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USGS2013

U.S. Department of the Interior South Central Climate Science Center strategic science plan, 2013--18

The Department of the Interior (DOI) recognizes and embraces the unprecedented challenges of maintaining our Nation’s rich natural and cultural resources in the 21st century. The magnitude of these challenges demands that the conservation community work together to develop integrated adaptation and mitigation strategies that collectively address the impacts of climate change and other landscape-scale stressors. On September 14, 2009, DOI Secretary Ken Salazar signed Secretarial Order 3289 (amended February 22, 2010) entitled, “Addressing the Impacts of Climate Change on America’s Water, Land, and Other Natural and Cultural Resources.” The Order establishes the foundation for two partner-based conservation science entities to address these unprecedented challenges: Climate Science Centers (CSCs and Landscape Conservation Cooperatives (LCCs). CSCs and LCCs are the Department-wide approach for applying scientific tools to increase understanding of climate change and to coordinate an effective response to its impacts on tribes and the land, water, ocean, fish and wildlife, and cultural-heritage resources that DOI manages. Eight CSCs have been established and are managed through the U.S. Geological Survey (USGS) National Climate Change and Wildlife Science Center (NCCWSC); each CSC works in close collaboration with their neighboring CSCs, as well as those across the Nation, to ensure the best and most efficient science is produced. The South Central CSC was established in 2012 through a cooperative agreement with the University of Oklahoma, Texas Tech University, Louisiana State University, the Chickasaw Nation, the Choctaw Nation of Oklahoma, Oklahoma State University, and NOAA’s Geophysical Fluid Dynamics Lab; hereafter termed the ”Consortium” of the South Central CSC. The Consortium has a broad expertise in the physical, biological, natural, and social sciences to address impacts of climate change on land, water, fish and wildlife, ocean, coastal, and cultural resources. The South Central CSC will provide scientific information, tools, and techniques that managers and other parties interested in land, water, wildlife, and cultural resources can use to anticipate, monitor, and adapt to climate change, actively engaging LCCs and other partners in translating science into management decisions. This document is the first Strategic Science Plan for the South Central CSC (2013-18). Using the January 2011 DOI guidance as a model, this document (1) describes the role and interactions of the South Central CSC among partners and stakeholders including Federal, State, and non-governmental organizations throughout the region; (2) describes a concept of what the center will provide to its partners; (3) defines a context for climate impacts in the south central United States; and (4) establishes the science priorities the center will address through research. Science priorities are currently organized as immediate or future research needs; however, this document is intended to be reevaluated and modified as partner needs change and as scientific work progresses.

Open-File Report↗
USGS2005

Occurrence of fecal-indicator bacteria and protocols for identification of fecal-contamination sources in selected reaches of the West Branch Brandywine Creek, Chester County, Pennsylvania

The presence of fecal-indicator bacteria indicates the potential presence of pathogens originating from the fecal matter of warm-blooded animals. These pathogens are responsible for numerous human diseases ranging from common diarrhea to meningitis and polio. The detection of fecal-indicator bacteria and interpretation of the resultant data are, therefore, of great importance to water-resource managers. Current (2005) techniques used to assess fecal contamination within the fluvial environment primarily assess samples collected from the water column, either as grab samples or as depth- and (or) width-integrated samples. However, current research indicates approximately 99 percent of all bacteria within nature exist as attached, or sessile, bacteria. Because of this condition, most current techniques for the detection of fecal contamination, which utilize bacteria, assess only about 1 percent of the total bacteria within the fluvial system and are, therefore, problematic. Evaluation of the environmental factors affecting the occurrence and distribution of bacteria within the fluvial system, as well as the evaluation and modification of alternative approaches that effectively quantify the larger population of sessile bacteria within fluvial sediments, will present water-resource managers with more effective tools to assess, prevent, and (or) eliminate sources of fecal contamination within pristine and impaired watersheds. Two stream reaches on the West Branch Brandywine Creek in the Coatesville, Pa., region were studied between September 2002 and August 2003. The effects of sediment particle size, climatic conditions, aquatic growth, environmental chemistry, impervious surfaces, sediment and soil filtration, and dams on observed bacteria concentrations were evaluated. Alternative approaches were assessed to better detect geographic sources of fecal contamination including the use of turbidity as a surrogate for bacteria, the modification and implementation of sandbag bacteria samplers, and the use of optical brighteners. For the purposes of this report, sources of bacteria were defined as geographic locations where elevated concentrations of bacteria are observed within, or expected to enter, the main branch of the West Branch Brandywine Creek. Biologic sources (for example, waterfowl) were noted where applicable; however, no specific study of biologic sources (such as bacterial source tracking) was conducted. Data indicated that specific bacterial populations within fluvial sediments could be related to specific particle-size ranges. This relation is likely the result of the reduced porosity and permeability associated with finer sediments and the ability of specific bacteria to tolerate particular environments. Escherichia coli (E. coli) showed a higher median concentration (2,160 colonies per gram of saturated sediment) in the 0.125 to 0.5-millimeter size range of natural sediments than in other ranges, and enterococcus bacteria showed a higher median concentration (61,830 colonies per gram of saturated sediment) in the 0.062 to 0.25-millimeter size range of natural sediments than in other ranges. There were insufficient data to assess the particle-size relation to fecal coliform bacteria and (or) fecal streptococcus bacteria. Climatic conditions were shown to affect bacteria concentrations in both the water column and fluvial sediments. Drought conditions in 2002 resulted in lower overall bacteria concentrations than the more typically wet year of 2003. E. coli concentrations in fluvial sediment along the Coatesville study reach in 2002 had a median concentration of 92 colonies per gram of saturated sediment; in 2003, the median concentration had risen to 4,752 colonies per gram of saturated sediment. Symbiotic relations between bacteria and aquatic growth were likely responsible for increased bacteria concentrations observed within an impoundment area on the Coatesville study reach. This reach showed evidence of elevated aquatic growth and sharp increases in E. coli concentrations from upstream to downstream through the impoundment area in both 2002 and 2003. In 2003, E. coli concentrations within the waters column increased from 940 colonies per 100 milliliters upstream to 6,000 colonies per 100 milliliters at the dam crest. Given that these bacteria likely resulted from natural bacterial regrowth, the use of E. coli as an indicator of fecal contamination was severely impaired. Variable environmental conditions along the West Branch Brandywine Creek made the common field-chemical parameters of specific conductance, temperature, pH, and dissolved oxygen ineffective and (or) impossible to use for the determination of inputs of fecal contamination. Extreme variations in chemical gradients commonly were related to the urban/industrial signature of the watershed. For example, during base-flow sampling in 2002, specific-conductance values exceeding 1,000 microsiemens per centimeter observed in effluent from a local steel mill. This effluent raised the specific conductance within the West Branch Brandywine from just above 200 microsiemens per centimeter upstream from the outfall to just below 500 microsiemens per centimeter downstream from the outfall. These chemical gradients also, likely, had an effect on the initial colonization of bacteria, the formation of biofilms, and the persistence of certain types of bacteria along the study reach. Data collected in 2003 indicated that nutrients increased during both base-flow and stormflow conditions along the Coatesville study reach. For example, during base-flow sampling in 2003, 20 pounds of phosphorus was shown to enter the West Branch Brandywine Creek along the Coatesville study reach. The largest contributors to this base-flow nutrient load were likely two wastewater-treatment facilities adjacent to the study reach. During stormflow sampling in 2003, 480 pounds of phosphorus was shown to enter the West Branch Brandywine Creek along the Coatesville study reach. Data, along with other research, indicated the largest contributor to this stormflow nutrient load was likely remobilized sediment originating from a large dam impoundment. These elevated nutrient concentrations were considered sufficient to promote accelerated aquatic growth along the reach. Data collected in 2003 showed that wastewater constituents entered the West Branch Brandywine Creek largely from urban storm-sewer systems. Samples from the primary storm sewer for the city of Coatesville had detections for 20 of 69 wastewater constituents. These constituents included both strong and weak indicators of fecal contamination and generally indicated the storm-sewer system along the Coatesville study reach was a likely source of fecal-indicator bacteria and fecal contamination under base-flow conditions. By comparison, 5 constituents were detected in samples from the upstream end of the reach, and 10 constituents were detected in samples from the downstream end of the reach. During stormflow, numbers of detections were similar along the entire length of the study reach-five in samples from the upstream end, eight in samples from the center of the reach, and seven in samples from the downstream end of the reach. These data indicate that point sources (such as culverts and pipes, septic systems, and wastewater-treatment facilities) are not likely the origin of bacteria contamination during stormflow. The bacteria concentrations observed during stormflow events probably result from remobilized sessile bacteria stored within fluvial sediments. In this case, these bacteria should not be considered indicators of current fecal contamination. Impervious surfaces were found to increase bacteria concentrations along the West Branch Brandywine Creek because contaminated runoff from impervious areas generally flows into, and is concentrated within, the confines of the local storm-sewer system. During 2002, storm-sewer outfalls draining impervious areas were associated with all major locations of elevated bacterial concentrations (greater than 1,200 colonies per gram of saturated sediment) in fluvial sediments. During 2003, wetter conditions and overall bacteria concentrations higher than in 2002 resulted in point sources of bacterial contamination becoming less pronounced; however, the storm-sewer system, draining adjacent impervious areas, was still observed to be the primary source of bacteria along the reach. Where stormwater and (or) other runoff from these areas was allowed to infiltrate and (or) flow through wetland and riparian buffers, bacteria concentrations were not observed to be elevated above background levels commonly observed throughout similar areas of the same reach. Two run-of-the-river dams along the Coatesville study reach were evaluated for their effects on observed bacterial concentrations. These dams were shown to have greater or lesser effects on bacterial concentrations depending on the size of the structure and the capacity of the structure to impede flows. The smaller upstream dam had an approximate height of 3 feet and showed little observed effect on measured turbidity values; these data indicated that the dam did not effectively impede the flow of water or sediment within the West Branch Brandywine Creek. Consequently, this small dam did not show any observed effect on bacterial concentrations either upstream or downstream of the structure. The larger dam, near the middle of the reach, had an approximate height of 20 feet and showed greater effects on both turbidity and bacteria concentrations. The capacity of the larger dam to impede flows, combined with nutrients entering the reach, resulted in increased biologic activity throughout the impoundment area. Within this larger impoundment, enterococcus bacteria populations were observed to decrease sharply and E. coli bacteria populations were observed to increase sharply as flow approached the dam crest. All bacteria levels were then observed to drop to background levels, in both the water column and fluvial sediment, immediately downstream from the dam crest. Additional study is required to determine the cause for this rapid die off. Turbidity was assessed as a potential surrogate for E. coli bacteria. Regression analysis indicated higher turbidity levels usually can indicate higher concentrations of bacteria (R2 = 0.67), but the relation was too sporadic on the West Branch Brandywine Creek to use turbidity as a surrogate for estimated bacteria concentrations. Evaluation of data from individual base-flow and stormflow events resulted in variable and generally poor statistical relations between E. coli bacteria and turbidity (R2 values ranged from 0.02 to 0.94). Sandbag samplers were used in 2003 to determine their suitability for the assessment of fecal contamination. Sandbag samplers rely on the ability of bacteria to attach to surfaces and use the larger sessile bacteria populations instead of the more commonly used planktonic bacteria populations. E. coli bacteria concentrations observed in the sandbag samplers, after 1 week in place, were similar to those found within natural sediments collected concurrently. Enterococcus bacteria concentrations within the same sandbag samplers were not similar, and were generally lower, than those observed within the natural sediments. This discrepancy was likely because sand within the samplers was sieved to a size that was likely too coarse for enterococcus bacteria to persist. Optical-brightener samplers were installed along with each sandbag sampler. Optical brighteners are additives used in common household detergents; therefore, detection of optical brighteners, along with elevated fecal-indicator bacteria concentrations, strongly indicates a link to humans. Positive results for optical brighteners were detected only at the outfalls of two sewage-treatment facilities; because of treatment of the effluent from these facilities, these samples did not have elevated bacteria concentrations. The lack of additional positive results was largely because this method is not sensitive to low concentrations of optical brighteners.

Pennsylvania↗
USGS2019

Interactive mapping of nonindigenous species in the Laurentian Great Lakes

Nonindigenous species pose significant risks to the health and integrity of ecosystems around the world. Tracking and communicating the spread of these species has been of interest to ecologists and environmental managers for many years, particularly in the bi-national Laurentian Great Lakes of North America. In this paper, we introduce the Great Lakes Aquatic Nonindigenous Species Information System (GLANSIS) Map Explorer. The Map Explorer provides access to records of documented nonindigenous species and their spatial distributions. Users may view the distributions of well-known nonindigenous species (such as zebra mussels) as well as perform custom queries. Additional map layers allow users to compare the distribution of nonindigenous species to environmental conditions. This tool serves to communicate knowledge to diverse stakeholder groups and to enable further in-depth research on nonindigenous species.

Laurentian Great Lakes↗
USGS2019

Conservation research across scales in a national program: How to be relevant to local management yet general at the same time

Successfully addressing complex conservation problems requires attention to pattern and process at multiple spatial scales. This is challenging from a logistical and organizational perspective. In response to indications of worldwide declines in amphibian populations, the Amphibian Research and Monitoring Initiative (ARMI) of the United States Geological Survey was established in 2000. This national program is unique in its structure, organization, and success in integrating information at multiple scales. ARMI works under the principle that a good study design is tailored to specific questions, but stipulates the use of methods that result in unbiased parameter estimates (e.g., occupancy). This allows studies to be designed to address local questions but also to produce data that can easily be scaled up to accomplish the objectives of a broad-scale monitoring program. Here we describe how the implementation of the Amphibian Research and Monitoring Initiative results in research that is applicable across scales – global, in contributing to the understanding of amphibian decline phenomena; continental, in synthesizing local data to understand large-scale drivers; regional, by characterizing threats and assessing status of species at the range scale; and local, by working with National Park, Wildlife Refuge, and other Federal and State land managers to identify research needs and serve conservation-relevant research results to inform management decisions.

Biological Conservation↗
USGS2019

Integrating amphibian movement studies across scales better informs conservation decisions

Numerous papers have highlighted the need to integrate amphibian research and conservation across multiple scales. Despite this, most amphibian movement studies focus on a single level of organization (e.g., local population) and a single life stage (e.g., adults) and many suggest potential conservation actions or imply that the information is useful to conservation, yet these presumptions are rarely clarified or tested. Movement studies to date provide little information to guide conservation decisions directly because they fail to integrate movement across scales with individual or population parameters (i.e., fitness metrics); this is exacerbated by a general failure to set movement studies in a probabilistic context. An integrative approach allows prediction of population or metapopulation responses to environmental changes and different management actions, thus directly informing conservation decisions and ‘moving the needle’ towards an informed application of conservation actions. To support this perspective we: 1) revisit reviews of amphibian movement to illustrate the focus on single scales and to underscore the importance of movement – at all scales – to conservation; 2) make the case that movement, breeding, and other demographic probabilities are intertwined and studies executed at different temporal and spatial scales can aid in understanding species' responses to varying environmental and/or management conditions; 3) identify limitations of existing movement-related research to predict conservation action outcomes and inform decision-making; and 4) highlight under-utilized quantitative approaches that facilitate research that either connects movement to fitness metrics (individual-level studies) or estimates population and metapopulation vital rates in addition to, or associated with, movement probabilities.

Biological Conservation↗
USGS2024

The potential influence of genome-wide adaptive divergence on conservation translocation outcome in an isolated greater sage-grouse population

Conservation translocations are an important conservation tool commonly employed to augment declining or reestablish extirpated populations. One goal of augmentation is to increase genetic diversity and reduce the risk of inbreeding depression (i.e., genetic rescue). However, introducing individuals from significantly diverged populations risks disrupting coadapted traits and reducing local fitness (i.e., outbreeding depression). Genetic data are increasingly more accessible for wildlife species and can provide unique insight regarding the presence and retention of introduced genetic variation from augmentation as an indicator of effectiveness and adaptive similarity as an indicator of source and recipient population suitability. We used 2 genetic data sets to evaluate augmentation of isolated populations of greater sage-grouse ( Centrocercus urophasianus ) in the northwestern region of the species range (Washington, USA) and to retrospectively evaluate adaptive divergence among source and recipient populations. We developed 2 statistical models for microsatellite data to evaluate augmentation outcomes. We used one model to predict genetic diversity after augmentation and compared these predictions with observations of genetic change. We used the second model to quantify the amount of observed reproduction attributed to transplants (proof of population integration). We also characterized genome-wide adaptive divergence among source and recipient populations. Observed genetic diversity ( H O = 0.65) was higher in the recipient population than predicted had no augmentation occurred ( H O = 0.58) but less than what was predicted by our model ( H O = 0.75). The amount of shared genetic variation between the 2 geographically isolated resident populations increased, which is evidence of periodic gene flow previously assumed to be rare. Among candidate adaptive genes associated with elevated fixation index ( F ST ) (143 genes) or local environmental variables (97 and 157 genes for each genotype–environment association method, respectively), we found clusters of genes with related functions that may influence the ability of transplants to use local resources and navigate unfamiliar environments and their reproductive potential, all possible reasons for low genetic retention from augmentation.

Conservation Biology↗
USGS2026

Where will the cat cross the road? Comparing camera and GPS-based models for identifying wildlife corridors

Designing effective wildlife corridors is a critical conservation challenge in fragmented landscapes. GPS-based step selection functions strongly predict dispersal corridors and connectivity, but GPS collaring can be expensive and invasive. Camera-based occupancy models are widely used for connectivity analyses but may involve trade-offs in data resolution. Despite widespread use of both approaches, few studies have directly compared them using concurrent datasets. We developed a stacked single-species, single-season occupancy model and a Circuitscape connectivity surface for mountain lions (Puma concolor) on Washington’s Olympic Peninsula, USA, and compared them with a connectivity surface from an existing integrated step selection function. Both models predicted mountain lion GPS locations well, with binned Spearman rank correlations of 1 for Circuitscape and 0.96 for the step selection function, though step selection better identified habitat use by dispersers. Connectivity predictions were moderately correlated across the landscape ( r = 0.26), but agreement was strongest in human-dominated areas most critical for corridor planning. We conclude that GPS-based approaches are advantageous when data collection is feasible and the focus is on dispersal or fine-scale movement. However, camera-based approaches may be preferable for multi-species monitoring, large spatial and temporal scales, noninvasive sampling, when resources are limited, or when fine-scale or dispersal-specific inference is not required.

Washington↗
USGS2020

Carrying capacity of a population diffusing in a heterogeneous environment

The carrying capacity of the environment for a population is one of the key concepts in ecology and it is incorporated in the growth term of reaction-diffusion equations describing populations in space. Analysis of reaction-diffusion models of populations in heterogeneous space have shown that, when the maximum growth rate and carrying capacity in a logistic growth function vary in space, conditions exist for which the total population size at equilibrium (i) exceeds the total population that which would occur in the absence of diffusion and (ii) exceeds that which would occur if the system were homogeneous and the total carrying capacity, computed as the integral over the local carrying capacities, was the same in the heterogeneous and homogeneous cases. We review here work over the past few years that has explained these apparently counter-intuitive results in terms of the way input of energy or another limiting resource (e.g., a nutrient) varies across the system. We report on both mathematical analysis and laboratory experiments confirming that total population size in a heterogeneous system with diffusion can exceed that in the system without diffusion. We further report, however, that when the resource of the population in question is explicitly modeled as a coupled variable, as in a reaction-diffusion chemostat model rather than a model with logistic growth, the total population in the heterogeneous system with diffusion cannot exceed the total population size in the corresponding homogeneous system in which the total carrying capacities are the same.

Mathematics and Computers in Modern Science - Acou↗
USGS2015

Design and methods of the Southeast Stream Quality Assessment (SESQA), 2014

During 2014, the U.S. Geological Survey (USGS) National Water-Quality Assessment Program (NAWQA) assessed stream quality across the Piedmont and southern Appalachian Mountain regions of the southeastern United States. This Southeast Stream Quality Assessment (SESQA) simultaneously characterized watershed and stream-reach water-quality stressors along with instream biological conditions, in order to better understand regional stressor-effects relations. The goal of SESQA is to provide communities and policymakers with information about those human and environmental factors that have the greatest impact on stream quality across the region. The SESQA design focused on hydrologic alteration and urbanization because of their importance as ecological stressors of particular concern to Southeast region resource managers. Streamflow and land-use data were used to identify and select sites representing gradients in urbanization and streamflow alteration across the region. One hundred fifteen sites were selected and sampled for as many as 10 weeks during April, May, and June 2014 for contaminants, nutrients, and sediment. This water-quality “index” period culminated with an ecological survey of habitat, periphyton, benthic macroinvertebrates, and fish at all sites. Sediment was collected during the ecological survey for analysis of sediment chemistry and toxicity testing. Of the 115 sites, 59 were on streams in watersheds with varying degrees of urban land use, 5 were on streams with multiple confined animal feeding operations, and 13 were reference sites with little or no development in their watersheds. The remaining 38 “hydro” sites were on streams in watersheds with relatively little agricultural or urban development but with hydrologic alteration, such as a dam or reservoir. This report provides a detailed description of the SESQA study components, including surveys of ecological conditions, routine water sampling, deployment of passive polar organic compound integrative samplers for pesticides and contaminants of emerging concern, and synoptic sediment sampling and toxicity testing at all urban, confined animal feeding operation, and reference sites. Continuous water-quality monitoring and daily pesticide sampling efforts conducted at a subset of urban sites are also described.

Alabama, Georgia, North Carolina, South Carolina, ↗
USGS2015

California State Waters Map Series — Offshore of Point Reyes, California

This publication about the Offshore of Point Reyes map area includes ten map sheets that contain explanatory text, in addition to this descriptive pamphlet and a data catalog of geographic information system (GIS) files. Sheets 1, 2, and 3 combine data from four different sonar surveys to generate comprehensive high-resolution bathymetry and acoustic-backscatter coverage of the map area. These data reveal a range of physiographic features (highlighted in the perspective views on sheet 4) such as the flat, sediment-covered seafloor in Drakes Bay, as well as abundant “scour depressions” on the Bodega Head–Tomales Point shelf (see sheet 9) and local, tectonically controlled bedrock uplifts. To validate geological and biological interpretations of the sonar data shown in sheets 1, 2, and 3, the U.S. Geological Survey towed a camera sled over specific offshore locations, collecting both video and photographic imagery; these “ground-truth” surveying data are summarized on sheet 6. Sheet 5 is a “seafloor character” map, which classifies the seafloor on the basis of depth, slope, rugosity (ruggedness), and backscatter intensity and which is further informed by the ground-truth-survey imagery. Sheet 7 is a map of “potential habitats,” which are delineated on the basis of substrate type, geomorphology, seafloor process, or other attributes that may provide a habitat for a specific species or assemblage of organisms. Sheet 8 compiles representative seismic-reflection profiles from the map area, providing information on the subsurface stratigraphy and structure of the map area. Sheet 9 shows the distribution and thickness of young sediment (deposited over the last about 21,000 years, during the most recent sea-level rise) in both the map area and the larger Salt Point to Drakes Bay region, interpreted on the basis of the seismic-reflection data, and it identifies the Offshore of Point Reyes map area as lying within the Bodega Head–Tomales Point shelf, Point Reyes bar, and Bolinas shelf domains. Sheet 10 is a geologic map that merges onshore geologic mapping (compiled from existing maps by the California Geological Survey) and new offshore geologic mapping that is based on integration of high-resolution bathymetry and backscatter imagery (sheets 1, 2, 3), seafloor-sediment and rock samples (Reid and others, 2006), digital camera and video imagery (sheet 6), and high-resolution seismic-reflection profiles (sheet 8), as well as aerial-photographic interpretation of nearshore areas. The information provided by the map sheets, pamphlet, and data catalog have a broad range of applications. High-resolution bathymetry, acoustic backscatter, ground-truth-surveying imagery, and habitat mapping all contribute to habitat characterization and ecosystem-based management by providing essential data for delineation of marine protected areas and ecosystem restoration. Many of the maps provide high-resolution baselines that will be critical for monitoring environmental change associated with climate change, coastal development, or other forcings. High-resolution bathymetry is a critical component for modeling coastal flooding caused by storms and tsunamis, as well as inundation associated with longer term sea-level rise. Seismic-reflection and bathymetric data help characterize earthquake and tsunami sources, critical for natural-hazard assessments of coastal zones. Information on sediment distribution and thickness is essential to the understanding of local and regional sediment transport, as well as the development of regional sediment-management plans. In addition, siting of any new offshore infrastructure (for example, pipelines, cables, or renewable-energy facilities) will depend on high-resolution mapping. Finally, this mapping will both stimulate and enable new scientific research and also raise public awareness of, and education about, coastal environments and issues.

California↗
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↗
USGS2019

Integrating anthropogenic factors into regional-scale species distribution models — A novel application in the imperiled sagebrush biome

Species distribution models (SDM) that rely on regional-scale environmental variables will play a key role in forecasting species occurrence in the face of climate change. However, in the Anthropocene, a number of local-scale anthropogenic variables, including wildfire history, land-use change, invasive species, and ecological restoration practices can override regional-scale variables to drive patterns of species distribution. Incorporating these human-induced factors into SDMs remains a major research challenge, in part because spatial variability in these factors occurs at fine scales, rendering prediction over regional extents problematic. Here, we used big sagebrush (Artemisia tridentata Nutt.) as a model species to explore whether including human-induced factors improves the fit of the SDM. We applied a Bayesian hurdle spatial approach using 21,753 data points of field-sampled vegetation obtained from the LANDFIRE program to model sagebrush occurrence and cover by incorporating fire history metrics and restoration treatments from 1980 to 2015 throughout the Great Basin of North America.

Global Change Biology↗
USGS2018

A full annual-cycle conservation strategy for Sprague’s Pipit, Chestnut-collared and McCown’s Longspurs, and Baird’s Sparrow

Sprague’s Pipit ( Anthus spragueii ), Chestnut-collared Longspur ( Calcarius ornatus ), McCown’s Longspur ( Rhynchophanes mccownii ), and Baird’s Sparrow ( Centronyx bairdii ) [hereafter, “the Species”] are North American grassland-obligate songbirds whose populations have experienced significant annual population declines and are the focus of increasing conservation concern. The purpose of this strategy is to summarize current knowledge of the Species and identify priority research, monitoring and conservation actions required to improve their population status. Grasslands are among the most threatened ecosystems in the world with historic losses of 61-70% converted to other land uses, primarily cropland agriculture. Losses continue, with current conversion in the northern Great Plains occurring several times faster than grasslands can be protected. The Partners in Flight North American Landbird Conservation Plan (PIF NALCP) estimates current global populations of 900,000, 3,000,000, 600,000, and 2,000,000 for Sprague’s Pipit, Chestnut-collared Longspur, McCown’s Longspur, and Baird’s Sparrow, respectively. Over the period of 1967-2015, these populations have declined at -3.1, -4.2, -5.9 and -2.2% annually for estimated total losses of 78, 87, 94 and 65%, respectively. Habitat associations of breeding birds, especially at the local scale, represent the majority of the existing scientific literature on the Species’ biology. Landscape-scale associations are more poorly understood, and few studies have linked habitat, at any scale, to population vital rates. Increasing effort is focused on nonbreeding season and very little is known about migration. Current knowledge identifies three primary threats: 1) loss of native grasslands, 2) degradation and fragmentation of remaining native grasslands, and 3) disturbance inconsistent with needs of the Species. Top priorities for future research include: identification of population limiting factors, links between breeding habitat and demographics, identification of migratory habitat requirements, and identification of conditions promoting winter survival. Implementation strategies must focus on the protection, restoration, and enhancement (i.e., management) of grassland communities. Most imperative is the protection of remaining native grasslands from conversion to other uses. Actions supporting grass-based agriculture on privately-owned, native grasslands are paramount. These include incentive-based tools to support livestock grazing that benefits both priority birds and healthy ranching communities, which in turn prevent the conversion of native grasslands to cropland. Where cropland conversion has already taken place, conservation partners should work to continue and improve programs such as the Conservation Reserve Program (CRP) to restore and maintain permanent native cover. This strategy adopts the PIF NALCP objective, which is to reduce the rate of the Species’ decline in the first 10 years, then stabilize and ultimately increase the 2016 population by 5-15% over the subsequent 20 years. Ongoing monitoring programs such as the Breeding Bird Survey, Integrated Monitoring of Bird Conservation Regions, and eBird are critical for informing broadscale demographic and geographic trends for the Species. However, to achieve PIF NALCP goals, there is additional need for monitoring that links habitat conservation accomplishments to population performance within a strategic habitat conservation framework.

Report↗
USGS2020

Wind River subbasin restoration: Annual report of US..Geological Survey activities, January 2018 through December 2018

We sampled juvenile wild Steelhead Oncorhynchus mykiss in headwater streams of the Wind River, WA, to characterize populations and investigate life-history metrics, particularly migratory patterns. We used Passive Integrated Transponder (PIT)-tagging and a series of instream PIT-tag interrogation systems (PTISs) to track juveniles. The Wind River subbasin is considered a wild Steelhead refuge by Washington Department of Fish and Wildlife (WDFW). No hatchery Steelhead have been planted in the Wind River subbasin since 1997, and hatchery adults are estimated to be less than one percent of spawners in most years (pers comm. Thomas Buehrens, Washington Department of Fish and Wildlife). Our repeated headwater sampling of consistent sites in the Wind River subbasin has also allowed us to track relative abundance of Brook Trout, a non-native species to the Wind River. Our work is contributing to understanding of Steelhead population response to numerous restoration actions in the subbasin, including removal of Hemlock Dam from Trout Creek in 2009, where our PTISs are helping to quantify adult response. Data from our study, and companion work by Washington Department of Fish and Wildlife, are contributing to Bonneville Power Administration’s (BPA) Research Monitoring and Evaluation (RM&E) Program Strategy of Fish Population Status Monitoring (www.cbfish.org/ProgramStrategy.mvc/ViewProgramStrategySummary/1). Specifically this work addresses the sub-strategies of: 1) Assessing the Status and Trends of Diversity of Natural Origin Fish Populations and to Uncertainties Research regarding differing life histories of a wild Steelhead population, 2) Assessing the Status and Trend of Adult Natural Origin Fish Populations, and 3) Monitoring and Evaluating the Effectiveness of Tributary Habitat Actions Relative to Environmental, Physical, or Biological Performance Objectives. Our headwaters parr PIT tagging, WDFW parr, smolt, and adult tagging and our instream PTISs are providing data on movements and life histories of parr, smolt, and adult Steelhead. During summer 2018, we PIT-tagged 1,592 age-0 and age-1 Steelhead parr in headwater areas of the Wind River subbasin to characterize population traits and investigate life-history diversity, including growth and pre-smolt downstream movement. Repeat headwater sampling and smolt trap operations provide opportunities for recapture, and instream PTISs and Columbia River infrastructure provide opportunity for detection of PIT-tagged fish. Throughout the year, we maintained a series of six instream PTISs to monitor movement of tagged Steelhead parr, smolts, and adults. Detections at the instream PTISs have demonstrated trends of age-0 and age-1 parr emigration from natal areas during summer and fall, in addition to the expected movement of parr and smolts in spring. Substantial numbers of parr make downstream movements as age-1 fish. We have estimated that from 15 to 33 percent of parr tagged as age-0 fish make downstream migrations at age-1 for additional rearing. We have estimated that from 1 to 27 percent of parr tagged as age-1 fish make downstream migrations during fall. These findings raise many questions about parr rearing strategies, habitat use, and success of these migrants and suggest a need for broader monitoring of juvenile Steelhead in some river systems to fully document juvenile production. Long-term monitoring of PIT-tagged fish is providing information on contribution of various life-history strategies to smolt production and adult returns. Movements of PIT-tagged adult Steelhead were recorded at instream PTISs. These data have allowed assessment of adult returns to tributary watersheds within the Wind River subbasin. Detection efficiency of adult PIT-tagged Steelhead at our primary adult-monitoring PTIS in Trout Creek has been greater than 92 percent during 6 of the past 7 years. This is providing excellent data to estimate adult returns to this watershed. Determination of adult use of tributary watersheds is providing data to help evaluate the efficacy of the removal of Hemlock Dam on Trout Creek. Hemlock Dam, located at rkm 2.0 of Trout Creek, was removed in summer 2009. The dam contributed to hydrologic impairment of Trout Creek and had potential negative effects on Steelhead. The improvements made to the upper Wind River PTIS (site code WRU at rkm 28.3; better site characteristics and grid power) during 2016 and 2017, and a planned new site in the Mine Reach of the upper Wind River, will allow estimates of subbasin adult escapement like those in Trout Creek. During 2018, we also completed planning and permitting with U.S. Forest Service for a new PTIS site at rkm 36 of the Wind River (the Mine Reach, mentioned above). This site will replace two sites (one in Paradise Creek and one at rkm 41 of the Wind River), which had operational challenges due to lack of adequate solar power and winter difficulties. The new Mine Reach PTIS site at rkm 36, will have better solar exposure, fewer winter operations difficulties, and provide opportunity to detect fish from juvenile sampling sites that were downstream of the previous two PTISs. The more consistent operation of the new Mine Reach PTIS site will increase our ability to estimate migrant abundance as all the juveniles tagged upstream of it will be subject to the same potential detection history, instead of three different potential detection histories as before. Additionally, with the new Mine Reach PTIS site lower in the watershed, it will subject more PIT-tagged adult Steelhead to detection and provide ability to generate a nonbiased adult-detection efficiency estimate for the WRU PTIS at rkm 28.3 of the Wind River. This will provide the opportunity to estimate yearly adult Steelhead abundance to the upper Wind watershed area. Permitting is complete and some supplies have been purchased to build and install this new site in 2019. Repeat sampling at consistent locations in the subbasin has allowed investigation into juvenile Steelhead growth patterns. Growth rates (relative change in weight) of age-0 PIT-tagged parr during summer are similar across the subbasin, but lower for age-1 parr in the Trout Creek watershed than the upper Wind River watershed. Yearly growth for parr tagged at age-0 is similar across the subbasin. Yearly growth for parr tagged at age-1 is lowest in Martha Creek, but similar elsewhere. Non-native Brook Trout are present in portions of the subbasin, chiefly the Trout Creek watershed, and repeat sampling has allowed us to index their prevalence. Percentage of catch that is Brook Trout at each of four sample sites in Trout Creek have declined from the period 1998 – 2003 to the period 2011 – 2018. There was a pattern of decline in percent of catch and number of Brook Trout at the Trout Creek sites from 2011 through 2016, though a slight upward trend during 2017 and 2018 has been evident. Evaluating and planning restoration efforts are of interest to many managers and agencies to ensure efficient use of resources. The evaluation of various life-histories of Steelhead within the Wind River subbasin will provide information to better track populations, and to direct habitat restoration and water allocation planning. Movement of Steelhead parr raises many questions regarding estimating juvenile abundance, origin, and habitat use within watersheds. Improved PTISs and focused PIT tagging of age-0 and age-1 Steelhead parr are increasingly allowing us to investigate such questions. Increasingly detailed Viable Salmonid Population information, such as that provided by PIT-tagging and instream PTISs networks like those in the Wind River subbasin, provide data to inform policy and management, as life-history strategies and production bottlenecks are identified and understood.

Washington↗
USGS2020

Tests in a semi-natural environment suggest that bait and switch strategy could be used to control invasive Common Carp

Common Carp ( Cyprinus carpio Linnaeus, 1758), is a highly invasive species that has had profound effects on biodiversity and ecosystem services. Many Carp management methods have been applied including physical removal, pesticide treatments of whole lakes, and water drawdowns. Herein, we tested key elements of a potential “bait and switch” approach in which corn could be used to induce feeding aggregations of Carp and then switched for corn pellets with a pesticide Antimycin-A (ANT-A) to selectively target the Carp. First, laboratory experiments were used to determine if addition of lethal concentrations of ANT-A to corn pellets deterred Carp from eating corn-based food pellets. Second, a pond experiment tested if a corn-based bait containing ANT-A functioned as a species-specific Carp management tool in a semi-natural environment with three common native fishes: White Sucker ( Catostomus commersonii Lacepède, 1803), Yellow Perch ( Perca flavescens Mitchill, 1814), and Bluegill ( Lepomis macrochirus Rafinesque, 1819). The use of baited sites by Carp and native species was monitored using passive integrated transponder (PIT) tags. Mortality of each species and presence of corn in their digestive tracts was also monitored. Our laboratory experiment showed that presence of ANT-A did not deter Carp from consuming the pellets. The pond experiment showed that only Carp perished in significant numbers once toxic bait was applied. Further, only Carp increased their use of baited sites once baiting began, and only Carp had corn in their digestive tracts. Overall, our results indicate that corn might function as a species-specific Carp attractant in systems of North American Midwest and that corn-based bait can be used to effectively conceal a lethal dose of ANT-A. Further research is necessary to refine this potential management tool, specifically investigating the behavioral and social dynamics of Carp aggregating at sites baited with corn to enhance the temporal and spatial specificity of pesticide application.z

Management of Biological Invasions↗
USGS2017

Design and methods of the Pacific Northwest Stream Quality Assessment (PNSQA), 2015

In 2015, the U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) project conducted the Pacific Northwest Stream Quality Assessment (PNSQA) to investigate stream quality across the western part of the Pacific Northwest. The goal of the PNSQA was to assess the health of streams in the region by characterizing multiple water-quality factors that are stressors to in-stream aquatic life and by evaluating the relation between these stressors and the condition of biological communities. The effects of urbanization and agriculture on stream quality for the Puget Lowland and Willamette Valley Level III Ecoregions were the focus of this regional study. Findings will help inform the public and policymakers about human and environmental factors that are the most critical in affecting stream quality and, thus, provide insights into possible strategies to protect or improve the health of streams in the region. Land-use data were used in the study to identify and select sites within the region that ranged in levels of urban and agricultural development. A total of 88 sites were selected across the region—69 were on streams that explicitly spanned a range of urban land use in their watersheds, 8 were on streams in agricultural watersheds, and 11 were reference sites with little or no development in their watersheds. Depending on the type of land use, sites were sampled for contaminants, nutrients, and sediment for either a 4- or 10-week period during April, May, and June 2015. This water-quality “index period” was immediately followed with an ecological survey of all sites that included stream habitat, benthic algae, benthic macroinvertebrates, and fish. Additionally, streambed sediment was collected during the ecological survey for analysis of sediment chemistry and toxicity testing. This report provides a detailed description of the specific study components and methods of the PNSQA, including (1) surveys of stream habitat and aquatic biota, (2) discrete water sampling, (3) deployment of passive polar organic chemical integrative samplers for pesticides and pharmaceuticals, and (4) sampling of streambed sediment. At selected study sites, toxicity testing of streambed sediment, continuous water-quality monitoring, and daily pesticide sampling also were conducted and are described.

Oregon, Washington↗
USGS2009

Water-Quality and Biological Characteristics and Responses to Agricultural Land Retirement in Three Streams of the Minnesota River Basin, Water Years 2006-08

Water-quality and biological characteristics in three streams in the Minnesota River Basin were assessed using data collected during water years 2006-08. The responses of nutrient concentrations, suspended-sediment concentrations, and biological characteristics to agricultural land retirement also were assessed. In general, total nitrogen, suspended-sediment, and chlorophyll-a concentrations, and fish resource quality improved with increasing land retirement. The Chetomba Creek, West Fork Beaver Creek, and South Branch Rush River subbasins, which range in size from about 200 to 400 square kilometers, have similar geologic and hydrologic settings but differ with respect to the amount, type, and location of retired agricultural land. Total nitrogen concentrations were largest, with a mean of 15.0 milligrams per liter (mg/L), in water samples from the South Branch Rush River, a subbasin with little to no agricultural land retirement; total nitrogen concentrations were smaller in samples from Chetomba Creek (mean of 10.6 mg/L) and West Fork Beaver Creek (mean of 7.9 mg/L), which are subbasins with more riparian or upland land retirement at the basin scale. Total phosphorus concentrations were not related directly to differing land-retirement percentages with mean concentrations at primary data-collection sites of 0.259 mg/L in the West Fork Beaver Creek subbasin, 0.164 mg/L in the Chetomba Creek subbasin, and 0.180 mg/L in the South Branch Rush River subbasin. Temporal variation in water quality was characterized using data from in-stream water-quality monitors and storm-sediment data. Fish data indicate better resource quality for the West Fork Beaver Creek subbasin than for other subbasins likely due to a combination of factors, including habitat quality, food resources, and dissolved oxygen characteristics. Index of biotic integrity (IBI) scores increased as local land-retirement percentages (within 50 and 100 meters of the streams) increased. Data and analysis from this study can be used to evaluate the success of agricultural management practices and land-retirement programs for improving stream quality.

Scientific Investigations Report↗
USGS2019

Evaluation of an acoustic fish deterrent system in shallow water application at the Emiquon Preserve, Lewistown, IL.

Expansion of non-native fish have caused ecological and economic damage and can negatively impact native fish populations. Current research on deterrent technologies for bighead Hypophthalmichthys nobilis and silver carp H. molitrix have primarily focused on reducing upstream movement in large river lock approaches. However, there is also interest in excluding carp from smaller-scale locations. A water control structure at Emiquon Preserve, Lewistown, Illinois, USA reconnected the Preserve’s wetland lakes to the Illinois River, and is a pinch point that site managers seek to deter immigration of non-native fishes without restricting native fish movement. One possible deterrent strategy that was evaluated within the water control structure in 2017 was the use of a 100 hp boat motor acoustic stimulus. Two underwater speakers were installed in each of two culverts to discourage fish movement though the water control structure. Fish passage was monitored using a series of passive integrated transponder (PIT) antennas in a confined study area. A combination of 176 fish consisting of seven different species (native and non-native) were implanted with PIT tags and relocated downstream of the water control structure. Over 2 days of periodic playback of the acoustic stimulus, 29% of tagged silver carp that were detected crossed though the active underwater speaker array. The acoustic treatment did not significantly reduce silver carp or native centrarchid passage through the culverts. However, numerous silver carp were observed jumping out of the acoustically active culvert at the onset of the stimulus. The acoustic stimulus, especially the frequencies to which silver carp are most sensitive to (< 2000 Hz), rapidly attenuated in the water control structure (water depth 0.55–0.38 m). Depth related attenuation observed in and around the water control structure may have reduced the efficacy of the acoustic fish deterrent system at this location.

Illinois↗