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At least 19 recordsLinked to original sources

Mapping ecological states in the upper Colorado River basin: Implications for fire management

Spatially explicit information on ecosystem dynamics that offers a mechanistic understanding of ecological processes can benefit environmental management. Broad-scale maps based on state-and-transition models provide valuable insight into transitions among ecological states resulting from specific drivers within areas sharing similar climatic and edaphic characteristics ecological sites (ES). We aimed to quantify ecological dynamics of two ES groups in the Upper Colorado River Basin from 1986 to 2022 through annual maps of ecological states and assess potential drivers of observed state change. This region comprises important sagebrush shrublands and pinyon-juniper woodlands affected by non-native annual grass invasion, wildfires, and drought-induced tree mortality. Using field-based and remote sensing data, we modeled vegetation states using random forest models and mapped the states annually from 1986 to 2022. To demonstrate the utility of the state maps for monitoring and management, we used this time series of maps to investigate the influences of fire and drought on state occurrence. Our findings revealed a statistically significant increase in states invaded by non-native annual species (Invaded state), which replaced Grassland and Shrubland states, while Shrubland states decreased significantly, transitioning to invaded and Woodland states. Invaded states had the highest likelihood of burning, followed by Woodlands. Drought was associated with increased area of Grassland and Bare states, but with decreased area of invaded and Shrubland states. These results indicate an accelerating fire cycle is potentially leading to ongoing regional environmental degradation. Despite increasing drought conditions during the study period, the invaded states continued to increase in area, indicating additional underlying mechanisms. Our reproducible, broad-scale, ecologically-driven state mapping process enhances understanding of how drought, fire, and invasion by non-native plants can transform semiarid landscapes of the western USA.

Arizona, Colorado, New Mexico, Utah, Wyoming

Sentinel imagery detects the presence of live trees following large wildfires in California

Identifying live tree presence following wildfire is important for burn damage assessments and decision making, as these trees serve as seed sources for recovery. Satellite-based remote sensing offers an efficient means to assess burn severity with products representing vegetation greenness and char/ash presence and their change from pre- to post-fire imagery. While effective at assessing burn severity (e.g. ecosystem change), there remain limitations in identifying fire refugia (surviving trees), due to the difficulty of teasing apart different green vegetation types (e.g. trees, shrubs, grasses). In this paper, we use 10 m Sentinel-2 satellite data to predict live tree presence across three sites impacted by the 2021 California fire season. We used vegetation indices (VIs) from post-fire imagery (normalized difference vegetation index [NDVI], normalized burn ratio [NBR], normalized difference water index [NDWI], visible atmospherically resistant index [VARI], and burn area index [BAI]), differential VIs from pre- and post-fire imagery (dNDVI, dNBR, RdNBR, dNDWI, dVARI), and direct reflectance bands (all bands model; visible, near-infrared, and shortwave infrared; B1–B12) to predict live tree presence via random forest modeling. To calibrate and validate the random forest models, we photointerpreted ∼2300 pixels per fire region using 2022 National Agriculture Imagery Program imagery. We performed additional field-based validation using tree presence/absence data two years post-fire ( n = 296 observations across two sites). At the site level, the all bands model outperformed the vegetation index-based models (80%–85% vs 65%–79% accuracy). Errors were mainly false positives attributed to pixels with green understory vegetation but no live trees. In cross-site inference, which involved pooling two sites for model calibration to test on the third site, the all bands model retained good performance (76%–81% accuracy). Evaluation against field survey data demonstrated a larger range of performance (50%–87% accuracy) that highlights limitations based on tree isolation and crown percent greenness. Relative to differential-based VIs, our results highlight potential advantages of using post-fire Sentinel-2 imagery and random forest modeling for identifying live tree presence and scaling to full fire extents.

California

Initial condition uncertainty exerts a large and persistent influence on model simulations of ecosystem carbon dynamics in California

Uncertainties in terrestrial ecosystem models limit their predictive power. Efforts to reduce projection error have rarely focused on constraining uncertainty in the initial state of the ecosystem, however, despite evidence that matching model initial conditions to real-world observations reduces overall model bias. Here we use an integrated land change and carbon gain-loss model to evaluate the influence of initial condition uncertainty on simulations of California wildland ecosystems during the years 1985–2020. We generated 36 initial conditions scenarios by varying the source data used to initialize state variables and then ran simulations based on each of these scenarios under a constant set of historical conditions. We found that discrepancies in initial forest extent and initial forest age among scenarios generated wide uncertainty ranges in model estimates of terrestrial ecosystem carbon stocks and flux rates at the outset of the simulation period, but differences in initial forest composition had no impact. Over time, forest age became more homogeneous across model scenarios leading to exponential rates of decline in the uncertainty ranges of live biomass and dead wood carbon but little to no impact on uncertainties in litter and soil organic carbon. Uncertainties in individual carbon flux rates were consistent with uncertainties in their source pools. In contrast, model estimates of ecosystem carbon balance demonstrated a shift in system behavior not apparent in trends for individual carbon stocks and fluxes. Specifically, estimates of ecosystem carbon balance converged across scenarios for the first 20 years of the simulation period but then began to diverge at an accelerating rate, possibly due to weakened resilience to the increased frequency and severity of climate-driven disturbances. Our results demonstrate that uncertainty in the initial state of the system can have large and persistent impacts on the predictability of ecosystem carbon dynamics, and that ongoing shifts in external forcing by climate and climate-driven disturbances can exacerbate these impacts.

California

Linking environmental variability to population and community dynamics

Linking population and community responses to environmental variability lies at the heart of ecology, yet methodological approaches vary and existence of broad patterns spanning taxonomic groups remains unclear. We review the characteristics of environmental and biological variability. Classic approaches to link environmental variability to population and community variability are discussed as are the importance of biotic factors such as life history and community interactions. In addition to classic approaches, newer techniques such as information theory and artificial neural networks are reviewed. The establishment and expansion of observing networks will provide new long-term ecological time-series data, and with it, opportunities to incorporate environmental variability into research. This review can help guide future research in the field of ecological and environmental variability.

Book chapter

Biosafety practices when working with bats: A guide to field research considerations

Introduction: Field work with bats is an important contribution to many areas of research in environmental biology and ecology, as well as microbiology. Work with bats poses hazards such as bites and scratches, and the potential for exposure to infectious pathogens such as rabies virus. It also exposes researchers to many other potential hazards inherent to field work, such as environmental conditions, delayed emergency responses, or challenging work conditions. Methods: This article discusses the considerations for a thorough risk assessment process around field work with bats, pre- and post-occupational health considerations, and delves into specific considerations for areas related to biosafety concerns—training, personal protective equipment, safety consideration in field methods, decontamination, and waste. It also touches on related legal and ethical issues that sit outside the realm of biosafety, but which must be addressed during the planning process. Discussion: Although the focal point of this article is bat field work located in northern and central America, the principles and practices discussed here are applicable to bat work elsewhere, as well as to field work with other animal species, and should promote careful considerations of how to safely conduct field work to protect both researchers and animals.

Applied Biosafety

Bayesian applications in environmental and ecological studies with R and Stan

Modern ecological and environmental sciences are dominated by observational data. As a result, traditional statistical training often leaves scientists ill-prepared for the data analysis tasks they encounter in their work. Bayesian methods provide a more robust and flexible tool for data analysis, as they enable information from different sources to be brought into the modelling process. Bayesian Applications in Evnironmental and Ecological Studies with R and Stan provides a Bayesian framework for model formulation, parameter estimation, and model evaluation in the context of analyzing environmental and ecological data. Features: An accessible overview of Bayesian methods in environmental and ecological studies Emphasizes the hypothetical deductive process, particularly model formulation Necessary background material on Bayesian inference and Monte Carlo simulation Detailed case studies, covering water quality monitoring and assessment, ecosystem response to urbanization, fisheries ecology, and more Advanced chapter on Bayesian applications, including Bayesian networks and a change point model Complete code for all examples, along with the data used in the book, are available via GitHub The book is primarily aimed at graduate students and researchers in the environmental and ecological sciences, as well as environmental management professionals. This is a group of people representing diverse subject matter fields, who could benefit from the potential power and flexibility of Bayesian methods.

Book

Hepatic pathologies in the brackish water catfish (Chrysichthys nigrodigitatus) from contaminated locations of the Lagos lagoon complex

Several toxicological studies into the effects of aquatic pollutants on the liver of teleost fish exist in literature. The focus on the liver in these studies is predicated on its central nature in the scheme of biotransformation and excretion of xenobiotics following exposure in polluted water bodies. As a consequence of the latter primary role of the liver in these processes it is regarded as a predilective site for the sub lethal effects of xenobiotics on the organism usually detectable at histological level. Hepatic histopathology recorded in livers from feral populations of the brackish water catfish Chrysichthys nigrodigitatus from locations on the Lagos lagoon complex with significant anthropogenic inputs from denizen populations and industries are presented. Liver sections from sixty specimens from two locations on the Lagos lagoon complex (Badagry lagoon: 6°24'N, 2°56'E; and Lagos lagoon: 6°29'N, 3°22'E) were analysed. Observed pathologies included hydropic degeneration (58%), portal / sinusoidal congestion (33%), hepatic necrosis (26%), hemosiderosis (12%) and foci of cellular alterations (FCA's). No obvious oncologic features were observed; the presence of the hydropic Vacuolation lesion was taken as prelude to the development of neoplasms and discussed as such.

Badagry Lagoon, Lagos Lagoon

Improving ecological data science with workflow management software

Pressing environmental research questions demand the integration of increasingly diverse and large-scale ecological datasets as well as complex analytical methods, which require specialized tools and resources. Computational training for ecological and evolutionary sciences has become more abundant and accessible over the past decade, but tool development has outpaced the availability of specialized training. Most training for scripted analyses focuses on individual analysis steps in one script rather than creating a scripted pipeline, where modular functions comprise an ecosystem of interdependent steps. Although current computational training creates an excellent starting place, linear styles of scripting can risk becoming labor- and time-intensive and less reproducible by often requiring manual execution. Pipelines, however, can be easily automated or tracked by software to increase efficiency and reduce potential errors. Ecology and evolution would benefit from techniques that reduce these risks by managing analytical pipelines in a modular, readily parallelizable format with clear documentation of dependencies. Workflow management software (WMS) can aid in the reproducibility, intelligibility and computational efficiency of complex pipelines. To date, WMS adoption in ecology and evolutionary research has been slow. We discuss the benefits and challenges of implementing WMS and illustrate its use through a case study with the targets r package to further highlight WMS benefits through workflow automation, dependency tracking and improved clarity for reviewers. Although WMS requires familiarity with function-oriented programming and careful planning for more advanced applications and pipeline sharing, investment in training will enable access to the benefits of WMS and impart transferable computing skills that can facilitate ecological and evolutionary data science at large scales.

Methods in Ecology and Evolution

Ground level environmental protein concentrations in various ecuadorian environments: potential uses of aerosolized protein for ecological research

Large quantities of free protein in the environment and other bioaerosols are ubiquitous throughout terrestrial ground level environments and may be integrative indicators of ecosystem status. Samples of ground level bioaerosols were collected from various ecosystems throughout Ecuador, including pristine humid tropical forest (pristine), highly altered secondary humid tropical forest (highly altered), secondary transitional very humid forest (regrowth transitional), and suburban dry montane deforested (suburban deforested). The results explored the sensitivity of localized aerosol protein concentrations to spatial and temporal variations within ecosystems, and their value for assessing environmental change. Ecosystem specific variations in environmental protein concentrations were observed: pristine 0.32 ± 0.09 μg/m3, highly altered 0.07 ± 0.05 μg/m 3 , regrowth transitional 0.17 ± 0.06 μg/m 3 , and suburban deforested 0.09 ± 0.04 μg/m 3 . Additionally, comparisons of intra-environmental differences in seasonal/daily weather (dry season 0.08 ± 0.03 μg/m 3 and wet season 0.10 ± 0.04 μg/m 3 ), environmental fragmentation (buffered 0.19 ± 0.06 μg/m 3 and edge 0.15 ± 0.06 μg/m 3 ), and sampling height (ground level 0.32 ± 0.09 μg/m 3 and 10 m 0.24 ± 0.04 μg/m 3 ) demonstrated the sensitivity of protein concentrations to environmental conditions. Local protein concentrations in altered environments correlated well with satellite-based spectral indices describing vegetation productivity: normalized difference vegetation index (NDVI) (r 2 = 0.801), net primary production (NPP) (r 2 = 0.827), leaf area index (LAI) (r 2 = 0.410). Moreover, protein concentrations distinguished the pristine site, which was not differentiated in spectral indices, potentially due to spectral saturation typical of highly vegetated environments. Bioaerosol concentrations represent an inexpensive method to increase understanding of environmental changes, especially in densely vegetated ecosystems with high canopies or in areas needing high spatial and temporal resolution. Further research to expand understanding of the applicability of bioaerosol concentrations for environmental monitoring is supported by this pilot study.

Ecological Indicators

Progress and challenges in coupled hydrodynamic-ecological estuarine modeling

Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational power, and incorporation of uncertainty. Coupled hydrodynamic-ecological models have been used to assess ecosystem processes and interactions, simulate future scenarios, and evaluate remedial actions in response to eutrophication, habitat loss, and freshwater diversion. The need to couple hydrodynamic and ecological models to address research and management questions is clear because dynamic feedbacks between biotic and physical processes are critical interactions within ecosystems. In this review, we present historical and modern perspectives on estuarine hydrodynamic and ecological modeling, consider model limitations, and address aspects of model linkage, skill assessment, and complexity. We discuss the balance between spatial and temporal resolution and present examples using different spatiotemporal scales. Finally, we recommend future lines of inquiry, approaches to balance complexity and uncertainty, and model transparency and utility. It is idealistic to think we can pursue a “theory of everything” for estuarine models, but recent advances suggest that models for both scientific investigations and management applications will continue to improve in terms of realism, precision, and accuracy.

Estuaries and Coasts

Used-habitat calibration plots: A new procedure for validating species distribution, resource selection, and step-selection models

“Species distribution modeling” was recently ranked as one of the top five “research fronts” in ecology and the environmental sciences by ISI's Essential Science Indicators (Renner and Warton 2013), reflecting the importance of predicting how species distributions will respond to anthropogenic change. Unfortunately, species distribution models (SDMs) often perform poorly when applied to novel environments. Compounding on this problem is the shortage of methods for evaluating SDMs (hence, we may be getting our predictions wrong and not even know it). Traditional methods for validating SDMs quantify a model's ability to classify locations as used or unused. Instead, we propose to focus on how well SDMs can predict the characteristics of used locations. This subtle shift in viewpoint leads to a more natural and informative evaluation and validation of models across the entire spectrum of SDMs. Through a series of examples, we show how simple graphical methods can help with three fundamental challenges of habitat modeling: identifying missing covariates, non-linearity, and multicollinearity. Identifying habitat characteristics that are not well-predicted by the model can provide insights into variables affecting the distribution of species, suggest appropriate model modifications, and ultimately improve the reliability and generality of conservation and management recommendations.

Ecography

Great Lakes lake trout thiamine monitoring program annual report

The U.S. Geological Survey’s Great Lakes Science Center (GLSC), Eastern Ecological Science Center, and Columbia Environmental Research Center (CERC), and the State University of New York (SUNY) Brockport have conducted in collaboration with partner agencies a cooperative program to monitor thiamine concentrations in lake trout eggs since the late 1990s. In 2021, egg thiamine concentrations were highly variable at each sampling site. No eggs samples with thiamine concentrations less than the 4 nmol/g threshold recommended for successful lake trout reproduction were collected in Lakes Superior, Huron, Erie, and Champlain. In contrast, every site in Lakes Michigan and Ontario and Cayuga Lake had some lake trout eggs below 4 nmol/g. Time series of mean lake trout egg thiamine concentrations showed high temporal and spatial variability within the Great Lakes region.

Great Lakes

Great Lakes lake trout (Salvelinus namaycush) thiamine monitoring program annual report

Thiamine deficiency in lake trout eggs has been identified to induce early life-stage mortality in the Great Lakes in the 1960s through the 1990s and potentially affecting lake trout recruitment. As a results, the U.S. Geological Survey’s Great Lakes Science Center (GLSC), Eastern Ecological Science Center, and Columbia Environmental Research Center (CERC), and the State University of New York (SUNY) Brockport, in collaboration with partner agencies, have conducted a cooperative program to monitor thiamine concentrations in lake trout Salvelinus namaycush eggs since the late 1990s. In 2023, egg thiamine concentrations were highly variable at each sampling site. No egg samples with thiamine concentrations less than the 4 nmol/g threshold recommended for successful lake trout reproduction were collected in Lakes Superior or Huron. In contrast, 3 to 52% of the lake trout collected at sites in Lakes Michigan, Huron, Ontario and Champlain, and Cayuga Lake had eggs below 4 nmol/g. Time series of mean lake trout egg thiamine concentrations showed high temporal and spatial variability within the Great Lakes region.

Cayuga Lake, Lake Champlain, Lake Erie, Lake Huron

Identifying management-relevant research priorities for responding to disease-associated amphibian declines

A research priority can be defined as a knowledge gap that, if resolved, identifies the optimal course of conservation action. We (a group of geographically distributed and multidisciplinary research scientists) used tools from nominal group theory and decision analysis to collaboratively identify and prioritize information needs within the context of disease-associated amphibian decline , in order to develop a strategy that would support US management agency needs. We developed iterated influence diagrams to create and assess a unified research strategy. We illustrated a transparent process for identifying specific knowledge gaps in amphibian disease ecology relevant to environmental management, and then constructed a research plan to address these uncertainties. The resulting priorities include a need to: (1) understand the drivers of the community-disease relationship, (2) determine the mechanisms by which exposure to contaminants influence disease outcomes, (3) identify elements of terrestrial and aquatic habitats that stabilize host-pathogen dynamics, (4) discuss how metapopulations may be managed to reduce the speed and intensity of disease outbreaks, and (5) define the relationship between habitat management and the environmental and host microbiomes. Along with identifying research priorities for disease management, we present the details of the process used to develop a consensus plan for addressing disease-related declines in amphibians on federally managed lands of the United States.

Global Ecology and Conservation

Early avian research at the Savannah River Site, South Carolina: historical highlights and possibilities for the future

Avian biology and collection of baseline population data was a major part of the first decade (1951-1961) of field research at the Savannah River Site (SRS). Baseline inventories involving organisms and land-use types were part of the mission in the early contracts between the Atomic Energy Commission (now the Department of Energy) and the University of Georgia prior to the establishment of the Savannah River Ecology Laboratory (SREL) as a National Environmental Research Park Laboratory. About 27% of the SREL publications during this first decade dealt with birds. Since that time, research on the SRS landscape has expanded and broadened with less than 10% of the publications dealing with birds. SRS changed also from an agriculturally dominated area with ca. 40% open areas (fields, crops, pastures) to a timber-managed area with ca. 80% forests, 12% open areas, and 2% open water impoundments. Baseline breeding bird populations of the SRS in the 1950s were typical for the region with avian species richness and density increasing with the age and succession of the vegetation (0-26 species and densities of 0-741 pairs/km2 for the habitats surveyed). During the first decade at the SRS, the resident game bird population of Northern Bobwhites (Colinus virginianus) increased and the Mourning Dove (Zenaida rnacroura) population, a migratory upland game bird, remained stable. Current avian research efforts, as well as new opportunities to reexamine the breeding bird populations and the landscape of SRS, will provide a better understanding of the potential causes of declines of neotropical migratory birds, declines of resident and migratory game birds, and how habitat influences invasions and extinctions of breeding birds in the region. Emphasis for future research and monitoring should be on neotropical migratory bird populations in decline (Yellow-billed Cuckoo, Coccyzus americanus; Eastern Wood-Pewee, Contopus virens; Wood Thrush, Hylocichla mustelina; Prairie Warbler, Dendroica discolor; and Painted Bunting, Passerina ciris), resident species in decline (e.g., Loggerhead Shrike, Lanius ludovicianus), certain species groups (e.g., waterfowl and wading birds), important habitat, and recent invasions and extinctions of breeding species. Old growth forested wetlands should be monitored because of the large number of neotropical migratory birds that depend on this habitat in the southeastern United States. A variety of survey techniques will be needed to determine population trends: line transects, call or song playbacks, roadside point surveys (call counts for game birds), aerial surveys, and presence or absence of species within stratified areas of SRS. The SRS provides opportunity for avian research at the landscape level with the potential to solve problems important to the survival of many bird populations as well as to increase our knowledge on how to manage and conserve our avian natural resources for the future.

Book chapter

Global assessment of aquatic Isoëtes species ecology

Isoëtes are iconic but understudied wetland plants, despite having suffered severe losses globally mainly because of alterations in their habitats. We therefore provide the first global ecological assessment of aquatic Isoëtes to identify their environmental requirements and to evaluate if taxonomically related species differ in their ecology. The assessment resulted in an extensive new database on aquatic Isoëtes , ecological niche analyses, and descriptive species accounts. We compiled a global database that includes all known environmental data collected from 1935 to 2023 regarding aquatic Isoëtes. We then evaluated the environmental drivers of 16 species using 2,179 global records. Additionally, we used hypervolume analysis to quantify the ecological niches of the two species with the greatest number of records, finding significant differences and evidence that Isoëtes echinospora occupies a wider ecological niche than Isoëtes lacustris . Fifty-nine species (30% of the c. 200 Isoëtes species known today) were categorised as aquatic and were mainly reported in the Americas and northern Europe. About 38% of the aquatic species are threatened with extinction or are endemic to a small region, according to the International Union for Conservation of Nature's Red List in 2023. Many species were determined to be sensitive to certain water physical and chemical factors, generally preferring oligotrophic conditions such as low total phosphorus, moderate total nitrogen, moderate to low pH, and low conductivity. This analysis includes ecological data in the assessment of rare/threatened aquatic plants globally. This new database and the ecological analyses completed defined the ecological requirements of several species and identified knowledge gaps, which can aid management actions and future research. This paper highlights ecological significance and environmental sensitivities of aquatic Isoëtes . The current level of knowledge is inadequate for a large proportion of known taxa. We affirm the extreme need to support global, collaborative initiatives on which to build future conservation strategies.

Freshwater Biology

Planning long-term vegetation studies at landscape scales

Long-term ecological research is receiving more attention now than ever before. Two recent books, Long-term Studies in Ecology: Approaches and Alternatives , edited by Gene Likens (1989), and Long-term Ecological Research: An International Perspective , edited by Paul Risser (1991), prompt the question, “Why are these books so thin?” Except for data from paleoecological, retrospective studies (see below), there are exceptionally few long-term data sets in terrestrial ecology (Strayer et al. 1986; Tilman 1989; this volume). In a sample of 749 papers published in Ecology , Tilman (1989) found that only 1.7% of the studies lasted at least five field seasons. Only one chapter in each of the review books dealt specifically with expanding both the temporal and the spatial scales of ecological research (Berkowitz et al. 1989; Magnuson et al. 1991). Judging by the growing number of landscape-scale long-term studies, however, such as the Long-Term Ecological Research (LTER) Program (Callahan 1991), the U.S. Environmental Protection Agency’s Environmental Monitoring and Assessment Program (EMAP; Palmer et al. 1991), the U.S. Army’s Land Condition-Trend Analysis (LCTA) Program (Diersing et al. 1992), and various agencies’ global change research programs (CEES 1993), there is a growing interest to expand ecological research both temporally and spatially.

Book chapter

Sustaining visitor use in protected areas: Future opportunities in recreation ecology research based on the USA experience

Recreation ecology, the study of environmental consequences of outdoor recreation activities and their effective management, is a relatively new field of scientific study having emerged over the last 50 years. During this time, numerous studies have improved our understanding of how use-related, environmental and managerial factors affect ecological conditions and processes. Most studies have focused on vegetation and soil responses to recreation-related trampling on trails and recreation sites using indicators such as percent vegetation cover and exposed mineral soil. This applied approach has and will continue to yield important information for land managers. However, for the field to advance, more attention needs to be given to other ecosystem attributes and to the larger aspects of environmental conservation occurring at landscape scales. This article is an effort at initiating a dialog on needed advances in the field. We begin by reviewing broadly generalizable knowledge of recreation ecology, to separate what is known from research gaps. Then, based on the authors’ perspective of research in the USA and North America, several research directions are suggested as essential for continued progress in this field including theoretical development, broadening scale, integration with other disciplines, and examination of synergistic effects.

Environmental Management