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At least 757 records · Page 42Linked to original sources

USGS2021

Socio-technical scales in socio-environmental modeling: Managing a system-of-systems modeling approach

System-of-systems approaches for integrated assessments have become prevalent in recent years. Such approaches integrate a variety of models from different disciplines and modeling paradigms to represent a socio-environmental (or social-ecological) system aiming to holistically inform policy and decision-making processes. Central to the system-of-systems approaches is the representation of systems in a multi-tier framework with nested scales. Current modeling paradigms, however, have disciplinary-specific lineage, leading to inconsistencies in the conceptualization and integration of socio-environmental systems. In this paper, a multidisciplinary team of researchers, from engineering, natural and social sciences, have come together to detail socio-technical practices and challenges that arise in the consideration of scale throughout the socio-environmental modeling process. We identify key paths forward, focused on explicit consideration of scale and uncertainty, strengthening interdisciplinary communication, and improvement of the documentation process. We call for a grand vision (and commensurate funding) for holistic system-of-systems research that engages researchers, stakeholders, and policy makers in a multi-tiered process for the co-creation of knowledge and solutions to major socio-environmental problems.

Environmental Modelling and Software↗

USGS2018

Inferring watershed hydraulics and cold-water habitat persistence using multi-year air and stream temperature signals

Streams strongly influenced by groundwater discharge may serve as “climate refugia” for sensitive species in regions of increasingly marginal thermal conditions. The main goal of this study is to develop paired air and stream water annual temperature signal analysis techniques to elucidate the relative groundwater contribution to stream water and the effective groundwater flowpath depth. Groundwater discharge to streams attenuates surface water temperature signals, and this attenuation can be diagnostic of groundwater gaining systems. Additionally, discharge from shallow groundwater flowpaths can theoretically transfer lagged annual temperature signals from aquifer to stream water. Here we explore this concept using multi-year temperature records from 120 stream sites located across 18 mountain watersheds of Shenandoah National Park, VA, USA and a coastal watershed in Massachusetts, USA. Both areas constitute important cold-water habitat for native brook trout ( Salvelinus fontinalis ). Observed annual temperature signals indicate a dominance of shallow groundwater discharge to streams in the National Park, in contrast to the coastal watershed that has strong, apparently deeper, groundwater influence. The average phase lag from air to stream signals in Shenandoah National Park is 11 d; however, extended lags of approximately 1 month were observed in a subset of streams. In contrast, the coastal stream has pronounced attenuation of annual temperature signals without notable phase lag. To better understand these observed differences in signal characteristics, analytical and numerical models are used to quantify mixing of the annual temperature signals of surface and groundwater. Simulations using a total heat budget numerical model indicate groundwater-induced annual temperature signal phase lags are likely to show greater downstream propagation than the related signal amplitude attenuation. The measurement of multi-seasonal paired air and water temperatures offers great promise toward understanding catchment processes and informing current cold-water habitat management at ecologically-relevant scales.

Virginia↗

USGS2021

Ontogenetic trait shifts: Seedlings display high trait variability during early stages of development

Characterizing variation in plant functional traits is often key to understanding community-level processes and predicting ecosystem responses to environmental change. Trait-based ecology has focused on interspecific trait variation, but sources and consequences of within-species ontogenetic trait variation, particularly during early stages of development, remain understudied. Using a manipulative greenhouse experiment, we investigated trait variation during early stages of seedling development in seven dominant perennial plant species in the western United States. We examined variability in key trait values (i.e. SLA, root:shoot ratio (RSR), specific root length (SRL) and root dry matter content (RDMC)) of 20- to 62-day-old seedlings grown under low and high levels of water availability. We also compared these to compiled trait databases to assess how representative these readily available data sources are of seedling trait values. Early seedling trait values shifted greatly during early stages of development and generally differed from average plant trait database values. Trait shifts were greatest in forbs versus grasses. Overall, observed trait shifts suggested a transition from fast-growing resource acquisitional strategies towards more slow-growing conservative strategies over time. For example, seedling SLA decreased while RSR and RDMC increased over time. That seedling trait values aconsistently differed from trait database values indicates that plant trait database values may be poor predictors of seedling trait values. Such mismatches in species trait information could result in inaccurate predictions of community assembly outcomes or incongruities between seedling traits and environmental filters experienced by seedlings during early stages of recruitment in applied settings. We suggest that additional work is needed to characterize intraspecific trait variation across plant ontogeny, and that this information should be incorporated into studies ranging from understanding early plant growth and survival to evaluating the outcomes of ecological restoration.

Functional Ecology↗

USGS2005

Coastal change rates and patterns: Kaloko-Honokohau National Historical Park, Hawai'i

A collaborative project between the U.S. Geological Survey's Coastal and Marine Geology Program and the National Park Service (NPS) has been developed to create an inventory of geologic resources for National Park Service lands on the Big Island of Hawai'i. The NPS Geologic Resources Inventories are recognized as essential for the effective management, interpretation, and understanding of vital park resources. In general, there are three principal components of the inventories: geologic bibliographies, digital geologic maps, and geologic reports. The geologic reports are specific to each individual park and include information on the geologic features and processes that are important to the management of park resources, including ecological, cultural and recreational resources. This report summarizes a component of the geologic inventory concerned specifically with characterizing the coastal geomorphology of the beach system within Kaloko-Honokohau National Historical Park (NHP) and describes an analysis that utilizes georeferenced and orthorectified aerial photography to understand the spatial and temporal trends in shoreline change from 1950 to 2002. In addition, spatial patterns of beach change were examined and a beach stability map was developed. Both the shoreline change rates and the beach stability map are designed to help Park personnel effectively manage the valuable park resources within the context of understanding natural changes to the KAHO beach system.

Hawaii↗

USGS2023

Genomes & islands & evolution: Oh my!

A central question in evolutionary biology is how lineages quickly diversify to occupy different ecological niches, along with determining genomic factors that facilitate evolutionary change. Isolated, oceanic archipelagos are famous for adaptive radiations characterized by endemic, species-rich clades with substantial ecological variation, yet genome resources key to determining eco-evo processes are generally lacking. Here I present a comparison of the number of genome reference assemblies available (as of May 31, 2023) for three major eukaryotic lineages, briefly describe genome sequencing and benchmarking strategies, and highlight as a case study a genome assembly project for Bidens hawaiensis (Koʻokoʻolau, Asteraceae or Compositae; Coreopsidae), a member of a hexaploid Hawaiian plant adaptive radiation. The total number of plant genome references (1,394) was found to substantially lag the total number of genome references for animal (6,003) and fungi (4,400). Improvements to the quality of de novo assembled genomes are fueled by second- and third-generation long-read sequencing advancements, among other sequencing approaches. In conjunction, strategies to improve genome contiguity include optical maps, Hi-C chromatin capture, or trio binning. Continual improvements to genome sequencing and assembly algorithms have brought within reach telomere-to-telomere genome assemblies, albeit this level of sequencing has to date only been achieved in a few cases. With improvements in sequencing techniques and per-base pair costs that continue to trend downward, the number of high-quality genomes is anticipated to continue to increase, leading to the filling in of taxonomic gaps and sampling of groups of taxa from under sampled geographic areas. Increasing the number of plant genome resources available for the study of island endemism could help to shed light on genome-phenome relationships and genome characteristics that have produced the stunning biological diversity that we now observe across the globe.

Capitulum↗

USGS2001

The robust design for capture-recapture studies: analysis using program MARK

Collecting capture-recapture data under Pollock?s robust design provides an additional source of information on capture probability that can be used to provide less biased and more efficient estimates of population dynamics parameters. In addition, it can be used to estimate the probability of being available for capture, which in some cases (e.g., breeding proportion) has ecological significance. This phenomenon can be modeled as a completely random process, Markovian, or with temporary trap dependence. Analysis of this type of data is one of the options in program MARK. By using MARK the relationship between parameters and covariates can be modeled, and various approaches to goodness of fit, model selection, and model averaging can be implemented.

Book chapter↗

USGS2016

Application of decision science to resilience management in Jamaica Bay

This book highlights the growing interest in management interventions designed to enhance the resilience of the Jamaica Bay socio-ecological system. Effective management, whether the focus is on managing biological processes or human behavior or (most likely) both, requires decision makers to anticipate how the managed system will respond to interventions (i.e., via predictions or projections). In systems characterized by many interacting components and high uncertainty, making probabilistic predictions is often difficult and requires careful thinking not only about system dynamics, but also about how management objectives are specified and the analytic method used to select the preferred action(s). Developing a clear statement of the problem(s) and articulation of management objectives is often best achieved by including input from managers, scientists and other stakeholders affected by the decision through a process of joint problem framing (Marcot and others 2012; Keeney and others 1990). Using a deliberate, coherent and transparent framework for deciding among management alternatives to best meet these objectives then ensures a greater likelihood for successful intervention. Decision science provides the theoretical and practical basis for developing this framework and applying decision analysis methods for making complex decisions under uncertainty and risk.

Book chapter↗

USGS2023

Movement beyond the mean: decoupling sources of individual variation in brook trout movement across seasons

Movement is an important eco-evolutionary process that can shape population and ecosystem structure and function. Accordingly, a firm understanding of species movement ecology is often foundational to effective management and conservation. However, despite movement being an inherently individual-level behavior, there remains a tendency to describe dispersal and migration patterns using simple population-level processes and effects. Overlooking within- and among-individual variation in movement risks incomplete understanding of the intrinsic and extrinsic factors that govern dispersal dynamics and could potentially result in inadequate management of critical behavioral phenotypes. In this study, we monitored movement of over 100 brook trout ( Salvelinus fontinalis ) and quantified the effect of individual-level traits, season, and their interactions to better understand factors that influence vagility. Our results suggest that movement was higher in fall than in summer, particularly for fish in poor condition. But we found no significant main effects for sex, providing no evidence for sex-biased dispersal. To better understand sources of individual variation, we also allowed for sex- and season-specific residual standard deviations. In doing so, we found that, on average, movement was more variable in fall compared to summer, and that females were more variable than males in vagility. Taken together, these results demonstrate how intrinsic, individual-level traits can interact with abiotic environmental conditions to determine movement. They also highlight the potential for simple explanations of movement ecology to overlook important traits that may help predict individual-level behaviors.

Pennsylvania↗

USGS2016

Ecological resilience

Resilience is the capacity of complex systems of people and nature to withstand disturbance without shifting into an alternate regime, or a different type of system organized around different processes and structures (Holling, 1973). Resilience theory was developed to explain the non-linear dynamics of complex adaptive systems, like social-ecological systems (SES) (Walker & Salt, 2006). It is often apparent when the resilience of a SES has been exceeded as the system discernibly changes, such as when a thriving city shifts into a poverty trap, but it is difficult to predict when that shift might occur because of the non-linear dynamics of complex systems. Ecological resilience should not be confused with engineering resilience (Angeler & Allen, 2016), which emphasizes the ability of a SES to perform a specific task consistently and predictably, and to re-establish performance quickly should a disturbance occur. Engineering resilience assumes that complex systems are characterized by a single equilibrium state, and this assumption is not appropriate for complex adaptive systems such as SES. In the risk governance context this means that compounded perturbations derived from hazards or global change can have unexpected and highly uncertain effects on natural resources, humans and societies. These effects can manifest in regime shifts, potentially spurring environmental degradation that might lock SES in an undesirable system state that can be difficult to reverse, and as a consequence economic crises, conflict, human health problems.

Book chapter↗

USGS2007

Estimating species-specific suvival and movement when species identification is uncertain

Incorporating uncertainty in the investigation of ecological studies has been the topic of an increasing body of research. In particular, mark-recapture methodology has shown that incorporating uncertainty in the probability of detecting individuals in populations enables accurate estimation of population-level processes such as survival, reproduction, and dispersal. Recent advances in mark-recapture methodology have included estimating population-level processes for biologically important groups despite the misassignment of individuals to those groups. Examples include estimating rates of apparent survival despite less than perfect accuracy when identifying individuals to gender or breeding state. Here we introduce a method for estimating apparent survival and dispersal in species that co-occur but that are difficult to distinguish. We use data from co-occurring populations of meadow voles (Microtus pennsylvanicus) and montane voles (M. montanus) in addition to simulated data to show that ignoring species uncertainty can lead to biased estimates of population processes. The incorporation of species uncertainty in mark-recapture studies should aid future research investigating ecological concepts such as interspecific competition, niche differentiation, and spatial population dynamics in sibling species.

Ecology↗

USGS2015

Landscape genomics of Sphaeralcea ambigua in the Mojave Desert: a multivariate, spatially-explicit approach to guide ecological restoration

Local adaptation influences plant species’ responses to climate change and their performance in ecological restoration. Fine-scale physiological or phenological adaptations that direct demographic processes may drive intraspecific variability when baseline environmental conditions change. Landscape genomics characterize adaptive differentiation by identifying environmental drivers of adaptive genetic variability and mapping the associated landscape patterns. We applied such an approach to Sphaeralcea ambigua , an important restoration plant in the arid southwestern United States, by analyzing variation at 153 amplified fragment length polymorphism loci in the context of environmental gradients separating 47 Mojave Desert populations. We identified 37 potentially adaptive loci through a combination of genome scan approaches. We then used a generalized dissimilarity model (GDM) to relate variability in potentially adaptive loci with spatial gradients in temperature, precipitation, and topography. We identified non-linear thresholds in loci frequencies driven by summer maximum temperature and water stress, along with continuous variation corresponding to temperature seasonality. Two GDM-based approaches for mapping predicted patterns of local adaptation are compared. Additionally, we assess uncertainty in spatial interpolations through a novel spatial bootstrapping approach. Our study presents robust, accessible methods for deriving spatially-explicit models of adaptive genetic variability in non-model species that will inform climate change modelling and ecological restoration.

California, Nevada↗

USGS2016

Common carp disrupt ecosystem structure and function through middle-out effects

Middle-out effects or a combination of top-down and bottom-up processes create many theoretical and empirical challenges in the realm of trophic ecology. We propose using specific autecology or species trait (i.e. behavioural) information to help explain and understand trophic dynamics that may involve complicated and non-unidirectional trophic interactions. The common carp ( Cyprinus carpio ) served as our model species for whole-lake observational and experimental studies; four trophic levels were measured to assess common carp-mediated middle-out effects across multiple lakes. We hypothesised that common carp could influence aquatic ecosystems through multiple pathways (i.e. abiotic and biotic foraging, early life feeding, nutrient). Both studies revealed most trophic levels were affected by common carp, highlighting strong middle-out effects likely caused by common carp foraging activities and abiotic influence (i.e. sediment resuspension). The loss of water transparency, submersed vegetation and a shift in zooplankton dynamics were the strongest effects. Trophic levels furthest from direct pathway effects were also affected (fish life history traits). The present study demonstrates that common carp can exert substantial effects on ecosystem structure and function. Species capable of middle-out effects can greatly modify communities through a variety of available pathways and are not confined to traditional top-down or bottom-up processes.

Marine and Freshwater Research↗

USGS2026

Advances and applications of Unoccupied Aerial Systems (UAS) research in landscape ecology

Landscape ecologists have long depended on satellite and aerial remote sensing to address questions about landscape pattern and process, structure, and change (Foody 2023 ). Unoccupied aerial systems/vehicles (UAS/UAV, a.k.a. drones) technology is becoming an increasingly popular research tool in environmental sciences allowing scientists to generate low-cost, high-quality, and high-resolution imagery on demand that can be tailored to specific research questions. While satellite data are of a fixed resolution and temporal interval, UAS offer researchers control and flexibility to design studies and collect data at resolutions and scales that provide ecologically relevant information at finer spatial resolutions (e.g., < 30 cm) than what is currently available from satellite platforms (typically > 3m), thus helping capture objects such as individual plant canopies, micro-topography, and individual animals. Unlike satellites with fixed orbits, UAS can be deployed at more optimal temporal frequencies for ecological monitoring. We organized the special collection “Advances and Applications of Unoccupied Aerial Systems (UAS) Research in Landscape Ecology” to showcase the many ways that UAS tools and technologies are currently applied to advance landscape ecological research. When we announced the collection in 2023, only 11 papers published in the journal Landscape Ecology used UAS data, which was a notably small number compared to many other general ecology, environmental science and remote sensing journals. In an attempt to understand why UAS were not more widely used in landscape ecology and provide possible solutions, we published a review article (Villarreal et al. 2025) that identified the challenges, knowledge gaps, and obstacles for the adoption of UAS technologies in landscape ecology research. The main issues we identified include: (1) an abundance of UAS methods papers in the existing literature, with comparatively few studies demonstrating how UAS can be applied to address ecological questions; (2) a perceived scale mismatch between the geographic extent of UAS data collection (local) compared to larger study areas (landscapes) and a need to design robust scaling approaches to connect fine-scale UAS data with broader ecological patterns; and (3) a need for improved integration of UAS data with other commonly used remote sensing datasets including historical high resolution aerial imagery. Additionally, researchers new to UAS remote sensing may be discouraged or overwhelmed by the general lack of scientific consensus and standardized protocols for typical tasks such as data collection, vegetation classification, and change detection, as well as restrictive and/or confusing policy, regulatory, and legal issues surrounding UAS operations (Villarreal et al. 2025).

Landscape Ecology↗

USGS2019

A multi-indicator spatial similarity approach for evaluating ecological restoration scenarios

Context The greater Everglades region in Florida (USA) is an area of wetlands that has been altered and reduced to 50% of its original area and faces multiple threats. Spatial landscape analysis can help guide a large and complex ecosystem restoration process, involving billions of dollars and multiple groups of stakeholders. Objectives To guide Everglades restoration efforts, we evaluated ecological performance of different hydrologic restoration scenarios using a novel technique, the structural similarity index (SSIM), which quantitatively compares similarity between pairs of gridded maps in terms of mean, variance, and covariance. Methods Using the SSIM, we evaluated system-wide performance of apple snails, American alligators, Great egrets, and long- and short-hydroperiod vegetation types under multiple restoration scenarios that varied in water management strategies, amounts of water storage, removal of levees and canals (decompartmentalization), and seepage control barriers. We then compared species and habitat responses under each restoration scenario to a target scenario simulating the historical, natural system. Results The SSIM approach provides a reliable means of scenario comparison, accounting for both the local magnitude and spatial structure of the underlying data. Our results demonstrated that decompartmentalization benefits the indicator species. In general, scenarios with increased water storage were closer to the target scenario. Conclusions This spatial comparison technique is useful for evaluating restoration efforts at multiple spatial scales, ranging from the entire ecosystem down to individual compartments or sub-compartments. The results can be used to inform management and restoration efforts and to guide policy for the greater Everglades area.

Florida↗

USGS2024

Treed Gaussian processes for animal movement modeling

Wildlife telemetry data may be used to answer a diverse range of questions relevant to wildlife ecology and management. One challenge to modeling telemetry data is that animal movement often varies greatly in pattern over time, and current continuous-time modeling approaches to handle such nonstationarity require bespoke and often complex models that may pose barriers to practitioner implementation. We demonstrate a novel application of treed Gaussian process (TGP) modeling, a Bayesian machine learning approach that automatically captures the nonstationarity and abrupt transitions present in animal movement. The machine learning formulation of TGPs enables modeling to be nearly automated, while their Bayesian formulation allows for the derivation of movement descriptors with associated uncertainty measures. We demonstrate the use of an existing R package to implement TGPs using the familiar Markov chain Monte Carlo algorithm. We then use estimated movement trajectories to derive movement descriptors that can be compared across individuals and populations. We applied the TGP model to a case study of lesser prairie-chickens ( Tympanuchus pallidicinctus ) to demonstrate the benefits of TGP modeling and compared distance traveled and residence times across lesser prairie-chicken individuals and populations. For broad usability, we outline all steps necessary for practitioners to specify relevant movement descriptors (e.g., turn angles, speed, contact points) and apply TGP modeling and trajectory comparison to their own telemetry datasets. Combining the predictive power of machine learning and the statistical inference of Bayesian methods to model movement trajectories allows for the estimation of statistically comparable movement descriptors from telemetry studies. Our use of an accessible R package allows practitioners to model trajectories and estimate movement descriptors, facilitating the use of telemetry data to answer applied management questions.

Ecology and Evolution↗

USGS2005

Phytoplankton community ecology: Principles applied in San Francisco Bay

In his seminal 1961 paper 'The paradox of the plankton' Am Nat 95:137-147, G. E. Hutchinson asked why many species of phytoplankton can coexist while competing for a small number of limiting resources in an unstructured habitat. Hutchinson anticipated the resolution of his paradox, recognizing that communities are organized by processes beyond resource competition including species interactions, habitat variability and dispersal. Since 1961 we have made fundamental discoveries that have revolutionized our conceptual understanding of pelagic ecology, including (1) habitat heterogeneity at all scales relevant to plankton population dynamics, (2) community shifts in response to global climate cycles, (3) fast and selective predation as a powerful top-down force to shape phytoplankton communities, (4) turbulent mixing as a physical process that selects species on the basis of their size and form, (5) mixotrophy that allows some algal species to tap organic nutrient pools and function at multiple trophic levels, (6) taxon-specific life cycles including alternating vegetative and resting stages, and (7) the pelagic as an open system where communities are continually reshaped by species immigration. Here we synthesize these discoveries to show how they validate and amplify Hutchinson's hypothesis that phytoplankton communities are assembled by many processes. Our synthesis is built around observations of phytoplankton species composition from a decade of study in San Francisco Bay, used as a case study to illustrate the contemporary principles of phytoplankton community ecology. We apply these principles to address 2 central questions: (1) What processes assemble phytoplankton communities? (2) How does phytoplankton community composition influence ecosystem functions such as production in pelagic and benthic food webs?

California↗

USGS2000

Ground-water microbiology and geochemistry

Up-to-date coverage and a unique, multidisciplinary approach The ongoing effort to protect our valuable ground-water resources necessarily involves scientists and engineers from many disciplines. Ground-Water Microbiology and Geochemistry, Second Edition is designed to bridge the historical lack of communication among these disciplines by detailing-in language that cuts across specialties-the impact of microorganisms and microbial processes on ground-water systems. Carefully revised to reflect the many recent discoveries that have been made in the field, the Second Edition begins with an overview of microbiology, ideal for hydrologists and others who may lack formal training in the field. These initial chapters systematically cover the kinds of microorganisms found in subsurface environments, focusing on their growth, metabolism, genetics, and ecology. The second part of the book offers a hydrologic perspective on how microbial processes affect ground-water geochemistry in pristine systems. It also introduces the different classes of ground-water systems, and gives an overview of techniques for sampling subsurface environments. Readers gain an understanding of biogeochemical cycling in ground-water systems-in coverage unique to this book-and how ground-water chemistry can be used to study microbial processes in aquifer systems. The final section of the book deals with the biodegradation of human-introduced contaminants in ground-water systems, with an up-to-date review of the physiology, biochemistry, and redox conditions that favor biodegradation processes. Ground-Water Microbiology and Geochemistry, Second Edition is important reading for geoscientists, hydrologists, and environmental engineers, as well as for water planners and lawyers involved in environmental issues. It also serves as a compelling text for upper-level undergraduate and graduate courses in ground-water chemistry.

Book↗

USGS2025

A partner-driven decision support model to inform the reintroduction of bull trout

Assessments of species reintroductions involve a series of complex decisions that include human perspectives and ecological contexts. Here, we present a reintroduction assessment involving bull trout ( Salvelinus confluentus ) using a structured decision-making process. We approached this assessment by engaging partners representing public utilities, government agencies, and Tribes with shared interests in a potential reintroduction. These individuals identified objectives, decision alternatives, and ecological scenarios that were incorporated into a co-produced simulation-based model of potential reintroduction outcomes. The model included mathematical representations of habitat availability, life history expression, and assumptions regarding constraints on potential bull trout populations. Within each recipient stream, partners chose to explore a wide range of decision alternatives and simulated scenarios affecting reintroduction success. Results suggested that 1) reintroductions using eggs or adults were most optimal, 2) adding more individuals resulted in diminishing returns, 3) access to migratory habitat could improve success, and 4) the diversity of opportunities for life history expression led to improved reintroduction opportunities. In addition, modeled scenarios indicated some recipient streams consistently produced lower abundance of reintroduced bull trout. This work contributes a novel example to a growing portfolio of reintroduction assessments that may inform future conservation for bull trout and many other species facing similar challenges.

Washington↗