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USGS2020

Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River Fall Chinook Salmon ESU: January 2019 - December 2019

The portion of the Snake River fall Chinook salmon Oncorhynchus tshawytscha evolutionary significant unit (ESU) that spawns upstream of Lower Granite Dam transitioned from low to high abundance during 19922019 in association with U.S. Endangered Species Act recovery efforts and other federally mandated actions. This annual report focuses on (1) numeric and habitat use responses by natural- and hatchery-origin spawners, (2) phenotypic and numeric responses by natural-origin juveniles, and (3) use of a small unmanned aerial system (sUAS) to search for fall Chinook salmon redds and carcasses. Spawners have located and used most of the available spawning habitat and that habitat is gradually approaching redd capacity. Timing of spawning and fry emergence have been relatively stable, but effects of density dependence are evident in juvenile life stages. Apparent abundance of juvenile fall Chinook salmon has increased and we noted the following responses: parr dispersal from riverine rearing habitat into Lower Granite Reservoir has become earlier; growth rate (g/d) and dispersal size of parr declined; and passage timing of smolts from the two Snake River reaches has become earlier and downstream movement rate faster. These findings coupled with stock-recruitment analyses presented in this report provide evidence for density-dependence in the Snake River reaches and in Lower Granite Reservoir that was influenced by the expansion of the recovery program. The long-term goal is to use this information in a comprehensive modeling effort to conduct action-effectiveness and uncertainty research and to inform Fish Population, Hydrosystem, Harvest, Hatchery, and Predation and Invasive Species Management Research, Monitoring, and Evaluation (RM&E) progams. In 2019, the U.S. Geological Survey (USGS) shifted survey efforts in the Snake River toward deepwater redd searches and fish collection for parentage-based tagging (PBT) analyses because all unmanned aerial system (UAS) activities were suspended by the Department of the Interior two weeks into the spawning season. We counted 81 deepwater redds at 17 of the 29 sites surveyed. Redd depths averaged 3.6 m. We collected a total of 123 live fall Chinook salmon from 16 unique geographic locations that spanned 55 river kilometers. Forty-six fish were recovered at Eureka Bar (rkm 307.1) and Kirby Creek (rkm 352.0), which accounted for 37% of all collected fish in 2019. Most (73 fish) post-spawned salmon were collected from early to mid-November just after peak spawning. A summary of 2019 PBT results can be found in Appendix A.1. In 2019, we PIT tagged subyearling fall Chinook salmon in both the Snake and Clearwater rivers. In the Snake River, we tagged 410 fish with 8-mm tags, 666 fish with 9-mm tags, and 1,082 fish 12-mm tags. During seining, our recapture rate of previously tagged fish was slightly higher in the lower reach at 11.4% than in the upper reach at 10.6%. In an effort to represent more of the population through tagging, we tagged fish as small as 45 mm with 8-mm tags at one site in the upper reach. This allowed us to increase the number of fish tagged in that reach by 17.7%. An additional 10.6% of collected fish could have been tagged in the lower reach had we used 8-mm tags in that reach. In the Clearwater River, we tagged 2,451 subyearlings and recaptured 260 (10.6%) fish in the river and 66 fish (48 tagged by USGS, 18 tagged by the Nez Perce Tribe) at Lower Granite Dam during October to provide information for growth estimation. Within riverine habitats, growth in both length and mass were higher for fish tagged with 8-mm tags than with 9- and 12-mm tags. Estimated growth in length and mass of subyearlings was higher in Lower Granite Reservoir than in riverine habitats. We adapted existing statistical models used to estimate abundance of steelhead and spring/summer Chinook salmon for fall Chinook salmon passing Lower Granite Dam. Run reconstruction efforts to date at Lower Granite Dam for Snake River fall Chinook salmon have provided estimates of the number of returning adults but with no measure of uncertainty about the estimates. The objective of this study was to estimate the abundance, with uncertainty, of marked (coded-wire tagged CWT or adipose clipped) and unmarked fall Chinook salmon past Lower Granite Dam for return years 20032018. Estimating uncertainty is important for informing the state-space life cycle model (Chapter 5), which incorporates both observation and process uncertainty into parameter estimates. The coefficient of variation (CV) for log- abundance was 1.0% or less in all years, whereas the CV for abundance averaged 4.2% and ranged from 1.4% to 10.4% among years. Over the past five years, we have been developing a two-stage state-space life-cycle model for naturally produced fall Chinook salmon in the Snake River basin. Initial efforts focused on generating juvenile and adult abundance estimates, with estimates of uncertainty, for informing the life-cycle model. In this report we 1) describe the statistical life-cycle model and improvements made since our last report to the Independent Scientific Advisory Board (ISAB), 2) estimate the effects of covariates on key demographic parameters, and 3) use the fitted life- cycle model to simulate population trajectories under hydrosystem actions proposed for the NOAA 2020 Biological Opinion (hereafter, the Proposed Action). Major recent advancements to the model include revised juvenile abundance estimates, the ability to estimate smolt-to-adult return rates (SAR) separately for subyearling and yearling juvenile fall Chinook salmon, and improvements in the observation model for estimating age, sex, and outmigration structure in adult returns. We examined the effect of numerous environmental, hydrosystem, and ocean covariates on key demographic parameters but only a few covariates were significant. For the adult-to-juvenile transition, we found the maximum weekly river flows during the winter egg- incubation period had a significant negative effect on the juvenile outmigrant abundance from that brood year. For subyearling outmigrants, percent spill during the summer had a significant positive effect on SAR and the mean winter PDO (Pacific Decadal Oscillation) had a significant negative effect on SAR. For yearling outmigrants, NPGO (North Pacific Gyre Oscillation) had a significant positive effect on SAR. We used the fitted model to simulate population trajectories under the Proposed Action, and the median 10-year geometric mean abundance was 8,222 female spawners (interquartile range: 2,592 26,714). Overall, the probability of quasi- extinction (probability of falling below 50 female spawners for 4 consecutive years) was low, with only 1.6% of all simulations having a quasi-extinction probability >0.95. Although quasi-extinction probability was low, we did not assess the additional effect of climate change, which would be expected to increase quasi-extinction probability.

Idaho, Oregon, Washington↗

USGS2021

Microbial and viral indicators of pathogens and human health risks from recreational exposure to waters impaired by fecal contamination

Fecal indicator bacteria (FIB) (e.g., fecal coliforms, Escherichia coli , and enterococci) have been used for decades to monitor for and protect the public from waterborne pathogens from fecal contamination. However, FIB may not perform well at predicting the presence of waterborne pathogens or human health outcomes from recreational exposure to fecal-contaminated surface waters. Numerous factors can influence the relationship between FIB and pathogens or human health outcomes, including the source(s) of contamination, the type of pathogen(s) present, differences in the survival and behavior of FIB and pathogens in the wastewater conveyance and treatment process, and varying environmental conditions. As a result, different indicators, such as source-specific microbial source tracking (MST) markers and viral fecal indicators, have been used as possible surrogates to better approximate pathogen abundance and human health risks in recreational waters. The performance of these alternative indicators has been mixed, with some promise of viral indicators better approximating viral pathogens than bacterial fecal indicators, and FIB generally more closely associated with bacterial and protozoal pathogen presence than human MST markers. Many of the assays to detect and quantify fecal indicators and pathogens are polymerase chain reaction-based assays, which detect and quantify nucleic acid [deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)] sequences specific to a target of interest. Recent advances in DNA and RNA sequencing technologies may push the field toward metabarcoding approaches, where multiple targets can be detected and quantified simultaneously. Metabarcoding is currently more applicable to bacterial and protozoal assessments than viral assessments based on a lack of universal metabarcoding markers for viruses. Innovative technologies, such as biosensors and nanotechnologies, may provide more sensitive and accurate tools to detect and quantify pathogens. When a specific pathogen is of concern for a recreational water body, a practical approach in estimating the likelihood of human health outcomes is the application of quantitative microbial risk assessments (QMRAs). Quantitative microbial risk assessments can be used to model the likelihood of pathogen-specific human health outcomes from recreational exposure as a function of a surrogate indicator. Inputs for QMRAs include the ratio between the indicator to be monitored and the pathogen of interest, the concentration of the indicator, the amount of water ingested, and the likelihood of the health outcome based on the estimated amount of pathogen consumed. There are numerous unknowns about the behavior and survival of fecal indicators and pathogens in environmental waters. Developing accurate models to predict pathogen concentrations from fecal indicators in recreational waters will require a better understanding of these unknowns. Current methods and technologies for detecting and quantifying fecal indicators and pathogens are limited due to the rare and patchy nature of pathogens. Technological advances may help improve sensitivity for detecting and quantifying pathogens.

Journal of Sustainable Water in the Built Environm↗

USGS2022

Using piecewise regression to identify biological phenomena in biotelemetry datasets

1. Technological advances in the field of animal tracking have greatly expanded the potential to remotely monitor animals, opening the door to exploring how animals shift their behavior over time or respond to external stimuli. A wide variety of animal-borne sensors can provide information on an animal’s location, movement characteristics, external environmental conditions, and internal physiological status. 2. Here, we demonstrate how piecewise regression can be used to identify the presence and timing of potential shifts in a variety of biological responses using GPS telemetry and other biologging data streams. Different biological latent states can be inferred by partitioning a time-series into multiple segments based on changes in modeled responses (e.g., their mean, variance, trend, degree of autocorrelation) and specifying a unique model structure for each interval. 3. We provide six example applications highlighting a variety of taxonomic species, data streams, timescales and biological phenomena. These examples include a short-term behavioural response (flee and return) by a trumpeter swan Cygnus buccinator following a GPS collar deployment; remote identification of parturition based on movements by a pregnant moose Alces alces ; a physiological response (spike in heart-rate) in a black bear Ursus americanus to a stressful stimulus(presence of a drone); a mortality event of a trumpeter swan signalled by changes in collar temperature and overall dynamic body acceleration; an unsupervised method for identifying the onset, return, duration and staging use of sandhill crane Antigone canadensis migration; and estimation of the transition between incubation and brood-rearing (i.e. hatching) for a breeding trumpeter swan. 4. We implement analyses using the MCP package in R, which provides functionality for specifying and fitting a wide variety of user-defined model structures in a Bayesian framework and methods for assessing and comparing models using information criteria and cross-validation measures.

Journal of Animal Ecology↗

USGS2012

Approaches in highly parameterized inversion-PESTCommander, a graphical user interface for file and run management across networks

Models of environmental systems have become increasingly complex, incorporating increasingly large numbers of parameters in an effort to represent physical processes on a scale approaching that at which they occur in nature. Consequently, the inverse problem of parameter estimation (specifically, model calibration) and subsequent uncertainty analysis have become increasingly computation-intensive endeavors. Fortunately, advances in computing have made computational power equivalent to that of dozens to hundreds of desktop computers accessible through a variety of alternate means: modelers have various possibilities, ranging from traditional Local Area Networks (LANs) to cloud computing. Commonly used parameter estimation software is well suited to take advantage of the availability of such increased computing power. Unfortunately, logistical issues become increasingly important as an increasing number and variety of computers are brought to bear on the inverse problem. To facilitate efficient access to disparate computer resources, the PESTCommander program documented herein has been developed to provide a Graphical User Interface (GUI) that facilitates the management of model files ("file management") and remote launching and termination of "slave" computers across a distributed network of computers ("run management"). In version 1.0 described here, PESTCommander can access and ascertain resources across traditional Windows LANs: however, the architecture of PESTCommander has been developed with the intent that future releases will be able to access computing resources (1) via trusted domains established in Wide Area Networks (WANs) in multiple remote locations and (2) via heterogeneous networks of Windows- and Unix-based operating systems. The design of PESTCommander also makes it suitable for extension to other computational resources, such as those that are available via cloud computing. Version 1.0 of PESTCommander was developed primarily to work with the parameter estimation software PEST; the discussion presented in this report focuses on the use of the PESTCommander together with Parallel PEST. However, PESTCommander can be used with a wide variety of programs and models that require management, distribution, and cleanup of files before or after model execution. In addition to its use with the Parallel PEST program suite, discussion is also included in this report regarding the use of PESTCommander with the Global Run Manager GENIE, which was developed simultaneously with PESTCommander.

Techniques and Methods↗

USGS2005

Advanced Very High Resolution Radiometer Normalized Difference Vegetation Index Composites

The Advanced Very High Resolution Radiometer (AVHRR) is a broad-band scanner with four to six bands, depending on the model. The AVHRR senses in the visible, near-, middle-, and thermal- infrared portions of the electromagnetic spectrum. This sensor is carried on a series of National Oceanic and Atmospheric Administration (NOAA) Polar Orbiting Environmental Satellites (POES), beginning with the Television InfraRed Observation Satellite (TIROS-N) in 1978. Since 1989, the United States Geological Survey (USGS) Center for Earth Resources Observation and Science (EROS) has been mapping the vegetation condition of the United States and Alaska using satellite information from the AVHRR sensor. The vegetation condition composites, more commonly called greenness maps, are produced every week using the latest information on the growth and condition of the vegetation. One of the most important aspects of USGS greenness mapping is the historical archive of information dating back to 1989. This historical stretch of information has allowed the USGS to determine a 'normal' vegetation condition. As a result, it is possible to compare the current week's vegetation condition with normal vegetation conditions. An above normal condition could indicate wetter or warmer than normal conditions, while a below normal condition could indicate colder or dryer than normal conditions. The interpretation of departure from normal will depend on the season and geography of a region.

Fact Sheet↗

USGS2020

Groundwater quality and geochemistry of West Virginia’s southern coal fields

Coal mining has been the dominant industry and land use in West Virginia’s southern coal fields since the mid-1800s. Mortality rates for a variety of serious chronic conditions, such as diabetes, heart disease, and some forms of cancer in Appalachian coal mining regions, are higher than in areas lacking substantial coal mining activity within the Appalachian Region or elsewhere in the United States. Causes of the increased mortality and morbidity are not clear, but poor diet, high rates of smoking, socioeconomic factors, and the quality of groundwater used by area residents are all possible contributing factors. This study was conducted by the U.S. Geological Survey in cooperation with the West Virginia Department of Health and Human Resources and the West Virginia Department of Environmental Protection, with grant support from the Centers for Disease Control and Prevention (CDC) to assess the quality of groundwater in southern West Virginia. The data from this assessment of groundwater quality may be used by the CDC and other agencies to potentially investigate the role or lack thereof of groundwater quality with respect to mortality and morbidity rates in the region. The study was conducted in a region where a high density of current or past coal mining combined with a lack of advanced sewage treatment could affect concentrations of commonly occurring constituents plus contaminants, including nitrate, trace metals, major ions, indicator bacteria, radon, hydrogen sulfide, and dissolved hydrocarbons. Because rural residential wells and mine outfalls are considered private sources of water in the region, and are therefore unregulated and unmonitored, water-quality data are sparse. To fill the data gap and assess the groundwater quality in the region, water-quality samples were collected from 60 sites in a 10-county area. The 60 sites sampled included 46 rural residential homeowner wells and 14 mine outfall discharges used for residential supply. For this study, all samples were collected prior to any filtration or other treatments, typically at the pressure tank, and are indicative of total and dissolved constituents in the untreated water. Generally, data for the 60 sites indicate that most waters sampled do not exceed thresholds for most U.S. Environmental Protection Agency (EPA) drinking-water standards and U.S. Geological Survey (USGS) drinking-water screening criteria. However, there were several notable exceptions. Turbidity exceeded the 5-Nephelometric Turbidity Unit (NTU) EPA treatment technique (TT) drinking-water standard in 14 of 60 (23 percent) sites sampled and exceeded the 1-NTU TT standard in 51 of 60 (85 percent) sites sampled. Turbidity is common in many wells in southern West Virginia and may be attributed to iron oxyhydroxide precipitates, sediment carried into the aquifers from the shallow soil zone due to improperly constructed or cased wells or transported to the aquifer in shallow stress-relief fracture zones or through permeable bedding-plane partings. For the sites sampled, 31 of 60 (52 percent) had pH values at, above, or below the upper and lower range of the EPA Secondary Maximum Contaminant Level (SMCL, 6.5–8.5 standard units). Of those 31 sites, 28 (90 percent) were indicative of acidic corrosive water and 3 (10 percent) were indicative of alkaline water. The Langelier Saturation Index (LSI), which is a measure of the corrosivity of the water, was computed for all sites sampled for the study. Eighty-two percent of the sites sampled had waters that were classified as corrosive, based on a LSI less than −0.5. Corrosive water has the potential to leach lead, copper, and other metals from lead, copper, galvanized, or lead-tin soldered connections in water lines. The chloride to sulfate mass ratio also was assessed with the alkalinity to indicate the potential to promote galvanic corrosion (PPGC) of water lines and plumbing fixtures. Only one of the sites (1.7 percent) classified as a corrosive water site, had a PPGC considered high; the remaining sites were classified as having either a moderate (53.3 percent) or low (45 percent) PPGC. Therefore, the type of plumbing systems sampled for this study may be affected by corrosive water, but the potential for leaching trace metals and other constituents from residential plumbing systems containing older galvanized pipes or lead-tin soldered copper pipes is moderate to low. The indicator bacteria total coliform and Escherichia coli ( E. coli ) also were detected in groundwater samples to varying degrees. Total coliforms, which are a broad class of indicator bacteria, are common in groundwater in southern West Virginia and were detected in 39 of the 60 sites (65 percent) sampled. The presence of total coliform bacteria is a potential indicator of surface contamination, due to improperly constructed or cased wells, or infiltration of soil or other surface contaminants into the aquifer or well bore. E. coli bacteria, however, are much more indicative of fecal contamination of groundwater from either human or animal sources, and 14 of the 60 (23 percent) sites sampled had detections of E. coli . Although only a few strains of E. coli are known pathogens, their presence in groundwater may be an indicator of other related pathogens such as viruses and should be regarded as a serious potential issue. Water treatment such as chlorination, ozonation, or ultraviolet light may be appropriate to kill potential pathogenic bacteria or viruses in the source water. Manganese and iron were prevalent contaminants in the groundwater samples collected for this study, with 30 of 60 (50 percent) sites analyzed for manganese and 25 of 60 (42 percent) sites analyzed for iron exceeding the proposed 50- and 300-micrograms per liter (µg/L) SMCL drinking-water standards, respectively, for aesthetic criteria such as taste, odor, or staining of plumbing fixtures. Fourteen of the 60 sites sampled (23 percent) had concentrations of manganese that exceeded the 300-µg/L USGS health-based screening level, and 1 site exceeded the 1,600-µg/L EPA drinking-water equivalent level, which is based on a lifetime exposure level. Sodium is another common constituent in groundwater within the study area. Sodium has an EPA health-based value (HBV) of 20 milligrams per liter (mg/L) for individuals who are on a sodium-restricted diet for blood pressure or other health reasons. Sodium concentrations exceeded the 20-mg/L EPA HBV in 27 of 60 (45 percent) samples. Radon, a naturally occurring carcinogenic radioactive gas known to cause lung cancer, was detected at concentrations at or exceeding the proposed 300-picocuries per liter (pCi/L) EPA Maximum Contaminant Level (MCL) in 12 of the 60 (20 percent) sites sampled. Sites with radon gas concentrations exceeding the 300-pCi/L proposed MCL have the potential for airborne concentrations of radon to exceed the 4-pCi/L indoor air standard. Inhalation of radon can cause lung cancer, and the 4-pCi/L indoor air standard is based on an inhalation standard. Therefore, homeowners whose wells have radon gas concentrations exceeding 300 pCi/L may be advised to have their indoor air tested to determine if indoor air concentrations exceed the 4-pCi/L indoor air standard established by the EPA. Various factors were analyzed statistically and graphically to determine whether they have an influence on groundwater quality within the study area, including topographic setting, well depth, type of mining (surface or underground), type of site (well or mine outfall), and geologic formation. Only geologic formation and the type of site sampled had strong statistical correlations with one or more of the constituents of concern for this study. The overall chemistry of outfalls (mine outfalls) and wells was significantly different, with a much higher dissolved oxygen content in outfalls than in wells. The dissolved oxygen content is the primary component driving the oxidation and reduction of minerals, and the precipitation of minerals that are saturated or super saturated with respect to various cations and anions. Median dissolved oxygen concentrations for the outfalls sampled was 8.75 mg/L, and only 0.4 mg/L for the wells sampled. Median concentrations of sulfate and selenium were much higher in waters from the outfalls sampled, with median concentrations of 73.75 mg/L and 2.35 µg/L, respectively, compared to the wells sampled, which had median concentrations of 18.3 mg/L and less than (<) the 0.05-µg/L method detection limit, respectively. The maximum selenium concentration was for a well, with a concentration of 16.6 µg/L. The geochemical processes that control sulfate and selenium concentrations in groundwater are similar and are the result of the oxidation of sulfide minerals such as pyrite and ferroselite. Iron and manganese concentrations were elevated in most of the wells sampled, with median concentrations of 269.5 and 124.5 µg/L, respectively, but were rarely detected in the outfalls sampled, with median concentrations of < 4.0 and < 0.4 µg/L, respectively. The difference in iron and manganese between wells and outfalls is indicative of the role of dissolved oxygen on processes controlling groundwater chemistry in the region. Three principal geologic formations were assessed for the study, and the overall chemistry for the Pocahontas, New River, and Kanawha Formations varied substantially with respect to several constituents. Concentrations of calcium, magnesium, and total dissolved solids were highest for sites sampled in the Pocahontas Formation, with median concentrations of 41.9, 18.6, and 312 mg/L, respectively. For constituents that are commonly associated with mining activity, the highest concentrations were for sites sampled in the New River Formation, with median concentrations of iron and manganese of 2,450 µg/L and 482 µg/L, respectively, and a median pH of 6.35 standard units. Concentrations of barium also were elevated in samples collected from sites in the New River Formation, with a median barium concentration of 184 µg/L. The source of the barium is not fully known but may be associated with commingling of shallow groundwater with deeper brines or dissolution of the mineral barite. The highest median sulfate concentrations were from sites sampled in the Pocahontas Formation, with a median concentration of 64.0 mg/L. Of the 12 sites at or exceeding the 300-pCi/L proposed drinking-water standard for radon, 8 (67 percent of MCL exceedances) were for sites deriving water from the Kanawha Formation, 3 (25 percent of MCL exceedances) were for sites deriving water from the New River Formation, and only 1 site was for water from the Pocahontas Formation (8 percent of proposed MCL exceedances). Dissolved hydrocarbons, including methane, ethane, propane, propene, n - and i -butane, 1-butene, n - and i -pentane, pentane, 2- and 3-ethyl pentane, hexane, and benzene were analyzed in samples collected from 59 of the 60 sites to assess the potential occurrence and sources of these trace gases in groundwater within the study area. Results of the analysis indicate that most of the gas is of shallow biogenic origin, possibly associated with coal-bed methane, but a subset of samples has a gas signature and a chloride to bromide ratio indicative of potential mixing with deeper thermogenic gases. Only 2 of the 59 (3.3 percent) sites sampled had concentrations of methane gas, which is a highly combustible and explosive gas, exceeding the 10 milligrams per kilogram level of concern established by the U.S. Office of Surface Mining Reclamation and Enforcement. Principal components analysis was used to assess the primary geochemical processes occurring in the aquifers sampled. The first principal component had significant positive loadings for bromide, chloride, silica, ammonia, barium, iron, manganese, and arsenic, and significant negative loadings for dissolved oxygen, potassium, nitrate, and uranium, and reflects reduction and oxidation (redox) processes occurring in deeper anoxic groundwater or shallow oxic groundwater. The strong positive loadings for iron, manganese, barium, and arsenic are correlated with reducing conditions often found deeper in the aquifer. More oxic water is correlated with oxidation of nitrogen species to nitrate and environmental mobilization of uranium and sulfate in shallow wells and mine outfalls.

West Virginia↗

USGS2009

EAARL Coastal Topography-Pearl River Delta 2008: Bare Earth

These remotely sensed, geographically referenced elevation measurements of Lidar-derived bare earth (BE) topography were produced as a collaborative effort between the U.S. Geological Survey (USGS), Florida Integrated Science Center (FISC), St. Petersburg, FL; the University of New Orleans (UNO), Pontchartrain Institute for Environmental Sciences (PIES), New Orleans, LA; and the National Aeronautics and Space Administration (NASA), Wallops Flight Facility, VA. This project provides highly detailed and accurate datasets of a portion of the Pearl River Delta in Louisiana and Mississippi, acquired March 9-11, 2008. The datasets are made available for use as a management tool to research scientists and natural resource managers. An innovative airborne Lidar instrument originally developed at the NASA Wallops Flight Facility, and known as the Experimental Advanced Airborne Research Lidar (EAARL), was used during data acquisition. The EAARL system is a raster-scanning, waveform-resolving, green-wavelength (532-nanometer) Lidar designed to map near-shore bathymetry, topography, and vegetation structure simultaneously. The EAARL sensor suite includes the raster-scanning, water-penetrating full-waveform adaptive Lidar, a down-looking red-green-blue (RGB) digital camera, a high-resolution multi-spectral color infrared (CIR) camera, two precision dual-frequency kinematic carrier-phase GPS receivers, and an integrated miniature digital inertial measurement unit, which provide for submeter georeferencing of each laser sample. The nominal EAARL platform is a twin-engine Cessna 310 aircraft, but the instrument may be deployed on a range of light aircraft. A single pilot, a Lidar operator, and a data analyst constitute the crew for most survey operations. This sensor has the potential to make significant contributions in measuring sub-aerial and submarine coastal topography within cross-environmental surveys. Elevation measurements were collected over the survey area using the EAARL system, and the resulting data were then processed using the Airborne Lidar Processing System (ALPS), a custom-built processing system developed in a NASA-USGS collaboration. ALPS supports the exploration and processing of Lidar data in an interactive or batch mode. Modules for presurvey flight line definition, flight path plotting, Lidar raster and waveform investigation, and digital camera image playback have been developed. Processing algorithms have been developed to extract the range to the first and last significant return within each waveform. ALPS is used routinely to create maps that represent submerged or first surface topography. Specialized filtering algorithms have been implemented to determine the 'bare earth' under vegetation from a point cloud of last return elevations.

Data Series↗

USGS2009

EAARL Coastal Topography-Pearl River Delta 2008: First Surface

These remotely sensed, geographically referenced elevation measurements of Lidar-derived first surface (FS) topography were produced as a collaborative effort between the U.S. Geological Survey (USGS), Florida Integrated Science Center (FISC), St. Petersburg, FL; the University of New Orleans (UNO), Pontchartrain Institute for Environmental Sciences (PIES), New Orleans, LA; and the National Aeronautics and Space Administration (NASA), Wallops Flight Facility, VA. This project provides highly detailed and accurate datasets of a portion of the Pearl River Delta in Louisiana and Mississippi, acquired March 9-11, 2008. The datasets are made available for use as a management tool to research scientists and natural resource managers. An innovative airborne Lidar instrument originally developed at the NASA Wallops Flight Facility, and known as the Experimental Advanced Airborne Research Lidar (EAARL), was used during data acquisition. The EAARL system is a raster-scanning, waveform-resolving, green-wavelength (532-nanometer) Lidar designed to map near-shore bathymetry, topography, and vegetation structure simultaneously. The EAARL sensor suite includes the raster-scanning, water-penetrating full-waveform adaptive Lidar, a down-looking red-green-blue (RGB) digital camera, a high-resolution multi-spectral color infrared (CIR) camera, two precision dual-frequency kinematic carrier-phase GPS receivers, and an integrated miniature digital inertial measurement unit, which provide for submeter georeferencing of each laser sample. The nominal EAARL platform is a twin-engine Cessna 310 aircraft, but the instrument may be deployed on a range of light aircraft. A single pilot, a Lidar operator, and a data analyst constitute the crew for most survey operations. This sensor has the potential to make significant contributions in measuring sub-aerial and submarine coastal topography within cross-environmental surveys. Elevation measurements were collected over the survey area using the EAARL system, and the resulting data were then processed using the Airborne Lidar Processing System (ALPS), a custom-built processing system developed in a NASA-USGS collaboration. ALPS supports the exploration and processing of Lidar data in an interactive or batch mode. Modules for presurvey flight line definition, flight path plotting, Lidar raster and waveform investigation, and digital camera image playback have been developed. Processing algorithms have been developed to extract the range to the first and last significant return within each waveform. ALPS is used routinely to create maps that represent submerged or first surface topography. Specialized filtering algorithms have been implemented to determine the 'bare earth' under vegetation from a point cloud of last return elevations.

Data Series↗

USGS2023

Coproduction and modeling spatial contact networks prevent bias about infectious hematopoietic necrosis virus transmission for Snake River Basin salmonids

Much remains unknown about variation in pathogen transmission across the geographic range of a free-ranging fish or animal species and about the influence of movement (associated with husbandry practices or animal behavior) on pathogen transmission. Salmonid hatcheries are an ideal system in which to study these processes. Salmonid hatcheries are managed for endangered species recovery, supplementation of threatened or at-risk fish stocks, support of fisheries, and ecosystem stability. Infectious hematopoietic necrosis virus (IHNV) is a rhabdovirus of significant concern to salmon aquaculture. Landscape IHNV transmission dynamics previously had been estimated only for salmonid hatcheries in the Lower Columbia River Basin (LCRB). The objectives of this study were to estimate IHNV transmission dynamics in a unique geographic region, the Snake River Basin (SRB), and to quantitatively estimate the effect of model coproduction on inference because previous assessments of coproduction have been qualitative. In contrast to the LCRB, the SRB has hatchery complexes consisting of a main hatchery and ≥1 satellite facility. Knowledge about hatchery complexes was held by a subset of project researchers but would not have been available to project modelers without coproduction. Project modelers generated and tested multiple versions of Bayesian susceptible-exposedinfected models to realistically represent the SRB and estimate the effect of coproduction. Models estimated the frequency of transmission routes, route-specific infection probabilities, and infection probabilities for combinations of salmonid hosts and IHNV lineages. Model results indicated that in the SRB, avoiding exposure to IHNV-positive adult salmonids is the most important action to prevent juvenile infections. Migrating adult salmonids exposed juvenile cohort-sites most frequently, and the infection probability was greatest following exposure to migrating adults. Without coproduction, the frequency of exposure by migrating adults would have been overestimated by 70 cohort-sites, and the infection probability following exposure to migrating adults would have been underestimated by∼0.09. The coproduced model had less uncertainty in the infection probability if no transmission route could be identified (Bayesian credible interval (BCI) width = 0.12) compared to the model without coproduction (BCI width = 0.34). Evidence for virus lineage MD specialization on steelhead and rainbow trout (both Oncorhynchus mykiss) was apparent without model coproduction. In the SRB, we found a greater probability of virus lineage UC infection in Chinook salmon (Oncorhynchus tshawytscha) compared to in O. mykiss, whereas in the LCRB, UC more clearly exhibited a generalist approach. Coproduction influenced estimates that depended on transmission routes, which operated differently at main hatcheries and satellite sites within hatchery complexes. Hatchery complexes are found outside of the SRB and are not specific to salmonid hatcheries alone. There is great potential for coproduction and modeling spatial contact networks to advance understanding about infectious disease transmission in complex production systems and surrounding free-ranging animal populations.

Idaho, Oregon, Washington↗

USGS2013

Spatial and temporal genetic diversity of lake whitefish (Coregonus clupeaformis (Mitchill)) from Lake Huron and Lake Erie

Lake whitefish (Coregonus clupeaformis (Mitchill)) are important commercially, culturally, and ecologically in the Laurentian Great Lakes. Stocks of lake whitefish in the Great Lakes have recovered from low levels of abundance in the 1960s. Reductions in abundance, loss of habitat and environmental degradation can be accompanied by losses of genetic diversity and overall fitness that may persist even as populations recover demographically. Therefore, it is important to be able to identify stocks that have reduced levels of genetic diversity. In this study, we investigated patterns of genetic diversity at microsatellite DNA loci in lake whitefish collected between 1927 and 1929 (historical period) and between 1997 and 2005 (contemporary period) from Lake Huron and Lake Erie. Genetic analysis of lake whitefish from Lakes Huron and Erie shows that the amount of population structuring varies from lake to lake. Greater genetic divergences among collections from Lake Huron may be the result of sampling scale, migration patterns and demographic processes. Fluctuations in abundance of lake whitefish populations may have resulted in periods of increased genetic drift that have resulted in changes in allele frequencies over time, but periodic genetic drift was not severe enough to result in a significant loss of genetic diversity. Migration among stocks may have decreased levels of genetic differentiation while not completely obscuring stock boundaries. Recent changes in spatial boundaries to stocks, the number of stocks and life history characteristics of stocks further demonstrate the potential of coregonids for a swift and varied response to environmental change and emphasise the importance of incorporating both spatial and temporal considerations into management plans to ensure that diversity is preserved.

Lake Erie, Lake Huron↗

USGS2003

Selected applications of hydrologic science and research in Maryland, Delaware, and Washington, D.C., 2001-2003

One of the roles of the U.S. Geological Survey (USGS) is to provide reliable water data and unbiased water science needed to describe and understand the Nation?s water resources. This fact sheet describes selected techniques that were used by the USGS to collect, transmit, evaluate, or interpret data, in support of investigations that describe the quantity and quality of water resources in Maryland (MD), Delaware (DE), and the District of Columbia (D.C.). These hydrologic investigations generally were performed in cooperation with universities, research centers, and other Federal, State, and local Government agencies. The applications of hydrologic science and research that were selected for this fact sheet were used or tested in the MD-DE-DC District from 2001 through 2003, and include established methods, new approaches, and preliminary research. The USGS usually relies on standard methods or protocols when conducting water-resources research. Occasionally, traditional methods must be modified to address difficult environmental questions or challenging sampling conditions. Technologies developed for other purposes can sometimes be successfully applied to the collection or dissemination of water-resources data. The USGS is continually exploring new ways to collect, transmit, evaluate, and interpret data. The following applications of hydrologic science and research illustrate a few of the recent advances made by scientists working for and with the USGS.

Fact Sheet↗

USGS2013

Dynamics of land-use change and conservation in the Prairie Pothole Region of the United States: environmental and economic implications with linkages to rural community well-being

Rural America has changed dramatically over the last century, from having over half the population living in rural settings to only 20 percent residing in a rural area today, and outmigration of younger populations from rural communities remains a constant issue for local governing officials. A declining tax base and concurrent rising costs for maintenance and repair of aging infrastructure add further challenges to policy decisions. Reduced enrollment has caused school closures or mergers. Farm consolidation and technical advances reduced the demand for local labor. On the positive side, however, record-high commodity prices have amplified farm income to new heights. The increased revenues can lead to farmers spending additional money within the local region, while at the same time increased transportation of products has impacted local infrastructure such as roads and bridges. Such dynamics present challenges for municipal leaders charged with promoting economic development and balanced spending, while at the same time maintaining the way of life and rural character that are so important to area residents. The Prairie Pothole Region (PPR) of the United States covers much of the Northern Great Plains, including parts of North and South Dakota, Minnesota, Iowa, and a small part of Montana, and extends across a broad swath of Alberta and Saskatchewan. The region is defined largely by its rural character but has experienced extensive land conversion over the last century, with agricultural areas replacing native prairie habitat. Additional pressures arise from oil and gas development, global markets for agricultural production, and increased demands for biofuel feedstocks. Record-high commodity prices increase pressure on the native prairie as farmers look for new cropland acres. The volatility of commodity prices has raised fears over the intensity of land conversion to row-crop agriculture, the economic health and resiliency of rural communities, and ultimately, population dynamics and outmigration of younger generations. Land-use pressures are increased by the exponential growth of oil and gas production in the region, where some 8,200 wells are now in production within the Williston Basin of North Dakota, accompanied by increased population pressures on housing and municipal services. The U.S. Department of Agriculture’s Conservation Reserve Program (CRP)--a cropland retirement program with close to 4.8 million acres enrolled in the PPR--faces uncertainty in upcoming legislative actions, with a large majority of property enrollments scheduled to expire by 2017. The CRP historically has provided improved habitat conditions, reductions of soil damage through erosion and loss of nutrients, and sequestration of millions of tons of atmospheric carbon. In turn, wildlife-related recreation levels have increased in many parts of the PPR, with money spent in local communities. Contemporary resource-management and rural-development planning increasingly emphasize the need for diversification and integration of resource-extractive industries with nonmarket-based recreational and amenity values that tie into quality of life. Ultimately, each community is unique in its environmental, social, economic, and fiscal endowments. One rural-development policy may work better in one community than another. In addition, rural-development issues such as migration, job growth, and taxes are diverse in themselves. The goal of this report is to qualitatively and quantitatively discuss the economic impacts of land-use decisions in rural areas, particularly in the PPR.

Professional Paper↗

USGS2017

Shorebirds adjust spring arrival schedules with variable environmental conditions: Four decades of assessment on the Yukon–Kuskokwim Delta, Alaska

Arctic summers are brief, and there has been strong selection for migratory birds to arrive in Arctic nesting areas as early as possible to time breeding with peak food availability and complete reproduction. The timing of emergence of nesting habitat in spring is, however, extremely variable in the Arctic, and few long-term studies have examined the ability of avian migrants to track spring conditions to assure optimal nesting. Such studies require long-term migration monitoring under variable spring habitat conditions. These conditions were met during our long-term (1977–2008) study of the timing of arrival of shorebirds to their nesting grounds on the central Yukon–Kuskokwim (Y-K) Delta, in western Alaska. Over this period, the timing of arrival on the nesting grounds of 12 species of shorebirds varied significantly, with the Black-bellied Plover (Pluvialis squatarola) generally arriving first (mean arrival of 4 May), the Red Phalarope (Phalaropus fulicarius) usually arriving last (mean arrival of 20 May). The Western Sandpiper (Calidris mauri), Dunlin (Calidris alpina), and Red-necked Phalarope (Phalaropus lobatus), the most common breeding shorebird species we studied, all arrived about the same time each year (7–9 May). From year to year, first arrival of all species varied significantly by more than 2 weeks, but there was no long-term trend in arrival times over the length of our study. Shorebird arrival was highly correlated with the timing of the break-up of ice on the Kashunuk River, which in turn was correlated with decreasing snow cover and increasing ambient temperature. The date of break-up of river ice also varied by year but did not advance significantly during our study. After arriving on the breeding grounds, Arctic-nesting shorebirds rely on local food resources, which on the Y-K Delta they achieve by timing their arrival to coincide with availability of snow-free habitat. Temperatures along the terminal portions of the spring migration route were significantly correlated with both conditions on the breeding ground and the timing of shorebirds’ arrival there, which suggests that shorebirds may use environmental cues during spring migration to regulate its pace. Ours is one of the few multi-decadal studies to evaluate the responses of a suite of migrant species to annual variation in conditions in their Arctic breeding habitat. Shorebirds’ adaptations to variable conditions on the Y-K Delta are probably rooted in frequent changes to the landscape since the last glacial maximum. Such inherent flexibility may serve them well under future scenarios associated with a changing climate.

Alaska↗

USGS2023

A recruitment niche framework for improving seed-based restoration

As larger tracts of land experience degradation, seed-based restoration (SBR) will be a primary tool to reestablish vegetation and ecosystem function. SBR has advanced in terms of technical and technological approaches, yet plant recruitment remains a major barrier in some systems, notably drylands. There is an unmet opportunity to test science-based approaches to seed mix design and application, based not only on diversity or local provenance, but on the unique recruitment strategies of species. We lay out a framework that uses a quantitative representation of species' recruitment niches to match them to targeted goals (e.g. drought or invasion resistance) and methods (e.g. precision tools and technologies) in SBR. We first describe how to quantify the recruitment niche with seed and seedling traits tied to observed recruitment responses to environmental factors. We then show how a quantified recruitment niche framework can serve as the foundation to address three major restoration challenges: (1) designing forward-looking seed mixes that increase resilience to future climate and disturbance, (2) accounting for natural recovery in SBR planning, and (3) applying precision seeding practices to maximize restoration success. Finally, we demonstrate these ideas with existing data and discuss key challenges to adoption in SBR practice. While the ideas in this framework are based in ecological theory, they will require substantial testing and refinement by scientists engaged in SBR efforts. If this framework is integrated into research agendas, we believe it has the potential to unify and advance diverse elements of seed-based restoration ecology and improve restoration outcomes.

Restoration Ecology↗

USGS2015

Volcano warning systems: Chapter 67

Messages conveying volcano alert level such as Watches and Warnings are designed to provide people with risk information before, during, and after eruptions. Information is communicated to people from volcano observatories and emergency management agencies and from informal sources and social and environmental cues. Any individual or agency can be both a message sender and a recipient and multiple messages received from multiple sources is the norm in a volcanic crisis. Significant challenges to developing effective warning systems for volcanic hazards stem from the great diversity in unrest, eruption, and post-eruption processes and the rapidly advancing digital technologies that people use to seek real-time risk information. Challenges also involve the need to invest resources before unrest to help people develop shared mental models of important risk factors. Two populations of people are the target of volcano notifications–ground- and aviation-based populations, and volcano warning systems must address both distinctly different populations.

Book chapter↗

USGS2025

Factors structuring macrofaunal communities of hydrocarbon seeps along the Cascadia margin

Cold seeps, fueled by hydrocarbon-based chemosynthesis, support unique benthic communities that can vary across small spatial scales influenced by local geochemistry. We examined the community structure and function of macrofauna in cold seeps along the Cascadia margin on the edge of gas hydrate stability—a dynamic environment that may fluctuate as seafloor temperatures change. These communities were assessed in relation to their sediment environment to provide baseline data for these previously uninvestigated seeps and decipher the most significant variables structuring them. Specific environmental drivers investigated include sediment organic carbon, total nitrogen, C:N ratios, stable isotopes (δ 13 C and δ 15 N), redox potential, grain size, and porefluid chemistry. Macrofaunal community composition varied across locations separating into twelve distinct clusters. Several co-located cores clustered separately, indicating high heterogeneity in these communities at small spatial scales. Significant drivers of macrofauna communities included clay and sand content, C:N, δ 15 N values, organic carbon content, and depth. Functional trait composition was influenced by similar drivers, including depth, δ 15 N values, C:N, and sand content. Our results indicate similar environmental variables structure macrofaunal community composition and function across small- and large-scale gradients, contributing to our understanding of heterogeneity in local and regional factors that shape seep macrofaunal communities. This is the first investigation of macrofauna at these recently discovered seeps and provides baseline data on the hydrate stability zone for future comparisons, advancing our knowledge of broad-scale trends in seep macrofauna ecology.

California, Oregon, Washington↗

USGS2022

Opportunities for businesses to use and support development of SEEA-aligned natural capital accounts

Global understanding of the interconnections between the environment and economy has increased, driving the development of frameworks and standards that support the measurement and valuation of natural capital and ecosystem services by both governments and businesses. This paper outlines how businesses can use natural capital accounts (NCA) aligned to the System of Environmental Economic Accounting (SEEA) standard described in this special issue to support identification, management, and valuation of natural capital not typically listed on corporate balance sheets. Such accounts have direct applications for business strategic planning, investment decisions, supply chain management , operations management, risk management, and corporate reporting. Businesses also have important roles to play in advancing SEEA-aligned NCA by providing information that would be useful to include in the accounts and by helping to shape accounts to provide decision-relevant information for both the private and the public sectors. Current pilot SEEA-aligned NCA data and analyses developed for the United States can help address some of the common challenges that businesses face in using natural capital data such as accessibility, quality, and credibility, important for business decision making. However, improvements are needed to fill data gaps and produce more frequent and timely estimates aligned to the temporal resolution needed by businesses.

Ecosystem Services↗

USGS2021

Establishment of baseline cytology metrics in nestling American kestrels (Falco sparverius): Immunomodulatory effects of the flame retardant isopropylated triarylphosphate isomers

Avian populations must mount effective immune responses upon exposure to environmental stressors such as avian influenza and xenobiotics. Although multiple immune assays have been tested and applied to various avian species, antibody-mediated immune responses in non-model avian species are not commonly reported due to the lack of commercially available species-specific antibodies. The objectives of the present study were to advance methods for studying wild bird immune responses and to apply these to the evaluation of cytological responses after exposure of American kestrels, Falco sparverius, to a commercial flame retardant mixture containing isopropylated triarylphosphate isomers (ITP). Hatchlings were gavaged daily with safflower oil or 1.5 ug/g bw/day of ITP suspended in safflower oil, then bled on days 9, 17, and 21. The ITP treatment group ( n = 18) and a subset of controls (Poly I:C treatment group; n = 10) were injected on days 9 and 15 with a synthetic analog of viral double-stranded RNA, polyinosinic:polycytidylic acid (Poly I:C), a toll-like receptor ligand and synthetic viral mimic, and responses compared to a sham injected control group (n = 8). The hypotheses tested whether kestrels showed immunological differences among treatment groups, genetic sex, and/or white blood cell (WBC) subpopulation type over time. A flow cytometry (FCM) gating strategy categorized heterophils (H), lymphocytes (L), and monocytes (M) and their proportions, and measured relative fluorescence in response to anti-chicken CD4 binding. Fluorescent cell surfaces and some granular/vacuolar inclusions were visualized by epifluorescence microscopy. A fourth subpopulation with higher levels of granularity than M but less than H became increasingly apparent with time and was gated along with the H subpopulation; its frequency of occurrence was lowest in the ITP group ( P = 0.0023). The percentages of cells differed among treatment groups, days, and sexes ( P = 0.0001). For both sexes, percentages of H and L were higher than M in control and Poly I:C. In the ITP group, L percentages were higher than H and M ( P = 0.0457), and H and L were higher than M on days 9 and 21 ( P = 0.0001). The ratios of H:L and H:WBC, indicators of robust immunity, were also higher on days 9 and 21 than on 17 ( P = 0.0079). For each sex, the highest levels of activity measured by FCM geometric means (GEO) of fluorescence (indicative of antibody binding) were observed on day 9 ( P = 0.0001 female, and P = 0.0011 male) in H over both L and M ( P < 0.0001 for each). In males, GEO of the Poly I:C group was higher than that of the ITP group ( P = 0.0374), with no difference observed among females over all days. By using a FCM algorithm for population comparisons of fluorescence to investigate binding within H, the T(x) scores indicated higher fluorescence in control and Poly I:C groups over ITP ( P = 0.0001). Unlike chickens, Gallus gallus , which express CD4 primarily on L, kestrels bound the commercial antibody primarily within the gated H subpopulation, suggesting an immunophenotypic difference between taxa, despite a ~60% identity of Falco CD4 amino acid sequences with chicken CD4. The emergent cell subset within the gated H presented dendritic-like cell (DLC) morphological and functional properties, apparently serving as an effector cell. This study adds interpretive context to ecological investigations of infection and of potential immunomodulation by emerging compounds, whereby the early innate responses are mediated by the various cell subsets serving as useful quantitative markers of immunological condition. Data showed that dietary exposure to ITP was immunosuppressive for male and female kestrels over the course of the experiment, reducing DLC frequency compared to the Poly I:C controls. Heterophils and DLC were important in facilitating innate immunological responses.

Environment International↗