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Landscape change in the Southern Piedmont: Challenges, solutions and uncertainty across scales

The southern Piedmont of the southeastern United States epitomizes the complex and seemingly intractable problems and hard decisions that result from uncontrolled urban and suburban sprawl. Here we consider three recurrent themes in complicated problems involving complex systems: (1) scale dependencies and cross-scale, often nonlinear relationships; (2) resilience, in particular the potential for complex systems to move to alternate stable states with decreased ecological and/or economic value; and (3) uncertainty in the ability to understand and predict outcomes, perhaps particularly those that occur as a result of human impacts. We consider these issues in the context of landscape-level decision making, using as an example water resources and lotic systems in the Piedmont region of the southeastern United States. Copyright ?? 2003 by the author(s). Published here under licence by The Resilience Alliance.

Ecology and Society

Bayesian models: A statistical primer for ecologists

Bayesian modeling has become an indispensable tool for ecological research because it is uniquely suited to deal with complexity in a statistically coherent way. This textbook provides a comprehensive and accessible introduction to the latest Bayesian methods—in language ecologists can understand. Unlike other books on the subject, this one emphasizes the principles behind the computations, giving ecologists a big-picture understanding of how to implement this powerful statistical approach. Bayesian Models is an essential primer for non-statisticians. It begins with a definition of probability and develops a step-by-step sequence of connected ideas, including basic distribution theory, network diagrams, hierarchical models, Markov chain Monte Carlo, and inference from single and multiple models. This unique book places less emphasis on computer coding, favoring instead a concise presentation of the mathematical statistics needed to understand how and why Bayesian analysis works. It also explains how to write out properly formulated hierarchical Bayesian models and use them in computing, research papers, and proposals. This primer enables ecologists to understand the statistical principles behind Bayesian modeling and apply them to research, teaching, policy, and management. Presents the mathematical and statistical foundations of Bayesian modeling in language accessible to non-statisticians Covers basic distribution theory, network diagrams, hierarchical models, Markov chain Monte Carlo, and more Deemphasizes computer coding in favor of basic principles Explains how to write out properly factored statistical expressions representing Bayesian models

Book

Fish out of water: Insights from a case study of a highly social animal that failed the mirror self-recognition test

Mirror self-recognition (MSR) tests have been conducted with a variety of species with the aim of examining whether subject animals have the capacity for self-awareness. To date, the majority of animals that have convincingly passed are highly social mammals whose wild counterparts live in complex societies, though there is much debate concerning what constitutes passing and what passing means in terms of self-awareness. Amid recent reports that a fish (cleaner wrasse, Labroides dimidiatus ) passed, it is intriguing that a mammal as highly social, tolerant, attentive, and cooperative as the grey wolf ( Canis lupus ) reportedly failed the test. Given the many possible reasons for failure, we aimed to elucidate the wolves’ responses at various stages of the MSR test to pinpoint potential problem areas where species-appropriate modifications to the test may be needed. Thus, we evaluated 6 socialized, captive grey wolves as a case study of failed MSR in socially complex canids. At a minimum, wolves did not respond to their reflection as an unfamiliar conspecific. Unfortunately, the wolves rapidly lost interest in the mirror and were uninterested in the applied marks. We note limitations of the MSR test for this species, recommend changes for future MSR tests of wolves, discuss other emerging self-cognizance methods for socially complex canids, and highlight the need for a suite of ecologically relevant, potentially scalable self-cognizance methods. Our findings and recommendations may aid in understanding self-cognizance in other untested highly social, cooperatively-hunting, coursing, terrestrial carnivores such as African wild dogs ( Lycaon pictus ), spotted hyenas ( Crocuta crocuta ), and African lions ( Panthera leo ).

International Journal of Comparative Psychology

Assessing contaminants of emerging concern in the Great Lakes Ecosystem: A decade of method development and practical application

Assessing the ecological risk of contaminants in the field typically involves consideration of a complex mixture of compounds which may or may not be detected via instrumental analyses. Further, there are insufficient data to predict the potential biological effects of many detected compounds, leading to their being characterized as contaminants of emerging concern (CECs). Over the past several years, advances in chemistry, toxicology, and bioinformatics have resulted in a variety of concepts and tools that can enhance the pragmatic assessment of the ecological risk of CECs. The present Focus article describes a 10+- year multiagency effort supported through the U.S. Great Lakes Restoration Initiative to assess the occurrence and implications of CECs in the North American Great Lakes. State-of-the-science methods and models were used to evaluate more than 700 sites in about approximately 200 tributaries across lakes Ontario, Erie, Huron, Michigan, and Superior, sometimes on multiple occasions. Studies featured measurement of up to 500 different target analytes in different environmental matrices, coupled with evaluation of biological effects in resident species, animals from in situ and laboratory exposures, and in vitro systems. Experimental taxa included birds, fish, and a variety of invertebrates, and measured endpoints ranged from molecular to apical responses. Data were integrated and evaluated using a diversity of curated knowledgebases and models with the goal of producing actionable insights for risk assessors and managers charged with evaluating and mitigating the effects of CECs in the Great Lakes. This overview is based on research and data captured in approximately about 90 peer-reviewed journal articles and reports, including approximately about 30 appearing in a virtual issue comprised of highlighted papers published in Environmental Toxicology and Chemistry or Integrated Environmental Assessment and Management . Environ Toxicol Chem 2023;42:2506–2518. © 2023 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Environmental Toxicology and Chemistry

Functional variability of habitats within the Sacramento-San Joaquin Delta: Restoration implications

We have now entered an era of large-scale attempts to restore ecological functions and biological communities in impaired ecosystems. Our knowledge base of complex ecosystems and interrelated functions is limited, so the outcomes of specific restoration actions are highly uncertain. One approach for exploring that uncertainty and anticipating the range of possible restoration outcomes is comparative study of existing habitats similar to future habitats slated for construction. Here we compare two examples of one habitat type targeted for restoration in the Sacramento-San Joaquin River Delta. We compare one critical ecological function provided by these shallow tidal habitats - production and distribution of phytoplankton biomass as the food supply to pelagic consumers. We measured spatial and short-term temporal variability of phytoplankton biomass and growth rate and quantified the hydrodynamic and biological processes governing that variability. Results show that the production and distribution of phytoplankton biomass can be highly variable within and between nearby habitats of the same type, due to variations in phytoplankton sources, sinks, and transport. Therefore, superficially similar, geographically proximate habitats can function very differently, and that functional variability introduces large uncertainties into the restoration process. Comparative study of existing habitats is one way ecosystem science can elucidate and potentially minimize restoration uncertainties, by identifying processes shaping habitat functionality, including those that can be controlled in the restoration design.

California

Glacial vicariance and secondary contact shape demographic histories in a freshwater mussel species complex

Characterizing the mechanisms influencing the distribution of genetic variation in aquatic species can be difficult due to the dynamic nature of hydrological landscapes. In North America’s Central Highlands, a complex history of glacial dynamics, long-term isolation, and secondary contact have shaped genetic variation in aquatic species. Although the effects of glacial history have been demonstrated in many taxa, responses are often lineage- or species-specific and driven by organismal ecology. In this study, we reconstruct the evolutionary history of a freshwater mussel species complex using a suite of mitochondrial and nuclear loci to resolve taxonomic and demographic uncertainties. Our findings do not support Pleurobema rubrum as a valid species, which is proposed for listing as threatened under the U.S. Endangered Species Act. We synonymize P. rubrum under Pleurobema sintoxia —a common and widespread species found throughout the Mississippi River Basin. Further investigation of patterns of genetic variation in P. sintoxia identified a complex demographic history, including ancestral vicariance and secondary contact, within the Eastern Highlands. We hypothesize these patterns were shaped by ancestral vicariance driven by the formation of Lake Green and subsequent secondary contact after the last glacial maximum. Our inference aligns with demographic histories observed in other aquatic taxa in the region and mirrors patterns of genetic variation of a freshwater fish species ( Erimystax dissimilis ) confirmed to serve as a parasitic larval host for P. sintoxia . Our findings directly link species ecology to observed patterns of genetic variation and may have significant implications for future conservation and recovery actions of freshwater mussels.

Mississippi River basin

Spatial and temporal patterns in Arctic mosquito abundance

Organisms that undergo a shift in ontogeny and habitat type often change their spatial distribution throughout their life cycle, but how this affects population dynamics remains poorly understood. We examined spatial and temporal patterns in Aedes nigripes abundance, a widespread univoltine Arctic mosquito species (Diptera: Culicidae), hypothesizing that the spatial distribution of adults would be closely tied to aquatic habitat. We tracked adult densities of A. nigripes near Kangerlussuaq, Greenland using emergence traps, CO 2 -baited traps, and sweep-nets. In back-to-back years of sampling (2017 and 2018) we found two-fold variation in overall abundance. Adults were spatially patchy when first emerging from aquatic habitats but within a week, mean capture rates for host-seeking adult females were similar across locations, even in places far from larval habitat. Daily variation in mosquito captures was primarily explained by weather, with virtually no mosquito activity when temperatures averaged less than 8°C or wind speeds exceeded 6 m/s. Gravid females (3% of resting adults) were spatially patchy on the landscape, but not always in the same places where most adults emerged. The spatial distribution of adults is quickly uncoupled from the spatial distribution of larvae because A. nigripes females may disperse far from their natal habitats in search of a blood-meal and high-quality oviposition habitat. 8. This research highlights the value of studying ecological processes that act at disparate life stages for understanding the population biology of organisms with complex life cycles.

Ecological Applications

The early bird gets the shrimp: Confronting assumptions of isotopic equilibrium and homogeneity in a wild bird population

1. Because stable isotope distributions in organic material vary systematically across energy gradients that exist in ecosystems, community and population structures, and in individual physiological systems, isotope values in animal tissues have helped address a broad range of questions in animal ecology. It follows that every tissue sample provides an isotopic profile that can be used to study dietary or movement histories of individual animals. Interpretations of these profiles depend on the assumption that metabolic pools are isotopically well mixed and in equilibrium with dietary resources prior to tissue synthesis, and they extend to the population level by assuming isotope profiles are identically distributed for animals using the same proximal dietary resource. As these assumptions are never fully met, studying structure in the variance of tissue isotope values from wild populations is informative. 2. We studied variation in δ 13 C, δ 15 N, δ 2 H and δ 18 O data for feathers from a population of eared grebes (Podiceps nigricollis) that migrate to Great Salt Lake each fall to moult feathers. During this time, they cannot fly and feed almost exclusively on superabundant brine shrimp (Artemia franciscana). The ecological simplicity of this situation minimized the usual spatial and trophic complexities often present in natural studies of feather isotope values. 3. Ranges and variances of isotope values for the feathers were larger than those from previously published studies that report feather isotopic variance, but they were bimodally distributed in all isotope dimensions. Isotope values for proximal dietary resources and local surface water show that some of the feathers we assumed to have been grown locally must have been grown before birds reached isotopic equilibrium with local diet or immediately prior to arrival at Great Salt Lake. 4. Our study provides novel insights about resource use strategies in eared grebes during migration. More generally, it demonstrates the utility of studying variance structures and questioning assumptions implicit in the interpretation of stable isotope data from wild animals.

Utah

Estimation of parental abundance using hierarchical Bayesian modeling with data augmentation

Pedigree-based estimation methods leverage the fact that each offspring in a cohort is genotypically “marked” by its parents and represent a recent and promising toolset for estimating population dynamics. This includes pedigree accumulation estimators that model the “accumulation” of inferred unique parents within a given cohort to estimate parental abundance. Unlike close-kin mark-recapture approaches, which rely on intercohort comparisons, pedigree accumulation modeling can be completed solely using intracohort samples. This is particularly advantageous for semelparous species, where intercohort pairs are impossible and adult life stages can be difficult to sample without affecting their likelihood of successfully reproducing. Previous work has evaluated a range of estimators for such datasets, concluding that the non-parametric Chao estimator provides the most accurate and precise estimates for feasible levels of sampling effort. We used simulated data to evaluate an alternative estimator based on hierarchical modeling and data augmentation in a Bayesian framework. Results indicate that estimates from the hierarchical Bayesian estimator had comparable accuracy and better precision than both the previously tested Chao1 estimator and the improved iChao formulation across a range of sample sizes and sex ratios. Furthermore, the Bayesian estimator was far more robust to simulated errors in pedigree reconstruction, especially the presence of false negatives. Hierarchical Bayesian pedigree accumulation models can also provide additional insight into underlying reproductive ecology through their use of an explicit observation process, allowing for the incorporation or estimation of species- and population-specific reproductive dynamics. More broadly, the parametric nature of these models offers opportunities to efficiently pool information among datasets as well as to propagate uncertainty within more complex models.

Ecology and Evolution

Ecological and social strategies for managing fisheries using the Resist-Accept-Direct (RAD) framework

Fisheries management is a complex task made even more challenging by rapid and unprecedented socioecological transformations associated with climate change. The Resist-Accept-Direct (RAD) framework can be a useful tool to support fisheries management in facing the high uncertainty and variability associated with aquatic ecosystem transformations. Here, RAD strategies are presented to address ecological goals for aquatic ecosystems and social goals for fisheries. These strategies are mapped on a controllability matrix which explores the ability to guide a system's behaviour towards a desired state based on ecological responsiveness and societal receptivity to change. Understanding and improving the controllability of aquatic systems and fisheries can help managers to maintain the broadest suite of available RAD management strategies.

Fisheries Management and Ecology

Data management challenges in species distribution modeling

An important component in the fields of ecology and conservation biology is understanding the environmental conditions and geographic areas that are suitable for a given species to inhabit. A common tool in determining such areas is species distribution modeling which uses computer algorithms to determine the spatial distribution of organisms. Most commonly the correlative relationships between the organism and environmental variables are the primary consideration. The data requirements for this type of modeling consist of known presence and possibly absence locations of the species as well as the values of environmental or climatic covariates thought to define the species habitat suitability at these locations. These covariate data are generally extracted from remotely sensed imagery, interpolated/gridded historical climate data, or downscaled climate model output. Traditionally, ecologists and biologists have constructed species distribution models using workflows and data that reside primarily on their local workstations or networks. This workflow is becoming challenging as scientists increasingly try to use these modeling techniques to inform management decisions under different climate change scenarios. This challenge stems from the fact that remote sensing products, gridded historical climate, and downscaled climate models are not only increasing in spatial and temporal resolution but proliferating as well. Any rigorous assessment of uncertainty requires a computationally intensive sensitivity analysis accounting for various sources of uncertainty. The scientists fitting these models generally do not have the background in computer science required to take advantage of recent advances in web-service based data acquisition, remote high-powered data processing, or scientific workflow systems. Ecologists in the field of modeling are in need of a tractable platform that abstracts the inherent computational complexity required to incorporate the burgeoning field of coupled climate and ecological response modeling. In this paper we describe the computational challenges in species distribution modeling and solutions using scientific workflow systems. We focus on the Software for Assisted Species Modeling (SAHM) a package within VisTrails, an open-source scientific workflow system.

Bulletin of the Technical Committee on Data Engine

Partial observability and management of ecological systems

The actual state of ecological systems is rarely known with certainty, but management actions must often be taken regardless of imperfect measurement (partial observability). Because of the difficulties in accounting for partial observability, it is usually treated in an ad hoc fashion, or simply ignored altogether. Yet incorporating partial observability into decision processes lends a realism that has the potential to improve ecological outcomes significantly. We review frameworks for dealing with partial observability, focusing specifically on dynamic ecological systems with Markovian transitions, i.e., transitions among system states that are influenced by the current system state and management action over time. Fully observable states are represented in an observable Markov decision process (MDP), whereas obscure or hidden states are represented in a partially observable process (POMDP). POMDPs can be seen as a natural extension of observable MDPs. Management under partial observability generalizes the situation for complete observability, by recognizing uncertainty about the system's state and incorporating sequential observations associated with, but not the same as, the states themselves. Decisions that otherwise would depend on the actual state must be based instead on state probability distributions (“belief states”). Partial observability requires adaptation of the entire decision process, including the use of belief states and Bayesian updates, valuation that includes expectations over observations, and optimal strategy that identifies actions for belief states over a continuous belief space. We compare MDPs and POMDPs and highlight POMDP applications to some common ecological problems. We clarify the structure and operations, approaches for finding solutions, and analytic challenges of POMDPs for practicing ecologists. Both observable and partially observable MDPs can use an inductive approach to identify optimal strategies and values, with a considerable increase in mathematical complexity with POMDPs. Better understanding of POMDPs can help decision makers manage imperfectly measured ecological systems more effectively.

Ecology and Evolution

An ecological and conservation perspective

Natural ecosystems are facing unprecedented threats which directly threaten human well-being through decreases in critical ecosystem services (IPBES 2019). The top five drivers causing the largest global impacts to biodiversity and ecosystem services include: 1) changes in land and sea use; 2) direct exploitation of organisms; 3) climate change; 4) pollution, and 5) invasive alien species (IPBES 2019). Although One Health acknowledges the link between the health of humans, animals, and the environment, One Health discussions have historically focused on the prevention and control of infectious disease at the human-animal interface rather than these large-scale drivers of health. While One Health has succeeded in bringing awareness to the need for proactive disease control measures such as strengthened biosecurity and vaccine development (e.g., Machalaba et al., 2018; Middleton et al., 2014), disease is only one component of health. In this chapter, we explore the potential for One Health to shift its focus from disease prevention to health promotion to more fully integrate solutions that protect the health of humans, animals, and the ecosystems on which we all depend for our economies, livelihoods, food security, and health. This shift will facilitate a more seamless inclusion of ecological health and environmental conservation in the One Health paradigm and can serve as the basis for a comprehensive approach to complex problems at the root of global health. We also suggest a framework for creating and applying health metrics for wildlife and ecological systems that will be essential for measuring the success of actions aimed at maintaining or shifting systems to desired states.

Book chapter

Aquatic–terrestrial linkages provide novel opportunities for freshwater ecologists to engage stakeholders and inform riparian management

Studies of aquatic–terrestrial ecosystem linkages explore the mechanisms by which components of one ecosystem, such as the aquatic insect community in a stream, directly affect components of an adjacent ecosystem, such as the density and diversity of riparian predators. On a human level, research into these linkages allows freshwater ecologists to form novel collaborations with stakeholders and other interest groups by emphasizing shared interests. To highlight this point, we use 3 case studies as examples of how aquatic–terrestrial linkages research can be leveraged to achieve multifaceted goals of improving riparian and freshwater management, engaging stakeholders, and advancing ecological understanding. In the 1 st case study, we describe a project in which consideration of the complex life histories of aquatic insects could have led to more effective outcomes for riparian bird restoration. The 2 nd case study provides an example of how studying contaminant transport through ecological subsidies has been incorporated into programs for contaminant management. In the 3 rd case, we use a study of terrestrial vertebrates feeding on adult aquatic insects to show how research into aquatic–terrestrial subsidies connects freshwater ecologists, youth groups, and commercial river guides. By focusing on how in-stream processes propagate onto land through ecological subsidies, we argue that freshwater ecologists also gain a platform for communicating their science to riparian managers and the public, which can improve the potential for stream and riparian co-management and restoration success.

Freshwater Science

Geomorphometry in landscape ecology: Issues of scale, physiography, and application

Topographic measures are frequently used in a variety of landscape ecology applications, in their simplest form as elevation, slope, and aspect, but increasingly more complex measures are being employed. We explore terrain metric similarity with changes in scale, both grain and extent, and examine how selecting the best measures is sensitive to changes in application. There are three types of topographic measures: 1) those that relate to orientation for approximating solar input, 2) those that capture variability in terrain configuration, and 3) those that provide metrics about landform features. Many biodiversity hotspots and predators have been found to coincide with areas of complexity, yet most complexity measures cannot differentiate between terrain steepness and uneven and broken terrain. Currently characterizing terrain in landscape-level analyses can be challenging, especially at coarser spatial resolutions but developing methods that improve landscape-level assessments include multivariate approaches and the use of neighborhood statistics. Some measures are sensitive to the spatial grain of calculation, the physiography of the landscape, and the scale of application. We show which measures have the potential to be multi-collinear, and illustrate with a case study how the selection of the best measures can change depending on the question at hand using mountain lion (Puma concolor) occurrence data. The case study showed a combination of infrequently employed metrics, such as view-shed analysis and focal statistics, outperform more commonly employed singular metrics. The use of focal statistics as a measure of topographic complexity shows promise for improving how mountain lions use terrain features.

Environment and Ecology Research

How wildlife respond to tropical cyclones: Short-term tactics and long-term impacts

From butterflies to lizards and from sharks to seabirds, wildlife exhibit tactics to survive the impacts of tropical cyclones, also known as hurricanes, cyclones, or typhoons depending on where they occur. Some species seek refuge during the storm by moving, some remain in place and ride it out, and others move longer distances, avoiding the main impacts of the storm altogether. Tropical cyclones can have direct impacts on wildlife (e.g. mortality) but can also have indirect effects by altering resources and habitat, with downstream impacts on abundance and recruitment. Using examples from across taxa and ecosystems, we explore the pathways by which tropical cyclones can influence wildlife populations and communities. We describe tactics demonstrated by wildlife that enable them to survive the immediate impacts of the storm, as well as the longer-term impacts after the storm. We give examples of tropical cyclones as a selective pressure and as a facilitator for the introduction of invasive species. We also describe how tropical cyclones may provide a net benefit to some native species. The ecological and evolutionary impacts of tropical cyclones on wildlife can be complex, as they are often intertwined with concurrent pressures from land-use change, human development, and climate change. As the frequency of intense tropical cyclones is predicted to increase globally, identifying the mechanisms by which wildlife cope with such disturbances can aid in understanding and mitigating the impacts of climate change on wildlife.

Biological Reviews

Deformity, erosion, lesion, tumor, and parasite (DELT) anomalies in fish communities of the Chesapeake Bay watershed, USA: A regional assessment and potential landscape drivers

Fish diseases in freshwater ecosystems pose significant ecological and socioeconomic challenges, yet monitoring them in wild populations is complex due to interactions between pathogens, hosts, and environmental conditions. We examine the prevalence and watershed-scale landscape drivers of external deformity, erosion, lesion, tumor, and parasite (DELT) anomalies in 57 riverine fish species using a large dataset (577,266 individuals collected 2008–2019) from the Chesapeake Bay watershed that originated from state and federal agencies. Overall, DELT prevalence was low (1.4%), but was higher in larger, longer-lived species, including Channel Catfish ( Ictalurus punctatus ) (18.9%), Rock Bass ( Ambloplites rupestris ) (7.6%), Smallmouth Bass ( Micropterus dolomieu ) (7.3%), Brown Bullhead ( Ameiurus nebulosus ) (5.6%), and Yellow Bullhead ( Ameiurus natalis ) (5.1%), signifying their potential as regional environmental health indicators. Spatial analysis indicated warmer temperatures increased the estimated probability of DELT occurrence, whereas higher precipitation often mitigated the probability of DELT occurrence. Conservation strategies (e.g., best management practices) had mixed effectiveness in reducing DELT occurrence probability across agricultural and urban landscapes. Across the landscape, various drivers, including harvested forest, impervious land, and pesticide use, influenced DELT occurrence probability differently across species. However, uncertainty remains partly due to low prevalence and variability in sampling methods across agencies. Despite low overall prevalence, DELT occurrence is a rapid fish health indicator. Future research could emphasize species-specific responses and longitudinal studies that incorporate life stages and health indicators. Understanding these intricate, multi-scale interactions is vital for effective monitoring, conservation, and adaptive management of freshwater ecosystems.

Chesapeake Bay watershed

Modulators of mercury risk to wildlife and humans in the context of rapid global change

Environmental mercury (Hg) contamination is an urgent global health threat. The complexity of Hg in the environment can hinder accurate determination of ecological and human health risks, particularly within the context of the rapid global changes that are altering many ecological processes, socioeconomic patterns, and other factors like infectious disease incidence, which can affect Hg exposures and health outcomes. However, the success of global Hg-reduction efforts depends on accurate assessments of their effectiveness in reducing health risks. In this paper, we examine the role that key extrinsic and intrinsic drivers play on several aspects of Hg risk to humans and organisms in the environment. We do so within three key domains of ecological and human health risk. First, we examine how extrinsic global change drivers influence pathways of Hg bioaccumulation and biomagnification through food webs. Next, we describe how extrinsic socioeconomic drivers at a global scale, and intrinsic individual-level drivers, influence human Hg exposure. Finally, we address how the adverse health effects of Hg in humans and wildlife are modulated by a range of extrinsic and intrinsic drivers within the context of rapid global change. Incorporating components of these three domains into research and monitoring will facilitate a more holistic understanding of how ecological and societal drivers interact to influence Hg health risks.

Ambio