USGS Science⌕ Search

SEARCH · USGS Science

Results for “Ecological Applications”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,315 records · Page 73Linked to original sources
USGS2022

Open removal models with temporary emigration and population dynamics to inform invasive animal management

Removal sampling data are the primary source of monitoring information for many populations (e.g., invasive species, fisheries). Population dynamics, temporary emigration, and imperfect detection are common sources of variation in monitoring data and are key parameters for informing management. We developed two open robust-design removal models for simultaneously modeling population dynamics, temporary emigration, and imperfect detection: a random walk linear trend model (estimable without ancillary information), and a 2-age class informed population model (InfoPM, closely related to integrated population models) that incorporated prior information for age-structured vital rates and relative juvenile availability. We applied both models to multiyear, removal trapping time-series of a large invasive lizard (Argentine black and white tegu, Salvator merianae ) in three management areas of South Florida to evaluate the effectiveness of management programs. Although estimates of the two models were similar, the InfoPMs generally returned more precise estimates, partitioned dynamics into births, deaths, net migration, and provided a decision support tool to predict population dynamics under different effort scenarios while accounting for uncertainty. Trends in tegu superpopulation abundance estimates were increasing in two management areas despite generally high removal rates. However, tegu abundance appeared to decline in the Core management area, where trapping density was the highest and immigration the lowest. Finally, comparing abundance predictions of no-removal scenarios to those estimated in each management area suggested significant population reductions due to management. These results suggest that local tegu population control via systematic trapping may be feasible with high enough trap density and limited immigration; and highlights the value of these trapping programs. We provided the first estimates of tegu abundance, capture probabilities, and population dynamics, which is critical for effective management. Furthermore, our models are applicable to a wide range of monitoring programs (e.g., carcass recovery or removal point-counts).

Ecology and Evolution↗
USGS2026

Adaptive capacity of freshwater organisms in North America: Current understanding and future applications

Freshwater species are increasingly threatened by climate change, yet our ability to assess their vulnerability remains incomplete. Typically, climate change vulnerability assessments (CCVAs) evaluate three components: exposure, sensitivity, and adaptive capacity. Adaptive capacity, defined as the ability of a species to adjust to changing conditions, provides critical insight into how species may persist under future scenarios and can strengthen conservation planning by highlighting opportunities for resilience and targeted management strategies. Trait-based approaches offer a promising path for managers to operationalize adaptive capacity by identifying measurable biological and ecological traits that influence climate change response strategies. However, these insights are rarely integrated into broader vulnerability frameworks that support conservation decision making. We build on previous research to synthesize current understanding of adaptive capacity for three freshwater taxa in North America: fishes, mussels, and crayfishes. Our objectives were to: (1) assess the relevance of adaptive capacity factors for fishes, mussels, and crayfishes; (2) identify key opportunities and gaps in linking trait-based information into adaptive capacity assessments; and (3) illustrate how incorporating adaptive capacity can enhance management decisions for freshwater species under climate change. We used an expert workshop, literature review, and case studies to identify relevant adaptive capacity factors, assess available information, and evaluate inclusion in management contexts. We found that all three taxa had sufficient information to inform adaptive capacity assessments. In addition to existing adaptive capacity factors, we identified Morphology as an important yet underutilized cross-cutting diagnostic category when information was limited. By explicitly linking trait-based approaches with adaptive capacity frameworks, we offer practical guidance for improving climate adaptation strategies and prioritizing management actions for freshwater biodiversity under accelerating global change.

Global Change Biology Communications↗
USGS2014

Investigations of novel unsaturated bile salts of male sea lamprey as potential chemical cues

Sulfated bile salts function as chemical cues that coordinate reproduction in sea lamprey, Petromyzon marinus . 7α, 12α, 24-trihydroxy-5α-cholan-3-one 24-sulfate (3kPZS) is the most abundant known bile salt released by sexually mature male sea lampreys and attracts ovulated females. However, previous studies showed that the male-produced pheromone consists of unidentified components in addition to 3kPZS. Here, analysis of water conditioned with mature male sea lampreys indicated the presence of 4 oxidized, unsaturated compounds with molecular weights of 466 Da, 468 Da, and 2 of 470 Da. These compounds were not detectable in water conditioned with immature male sea lampreys. By using mass spectrometry, 4 A-ring unsaturated sulfated bile salts were tentatively identified from male washings as 2 4-ene, a 1-ene, and a 1,4-diene analogs. These were synthesized to determine if they attracted ovulated female sea lampreys to spawning nests in natural streams. One of the novel synthetic bile salts, 3 keto-1-ene PZS, attracted ovulated females to the point of application at a concentration of 10 -12 M. This study reveals the structural diversity of bile salts in sea lamprey, some of which have been demonstrated to be pheromonal cues.

Journal of Chemical Ecology↗
USGS2014

An application of Social Values for Ecosystem Services (SolVES) to three national forests in Colorado and Wyoming

Despite widespread recognition that social-value information is needed to inform stakeholders and decision makers regarding trade-offs in environmental management, it too often remains absent from ecosystem service assessments. Although quantitative indicators of social values need to be explicitly accounted for in the decision-making process, they need not be monetary. Ongoing efforts to map such values demonstrate how they can also be made spatially explicit and relatable to underlying ecological information. We originally developed Social Values for Ecosystem Services (SolVES) as a tool to assess, map, and quantify nonmarket values perceived by various groups of ecosystem stakeholders. With SolVES 2.0 we have extended the functionality by integrating SolVES with Maxent maximum entropy modeling software to generate more complete social-value maps from available value and preference survey data and to produce more robust models describing the relationship between social values and ecosystems. The current study has two objectives: (1) evaluate how effectively the value index, a quantitative, nonmonetary social-value indicator calculated by SolVES, reproduces results from more common statistical methods of social-survey data analysis and (2) examine how the spatial results produced by SolVES provide additional information that could be used by managers and stakeholders to better understand more complex relationships among stakeholder values, attitudes, and preferences. To achieve these objectives, we applied SolVES to value and preference survey data collected for three national forests, the Pike and San Isabel in Colorado and the Bridger–Teton and the Shoshone in Wyoming. Value index results were generally consistent with results found through more common statistical analyses of the survey data such as frequency, discriminant function, and correlation analyses. In addition, spatial analysis of the social-value maps produced by SolVES provided information that was useful for explaining relationships between stakeholder values and forest uses. Our results suggest that SolVES can effectively reproduce information derived from traditional statistical analyses while adding spatially explicit, social-value information that can contribute to integrated resource assessment, planning, and management of forests and other ecosystems.

Colorado;Wyoming↗
USGS2026

Severity and certainty metric for kelp stressors: A tool for research, management, and conservation

Foundation species face multiple threats, and many are in decline worldwide. Kelps are no exception, with declines documented throughout their range. Stressors such as warming, eutrophication, and reduced water quality—often linked to human activities—are well recognized, yet their relative severity and certainty have not been systematically evaluated. Such a framework may aid scientific, regulatory, and conservation organizations in prioritizing actions and decision making. Here we build on a conceptual model of stressors to kelp in the Salish Sea by rating stressor severity and scientific certainty. We convened a panel of regional kelp experts to perform the rating exercise for two canopy taxa, Nereocystis luetkeana and Macrocystis tenuifolia , as well as a grouping for understory species, including both the sporophyte (adult) and gametophyte (juvenile) life stages for these algae. Our process produced a rich dataset which can be separated by stressor, taxa, and life stage allowing for broad applications. The panel identified temperature, low nutrients, and substrate change/benthic sedimentation as the most severe stressors to kelp, with relatively high certainty for most taxa. Certainty scores were relatively high for Nereocystis and Macrocystis sporophytes but were considerably lower for understory species and the gametophyte life stage, for most stressors, highlighting research gaps. Our data set could be applied for management prioritization, setting ecological baselines, and spatial modeling exercises. We encourage scientific, regulatory, and conservation organizations to consider both our data and our process when evaluating their needs. As foundation species continue to face threats, exercises such as this can provide scientists and managers with actionable indices that support strategies to stem degradation.

Ecological Indicators↗
USGS2019

Optimal spatial allocation of control effort to manage invasives in the face of imperfect detection and misclassification

Imperfect detection and misclassification errors are often ignored in the context of invasive species management. Here we present an approach that combines spatially explicit models and an optimization technique to design optimal search and destroy strategies based on noisy monitoring observations. We focus on two invasive plants, melaleuca ( Melaleuca quinquenervia ) and Old World climbing fern ( Lygodium microphyllum ), which continue to cause important damages to the Everglades ecosystem. We present a methodological framework that combines Hidden Markov Random Field (HMRF, initially developed for image analysis) and linear programming to optimally search for invasive species. A benefit of this approach is that it accounts for the spatial structure of the system by using a spatially explicit modeling approach (i.e. HMRF), and does not require repeated visits to model the probability of occurrence of species. We found on simulated cases that our approach can lead to substantial improvements in control efficiency when compared to state of the art model-free approaches. For example, in the case of the old world fern, simulations showed that the optimal strategy would allow managers to control up to 34% more sites than with model-free approaches that ignored misclassification and imperfect detection. For melaleuca it was possible to control up to 20% more sites. The vast increase in imagery data obtained from different sources (e.g. unmanned aerial systems, and satellite) provides great opportunities to improve management of natural resources by applying modern computational methods such as the one we present. Our approach can substantially increases the efficiency of invasive species control by accounting for imperfect detection, misclassification error and the spatial structure of the system. Our approach is applicable to other systems and problems, for example it could be applied to the control of plant pathogens, or optimal extraction of resources (e.g. minerals or biological resources).

Ecological Modelling↗
USGS2011

Development of a bioenergetics model for age-0 American shad

Bioenergetics modeling can be used as a tool to investigate the impact of non-native age-0 American shad ( Alosa sapidissima ) on reservoir and estuary food webs. The model can increase our understanding of how these fish influence lower trophic levels as well as predatory fish populations that feed on juvenile salmonids. Bioenergetics modeling can be used to investigate ecological processes, evaluate alternative research hypotheses, provide decision support, and quantitative prediction. Bioenergetics modeling has proven to be extremely useful in fisheries research (Ney et al. 1993,Chips and Wahl 2008, Petersen et al. 2008). If growth and diet parameters are known, the bioenergetics model can be used to quantify the relative amount of zooplankton or insects consumed by age-0 American shad. When linked with spatial and temporal information on fish abundance, model output can guide inferential hypothesis development to demonstrate where the greatest impacts of age-0 American shad might occur. Bioenergetics modeling is particularly useful when research questions involve multiple species and trophic levels (e.g. plankton communities). Bioenergetics models are mass-balance equations where the energy acquired from food is partitioned between maintenance costs, waste products, and growth (Winberg 1956). Specifically, the Wisconsin bioenergetics model (Hanson et al. 1997) is widely used in fisheries science. Researchers have extensively tested, reviewed, and improved on this modeling approach for over 30 years (Petersen et al. 2008). Development of a bioenergetics model for any species requires three key components: 1) determine physiological parameters for the model through laboratory experiments or incorporate data from a closely related species, 2) corroboration of the model with growth and consumption estimates from independent research, and 3) error analysis of model parameters. Wisconsin bioenergetics models have been parameterized for many of the salmonids and predatory fishes encountered in the lower Columbia River (Petersen and Ward 1999). The Wisconsin bioenergetics model has not been developed for American shad, however Limburg (1996) parameterized a simplified bioenergetics growth model for this species. A common application for the Wisconsin bioenergetics model is to estimate the consumption or growth of a fish population under different temperature and feeding scenarios (Ney 1993). One advantage of the bioenergetics approach is that consumption can be estimated without direct field measurements of predation rate (prey·predator -1 · day -1 ; Petersen and Ward 1999). Field estimates of fish consumption are time consuming and costly to determine, and estimates may show wide variance due to environmental and sampling variability. However, the consumption parameters used in a newly developed bioenergetics model must be verified with field and laboratory estimates of consumption (Ney 1993). The objective of this research was to parameterize a Wisconsin bioenergetics model for age-0 American shad using published physiological data on American shad and closely related alosine species. The American shad bioenergetics model will be used as a tool to explore various hypotheses about how age-0 American shad directly and indirectly affect Columbia River salmon through ecological interactions in lower Columbia River food webs. One over-arching focus of the larger research project was to identify potential interactions between age-0 American shad and juvenile salmonids, addressing potential outcomes through bioenergetics modeling scenarios. This report contains two bioenergetics modeling applications to demonstrate how these models can be used to address management questions and direct research effort. The first modeling application uses the American shad bioenergetics model described in this report to explore prey consumption by age-0 American shad (Chapter 1, this report). Dietary data on age-0 American shad and previously published reports on the diet of juvenile fall Chinook salmon (Rondorf et al. 1990, USGS unpublished data) suggested there might be considerable dietary overlap between these species in the lower Columbia River. The U.S. Geological Survey (USGS) was interested in using the American shad bioenergetics model to explore hypotheses concerning dietary overlap between age-0 American shad and emigrating fall Chinook salmon. The second modeling application uses the fall Chinook salmon bioenergetics model (Koehler et al. 2006) to explore the growth potential of juvenile fall Chinook salmon predating on age-0 American shad in the lower Columbia River. This modeling was based dietary information on a small number of age-0 fall Chinook salmon (n = 13) collected in John Day Reservoir in 1994 - 1996 (unpublished USGS data). Analysis of this dietary data found that these salmonids were feeding primarily on age-0 American shad (> 75% by weight).

Oregon↗
USGS2016

Application of effective discharge analysis to environmental flow decision-making

Well-informed river management decisions rely on an explicit statement of objectives, repeatable analyses, and a transparent system for assessing trade-offs. These components may then be applied to compare alternative operational regimes for water resource infrastructure (e.g., diversions, locks, and dams). Intra- and inter-annual hydrologic variability further complicates these already complex environmental flow decisions. Effective discharge analysis (developed in studies of geomorphology) is a powerful tool for integrating temporal variability of flow magnitude and associated ecological consequences. Here, we adapt the effectiveness framework to include multiple elements of the natural flow regime (i.e., timing, duration, and rate-of-change) as well as two flow variables. We demonstrate this analytical approach using a case study of environmental flow management based on long-term (60 years) daily discharge records in the Middle Oconee River near Athens, GA, USA. Specifically, we apply an existing model for estimating young-of-year fish recruitment based on flow-dependent metrics to an effective discharge analysis that incorporates hydrologic variability and multiple focal taxa. We then compare three alternative methods of environmental flow provision. Percentage-based withdrawal schemes outcompete other environmental flow methods across all levels of water withdrawal and ecological outcomes.

Environmental Management↗
USGS2019

A brief introduction to integrated pest management for aquatic systems

Aquatic invasive plants and animals are increasingly becoming a problem, causing severe economic and ecological damage to critical freshwater systems. The best strategy for controlling an invasive pest employs an integrated pest management (IPM) approach using a combination of biological, physical, chemical, and social/cultural control methods. Here, we examine the history and development of IPM and provide a discussion of the components of an IPM program involving development, evaluation, and management. Control approaches will be reviewed and the application of this technique to aquatic systems will be discussed. A discussion of the Great Lakes Fishery Commission's (GLFC) Integrated Management of Sea Lamprey Petromyzon marinus Control Program will be provided to illustrate the application of IPM to an aquatic system.

North American Journal of Fisheries Management↗
USGS2011

Modelling the distribution of chickens, ducks, and geese in China

Global concerns over the emergence of zoonotic pandemics emphasize the need for high-resolution population distribution mapping and spatial modelling. Ongoing efforts to model disease risk in China have been hindered by a lack of available species level distribution maps for poultry. The goal of this study was to develop 1 km resolution population density models for China's chickens, ducks, and geese. We used an information theoretic approach to predict poultry densities based on statistical relationships between poultry census data and high-resolution agro-ecological predictor variables. Model predictions were validated by comparing goodness of fit measures (root mean square error and correlation coefficient) for observed and predicted values for 1/4 of the sample data which were not used for model training. Final output included mean and coefficient of variation maps for each species. We tested the quality of models produced using three predictor datasets and 4 regional stratification methods. For predictor variables, a combination of traditional predictors for livestock mapping and land use predictors produced the best goodness of fit scores. Comparison of regional stratifications indicated that for chickens and ducks, a stratification based on livestock production systems produced the best results; for geese, an agro-ecological stratification produced best results. However, for all species, each method of regional stratification produced significantly better goodness of fit scores than the global model. Here we provide descriptive methods, analytical comparisons, and model output for China's first high resolution, species level poultry distribution maps. Output will be made available to the scientific and public community for use in a wide range of applications from epidemiological studies to livestock policy and management initiatives.

Agriculture, Ecosystems and Environment↗
USGS1983

Evaluation of thematic mapper data for natural resource assessment

The U.S. Geological Survey EROS Data Center evaluated the utility of Landsat Thematic Mapper (TM) date for natural resource assessment, emphasizing manual interpretation and digital classification of the data for U.S. Department of the Interior applications. Substantially more information was derived from TM data than from Landsat Multispectral Scanner (MSS) data. Greater resolution of TM data aided in locating roads, small stock ponds, and many other land features that could be used as landmarks. The improved spatial resolution of TM data also permitted more efficient visual interpretations of land use, better identification of resource types, and improved assessment of ecological status of natural vegetation. TM data also provided a new source of spectral information that was useful for natural resource assessment. New mid-infrared spectral bands, TM band 5 and band 7, aided in distinguishing water resources, wetland vegetation resources, and other important terrain features. The added information was useful for both manual interpretation and digital data classification of vegetation resources and land features. Results from the analyses of both TM and TM simulator (TMS) spectral data suggest that the coefficient of variation for major land cover types is generally less for TM data than for MSS data taken from the same area. This reduction in variance should contribute to an improved multispectral analysis, contributing new information about vegetation in natural ecosystems. Although the amount of new information in TM bands 5 and 7 is mall, it is unique in that the same information cannot be derived from four-band Landsat MSS spectral data.

Conference Paper↗
USGS2021

Interagency Ecological Program long-term monitoring element review: Pilot approach and methods development (2020)

This report describes the first-year, pilot-phase of what is intended to be a larger, multiple-year review of all IEP core long-term monitoring elements (LTMEs). Here we hope to provide evidence that the review team arrangement and communication schedule was effective at developing a framework to objectively evaluate a suite of LTMEs. We focused on developing methods for an effective review, documenting the process of methods development, and compiling recommendations for applications of these methods to future reviews. We also gathered recommendations to improve data collection, catchability-adjustment, and record keeping processes which will be useful for all LTMEs regardless of when they are to be reviewed. Although we did not complete a comprehensive review of the long-term monitoring elements due to our short timeline, we believe this report represents a substantial effort towards that review and will serve as an invaluable guide for subsequent IEP LTME reviews.

Report↗
USGS2020

Applications of deep convolutional neural networks to predict length, circumference, and weight from mostly dewatered images of fish

Simple biometric data of fish aid fishery management tasks such as monitoring the structure of fish populations and regulating recreational harvest. While these data are foundational to fishery research and management, the collection of length and weight data through physical handling of the fish is challenging as it is time consuming for personnel and can be stressful for the fish. Recent advances in imaging technology and machine learning now offer alternatives for capturing biometric data. To investigate the potential of deep convolutional neural networks to predict biometric data, several regressors were trained and evaluated on data stemming from the FishL™ Recognition System and manual measurements of length, girth, and weight. The dataset consisted of 694 fish from 22 different species common to Laurentian Great Lakes. Even with such a diverse dataset and variety of presentations by the fish, the regressors proved to be robust and achieved competitive mean percent errors in the range of 5.5 to 7.6% for length and girth on an evaluation dataset. Potential applications of this work could increase the efficiency and accuracy of routine survey work by fishery professionals and provide a means for longer‐term automated collection of fish biometric data.

Illinois, Michigan, Ohio↗
USGS2015

A sea lamprey ( Petromyzon marinus ) sex pheromone mixture increases trap catch relative to a single synthesized component in specific environments

Spermiating male sea lamprey ( Petromyzon marinus ) release a sex pheromone, of which a component, 7α, 12α, 24-trihydoxy-3-one-5α-cholan-24-sulfate (3kPZS), has been identified and shown to induce long distance preference responses in ovulated females. However, other pheromone components exist, and when 3kPZS alone was used to control invasive sea lamprey populations in the Laurentian Great Lakes, trap catch increase was significant, but gains were generally marginal. We hypothesized that free-ranging sea lamprey populations discriminate between a partial and complete pheromone while migrating to spawning grounds and searching for mates at spawning grounds. As a means to test our hypothesis, and to test two possible uses of sex pheromones for sea lamprey control, we asked whether the full sex pheromone mixture released by males (spermiating male washings; SMW) is more effective than 3kPZS in capturing animals in traditional traps (1) en route to spawning grounds and (2) at spawning grounds. At locations where traps target sea lampreys en route to spawning grounds, SMW-baited traps captured significantly more sea lampreys than paired 3kPZS-baited traps (~10 % increase). At spawning grounds, no difference in trap catch was observed between 3kPZS and SMW-baited traps. The lack of an observed difference at spawning grounds may be attributed to increased pheromone competition and possible involvement of other sensory modalities to locate mates. Because fishes often rely on multiple and sometimes redundant sensory modalities for critical life history events, the addition of sex pheromones to traditionally used traps is not likely to work in all circumstances. In the case of the sea lamprey, sex pheromone application may increase catch when applied to specifically designed traps deployed in streams with low adult density and limited spawning habitat.

Journal of Chemical Ecology↗
USGS2024

Assessing and implementing the concept of Blue Economy in Laurentian Great Lakes fisheries: Lessons from coupled human and natural systems

Inland fisheries often receive little to no attention in global discussions about sustainable development. The consequences of overlooking inland fisheries in sustainability dialogues are increasingly problematic as fisheries stressors (e.g., overharvest, species invasion, climate change, habitat modification) intensify. Elevating the global profile of inland fisheries requires an approach for quantifying and clearly conveying the ecological, economic, and societal values of these systems. One such approach involves the Blue Economy, a multifaceted concept initially used to describe the intersection of marine conservation and sustainable use of marine resources for economic growth. Although conceptually powerful, the Blue Economy has rarely been applied to inland waters and fisheries. To address this knowledge gap, we conceptualized Laurentian Great Lakes fisheries from a Blue Economy perspective. In particular, we evaluated the utility of the coupled human and natural systems (CHANS) framework for characterizing the ecological, economic, and societal values of Laurentian Great Lakes fisheries and associated contributions to the Blue Economy (e.g., human livelihoods, food security, recreation, conservation, economic prosperity). There are numerous opportunities to leverage CHANS methods (e.g., metacoupling, telecoupling) and associated mathematical models to advance fisheries science, inform fisheries management, and ultimately move toward a Blue Economy in the Laurentian Great Lakes. To that end, we demonstrated applications of CHANS methods, discussed strategies for communicating with stakeholders, and provided insights for navigating challenges to developing a Blue Economy in the Laurentian Great Lakes—a model that could be used in the African Great Lakes and other large ecosystems in the world.

Laurentian Great Lakes↗
USGS2016

Model selection and assessment for multi­-species occupancy models

While multi-species occupancy models (MSOMs) are emerging as a popular method for analyzing biodiversity data, formal checking and validation approaches for this class of models have lagged behind. Concurrent with the rise in application of MSOMs among ecologists, a quiet regime shift is occurring in Bayesian statistics where predictive model comparison approaches are experiencing a resurgence. Unlike single-species occupancy models that use integrated likelihoods, MSOMs are usually couched in a Bayesian framework and contain multiple levels. Standard model checking and selection methods are often unreliable in this setting and there is only limited guidance in the ecological literature for this class of models. We examined several different contemporary Bayesian hierarchical approaches for checking and validating MSOMs and applied these methods to a freshwater aquatic study system in Colorado, USA, to better understand the diversity and distributions of plains fishes. Our findings indicated distinct differences among model selection approaches, with cross-validation techniques performing the best in terms of prediction.

Ecology↗
USGS2014

Stream classification of the Apalachicola-Chattahoochee-Flint River System to support modeling of aquatic habitat response to climate change

A stream classification and associated datasets were developed for the Apalachicola-Chattahoochee-Flint River Basin to support biological modeling of species response to climate change in the southeastern United States. The U.S. Geological Survey and the Department of the Interior’s National Climate Change and Wildlife Science Center established the Southeast Regional Assessment Project (SERAP) which used downscaled general circulation models to develop landscape-scale assessments of climate change and subsequent effects on land cover, ecosystems, and priority species in the southeastern United States. The SERAP aquatic and hydrologic dynamics modeling efforts involve multiscale watershed hydrology, stream-temperature, and fish-occupancy models, which all are based on the same stream network. Models were developed for the Apalachicola-Chattahoochee-Flint River Basin and subbasins in Alabama, Florida, and Georgia, and for the Upper Roanoke River Basin in Virginia. The stream network was used as the spatial scheme through which information was shared across the various models within SERAP. Because these models operate at different scales, coordinated pair versions of the network were delineated, characterized, and parameterized for coarse- and fine-scale hydrologic and biologic modeling. The stream network used for the SERAP aquatic models was extracted from a 30-meter (m) scale digital elevation model (DEM) using standard topographic analysis of flow accumulation. At the finer scale, reaches were delineated to represent lengths of stream channel with fairly homogenous physical characteristics (mean reach length = 350 m). Every reach in the network is designated with geomorphic attributes including upstream drainage basin area, channel gradient, channel width, valley width, Strahler and Shreve stream order, stream power, and measures of stream confinement. The reach network was aggregated from tributary junction to tributary junction to define segments for the benefit of hydrological, soil erosion, and coarser ecological modeling. Reach attributes are summarized for each segment. In six subbasins segments are assigned additional attributes about barriers (usually impoundments) to fish migration and stream isolation. Segments in the six sub-basins are also attributed with percent urban area for the watershed upstream from the stream segment for each decade from 2010–2100 from models of urban growth. On a broader scale, for application in a coarse-scale species-response model, the stream-network information is aggregated and summarized by 256 drainage subbasins (Hydrologic Response Units) used for watershed hydrologic and stream-temperature models. A model of soil erodibility based on the Revised Universal Soil Loss Equation also was developed at this scale to parameterize a model to evaluate stream condition. The reach-scale network was classified using multivariate clustering based on modeled channel width, valley width, and mean reach gradient as variables. The resulting classification consists of a 6-cluster and a 12-cluster classification for every reach in the Apalachicola-Chattahoochee-Flint Basin. We present an example of the utility of the classification that was tested using the occurrence of two species of darters and two species of minnows in the Apalachicola-Chattahoochee-Flint River Basin, the blackbanded darter and Halloween darter, and the bluestripe shiner and blacktail shiner.

Alabama, Florida, Georgia, Virginia↗
USGS2013

Identification of metrics to monitor salt marsh integrity on National Wildlife Refuges in relation to conservation and management objectives

Executive Summary Most salt marshes in the US have been degraded by human activities, and threats from physical alterations, surrounding land-use, species invasions, and global climate change persist. Salt marshes are unique and highly productive ecosystems with high intrinsic value to wildlife, and many National Wildlife Refuges (NWRs) have been established in coastal areas to protect large tracts of salt marsh and wetland-dependent species. Various management practices are employed routinely on coastal NWRs to restore and enhance marsh integrity and ensure ecosystem sustainability. Prioritizing NWR salt marshes for application of management actions and choosing among multiple management options requires scientifically-based methods for assessing marsh condition. Monitoring is integral to structured decision-making (SDM), a formal process for decomposing a decision into its essential elements. Within a natural resource context, SDM involves identifying management objectives, alternative management actions, and expected management outcomes. The core of SDM is a set of criteria for measuring system performance and evaluating management responses. Therefore, use of SDM to frame natural resource decisions leads to logical selection of monitoring attributes that are linked explicitly to management needs. We used SDM to guide selection of variables for monitoring the ecological integrity of salt marshes within the National Wildlife Refuge System (NWRS). Our objectives were to identify indicators of salt marsh integrity that are effective across large geographic regions, responsive to a wide range of threats, and feasible to implement within funding and staffing constraints of the NWRS. In April, 2008, we engaged interdisciplinary experts in a week-long rapid prototyping SDM workshop to define the essential elements of salt marsh management decisions on refuges throughout the northeastern, southwestern, and northwestern US, corresponding to respective Regions 5, 2, and 1 of the US Fish and Wildlife Service (FWS). Through this process we identified measurable attributes for monitoring salt marsh ecosystems that are integrated into conservation practice and target management objectives. The following salt marsh attributes were identified through the SDM process either for describing state condition to determine management needs or for evaluating the achievement of management objectives: historical condition and geomorphic setting; ditch density; surrounding land use; ratio of open water area to vegetation area; rate of pesticide application; environmental contaminant concentration; change in marsh surface elevation relative to sea level rise; tidal range and groundwater level; surface topography; salinity; and species composition and abundance of vegetation, invasive species, invertebrates, nekton, and breeding and wintering birds. The identified attributes were too broadly defined to serve as operational monitoring variables. Therefore, we tested specific metrics for quantifying most of these attributes in summers of 2008 and 2009. The first four attributes in the above list can be characterized by office-based analysis of existing GIS data layers. The remaining attributes require field-based methods for assessment. We were forced to exclude a small number of attributes from field tests due to inconsistent data (pesticide application rate, environmental contaminant concentrations) or requirements that exceeded the scope of this project (change in marsh surface elevation; surface topography; benthic invertebrates; wintering birds). We evaluated potential metrics for evaluating all remaining field attributes. In partnership with NWRS biologists, we tested rapid versus intensive metrics for monitoring field attributes (tidal range and groundwater level; marsh surface elevation; salinity; and species composition and abundance of vegetation, invasive species, nekton, and breeding birds) at coastal refuges throughout FWS Region 5. Seven refuges participated in metric testing in 2008: Rachel Carson (ME), Parker River (MA), Wertheim (NY), E. B. Forsythe (NJ), Bombay Hook (DE), Prime Hook (DE), and Eastern Shore of Virginia Complex (VA). These seven and two additional refuges participated in metric testing in 2009: Rhode Island Complex (RI) and Stewart B. McKinney (CT). We based all field metrics on existing protocols for salt marsh assessment. Sampling locations were determined randomly within delineated marsh study units (MSUs) at each refuge. Detailed field methods are provided in appendices to this report. Measurements for individual metrics were averaged across samples within MSUs during each year of sampling. Each year, correlation or regression analysis was conducted on average measurements across MSUs within each attribute set to identify redundant metrics. Statistical redundancy between a pair of metrics within an attribute set (i.e., correlation or regression slopes with p-values < 0.05) was considered justification for eliminating one of the pair from the regional set of monitoring metrics. Decisions regarding metric elimination versus retention were based on feasibility of monitoring, considering such factors as sampling time, resources required, and potential for regional standardization in implementation. The result of these tests is a reduced suite of monitoring metrics that targets NWRS management decisions and is practicable for implementing on a regional scale. Based on these tests, we recommend the following list of metrics for monitoring integrity of NWRS salt marshes (marsh attribute category is in parentheses): (historical condition and geomorphic setting) position of marsh in the landscape, marsh shape, degree of fill and/or fragmentation, degree of tidal flushing, amount of aquatic edge; (ditch density) ranking of ditch density from none to severe; (surrounding land use) relative proportion of agricultural land in a 150-m buffer around the marsh, relative proportion of natural land in a 150-m buffer around the marsh, relative proportion of natural land in a 1-km buffer around the marsh; (ratio of open water area to vegetation area) ratio of open water to emergent herbaceous wetlands within the marsh; (marsh surface elevation) elevation referenced to NAVD88 in a representative area of the marsh; (tidal range and groundwater level) percent of time the marsh surface is flooded during deployment of a continuous water-level monitor at a representative marsh location, mean depth of surface flooding as measured by a continuous water-level monitor at a representative location; (salinity) salinity measured in surface water; (vegetation community) vegetation species richness using the point-intercept method in 100-m diameter survey plots, percent cover of various marsh community types within 100-m diameter survey plots; (invasive species abundance) percent cover of invasive plant species measured using the point-intercept method in 100-m diameter survey plots; (nekton community) nekton density, nekton species richness, length of Fundulus heteroclitus ; (breeding bird community) abundance of Willets counted per point during standard call-broadcast surveys, summed abundance of tidal marsh obligate species (Clapper Rail, Willet, Saltmarsh Sparrow, Seaside Sparrow) counted per point during standard call-broadcast surveys. Metrics describing the historical condition, geomorphic setting, and broad landscape features can be assessed using existing GIS databases. Our results support use of rapid methods to assess the majority of field metrics; only those used to describe the nekton community must be measured using intensive methods (throw traps or ditch nets, dependant on habitat configuration). Implementation of these metrics for quantitative assessment of NWRS salt marsh integrity in FWS Region 5 requires developing sampling designs for each refuge. Additionally, it is important to determine how the monitoring information will be used within a management context. SDM should be used to complete the analysis of salt marsh management decisions. The next steps would involve 1) prioritizing and weighting the management objectives; 2) predicting responses to individual management actions in terms of objectives and metrics; 3) using multiattribute utility theory to convert all measurable attributes to a common utility scale; 4) determining the total management benefit of each action by summing utilities across objectives; and 5) maximizing the total management benefits within cost constraints for each refuge. This process would allow the optimum management decisions for NWRS salt marshes to be selected and implemented based directly on monitoring data and current understanding of marsh responses to management actions. Monitoring the outcome of management actions would then allow new monitoring data to be incorporated into subsequent decisions.

Connecticut, Delaware, Maine, Massachusetts, New J↗