout were tested. Finally, we demonstrated that gill snips were a suitable tissue for nonlethal detection of N. salmonis DNA in juvenile salmonids. Monitoring of juvenile salmonid fish in the Snake River over a 3-year period revealed low prevalence of N. salmonis in hatchery and wild Chinook salmon and wild steelhead but significantly higher prevalence in hatchery-derived steelhead. Routine monitoring of N. salmonis is not performed for all hatchery steelhead populations. At present, the possible contribution of this pathogen to delayed mortality of steelhead has not been determined.

Journal of Aquatic Animal Health↗

USGS2006

Survey and monitoring of species at risk at Camp Blanding Training Site, northeastern Florida

We studied the presence and distribution of 19 species at risk in northeastern Florida at the Camp Blanding Training Site (CBTS) during 2000-2001, seven years after the first major baseline surveys of CBTS were conducted. Much of the training conducted at CBTS deals with light infantry exercises, but the site is also used for mining, silviculture, hunting, fishing, emergency logistical support, and entertainment purposes. CBTS contains more than 2000 species of plants and animals in 14 natural communities, each impacted to various degrees by past and current land management. Adaptive management plans for species may be ineffective without continual feedback and the flexibility for change. Here we summarize and discuss the results of our surveys, compare these results with those of past surveys, identify differences between the surveys, and discuss the importance of systematic protocols and study design for CBTS environmental managers.

Southeastern Naturalist↗

USGS2017

Updated operational protocols for the U.S. Geological Survey Precipitation Chemistry Quality Assurance Project in support of the National Atmospheric Deposition Program

The U.S. Geological Survey Branch of Quality Systems operates the Precipitation Chemistry Quality Assurance Project (PCQA) for the National Atmospheric Deposition Program/National Trends Network (NADP/NTN) and National Atmospheric Deposition Program/Mercury Deposition Network (NADP/MDN). Since 1978, various programs have been implemented by the PCQA to estimate data variability and bias contributed by changing protocols, equipment, and sample submission schemes within NADP networks. These programs independently measure the field and laboratory components which contribute to the overall variability of NADP wet-deposition chemistry and precipitation depth measurements. The PCQA evaluates the quality of analyte-specific chemical analyses from the two, currently (2016) contracted NADP laboratories, Central Analytical Laboratory and Mercury Analytical Laboratory, by comparing laboratory performance among participating national and international laboratories. Sample contamination and stability are evaluated for NTN and MDN by using externally field-processed blank samples provided by the Branch of Quality Systems. A colocated sampler program evaluates the overall variability of NTN measurements and bias between dissimilar precipitation gages and sample collectors. This report documents historical PCQA operations and general procedures for each of the external quality-assurance programs from 2007 to 2016.

Open-File Report↗

USGS2005

Specific electrical conductance

Electrical conductance is a measure of the capacity of a substance to conduct an electrical current. The specific electrical conductance (conductivity) of water is a function of the types and quantities of dissolved substances it contains, normalized to a unit length and unit cross section at a specified temperature. This section of the National Field Manual (NFM) describes U.S. Geological Survey (USGS) guidance and protocols for measurement of conductivity in ground and surface waters.

Techniques of Water-Resources Investigations↗