Stuart R Borrett

University of North Carolina at Wilmington | UNCW · Department of Biology and Marine Biology

Nitrogen (N) removal from estuaries is driven in part by sedimentary microbial processes. The processes of denitrification and anaerobic ammonium oxidation (anammox) remove N from estuaries by producing N2 gas, and each can be coupled to N recycling pathways such as nitrification and dissimilatory nitrate reduction to ammonium (DNRA). Environmental...

Network analysis is a useful approach for investigating complex and relational data in many fields including ecology, molecular and evolutionary biology.Here, we introduce enaR , an r package for Ecosystem Network Analysis (ENA). ENA is an analytical tool set rooted in ecosystem ecology with over 30 years of development that examines the structure...

Network ecologists investigate the structure, function, and evolution of ecological systems using network models and analyses. For example, network techniques have been used to study community interactions (i.e., food-webs, mutualisms), gene flow across landscapes, and the sociality of individuals in populations. The work presented here uses a bibl...

Network Environ Analysis is a formal, quantitative methodology to describe an object's within system “environ”ment [Patten, B.C., 1978a. Systems approach to the concept of environment. Ohio Journal of Science 78, 206–222]. It provides a perspective of the environment, based on general system theory and input–output analysis. This approach is one ty...

Network analysis of complex systems is a rapidly growing field. Both theoretical and empirical network studies have permeated many different ecological, biological, social, and economic fields, investigating the interrelationships between nodes as structural and functional attributes in static, time-dynamic, or spatially explicit formats. We consid...

https://leopard.tu-braunschweig.de/servlets/MCRFileNodeServlet/dbbs_derivate_00048475/Verhandlungen%20der%20Gesellschaft%20f%C3%BCr%20%C3%96kologie%20Band%2050_2021.pdf

Network analyses applied to models of complex systems generally contain at least three levels of analyses. Whole-network metrics summarize general organizational features (properties or relationships) of the entire network, while node-level metrics summarize similar organization features but consider individual nodes. The network- and node-level me...

The continuing loss of global biodiversity has raised questions about the risk that species extinctions pose for the functioning of natural ecosystems and the services that they provide for human wellbeing. There is consensus that, on single trophic levels, biodiversity sustains functions; however, to understand the full range of biodiversity effec...

Ecological Network Analysis (ENA) has provided insights into the structure, function, and transformation of ecosystems for more than forty years. Key insights from ENA focus on how the patterns of directed weighted transactions among system components (e.g., species, functional groups, economic sectors) create emergent and often unexpected relation...

In this study, we describe the approach taken by the International Council for the Exploration of the Seas Irish Sea benchmark working group (WKIrish), to co-create diet information for six commercial species using fishers' and scientists knowledge and incorporate it into an existing Ecopath food web model of the Irish Sea. To understand how the co...

Understanding soil systems is critical because they form the structural and nutritional foundation for plants and thus every terrestrial habitat and agricultural system. In this paper, we encourage increased use of mathematical models to drive forward understanding of interactions in soil ecological systems. We discuss several distinctive features...

In this paper, we identified seven ecological network analysis (ENA) metrics that, in our opinion, have high potential to provide useful and practical information for environmental decision-makers and stakeholders. Measurement and quantification of the network indicators requires that an ecosystem level assessment is implemented. The ENA metrics co...

For complex ecosystem models to be used as tools to inform fisheries management, their development should incorporate all available data and stakeholder knowledge and steps to address inherent uncertainty. We included long-term stomach records and stakeholder knowledge (food webs and fishing effort trends) into an ecosystem model of the Irish Sea (...

Ecological Network Analysis (ENA) can inform marine management decisions by producing indicators that describe ecosystem health and function. Reporting ENA indicators with uncertainty boundaries lets end-users draw stronger inferences and can increase confidence in model results. However, few studies developing these indicators have estimated uncer...

Ecological Network Analysis (ENA) combines modeling and analysis used to investigate the structure, function, and evolution of ecosystems and other complex systems. ENA is applied to network models that trace the movement of thermodynamically conserved energy or matter through the system. Investigators use ENA to answer a range of questions such as...

For complex ecosystem models to be used as tools to inform fisheries management, their development should incorporate stakeholder knowledge and steps to address inherent uncertainty. Using an Ecopath with Ecosim model of the Irish Sea (developed as part of the first ICES Integrated Benchmark Assessment, WKIrish), we investigate how uncertainty in t...

Uncertainty analyses show how variability inherent in model parameters affects model outcomes. While conducting uncertainty analyses is considered best practice, technical and conceptual challenges limit applications for network models. This work adapts Linear Inverse Modeling (LIM) techniques to conduct uncertainty analysis on ecosystem flow netwo...

The management of Irish Sea fisheries is currently challenged by a lack of recovery in some fish populations (cod, whiting and sole) despite large reductions in fishing effort and increases in gear mesh size. In response, Irish Sea fisheries have transitioned from a cod, whiting and herring dominated fishery to one dominated by Nephrops and other s...

Network ecology provides a systems basis for approaching ecological questions, such as factors that influence biological diversity, the role of particular species or particular traits in structuring ecosystems, and long-term ecological dynamics (e.g., stability). Whereas the introduction of network theory has enabled ecologists to quantify not only...

Two mass-balanced network models of Hooghly Matla estuarine system, from two different time periods (less exploited phase → 1985–1990 and highly exploited phase → 1998–2003) have been constructed for quantitative comparison. The models are used to estimate the important biological interactions and relationships among different ecologically importan...

Network ecology provides a systems basis for approaching ecological questions, such as factors that influence biological diversity, the role of particular species or particular traits in structuring ecosystems, and long-term ecological dynamics (e.g., stability). Whereas the introduction of network theory has enabled ecologists to quantify not only...

Oyster reef restoration projects are increasing in number both to enhance oyster density and to retain valuable ecosystem services provided by oyster reefs. Although some oyster restoration projects have demonstrated success by increasing density and biomass of transient fish, it still remains a challenge to quantify the effects of oyster restorati...

Network analysis has revealed whole-network properties hypothesized to be general characteristics of ecosystems including pathway proliferation, and network non-locality, homogenization, amplification, mutualism, and synergism. Collectively these properties characterize the impact of indirect interactions among ecosystem elements. While ecosystem n...

Species extinctions are accelerating globally, yet the mechanisms that maintain local biodiversity remain poorly understood. The extinction of species that feed on or are fed on by many others (i.e. ‘hubs’) has traditionally been thought to cause the greatest threat of further biodiversity loss. Very little attention has been paid to the strength o...

Ecologists, ecosystem managers and ecological engineers often seek to identify which components of an ecosystem are most important to its functioning. Ecosystem Network Analyses (ENA) can be used as a tool to address this challenge while taking into consideration the complex direct and indirect interactions that occur in natural systems. One way th...

Although genetics in a single species is known to impact whole communities, little is known about how genetic variation influences species interaction networks in complex ecosystems. Here, we examine the interactions in a community of arthropod species on replicated genotypes (clones) of a foundation tree species, Populus angustifolia James (narrow...

Although genetics in a single species is known to impact whole communities, little is known about how genetic variation influences species interaction networks in complex ecosystems. Here, we examine the interactions in a community of arthropod species on replicated genotypes (clones) of a foundation tree species, Populus angustifolia James (narrow...

Plant species vary greatly in their responsiveness to nutritional soil mutualists, such as mycorrhizal fungi and rhizobia, and this responsiveness is associated with a trade-off in allocation to root structures for resource uptake. As a result, the outcome of plant competition can change with the density of mutualists, with microbe-responsive plant...

Ecological network analysis is a set of algorithms that provide a holistic approach to the study of ecosystems. These analyses operate on at least three different hierarchical levels: network, neighborhood, and node. Network level analyses capture whole-system interactions and provide a broad view of the system; neighborhood level analyses provide...

Compartmental, or “stock-and-flow”, models describe the storage and transfer of conservative energy or matter entering and leaving open systems. The storages are the standing “stocks”, and the intra-system and boundary transfers are transactional “flows”. Network environ analysis (NEA) provides network methods and perspectives for the quantitative...

The methods of network environ analysis (NEA) currently apply to steady-state models. Networks of real ecosystems are near steady-state in long-term mean characteristics, but are dynamic in short-term responses. A formal mathematical approach to dynamic NEA analysis has never been fully developed, though Hippe [Hippe, P.W., 1983. Environ analysis o...

We hypothesized that the catastrophic annual molt of penguins (Sphenisciformes) would lead to reduced intra-individual variation of mercury concentrations in body feathers. While mean mercury concentrations varied significantly among 8 penguin species, intra-individual variability did not differ among species and was three times lower than values o...

Ecology studies the relationships among living and non-living components. Ecological Network Analysis (ENA) provides a "macroscopic" view of relationships that captures system-wide information that is otherwise lost through reductionistic approaches. For example, ENA has been used to uncover the dominance of indirect pathways in the dynamics of bot...

Background/Question/Methods An enduring question for network analysis of ecosystem models for holistic ecosystem function is, to what extent do different model size, topology, and currency affect the results and conclusions of such studies? To address this question comparative network environ analysis (CNEA) was conducted on two ecosystem model t...

Network ecology is the investigation of complex ecological systems (e.g., metapopulations, communities, ecosystems, landscapes) by modeling them as networks of interactions and applying network analyses. It is a subdiscipline of both ecosystem ecology and network science. A network model is composed of set of nodes and one of edges that map a relat...

A core question in ecology concerns the relative functional importance of species in communities and ecosystems. This information is useful for fisheries management as it can identify ecosystem components relevant for managing target species. Here, we apply the centrality concept from social network analysis to characterize the relative importance...

Ecologists and conservation biologists need to identify the relative importance of species to make sound management decisions and effectively allocate scarce resources. We introduce a new method, termed environ centrality, to determine the relative importance of a species in an ecosystem network with respect to ecosystem energy-matter exchange. We...

Background/Question/Methods In an effort to elucidate the role of bacteria in the connectivity of food webs, we added bacterial loops to existing food web matrices. We examined the influence of these modifications on indirect connectivity by performing a power series of 2, 5, and 10 on the adjacency matrices. We also calculated dominant eigenvalu...

Environment is an ecologically important but often ill-defined concept. Environs are an operationalization of environments that let us study their organization and activity. Specifically, environs are the directed (input and output), within-system environments of species (or more generally holons) in ecosystems. Scientists primarily study environs...

A new understanding of the consequences of how ecosystem elements are interconnected is emerging from the development and application of Ecological Network Analysis. The relative importance of indirect effects is central to this understanding, and the ratio of indirect flow to direct flow (I/D) is one indicator of their importance. Two methods have...

Indirect effects are powerful influences in ecosystems that may maintain species diversity and alter apparent relationships between species in surprising ways. Here, we applied network environ analysis to 50 empirically-based trophic ecosystem models to test the hypothesis that indirect flows dominate direct flows in ecosystem networks. Further, we...

Background/Question/Methods In this study we added bacterial loops to existing food web matrices. We examined the influence of these modifications on indirect connectivity by performing a power series of n on the adjacency matrices. We also calculated dominant eigenvalues. The dominant eigenvalues are interpreted as evidence of strongly connected...

Background/Question/Methods Connectivity patterns of ecological elements are often the core concern of ecologists working at multiple levels of organization (e.g., communities, ecosystems, and landscapes) because these patterns often reflect the forces shaping the system's development as well as constraining their operation or function. One reason...

Connectivity patterns of ecological elements are often the core concern of ecologists working at multiple levels of organization (e.g., populations, communities, ecosystems, and landscapes) because these patterns often reflect the forces shaping the system’s development as well as constraining their operation. One reason these patterns of direct co...

Indirect effects are important components of ecological and evolutionary interactions that may maintain biodiversity, enable or inhibit invasive species, and challenge ecosystem assessment and management. A central hypothesis of Network Environ Analysis (NEA), one type of ecological network analysis, is that indirect flows tend to dominate direct f...

Understanding how data uncertainty influences ecosystem analysis is critical as we move toward ecosystem-based management. Here, we investigate how 18 Ecological Network Analysis (ENA) indicators that characterize ecosystem growth, development, and condition are affected by uncertainty in an ecosystem model of Lake Sidney Lanier (USA). We applied E...

Scientific modeling is a creative activity that can benefit from computational support. This chapter reports five challenges that arise in developing such aids, as illustrated by PROMETHEUS, a software environment that supports the construction and revision of explanatory models. These challenges include the paucity of relevant data, the need to in...

Background/Question/Methods Food webs and matrices are important tools assisting in the understanding of feeding relationships and ecology. One way of presenting the direct relationships between predators and prey is with an adjacency matrix, a binary matrix which utilizes with direct links shown as one’s and no direct link between nodes as zero’s...

Network environ analysis is motivated by a desire to investigate ecosystems from a holistic perspective. It provides a quantitative measure of the integral (direct plus indirect) relationship between compartments and their within-system environments. In this analysis, each compartment within a system has an incoming interactive network that brings...

An environ is a within-system partition of the environment associated with each ecosystem component. The methodologies for calculating throughflow-based and storage-based environs have heretofore been considered quantitatively and qualitatively different. Below, we show, from the fundamental environ equations, that these two approaches are mathemat...

Large-scale structural patterns commonly occur in network models of complex systems including a skewed node degree distribution and small-world topology. These patterns suggest common organizational constraints and similar functional consequences. Here, we investigate a structural pattern termed pathway proliferation. Previous research enumerating...

Knowledge of the complex life cycle of Phaeocystis is a key to understanding its role in marine ecosystems and global biogeochemistry. An existing life cycle model was modified and used to integrate understanding of the Phaeocystis life cycle. In model-driven research, models expose gaps in our understanding, empirical studies ensue, and feedback i...

Efiective environmental impact assessment and management requires improved un- derstanding of the organization and transformation of ecosystems in which inde- pendent agents are linked through an intricate network of energy, matter, and in- formational interactions. While advances have been made, we still lack a complete understanding of the proces...

In this paper, we introduce an approach for extracting constraints on process model construction. We begin by clarifying the type of knowledge produced by our method and how one may apply it. Next, we review the task of inductive process modeling, which provides the required data. We then introduce a logical formal- ism and a computational method f...

In this paper, we review the task of inductive process mod- eling, which uses domain knowledge to compose explanatory models of continuous dynamic systems. Next we discuss approaches to learning with missing values in time series, noting that these eorts are typically applied for descriptive modeling tasks that use little background knowl- edge. We...

In high latitude planktonic ecosystems where the prymnesiophyte alga Phaeocystis pouchetii is often the dominant primary producer, its importance in structuring planktonic food webs is well known. In this study we investigated how the base of the planktonic food web responds to a P. pouchetii colony bloom in controlled mesocosm systems with natural...

Scientists investigate the dynamics of complex systems with quantitative models, employing them to synthesize knowledge, to explain observations, and to forecast future system behavior. Complete specification of systems is impossible, so models must be simplified abstractions. Thus, the art of modeling involves deciding which system elements to inc...

Comparative network environ analysis (NEA) is used to holistically explore controlling relationships in ecosystems. The term, distributed control, for the present series of papers, is adopted to describe a diffuse and decentralized concept of control residing in the complexity of organization. Starting with “open-loop” control theory parlance, thre...

Indirect effects, the ability of one element in a system to impact another without direct interaction, are critical components of complex adaptive systems. Network environ analysis (NEA) is an environmental extension of economic input–output analysis that characterizes and quantifies indirect effects transmitted by a specific currency (e.g., carbon...

Network environ analysis (NEA) was used to analyze a seven-compartment, steady-state model of nitrogen flow in the Neuse River Estuary, North Carolina, USA. Four perspectives for analyzing network properties emerge: (1) throughflow-specific oriented to output environs; (2) throughflow-specific oriented to input environs; (2) storage-specific orient...

Network environ analysis (NEA) was used to analyze a seven-compartment, steady-state model of nitrogen flow in the Neuse River Estuary, North Carolina, USA. Four perspectives for analyzing network properties emerge: (1) throughflow-specific oriented to output environs; (2) throughflow-specific oriented to input environs; (2) storage-specific orient...

Integrated urban water management – a framework to understand, control, and optimize elements of the urban water infrastructure as an integrated system – is inherently complex. It becomes more complex and challenging, however, when public participation in management institutions is considered. This paper applies a systems perspective to explore ins...

In ecosystems network, structure determines adjacent (direct) and non-adjacent (indirect) pathways over which energy, matter, and information can flow. The more pathways, the more possible ways the conservative substance can move in zero-sum transactions between network nodes that the pathways interconnect, and the more possible non-conservative, n...

This chapter discusses that as the human influence on environment accelerates, it must be modulated for the benefit of both the people and the environment. Rational decisions in the face of overwhelming information are overloaded and it collectively adapts to the new status quo, with the concepts of sustainability and ecosystem health. A potentiall...

An iterative approach to working with a community's environmental concerns, at the interface between science and society, is presented. We call this adaptive community learning, within which the principles of adaptive environmental assessment and management are embedded. Handling uncertainty – indeed, gross uncertainty – is integral to our approach...

Indirect effects appear to play a significant role in the organization and transformation of complex adaptive systems (CAS). In ecosystems, one type of CAS, organisms and their environments are coupled by an intricate network of energy, matter, and information exchanges. This makes it possible for one species to affect the distribution, abundance,...