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USGS2010

Assessment and management of ecological integrity: Chapter 12

Assessing and understanding the impacts of human activities on aquatic ecosystems has long been a focus of ecologists, water resources managers, and fisheries scientists. While traditional fisheries management focused on single-species approaches to enhance fish stocks, there is a growing emphasis on management approaches at community and ecosystem levels. Of course, as fisheries managers shift their attention from narrow (e.g., populations) to broad organizational scales (e.g., communities or ecosystems), ecological processes and management objectives become more complex. At the community level, fisheries managers may strive for a fish assemblage that is complex, persistent, and resilient to disturbance. Aquatic ecosystem level objectives may focus on management for habitat quality and ecological processes, such as nutrient dynamics, productivity, or trophic interactions, but a long-term goal of ecosystem management may be to maintain ecological integrity. However, human users and social, economic, and political demands of fisheries management often result in a reduction of ecological integrity in managed systems, and this conflict presents a principal challenge for the modern fisheries manager. The concepts of biotic integrity and ecological integrity are being applied in fisheries science, natural resource management, and environmental legislation, but explicit definitions of these terms are elusive. Biotic integrity of an ecosystem may be defined as the capability of supporting and maintaining an integrated, adaptive community of organisms having a species composition, diversity, and functional organization comparable to that of a natural habitat of the region (Karr and Dudley 1981). Following that, ecological integrity is the summation of chemical, physical, and biological integrity. Thus, the concept of ecological integrity extends beyond fish and represents a holistic approach for ecosystem management that is especially applicable to aquatic systems. The more general term, ecological condition, refers to the state of the physical, chemical, and biological characteristics of the environment and the processes and interactions that connect them. While the concept of ecological integrity may appear unambiguous, its assessment and practice are much less clear. Ecological integrity made its debut in the USA with the Clean Water Act (CWA) of 1972 (Federal Water Pollution Control Act, as amended through Public Law 107–303, November 27, 2002), which states only one objective, “to restore and maintain the chemical, physical, and biological integrity of the Nation’s waters.” This legislation compelled resource managers to focus on chemical pollution from point effluent sources, such as industrial and municipal outflows, as well as give attention to diffuse, chronic, and watershed effects on ecological integrity. Further, the CWA allowed pursuit of restoration programs in degraded water bodies and catalyzed the science and practice of restoration ecology. The term ecosystem health is often raised in discussions of ecological integrity. Perhaps it is natural to anthropomorphize our concern for personal health to ecosystems, so it becomes a useful metaphor for understanding the concept of ecological integrity. However, whether or not an ecosystem should be considered an entity, such as a superorganism, is a debate without end that began with early ecologists and continues today (Clements 1916; Suter 1993; Simon 1999a). Regardless, the ecosystem is indeed a natural unit with a level of organization and properties beyond the collection of those species that occupy it and presents the most appropriate spatial and organizational scale in which to assess and study ecological integrity. Streams and rivers serve as integrators of chemical, physical, and biological conditions across the landscape, and while the theory and practice associated with ecological integrity of aquatic systems is easily applied to flowing waters and is emphasized in this chapter, they are broadly applicable among all aquatic systems.

Book chapter↗
USGS2012

Variability in stream chemistry in relation to urban development and biological condition in seven metropolitan areas of the United States, 1999-2004

Beginning in 1999, the U.S. Geological Survey National Water Quality Assessment Program investigated the effects of urban development on stream ecosystems in nine metropolitan study areas across the United States. In seven of these study areas, stream-chemistry samples were collected every other month for 1 year at 6 to 10 sites. Within a study area, the sites collectively represented a gradient of urban development from minimally to highly developed watersheds, based on the percentage of urban land cover; depending on study area, the land cover before urban development was either forested or agricultural. The stream-chemistry factors measured in the samples were total nitrogen, total phosphorus, chloride, and pesticide toxicity. These data were used to characterize the stream-chemistry factors in four ways (hereafter referred to as characterizations)—seasonal high-flow value, seasonal low-flow value, the median value (representing a single integrated value of the factor over the year), and the standard deviation of values (representing the variation of the factor over the year). Aquatic macroinvertebrate communities were sampled at each site to infer the biological condition of the stream based on the relative sensitivity of the community to environmental stressors. A Spearman correlation analysis was used to evaluate relations between (1) urban development and each characterization of the stream-chemistry factors and (2) the biological condition of a stream and the different characterizations of chloride and pesticide toxicity. Overall, the study areas where the land cover before urban development was primarily forested had a greater number of moderate and strong relations compared with the study areas where the land cover before urban development was primarily agriculture; this was true when urban development was correlated with the stream-chemistry factors (except chloride) and when chloride and pesticide toxicity was correlated with the biological condition. Except for primarily phosphorus in two study areas, stream-chemistry factors generally increased with urban development, and among the different characterizations, the median value typically indicated the strongest relations. The variation in stream-chemistry factors throughout the year generally increased with urban development, indicating that water quality became less consistent as watersheds were developed. In study areas with high annual snow fall, the variation in chloride concentrations throughout the year was particularly strongly related to urban development, likely a result of road salt applications during the winter. The relations of the biological condition to chloride and pesticide toxicity were calculated irrespective of urban development, but the overall results indicated that the relations were still stronger in the study areas that had been forested before urban development. The weaker relations in the study areas that had been agricultural before urban development were likely the results of biological communities having been degraded from agricultural practices in the watersheds. Collectively, these results indicated that, compared with sampling a stream at a single point in time, sampling at regular intervals during a year may provide a more representative measure of water quality, especially in the areas of high urban development where water quality fluctuated more widely between samples. Furthermore, the use of "integrated" values of stream chemistry factors may be more appropriate when assessing relations to the biological condition of a stream because the taxa composition of a biological community typically reflects the water-quality conditions over time.

Scientific Investigations Report↗
USGS2007

Use of chemical analysis and assays of semipermeable membrane devices extracts to assess the response of bioavailable organic pollutants in streams to urbanization in six metropolitan areas of the United States

Studies to assess the effects of urbanization on stream ecosystems are being conducted as part of the U.S. Geological Survey’s National Water-Quality Assessment (NAWQA) Program. The overall objectives of these studies are to (1) determine how hydrologic, geomorphic, water quality, habitat, and biological characteristics respond to land-use changes associated with urbanization in specific environmental settings, and (2) compare these responses across environmental settings. As part of an integrated assessment, semipermeable membrane devices (SPMDs) were deployed in streams along a gradient of urban land-use intensity in and around Atlanta, Georgia; Raleigh-Durham, North Carolina; and Denver-Fort Collins, Colorado, in 2003; and Dallas-Fort Worth, Texas; Milwaukee-Green Bay, Wisconsin; and Portland, Oregon, in 2004. Sites were selected to avoid point-source discharge and to minimize natural variability within each of the six metropolitan areas. In addition to standard chemical analysis for hydrophobic organic contaminants, three assays were used to address mixtures and potential toxicity: (1) Fluoroscan provides an estimate of the total concentration of polycyclic aromatic hydrocarbons (PAHs); (2) the P450RGS assay indicates the presence and levels of aryl hydrocarbon receptor agonists; and (3) Microtox® measures toxicological effects on photo-luminescent bacteria. Of the 140 compounds targeted or identified by gas chromatography/mass spectrometry analysis in this study, 67 were not detected. In terms of numbers and types of compounds, the following were detected: 2 wood preservatives, 6 insecticides (parent compounds), 5 herbicides, 22 polycyclic aromatic hydrocarbons, 2 dibenzofurans, 4 polychlorinated biphenyls, 7 compounds associated with fragrances or personal care products, 4 steroids associated with wastewater, 5 polydibromated diphenyl ethers (flame retardants), 3 plasticizers, 3 antimicrobials/disinfectants, and 3 detergent metabolites. Of the 73 compounds detected and three assays utilized, 29 were detected in 25 percent or more of the streams and were strongly related to increases in urban intensity (defined as having a Spearman’s rho > 0.5 with percent urban land cover) in at least one of the six metropolitan areas investigated. These 29 endpoints included 16 PAHs, a wood preservative (pentachloroanisole), 2 insecticides (chlorpyrifos and chlordane), 3 herbicides (benfluralin, trifluralin, and dacthal), a synthetic musk (hexahydrohexamethylcyclopentabenzopyran, HHCB), 2 furans (methyldibenzofuran and benzo[b]naphtho[2,3-d]furan), and a flame retardant (BDE 47). In addition, the number of compounds detected and results of the Fluoroscan and P450RGS assays were strongly related to urban intensity. Average water concentrations estimated from SPMDs were compared to screening benchmarks for the protection of human health and aquatic life; of the 14 compounds with available benchmarks, 3 compounds (anthracene, dieldrin, and diazinon) exceeded those levels in one or more streams. Both dieldrin and anthracene exceeded their respective benchmarks in seven streams, and diazinon in only one stream. There were more exceedances in Milwaukee-Green Bay and Raleigh-Durham than in the other metropolitan areas, and there were no exceedances in Dallas-Fort Worth. The six metropolitan areas studied differed in the number and types of endpoints related to urban intensity, probably from a combination of factors governing source strength, transport, and fate of hydrophobic compounds. The number of endpoints strongly related to urban intensity ranged from 3 in Dallas-Fort Worth and Portland to 21 in Raleigh-Durham. High frequencies of detection and strong correlations with urban land cover for pyrogenic PAHs (such as unsubstituted 4-ringed PAHs) in all six metropolitan areas indicate that these compounds are an important component of urbanization, regardless of location. Pentachloroanisole, dibenzofurans, and petrogenic PAHs (alkylated PAHs and heterocyclic dibenzothiophenes) were frequently detected and strongly related to urban intensity in Atlanta, Raleigh-Durham, Milwaukee-Green Bay, and Denver-Fort Collins. Two insecticides were related to urban intensity: chlorpyrifos in Atlanta, Raleigh-Durham, and Dallas-Fort Worth; and chlordane in Raleigh-Durham. Three herbicides were strongly related to urban intensity: trifluralin in Atlanta and Raleigh-Durham; benfluralin in Atlanta, and dacthal in Denver-Fort Collins. The detection frequencies for most wastewater indicator compounds were too low to establish relations with urban intensity. Of the wastewater compounds analyzed, HHCB in Raleigh-Durham and Denver-Fort Collins, and BDE 47 in Denver-Fort Collins and Dallas-Forth Worth, had the strongest relations with urban intensity. In addition to pyrogenic PAHs, levels of aryl hydrocarbon receptor agonists (as measured by the P450RGS assay) were strongly related to increasing urban intensity in all six metropolitan areas. PAHs were the only group of aryl hydrocarbon agonists consistently detected and related with urban intensity in all six metropolitan areas. It is unknown which compounds in the SPMDs caused the increased response in the P450RGS assay because the SPMDs likely contained many aryl hydrocarbon receptor agonists not quantified by chemical analysis. It is clear that bioavailable, aryl hydrocarbon receptor agonists increase in streams with increasing urban intensity in the basin. Potential toxicity mediated by this metabolic pathway should be considered in integrated assessments of the response of aquatic biota to urbanization.

Scientific Investigations Report↗
USGS1997

Organic carbon balance and net ecosystem metabolism in Chesapeake Bay

The major fluxes of organic carbon associated with physical transport and biological metabolism were compiled, analyzed and compared for the mainstem portion of Chesapeake Bay (USA). In addition, 5 independent methods were used to calculate the annual mean net ecosystem metabolism (NEM = production - respiration) for the integrated Bay. These methods, which employed biogeochemical models, nutrient mass-balances anti summation of individual organic carbon fluxes, yielded remarkably similar estimates, with a mean NEM of +50 g C m-2 yr-1 (?? SE = 751, which is approximately 8% of the estimated annual average gross primary production. These calculations suggest a strong cross-sectional pattern in NEM throughout the Bay, wherein net heterotrophic metabolism prevails in the pelagic zones of the main channel, while net autotrophy occurs in the littoral zones which flank the deeper central area. For computational purposes, the estuary was separated into 3 regions along the land-sea gradient: (1) the oligohaline Upper Bay (11% of total area); (2) the mesohaline Mid Bay (36% of area); and (3) the polyhaline Lower Bay (53% of area). A distinct regional trend in NEM was observed along this salinity gradient, with net here(atrophy (NEM = 87 g C m-2 yr-1) in the Upper Bay, balanced metabolism in the Mid Bay and net autotrophy (NEM = +92 g C m-2 yr-1) in the Lower Bay. As a consequence of overall net autotrophy, the ratio of dissolved inorganic nitrogen (DIN) to total organic nitrogen (TON) changed from DIN:TON = 5.1 for riverine inputs to DIN:TON = 0.04 for water exported to the ocean. A striking feature of this organic C mass-balance was the relative dominance of biologically mediated metabolic fluxes compared to physical transport fluxes. The overall ratio of physical TOC inputs (1) to biotic primary production (P) was 0.08 for the whole estuary, but varied dramatically from 2.3 in the Upper Bay to 0.03 in the Mid and Lower Bay regions. Similarly, ecosystem respiration was some 6-fold higher than the sum of all physical carbon sinks. This general negative correspondence between I:P ratio and NEM, which occurred among Bay regions, was also evident in data available for organic C fluxes in other coastal ecosystems. An inverse relationship between NEM and P, postulated in a previous study, did not apply to Chesapeake Bay, and closer examination of available data revealed the importance of the loading ratio of DIN:TOC as a key control on coastal NEM. It is proposed here that the general global trend of coastal eutrophication will lead to increasing values of NEM in estuaries worldwide. The management implications of this trend are complex, involving both increased potential fisheries harvest and decreased demersal habitat.

Marine Ecology Progress Series↗
USGS2014

A visualization tool to support decision making in environmental and biological planning

Large-scale ecosystem management involves consideration of many factors for informed decision making. The EverVIEW Data Viewer is a cross-platform desktop decision support tool to help decision makers compare simulation model outputs from competing plans for restoring Florida's Greater Everglades. The integration of NetCDF metadata conventions into EverVIEW allows end-users from multiple institutions within and beyond the Everglades restoration community to share information and tools. Our development process incorporates continuous interaction with targeted end-users for increased likelihood of adoption. One of EverVIEW's signature features is side-by-side map panels, which can be used to simultaneously compare species or habitat impacts from alternative restoration plans. Other features include examination of potential restoration plan impacts across multiple geographic or tabular displays, and animation through time. As a result of an iterative, standards-driven approach, EverVIEW is relevant to large-scale planning beyond Florida, and is used in multiple biological planning efforts in the United States.

Environmental Modelling and Software↗
USGS2022

Condition of macroinvertebrate communities in the Buffalo River Area of Concern following sediment remediation

The lower 10 km of the Buffalo River, a tributary to Lake Erie, was designated as an Area of Concern (AOC) in 1987 through the Great Lakes Water Quality Agreement because sediment contamination and habitat alteration from past industrialization caused several Beneficial Use Impairments (BUIs). Extensive remediation efforts conducted between 2011 and 2015 removed approximately 688,100 cubic meters of contaminated sediment from the Buffalo River AOC, and subsequent chemical analysis of sediments indicated that most remedial goals had been achieved. Benthic macroinvertebrate communities and sediment toxicity were evaluated in the AOC and an upstream reference area in 2017 and 2020 to determine whether remediation has improved benthic conditions sufficiently that the benthos BUI designation can be removed. Community condition was characterized using the New York State multi-metric index of biological integrity and bed sediments were used for 10-day toxicity tests with Chironomus dilutus and Hyalella azteca . Macroinvertebrate communities were classified as moderately to slightly impacted at most AOC sites compared to slightly impacted at most reference sites, but toxicity tests did not identify any evidence of toxicity in sediments from the AOC. A linear mixed effects model indicated that total organic carbon concentration in sediments, distance upstream from the river mouth, and the relative dominance of zebra mussels Dreissena polymorpha were the primary predictors of macroinvertebrate community condition. These findings are consistent with those from other AOCs in New York which indicate that contemporary benthic communities are generally shaped by legacy habitat alterations rather than AOC-specific sediment contamination and toxicity.

New York↗
USGS2017

Evaluating and improving count-based population inference: A case study from 31 years of monitoring Sandhill Cranes

Monitoring animal populations can be difficult. Limited resources often force monitoring programs to rely on unadjusted or smoothed counts as an index of abundance. Smoothing counts is commonly done using a moving-average estimator to dampen sampling variation. These indices are commonly used to inform management decisions, although their reliability is often unknown. We outline a process to evaluate the biological plausibility of annual changes in population counts and indices from a typical monitoring scenario and compare results with a hierarchical Bayesian time series (HBTS) model. We evaluated spring and fall counts, fall indices, and model-based predictions for the Rocky Mountain population (RMP) of Sandhill Cranes ( Antigone canadensis ) by integrating juvenile recruitment, harvest, and survival into a stochastic stage-based population model. We used simulation to evaluate population indices from the HBTS model and the commonly used 3-yr moving average estimator. We found counts of the RMP to exhibit biologically unrealistic annual change, while the fall population index was largely biologically realistic. HBTS model predictions suggested that the RMP changed little over 31 yr of monitoring, but the pattern depended on assumptions about the observational process. The HBTS model fall population predictions were biologically plausible if observed crane harvest mortality was compensatory up to natural mortality, as empirical evidence suggests. Simulations indicated that the predicted mean of the HBTS model was generally a more reliable estimate of the true population than population indices derived using a moving 3-yr average estimator. Practitioners could gain considerable advantages from modeling population counts using a hierarchical Bayesian autoregressive approach. Advantages would include: (1) obtaining measures of uncertainty; (2) incorporating direct knowledge of the observational and population processes; (3) accommodating missing years of data; and (4) forecasting population size.

The Condor↗
USGS2012

Monitoring of stream restoration habitat on the main stem of the Methow River, Washington, during the pre-treatment phase (October 2008-May 2012) with a progress report for activities from March 2011 to November 2011

Introduction The U.S. Geological Survey (USGS) received a request from the Bureau of Reclamation (Reclamation) to provide monitoring and an evaluation of the effectiveness of habitat actions that Reclamation plans to implement in the Upper Columbia River basin, which includes the Methow River. This monitoring and evaluation program is to partially fulfill Reclamations part of the 2008 Biological Opinion for the Federal Columbia River Power System that includes a Reasonable and Prudent Alternative (RPA) to protect listed salmon and steelhead across their life cycle. The target species in the Methow River for this monitoring and restoration effort include Upper Columbia River (UCR) spring Chinook salmon ( Oncorhynchus tshawytscha ), UCR steelhead ( O. mykiss ), and bull trout ( Salvelinus confluentus ), which are listed as threatened or endangered under the Endangered Species Act. This report covers UCR activities performed by USGS personnel from March 2011 to November 2011. It involves collecting and analyzing data collected during pre-implementation (2008–2012) there will be a follow-up after actions are completed (2012–2014). The goal of Reclamation is to maximize the potential of habitat and improve proposed limiting factors affecting the middle Methow River subwatershed (Reclamation, 2010). The Middle Methow (M2) reach (river kilometer mile [rkm] 843.065 to 843.080) of the Methow River was selected as the treatment reach for this study based on possible stream restoration plans by Reclamation (fig. 1). The upper Methow River (rkm 843.094 and 843.080), Chewuch River, and the Methow River downstream of the Twisp River (rkm 843.065) are being sampled as reference and control reaches in this study (fig. 2). This report covers the third year in the pre-evaluation of the M2 reach and its side channels. Restoration of the M2 reach is scheduled for 2012, which is planned to be followed by a multi-year intensive post-evaluation period. The intent of the summary of information provided in this report is to fulfill the objectives and tasks submitted in a statement of work to Reclamation in November 2010 (Connolly and Martens, 2011). The study design provides data by which to assess potential fish response to a Reclamation habitat restoration effort focused to improve juvenile salmonid rearing habitat in the M2, which runs between the towns of Winthrop and Twisp, Washington (fig. 1). The pre-treatment phase of the study is designed so that specific questions about the response of target fish species (spring Chinook salmon, steelhead, and bull trout) to the restoration actions can be addressed. Effectiveness is being determined by measuring fish productivity and habitat connectivity of the restoration reach and adjoining reaches, and their tributaries. The study includes sampling efforts directed to understand the relationships between stream habitat and the abundance of various fish species and to assess the response of the fish community. To complement these measurements, we will use models to predict response to treatment, and we will update the model with empirically derived data as these data become available. This modeling effort is expected to inform us of data gaps, sensitivity of key variables, and ability to detect response based on variability of the data. The approach and actions taken or planned by Reclamation to modify off-channel habitat are largely untested as to their effectiveness to improve target fish species’ productivity and survival needs. Those documented strategies that identify both physical parameters and biological relationships and benefits have been identified (Reclamation, 2008). To assess biological performance, we plan to compare age structure, growth, and age at smolting between those fish that stay in natal areas versus those fish that move. To assess retention in, and movement from or into, the restoration reach, we have used a combination of within-reach and out-of-reach sampling. We are using passive integrated transponder (PIT) tags, a network of instream PIT tag interrogation systems, and smolt traps to assess differences in biological performance and the magnitude of retention in, and movement from and into, the restoration reach.

Washington↗
USGS2020

A comparative phylogeographic approach to facilitate recovery of an imperiled freshwater mussel (Bivalvia: Unionida: Potamilus inflatus)

North American freshwaters are among the world’s most threatened ecosystems, and freshwater mussels are among the most imperiled inhabiting these systems. A critical aspect of conservation biology is delineating patterns of genetic diversity, which can be difficult when a taxon has been extirpated from a significant portion of its historical range. In such cases, evaluating conservation and recovery options may benefit by using surrogate species as proxies when assessing overall patterns of genetic diversity. Here, we integrate the premise of surrogate species into a comparative phylogeographic framework to hypothesize genetic relationships between extant and extirpated populations of Potamilus inflatus by characterizing genetic structure in co-distributed congeners with similar life histories and dispersal capabilities. Our mitochondrial and nuclear sequence data exhibited variable patterns of genetic divergence between Potamilus spp. native to the Mobile and Pascagoula + Pearl + Pontchartrain (PPP) provinces. However, hierarchical Approximate Bayesian Computation indicated that the diversification between Mobile and PPP clades was synchronous and represents a genetic signature of a common history of vicariance. Recent fluctuations in sea-level appear to have caused Potamilus spp. in the PPP to form a single genetic cluster, providing justification for using individuals from the Amite River as a source of brood stock to re-establish extirpated populations of P. inflatus. Future studies utilizing eDNA and genome-wide molecular data are essential to better understand the distribution of P. inflatus and establish robust recovery plans. Given the imperilment status of freshwater mussels globally, our study represents a useful methodology for predicting relationships among extant and extirpated populations of imperiled species.

Florida, Alabama, Mississippi, Louisiana↗
USGS2016

Evaluating the adequacy of a reference site pool for ecological assessments in environmentally complex regions

Many advances in the field of bioassessment have focused on approaches for objectively selecting the pool of reference sites used to establish expectations for healthy waterbodies, but little emphasis has been placed on ways to evaluate the suitability of the reference-site pool for its intended applications (e.g., compliance assessment vs ambient monitoring). These evaluations are critical because an inadequately evaluated reference pool may bias assessments in some settings. We present an approach for evaluating the adequacy of a reference-site pool for supporting biotic-index development in environmentally heterogeneous and pervasively altered regions. We followed common approaches for selecting sites with low levels of anthropogenic stress to screen 1985 candidate stream reaches to create a pool of 590 reference sites for assessing the biological integrity of streams in California, USA. We assessed the resulting pool of reference sites against 2 performance criteria. First, we evaluated how well the reference-site pool represented the range of natural gradients present in the entire population of streams as estimated by sites sampled through probabilistic surveys. Second, we evaluated the degree to which we were successful in rejecting sites influenced by anthropogenic stress by comparing biological metric scores at reference sites with the most vs fewest potential sources of stress. Using this approach, we established a reference-site pool with low levels of human-associated stress and broad coverage of environmental heterogeneity. This approach should be widely applicable and customizable to particular regional or programmatic needs.

California↗
USGS2008

Integrated impact of tropical cyclones on sea surface chlorophyll in the North Atlantic

Past studies have shown that surface chlorophyll-a concentrations increase in the wake of hurricanes. Given the reported increase in the intensity of North Atlantic hurricanes in recent years, increasing chlorophyll-a concentrations, perhaps an indication of increasing biological productivity, would be an expected consequence. However, in order to understand the impact of variable hurricane activity on ocean biology, the magnitude of the hurricane-induced chlorophyll increase relative to other events that stir or mix the upper ocean must be assessed. This study investigates the upper ocean biological response to tropical cyclones in the North Atlantic from 1997-2005. Specifically, we quantitatively compare the anomalous chlorophyll-a concentrations created by cyclone activity to the total distribution of anomalies in the subtropical waters. We show that the cyclone-induced chlorophyll-a increase has minimal impact on the integrated biomass budget, a result that holds even when taking into consideration the lagged and asymmetrical response of ocean color. Copyright 2008 by the American Geophysical Union.

Geophysical Research Letters↗
USGS1998

Integrating across scales: Effectively applying science for the successful conservation of Atlantic salmon (Salmo salar)

Atlantic salmon (Salmo salar) is an excellent species on which to focus synthetic, integrative investigations because it is an economically important species that captures the public imagination, is heavily impacted by humans, uses several ecosystems over its life, and is the subject of a large body of extant literature. The following 24 papers were solicited to provide the biological basis for effective and innovative approaches that biologists, managers, and social scientists can use to develop policies that sustain Atlantic salmon and related species. Together these papers highlight the need for and benefits of (a) synthesizing within populations, (b) choosing the appropriate scale, (c) comparing across populations using rigorous, focused, question-oriented methods, (d) integrating across disciplines, (e) incorporating the human perspective, (f) linking multiple ecosystems, and (g) applied problem solving. To show how Atlantic salmon can guide research and conservation efforts for other species in other systems, we review the justification for the supplement and summarize the defining concepts that emerge from the volume.

Conference Paper↗
USGS2024

Comparing risk of chronic wasting disease occurrence using Bayesian hierarchical spatial models and different surveillance types

Spatial modeling of wildlife diseases can be used to describe patterns of disease risk, understand biological mechanisms of disease occurrence, and for spatial prediction. Risk of wildlife disease occurrence in relation to environmental variables is often modeled and predicted using Markov chain Monte Carlo (MCMC) methods, which are unsuitable for large datasets and those covering large spatial extents. Integrated nested Laplace approximation (INLA) and INLA using the stochastic partial differential equation (INLA-SPDE) approach have become popular alternatives to MCMC for Bayesian inference because of their fast computational time and ability to process large datasets. Studies investigating risk of disease occurrence in wildlife, to our knowledge, have not yet compared Bayesian hierarchical spatial models over large spatial extents using real world data. Using chronic wasting disease (CWD) surveillance data from white-tailed deer ( Odocoileus virginianus ) collected in Pennsylvania, United States, as a case study, we first demonstrate how parameter estimates compare among MCMC, INLA, and INLA-SPDE modeling frameworks. We then model CWD (detected/non-detected) using INLA-SPDE over a much larger spatial extent than has been conducted previously for this disease to determine how surveillance type (e.g., hunter harvest, roadkill, or all surveillance) influences model parameters and predicted risk of CWD occurrence at locations not sampled. Fixed effects considered in the models included deer age and sex, elevation, slope, distance to streams, percent clay, and proportion of two habitat classes (forest and open) known to influence deer movements. We found INLA to produce comparable estimates to MCMC and permit modeling large datasets covering expansive spatial extents much faster and more efficiently than MCMC. We identified potential biases in surveillance types, indicating the value of including all surveillance in models rather than only a single type. Comparing modeling tools available for mapping diseases of wildlife in relation to ecological variables at large spatial extents will guide future modeling efforts for CWD and other wildlife diseases. Understanding spatial patterns of CWD using different surveillance types can help improve understanding of CWD disease outbreaks, assist with control of CWD through geographical targeting, and inform future CWD surveillance efforts.

Ecological Modeling↗
USGS2017

The Beringian coevolution project: Holistic collections of mammals and associated parasites reveal novel perspectives on evolutionary and environmental change in the North

The Beringian Coevolution Project (BCP), a field program underway in the high northern latitudes since 1999, has focused on building key scientific infrastructure for integrated specimen-based studies on mammals and their associated parasites. BCP has contributed new insights across temporal and spatial scales into how ancient climate and environmental change have shaped faunas, emphasizing processes of assembly, persistence, and diversification across the vast Beringian region. BCP collections also represent baseline records of biotic diversity from across the northern high latitudes at a time of accelerated environmental change. These specimens and associated data form an unmatched resource for identifying hidden diversity, interpreting past responses to climate oscillations, documenting contemporary conditions, and anticipating outcomes for complex biological systems in a regime of ecological perturbation. Because of its dual focus on hosts and parasites, the BCP record also provides a foundation for comparative analyses that can document the effects of dynamic change on the geographic distribution, transmission dynamics, and emergence of pathogens. By using specific examples from carnivores, shrews, lagomorphs, rodents and their associated parasites, we demonstrate how broad, integrated field collections provide permanent infrastructure that informs policy decisions regarding human impact and the effect of climate change on natural populations.

Arctic Science↗
USGS2018

Contaminant-associated health effects in fishes from the Ottawa and Ashtabula Rivers, Ohio

The health of resident fishes serves as a biologically relevant barometer of aquatic ecosystem integrity. Here, the health of the Ottawa River and Ashtabula River (both within the Lake Erie Basin) were assessed using morphological and immunological biomarkers in brown bullheads ( Ameiurus nebulosus ) and largemouth bass ( Micropterus salmoides ). Biomarker metrics were compared to fish collected from a reference site (Conneaut Creek). Data utilized for analyses were collected between 2003 and 2011. Fish collected from all three river systems had markedly different contaminant profiles. Total PCBs were the dominant contaminant class by mass. In bullhead, PCBs were highest in fish from the Ashtabula River and there were no differences in fish collected pre- or post-remediation of Ashtabula Harbor (median = 4.6 and 5.5 mg/kg respectively). Excluding PCBs, the Ottawa River was dominated by organochlorine pesticides. Liver tumor prevalence exceeded the 5% trigger level at both the Ashtabula (7.7%) and Ottawa Rivers (10.2%), but was not statistically different than that at the reference site. There was no statistically significant association between microscopic lesions, gross pathology and contaminant body burdens. Collectively, contaminant body burdens were generally negatively correlated with functional immune responses including bactericidal, cytotoxic-cell and respiratory burst activity in both species. Exceptions were positive correlations of HCB and heptachlor epoxide with respiratory burst activity in largemouth bass, and HCB with respiratory burst activity in bullhead and ΣBHC for all three functional assays in bullhead. Data here provide additional support that organochlorine contamination is associated with immunomodulation, and that species differences exist within sites.

Ohio↗
USGS2007

A Quantitative Threats Analysis for the Florida Manatee ( Trichechus manatus latirostris )

The Florida manatee (Trichechus manatus latirostris) is an endangered marine mammal endemic to the southeastern United States. The primary threats to manatee populations are collisions with watercraft and the potential loss of warm-water refuges. For the purposes of listing, recovery, and regulation under the Endangered Species Act (ESA), an understanding of the relative effects of the principal threats is needed. This work is a quantitative approach to threats analysis, grounded in the assumption that an appropriate measure of status under the ESA is based on the risk of extinction, as quantified by the probability of quasi-extinction. This is related to the qualitative threats analyses that are more common under the ESA, but provides an additional level of rigor, objectivity, and integration. In this approach, our philosophy is that analysis of the five threat factors described in Section 4(a)(1) of the ESA can be undertaken within an integrated quantitative framework. The basis of this threats analysis is a comparative population viability analysis. This involves forecasting the Florida manatee population under different scenarios regarding the presence of threats, while accounting for process variation (environmental, demographic, and catastrophic stochasticity) as well as parametric and structural uncertainty. We used the manatee core biological model (CBM) for this viability analysis, and considered the role of five threats: watercraft-related mortality, loss of warm-water habitat in winter, mortality in water-control structures, entanglement, and red tide. All scenarios were run with an underlying parallel structure that allowed a more powerful estimation of the effects of the various threats. The results reflect our understanding of manatee ecology (as captured in the structure of the CBM), our estimates of manatee demography (as described by the parameters in the model), and our characterization of the mechanisms by which the threats act on manatees. As an example of the type of results generated, we estimated that the probability of the manatee population falling to less than 250 adults on either the Atlantic or Gulf coasts (from a current statewide population size of near 3300) within 100 years is 8.6%. Complete removal of the watercraft threat alone would reduce this risk to 0.4%; complete removal of the warm-water threat to 4.2%; removal of both threats would reduce the risk to 0.1%. The modeling approach we have taken also allows us to consider partial removal of threats, as well as removal of multiple threats simultaneously. We believe the measure we have proposed (probability of quasi-extinction over y years, with quasi-extinction defined as dropping below a threshold of z on either coast) is a suitable measure of status that integrates a number of the elements that are relevant to interpretation under the ESA (it directly integrates risk of extinction and reduction of range, and indirectly integrates loss of genetic diversity). But the identification of the time frame of interest and the tolerable risk of quasi-extinction are policy decisions, and an ecology-based quasi-extinction threshold has not yet been determined. We have endeavored to provide results over a wide range of these parameters to give decision-makers useful information to assess status. This assessment of threats suggests that watercraft-related mortality is having the greatest impact on manatee population growth and resilience. Elimination of this single threat would greatly reduce the probability of quasi-extinction. Loss of warm-water is also a significant threat, particularly over the long-term. Red tide and entanglement, while noticeable threats, have had less of an impact on the manatee population. The effect of water control structures may have already been largely mitigated. We did not, however, consider an exhaustive list of threats. Other threats (e.g., reduction of food resources due to storms and development) may play a

Open-File Report↗
USGS2016

Introduction: Exotic annual Bromus in the western USA

The spread and impacts of exotic species are unambiguous, global threats to many ecosystems. A prominent example is the suite of annual grasses in the Bromus genus ( Bromus hereafter) that originate from Europe and Eurasia but have invaded or are invading large areas of the Western USA. This book brings a diverse, multidisciplinary group of authors together to synthesize current knowledge, research needs, and management implications for Bromus . Exotic plant invasions are multifaceted problems, and understanding and managing them requires the biological, ecological, sociological, and economic perspectives that are integrated in this book. Knowing how well information from one geographic or environmental setting can transfer to another is a key need for broadly distributed Bromus species especially given ongoing climate change. Thus, the chapters in the book compare and contrast invasibility of different ecoregions and invasiveness of different Bromus species. A universal theme is managing for ecosystems that are resilient to disturbance and resistant to invasion which will be essential for adaptation to the human-caused problem of Bromus in the Western USA.

Book chapter↗
USGS2007

Development of the Hydroecological Integrity Assessment Process for Determining Environmental Flows for New Jersey Streams

The natural flow regime paradigm and parallel stream ecological concepts and theories have established the benefits of maintaining or restoring the full range of natural hydrologic variation for physiochemical processes, biodiversity, and the evolutionary potential of aquatic and riparian communities. A synthesis of recent advances in hydroecological research coupled with stream classification has resulted in a new process to determine environmental flows and assess hydrologic alteration. This process has national and international applicability. It allows classification of streams into hydrologic stream classes and identification of a set of non-redundant and ecologically relevant hydrologic indices for 10 critical sub-components of flow. Three computer programs have been developed for implementing the Hydroecological Integrity Assessment Process (HIP): (1) the Hydrologic Indices Tool (HIT), which calculates 171 ecologically relevant hydrologic indices on the basis of daily-flow and peak-flow stream-gage data; (2) the New Jersey Hydrologic Assessment Tool (NJHAT), which can be used to establish a hydrologic baseline period, provide options for setting baseline environmental-flow standards, and compare past and proposed streamflow alterations; and (3) the New Jersey Stream Classification Tool (NJSCT), designed for placing unclassified streams into pre-defined stream classes. Biological and multivariate response models including principal-component, cluster, and discriminant-function analyses aided in the development of software and implementation of the HIP for New Jersey. A pilot effort is currently underway by the New Jersey Department of Environmental Protection in which the HIP is being used to evaluate the effects of past and proposed surface-water use, ground-water extraction, and land-use changes on stream ecosystems while determining the most effective way to integrate the process into ongoing regulatory programs. Ultimately, this scientifically defensible process will help to quantify the effects of anthropogenic changes and development on hydrologic variability and help planners and resource managers balance current and future water requirements with ecological needs.

Scientific Investigations Report↗