USGS ScienceSearch

Geology topics

Simeon Yurek

Publications and source records attributed to Simeon Yurek.

At least 19 recordsLinked to original sources

Synthesis of observed field salinity ranges for oyster and seagrass species in the U.S.

Oyster and seagrass are important sessile, habitat-forming species that may be impacted by changes in salinity regimes from anthropogenic or climatic drivers. While salinity tolerance literature is focused on controlled experiments, observed field salinity ranges of species are more disparate. The salinity ranges in which organisms are observed in the field may not align exactly with their experimentally (wet lab) determined physiological salinity tolerances, since other critical factors control species occurrence. We performed a systematic review to synthesize observed practical salinity ranges for 10 oyster and 12 seagrass species in coastal waters of the United States. Of initially returned search results for oysters and seagrass, only 11.4% and 6.5% met our review inclusion criteria, respectively, corresponding to 3 oyster species and 5 seagrass species. The majority (95%) of the 57 reviewed studies were along the Atlantic and Gulf coasts, with 68% focusing on Crassostrea virginica . Shorter studies following episodic events were more common than long-term monitoring. Observed field salinity ranges were as follows (ppt): Crassostrea virginica (0.1 – 42.8, mean: 19.6), Ostrea lurida (1.7 – 32.5, mean: 27.8), Thalassia testudinum (0 – 65, mean 31.8), Halodule wrightii (<0.5 – 68.7, mean: 18.5), Syringodium filiforme (13.7 – 68.7, mean: 30.4), Ruppia maritima (0 – 29.4, mean: 3.8), and Zostera marina (19.7 – 51.2, mean: 28.9). Place-based examples highlight how reported overlapping salinity ranges for oyster and seagrass species can be used to expand existing habitat suitability models, inform restoration, and provide considerations for guiding holistic management of freshwater inflows to estuaries.

Estuaries and Coasts

Foraging of wading birds on a patchy landscape: Simulating effects of social information, interference competition, and patch selection on prey intake and individual distribution

Foragers on patchy landscapes must acquire sufficient resources despite uncertainty in the location and amount of the resources. Optimal Foraging Theory posits that foragers deal with this uncertainty by using strategies that optimize resource intake within foraging periods. For species such as wading birds, this optimization is closely linked to their survival and reproductive success. Understanding the influence of patch selection on individual resource intake and foraging distribution is therefore crucial. In this study, we simulated how resource distribution, interference competition, and social cues—such as aggregation behaviors—influence resource intake and foraging spatial distribution. We employed an individual-based model simulating wading bird foraging behaviors, with 900 individuals simultaneously foraging across a landscape with unknown resource distribution. Birds employed one of three patch-finding strategies: random, cue-searching, or hybrid, which uses both searching strategies. Each bird decided whether to remain in a patch based on a prey density threshold. We compared the daily resource intake and foraging distribution of birds across different modeled patch-finding strategies, resource distribution patterns, and the presence or absence of interference competition. Wading birds exhibiting aggregation behavior displayed increased intake rates when resources were concentrated and interference minimal. Aggregation behavior led to a closer match with the ideal free distribution when the prey density threshold was optimal. These findings provide theoretical support that aggregation behavior is effective in scenarios where resources are concentrated in a few patches, social cues are used by relatively few individuals, and interference competition is limited.

Ecological Modelling

An expert elicitation to inform coastal management decision-making for mitigating future hazards

A scientific expert elicitation was conducted to address the feasibility of restoring coastal environments in response to future hazards to best meet management objectives. Subject matter experts produced probabilistic estimates of coastal change metrics used to evaluate decision objectives and alternatives informed by a stakeholder advisory group. Changes in salt marsh extents, storm surge flooding and barrier island morphology by the year 2050 were estimated for three scenarios of management actions (no action, interior headland restoration, beach and dune nourishment), while also considering the effects of future sea level rise (SLR). Collectively the participants were confident in their expectations of increased storm surge flooding with SLR, regardless of management interventions. Estimates of marsh response had large uncertainty, but experts generally hypothesized that marsh area would decrease with increasing SLR if no action was taken, especially in areas already experiencing marsh deterioration. There was agreement that dune heights and barrier island widths would decrease with SLR if no action was taken. Experts felt that beach and dune nourishment may reduce the amount of erosion under future SLR. All experts recognized the dynamic effects of SLR and feedback between bio-geo-physical processes that govern coastal systems. Participants agreed that size and location of management actions were important factors for influencing the coastal response. Expert elicitation is novel in the context of coastal management decision making and can be a useful tool for informing future scientific needs and providing rapid results to end users to inform reallocation of resources surrounding research and application.

Alabama, Mississippi

Visualizing wading bird optimal foraging decisions with aggregation behaviors using individual-based modeling

Foragers on patchy landscapes must efficiently balance time between searching for and consuming resources to meet their daily energetic requirements. Spatial aggregation foraging behaviors may improve foraging efficiency by sharing information on locations of resource hotspots. Wading birds are an example of patch foragers that form colonial aggregations during the breeding season to obtain sufficient prey energy to sustain themselves and their offspring each day. Here, we describe a spatially-explicit simulation model of wading bird optimal foraging that represents information sharing through visual cues. The overall purpose of the model is to describe how wading bird daily foraging and reproductive success may change with alternative water control management practices that determine spatial availability of prey for wading birds on the landscape, throughout their breeding seasons. Wading birds are simulated as individuals that operate independently, sampling and selecting among patches based on a prey density tolerance threshold, but also use information from other birds to inform their selection decisions. Foraging success is evaluated against the fundamental objectives of (a) fulfilling daily energetic demands and (b) minimizing predation exposure, by tracking individual daily energetic intake and time spent foraging. In this way, the model approximates population level dynamics of wading bird aggregations that emerge through collective decision making of birds simulated at the lower individual level. Key results of this study suggest that aggregation behaviors may improve population-level foraging success rates, and the optimal settling threshold may modulate when resources become more scarce or difficult to find. Thus, the model addresses ecological theory on the advantages of foraging in groups versus independently. This technique is appropriate for evaluating wading bird populations that forage on patchy landscapes, such as seasonally-pulsed wetlands, wherever sufficient information is available to describe (1) foraging behavior (e.g., feeding rate, flight speeds, patch selection decisions), (2) key landscape characteristics, (3) spatial distributions of prey densities among foraging patches, and (4) changes in prey densities through time. The model was designed to predict qualitative, testable spatial patterns of wading bird foraging movements which can be compared with empirical observations and empirically-derived habitat suitability models. These techniques can also be applied to other bird species, such as shorebirds, or more generally to any species that transits between discrete foraging patches.

Ecological Modelling

Quantifying uncertainty in coastal salinity regime for biological application using quantile regression

Salinity regimes in coastal ecosystems are highly dynamic and driven by complex geomorphic and hydrological processes. Estuarine biota are generally adapted to salinity fluctuation, but are vulnerable to salinity extremes. Characterizing coastal salinity regime for ecological studies therefore requires representing extremes of salinity ranges at time scales relevant to ecology (e.g., daily, monthly, and seasonally). Here, we propose a framework for modeling coastal salinity with these overall goals: (1) quantify uncertainty in salinity associated with important terrestrial and oceanographic drivers, (2) examine time scales of salinity response to river streamflow events, and (3) predict salinity continuously over space at key time scales. Salinity is modeled as quantile surfaces related to river discharge, tidal dynamics, wind, and spatial location, applied to Suwannee Sound estuary, FL, USA, where salinity has been monitored spatially since 1981. Each quantile level is regressed independently, and together they comprise a distribution of salinity uncertainty across space, with upper and lower quantiles describing salinity extremes. Effects of physical drivers on salinity are compared through four base models with various combinations of tide and wind variables, each including spatial coordinates and a single streamflow metric (in cubic meters per second). Multiple time scales of streamflow are considered by taking means across various periods, from 1 to 12 days, and at various lagged intervals prior to salinity sample, totaling 144 streamflow metrics. We found that the Suwannee coastal salinity regime is dynamic at multiple time scales and varies nonlinearly across space from the river effluence outward. Salinity increases nonlinearly with decreasing river flow rates below 200 m 3 /s, most prominently in the lower quantiles of salinity (τ = 0.05–0.25). Wind appears to have a stronger influence on salinity than astronomic tides for this estuary. The regression approach developed here can be applied to any coastal system that has sufficient spatial and temporal monitoring coverage to capture multiple flood and drought events. It is implemented with a simple R routine, and is less computationally-intensive than finite difference hydrodynamic modeling. The characterizations of salinity uncertainty developed in these analyses can be directly applied to future studies of fish and wildlife responses to changes in watershed management.

Florida

Decision science as a framework for combining geomorphological and ecological modeling for the management of coastal systems

The loss of ecosystem services due to climate change and coastal development is projected to have significant impacts on local economies and conservation of natural resources. Consequently, there has been an increase in coastal management activities such as living shorelines, oyster reef restoration, marsh restoration, beach and dune nourishment, and revegetation projects. Coastal management decisions are complex and include challenging trade-offs. Decision science offers a useful framework to address such complex problems. Here, we provide a synthesis about how decision science can help to integrate research from multiple disciplines (physical and life sciences) with management of coastal and marine systems. Specifically, we discuss the importance of considering concepts and techniques from ecology, coastal geology, geomorphology, climate science, oceanography, and decision analysis when developing conservation plans for coastal restoration. We illustrate the process with several coastal restoration studies. Our capstone example is based on a recent barrier island restoration assessment project at Dauphin Island, Alabama, which included the development of geomorphological and ecological models. We show how decision science can be used as a framework to combine geomorphological and ecological modeling to help inform management decisions while considering uncertainty about system changes and risk tolerance. We also build on our examples through a review of recently developed techniques for spatial conservation planning for land acquisition decisions and the application of adaptive management for sequential decisions.

Alabama

Wading bird foraging on a wetland landscape: A comparison of two strategies

Tactile-feeding wading birds, such as wood storks and white ibises, require high densities of prey such as small fishes and crayfish to support themselves and their offspring during the breeding season. Prey availability in wetlands is often determined by seasonal hydrologic pulsing, such as in the subtropical Everglades, where spatial distributions of prey can vary through time, becoming heterogeneously clumped in patches, such as ponds or sloughs, as the wetland dries out. In this mathematical modeling study, we selected two possible foraging strategies to examine how they impact total energetic intake over a time scale of one day. In the first, wading birds sample prey patches without a priori knowledge of the patches' prey densities, moving from patch to patch, staying long enough to estimate the prey density, until they find one that meets a predetermined satisfactory threshold, and then staying there for a longer period. For this case, we solve for a wading bird's expected prey intake over the course of a day, given varying theoretical probability distributions of patch prey densities across the landscape. In the second strategy considered, it is assumed that the wading bird samples a given number of patches, and then uses memory to return to the highest quality patch. Our results show how total intake over a day is impacted by assumptions of the parameters governing the spatial distribution of prey among patches, which is a key source of parameter uncertainty in both natural and managed ecosystems. Perhaps surprisingly, the foraging strategy that uses a prey density threshold generally led to higher maximum potential prey intake than the strategy for using memory to return to the best patch sampled. These results will contribute to understanding the foraging of wading birds and to the management of wetlands.

Mathematical Biosciences and Engineering

Hierarchical functional response of a forager on a wetland landscape

We show that for some foragers the form that a functional response takes depends on the temporal and spatial scales considered. In representing the consumption rate of an organism, it may be necessary to use a hierarchy of functional responses. Consider, for example, a wading bird foraging in wetland landscape characterized by a spatial distribution of potential foraging sites, such as ponds. At the smallest time scale of minutes or hours, during which a wading bird is foraging within a single site, the functional response will reflect the local density of prey, as well as features of the site that affect the feeding rate, such as water depth. At this short time scale, which is determined by the giving up time of the wading bird in a particular site, prey density may be relatively constant. The food intake from a particular pond is then the product of the time spent before giving-up time and moving to another site and the rate of prey consumption at that site. A prey-centered functional response is most appropriate for describing the prey consumption rate. We propose that over the longer time scale of a day, during which a wading bird may visit several foraging sites, the type of functional response can be considered to be patch centered. That is, it is influenced by the spatial configuration of sites with available prey and the wading bird’s strategy of choosing among different sites and decisions on how long to stay in any given sites. Over the time scale of a day, if the prey densities stay relatively constant, the patch-centered functional response for a constant environment is adequate. However, on the longer time scale of a breeding season, in which changing water levels result in temporal changes in the availability of prey in sites, a third hierarchical level may be relevant. At that scale, the way in which the landscape pattern changes through time, and how the wading bird responds, influences the functional response. This hierarchical concept applies to a colony of breeding wading birds foraging in wetlands such as the Everglades.

Frontiers in Ecology and Evolution

SiteOpt: An open-source R-package for site selection and portfolio optimization

Conservation planning involves identifying and selecting actions to best achieve objectives for managing natural, social and cultural resources. Conservation problems are often high dimensional when specified as combinatorial or portfolio problems and when multiple competing objectives are considered at varying spatial and temporal scales. Although analytical techniques such as modern portfolio theory (MPT) have been developed to address these complex problems, open source computational platforms for executing these approaches are not readily available. We present a user-friendly R-package called SiteOpt for optimization of binary decisions while explicitly considering environmental or economic uncertainty and the risk tolerance of decision makers. We illustrate the package with spatially-explicit site selection problems (i.e. spatial conservation planning), including an option for divestment (i.e. selling assets), when accounting for future uncertainties in designing conservation areas. The tool is applicable to both spatial and non-spatial problems, such as budget allocation or species selection. Constraints for spatial design and spatial dependencies (e.g. connectivity among sites) can also be specified in SiteOpt. Users can optimize site selection based on two competing objectives by solving for the Nash bargaining solution. Importantly, by quantifying uncertainty and asset spatial correlation, a measure of risk can be included as one such objective to be traded off against portfolio benefits. Thus, SiteOpt can be used to explicitly manage risk in portfolio-based spatial optimization. This tool facilitates decisions in a variety of problem settings, including reserve selection, invasive species management, allocation of law enforcement activities for conservation, budget allocation and asset selection under uncertainty and risk.

Ecography

Cape Romain partnership for coastal protection

This final report summarizes activities, outcomes, and lessons learned from a 3-year project titled “Climate Change Adaptation for Coastal National Wildlife Refuges” with the Cape Romain National Wildlife Refuge (NWR) and local partners in the surrounding South Carolina Lowcountry. The Lowcountry is classified as the 10-county area encompassing the coastal plain of South Carolina (this report specifically focuses on Berkeley, Charleston, and Georgetown Counties). The goals of this work, sponsored by the U.S. Geological Survey’s Southeast Climate Adaptation Science Center (SECASC), were to foster active engagement with stakeholders; to develop a comprehensive definition of adaptation problems faced by agencies, organizations, and individuals near the Cape Romain NWR that accounts for global change, local values, knowledge and perceptions; and to encourage social learning and building of effective networks and trust across South Carolina Lowcountry organizations and individuals. Although project scoping began at the scale of the Atlantic seaboard, by engaging with NWRs from Massachusetts to Florida, participating refuge personnel eventually selected the Cape Romain NWR to serve as a case study for testing our goals. The Cape Romain Partnership for Coastal Conservation was established to address global change impacts at a regional level and includes representation from Federal and State resource agencies, local conservation nongovernmental organizations, and organizations representing underserved community interests. Research topics, originating from discussions with Cape Romain Partnership for Coastal Conservation members, focused on quantifying key drivers of change including localized sea-level rise (SLR) predictions, estimates of coastal hurricane inundation as amplified by SLR, and urban growth trends and forecasts. These key drivers provided a foundation to engage stakeholders in planning exercises to begin a process of collective understanding and collaborative decision making. The goal of this process was to develop collective strategies of adaptation to enhance community and ecosystem resilience in the South Carolina Lowcountry. South Carolina’s Lowcountry is experiencing rapid environmental and social transformation because of SLR rates approaching twice the global average, chronic tidal flooding and catastrophic storm surges, erosion and loss of habitats that provide essential services to wildlife and humans, and increasing social polarization fueled by aggressive low-density urban growth and other forms of land conversion. To support characterizations of plausible future scenarios, we used available or, in some cases, developed new models to project future conditions of key environmental and social-economic drivers. Because of the imprecision of mean global SLR projections, the SECASC commissioned a climatological study to account for local conditions and multiple representative concentration pathways to project a tailored distribution of future sea levels. These projections were matched to SLR scenarios provided by existing models to anticipate the range of future coastal habitat changes in the South Carolina Lowcountry. SLR scenarios were also incorporated into existing storm-surge models, which do not account for alternate baseline sea levels, to project the local effects of future hurricanes. To evaluate the extent and effects of population growth and urban expansion, we relied on an existing urban-growth model to map the spatial distribution of land-conversion probabilities, the total area of which is predicted to increase twofold to threefold over the next 60 years. In addition to this simplified model, an econometric model is in development to account for nonlinear feedback dynamics in land value, land use, and ecosystem service production. Although not yet completed, the goals of this model are to produce more-detailed projections of growth dynamics and to allow predictions of development patterns resulting from alternate land-use planning policies and incentives. Collaborative planning for an uncertain future requires more than providing decision makers with information on future physical and ecological conditions; developing effective and consensual strategies must also integrate sociological values, multiple cultural perspectives, and an understanding of human behavior. To support broad stakeholder engagement in integrative approaches to adaptation planning, emphasis was placed on the importance of considering differences in how individuals perceive their environment and create meaning. Because cultural frameworks form the basis for perceptions and, ultimately, the behaviors of individuals and institutions, we describe a model of human behavior and how it can be used to understand the effect of cultural complexity and variation in perception on choices, behavioral change, and long-term maintenance of behaviors. We consider a model commonly used in the field of behavioral health that accommodates variation in human perception when describing stages of behavior and the dynamics of behavioral change. Tailoring communication and engagement activities to targeted stakeholders is likely to benefit from increased understanding of behavioral change processes. The complex nature of this problem limited the usefulness of a traditional decision-analytic approach, we explored alternative methods for engagement, collaborative learning and decision making. Recognizing that project partners and Lowcountry stakeholders may be at different stages of preparedness and interest level for modifying behavior as a function of global change, we facilitated a scenario-planning exercise to familiarize partners with this well-established approach for communicating the opportunities and threats arising under alternative, plausible futures. We developed narratives for four alternative South Carolina Lowcountry scenarios to be used in later strategic planning that focus on quantitative trends for three primary drivers with high impact and high uncertainty: manifestations of climate change, social-political shifts at a global level, and forces of local value and power structures. This scenario-planning exercise underscored the complex relation between the temporospatial scale of the production of ecological goods and services and the institutional scale at which they are managed. We then guided the partners through an assessment of the relevant strengths and weaknesses of the Cape Romain Partnership for Coastal Protection, using the threats and opportunities characterized by each scenario to understand how the partnership might respond when attempting to meet conservation and societal objectives. The partnership identified key strengths including partnership experience, outreach and technical capacities, a substantial conservation land base, and high social cohesion in the South Carolina Lowcountry. Limited communication expertise, institutional inertia, and insufficient staffing and funding were recognized as important weaknesses across the partnership. By examining and scoring combinations of internal strengths and weaknesses and external threats and opportunities, the partnership developed sets of prioritized strategies to consider in the context of a given scenario. Although we had insufficient time to examine all scenarios in detail, the intent was to identify a portfolio of strategic actions to address threats and opportunities represented in multiple plausible futures. Top-ranking strategies encompassed a range of actions that focused on strengthening the conservation community and communicating the benefits of nature (that is, ecosystem services) to leveraging partnerships to expand land protection. This report also details the methods and preliminary results of several models developed or applied in support of this project. Two parcel-selection algorithms were used to evaluate anticipated habitat changes and patterns of urban growth to guide decisions on optimal conservation reserve design to protect habitat communities. One approach used a widely available planning software (MARXAN) to maximize conservation benefits near the Cape Romain NWR, whereas the other approach was a novel application of economic theory to account for uncertainty in future conditions and for the risks of unanticipated habitat loss. This latter model applies modern portfolio theory to estimate the risk of investing in any portfolio of land parcels (that is, candidate “reserves”) under climate-change uncertainty by quantifying the variation and spatial correlation of conservation benefits derived from each portfolio. We expanded the range of actions beyond simply whether or not to invest in a set of land parcels, an approach commonly used in spatial conservation planning, to also include consideration of divestment from currently protected lands. Such refinements allow for better accounting of system dynamics and can evaluate the benefits of flexible conservation tools such as rolling easements. Model results were conditional on a decision maker’s risk tolerance but highlighted general strategies of land conservation to increase future habitat representation beyond what is expected under the current protected land base. We built models that may help inform coastal planning by estimating salinity dynamics and the performance of oyster reef restoration efforts to predict the combined effects of global change and management of freshwater flows on coastal habitats and the processes that contribute to their resilience. These models can support restoration decisions by evaluating the expected benefits of site locations for shoreline protection and fisheries production. Lastly, we developed a spatially explicit economic model that predicts feedback dynamics among land value, land-use change, and effects on ecosystem service provision to explore zoning policies and incentives on urban growth and ecosystem services. We summarize these efforts with insights and considerations for the Cape Romain Partnership for Coastal Protection to continue to engage stakeholders in effective adaptation planning. First, notions of place attachment (referred to as sense of place), and the role of culture in social discourse are increasingly being used to understand the complex interactions between society and the environment and how societies respond and adapt to climate change. Sense of place was a unifying theme whenever the future of the South Carolina Lowcountry was discussed. The contribution of the South Carolina Lowcountry’s environmental wealth, rich cultural heritage, and quality of life to sense of place has important implications for how adaptation planning might best be pursued. More community-based governance of the commons (in other words, natural and cultural resources held in common), in which broad stakeholder participation and power sharing are key elements, is considered important. This devolution of governance is characterized by polycentric institutions and self-organizing social networks that promote a local culture of knowledge sharing, problem solving, and learning. These so-called bridging organizations (or individuals) often provide the leadership necessary to bring together potentially disparate Government agencies and institutions, private organizations, and individuals in a collective process of problem solving. Our observations also suggest that the conservation community in the South Carolina Lowcountry views its activities as integral to the broader governance of social-ecological systems, in which responses to the forces of global change are mediated through culture, economics, and politics. Rather than directly competing with other interests, the South Carolina Lowcountry conservation community seems to embrace an interpretation of conservation in which the fundamental objective is the quality of human life rather than environmental protection. Fundamental to the types of governance reforms described above is the notion of coproduction, in which experts and users collaborate to develop a shared body of knowledge. In this approach, scientists work with stakeholders to help frame questions, design research, and collect and analyze data. Such sustained collaborations are increasingly believed to be an effective way to produce useable (or actionable) science. The emphasis on social learning, leveraging strong social networks, coordinating and deliberating among diverse stakeholders, and applying principles of adaptive management is an essential contribution to adaptive capacity. The diverse and robust set of scientific approaches, methods to help stakeholders collaborate in effective and goal-driven planning processes, and decision tools resulting from this project hopefully will assist Cape Romain NWR and its partners prepare for climatic, ecological, and social changes over the coming decades.

South Carolina

Estimating the influence of oyster reef chains on freshwater detention at the estuary scale using Landsat-8 imagery

Oyster reef chains grow in response to local hydrodynamics and can redirect flows, particularly when reef chains grow perpendicular to freshwater flow paths. Singularly, oyster reef chains can act as porous dams that may facilitate nearshore accumulation of fresh or low-salinity water, in turn creating intermediate salinities that support oyster growth and estuarine conditions. However, oyster-driven freshwater detention has only been confirmed by limited, point-scale observational data, and simplified models. Oyster reef-driven freshwater detention in real ecosystems at the estuary scale remains largely unexplored. In this study, we analyzed the visible bands in 30-m resolution remote sensing (RS) images recorded by the Operational Land Imager aboard Landsat-8 to characterize the freshwater detention effect of oyster reef chains across a set of hydrologic conditions. Our results support prior findings indicating that 30-m resolution RS images recorded by the Operational Land Imager aboard Landsat-8 are useful for analyzing coastal dynamics after atmospheric correction, despite having been originally designed for terrestrial studies. Statistical models of water-leaving reflectance revealed that freshwater detention by oyster reefs was evident across the estuary, with the greatest effect occurring in the region closest to shore. Additionally, statistical modeling results and spatial patterns apparent in the satellite images suggested that reef-driven freshwater detention occurred under high riverine discharge conditions, but was less evident when flow was low. Beyond offering insight on the potential role of oyster reefs as mediators of estuarine hydrology, this study presents a transferable methodological framework for exploring estuarine biophysical feedbacks in blackwater river estuaries using satellite remote sensing.

Florida

Modeling structural mechanics of oyster reef self-organization including environmental constraints and community interactions

Self-organization is a process of establishing and reinforcing local structures through feedbacks between internal population dynamics and external factors. In reef-building systems, substrate is collectively engineered by individuals that also occupy it and compete for space. Reefs are constrained spatially by the physical environment, and by mortality, which reduces production but exposes substrate for recruits. Reef self-organization therefore depends on efficient balancing of production and occupancy of substrate. To examine this, we develop a three-dimensional individual-based model (IBM) of oyster reef mechanics. Shell substrate is grown by individuals as valves, accumulates at the reef level, and degrades following mortality. Single restoration events and subsequent dynamics are simulated for a case study in South Carolina (USA). Variability in model processes is included on recruitment, spatial environmental constraints, and predation, over multiple independent runs and five predator community scenarios. The main goal for this study is to summarize trends in dynamics that are robust across this uncertainty, and from these generate new hypotheses and predictions for future studies. Simulation results demonstrate three phases following restoration: initial transient dynamics with considerable shell loss, followed by growth and saturation of the live population, and then saturation of settlement habitat several years later. Over half of simulations recoup initial shell losses as populations grow, while others continue in decline. The balance between population density, substrate supporting the reef, and exposed surfaces for settlement is mediated by overall population size and size structure, presence of predators, and relative amounts of live individuals and intact dead shells. The efficiency of settlement substrate production improves through time as population size structure becomes more complex, and the population of dead valves accumulates.

Ecological Modelling

Trends in oyster populations in the northeastern Gulf of Mexico: An assessment of river discharge and fishing effects over time and space

Within the Big Bend region of the northeastern Gulf of Mexico, one of the least developed coastlines in the continental USA, intertidal and subtidal populations of eastern oyster Crassostrea virginica (hereafter referred to as “oyster”) are a critical ecosystem and important economic constituent. We assessed trends in intertidal oyster populations, river discharge, and commercial fishing activity in the Suwannee River estuary within the Big Bend region using fisheries‐independent data from irregular monitoring efforts and publicly available environmental data. We used generalized linear models to evaluate counts of oysters from line‐transect surveys over time and space. We assessed model performance using simulation to understand potential bias and then evaluated whether these counts were related to freshwater inputs from the Suwannee River and commercial oyster fishing effort and landings at different time lags. We found that intertidal oyster counts have declined over time and that most of these declines are found in inshore intertidal oyster bars, which are becoming degraded. We also found a significant relationship between oyster counts and a 1‐year lag on mean daily Suwannee River discharge, but including commercial fishery trips or landings did not improve model fit. It is unclear whether declines in intertidal oyster bars are offset by formation of new oyster reefs elsewhere. These results quantify rapid declines in intertidal oyster reefs in a region of coastline with high conservation value that can be used to inform ongoing and proposed restoration projects in the region.

Florida

Spatial conservation planning under uncertainty using modern portfolio theory and nash bargaining solution

In recent years, researchers from interdisciplinary teams involving ecologists, economists and operations re- searchers collaborated to provide decision support tools to address the challenges of preserving biodiversity by optimizing the design of reserves. The goal of this paper is to further advance this area of research and provide new solutions to solve complex Spatial Conservation Planning (SCP) problems under uncertainty that consider risk preferences of decision makers. Our approach employs modern portfolio theory to address uncertainties in SCP problems, and involves two conflicting objectives: maximizing return and minimizing risk. We apply concepts from game theory such as the Nash bargaining solution to directly compute a desirable Pareto-optimal solution for the proposed bi-objective optimization formulation in natural resource management problems. We demonstrate with numerical examples that by directly computing a Nash bar- gaining solution, a Binary Quadratically Constrained Quadratic Program (BQCQP) can be solved. We show that our approach (implementable with commercial solvers such as CPLEX) can effectively solve the proposed BQCQP for much larger problems than previous approaches published in the ecological literature. Optimal solutions for problems with less than 400 parcels can be computed within a minute. Near optimal solutions (within at most 0.2% gap from an optimal solution) for high-dimensional problems involving up to 800 parcels can be computed within 8 hours on a standard computer. We have presented a new approach to solve SCP optimization problems while considering uncertainty and risk tolerance of decision makers. Our new approach expands considerably the applicability of such SCP optimization methods to address real conservation problems.

Ecological Modelling

Spatial conservation planning under uncertainty: Adapting to climate change risks using modern portfolio theory

Climate change and urban growth impact habitats, species, and ecosystem services. To buffer against global change, an established adaptation strategy is designing protected areas to increase representation and complementarity of biodiversity features. Uncertainty regarding the scale and magnitude of landscape change complicates reserve planning and exposes decision makers to risk of failing to meet conservation goals. Conservation planning tends to treat risk as an absolute measure, ignoring the context of the management problem and risk preferences of stakeholders. Application to conservation of risk management theory emphasizes diversification of portfolio of assets, with the goal of reducing the impact of system volatility on investment return. We use principles of Modern Portfolio Theory (MPT), which quantifies risk as the variance and correlation among assets, to formalize diversification as an explicit strategy for managing risk in climate‐driven reserve design. We extend MPT to specify a framework that evaluates multiple conservation objectives, allows decision makers to balance management benefits and risk when preferences are contested or unknown, and includes additional decision options such as parcel divestment when evaluating candidate reserve designs. We apply an efficient search algorithm that optimizes portfolio design for large conservation problems and a game theoretic approach to evaluate portfolio tradeoffs that satisfy decision makers with divergent benefit and risk tolerances, or when a single decision maker cannot resolve their own preferences. Evaluating several risk profiles for a case study in South Carolina, our results suggest that a reserve design may be somewhat robust to differences in risk attitude but that budgets will likely be important determinants of conservation planning strategies, particularly when divestment is considered a viable alternative. We identify a possible fiscal threshold where adequate resources allow protecting a sufficiently diverse portfolio of habitats such that the risk of failing to achieve conservation objectives is considerably lower. For a range of sea‐level rise projections, conversion of habitat to open water (14‐180%) and wetland loss (1‐7%) are unable to be compensated under the current protected network. In contrast, optimal reserve design outcomes are predicted to ameliorate expected losses relative to current and future habitat protected under the existing conservation estate.

South Carolina

Resource concentration mechanisms facilitate foraging success in simulations of a pulsed oligotrophic wetland

Context Movement of prey on hydrologically pulsed, spatially heterogeneous wetlands can result in transient, high prey concentrations, when changes in landscape features such as connectivity between flooded areas alternately facilitate and impede prey movement. Predators track and exploit these concentrations, depleting them as they arise. Objectives We sought to describe how prey pulses of fish rapidly form and persist on wetland landscapes, while enduring constant consumption by wading birds, without being fully depleted. Specifically, we questioned how is the predator–prey relationship mediated by interactions between animal movement and dynamic landscape connectivity? Methods Two models were developed of the predator–prey-landscape system with qualitatively different representations of space, to identify and quantify prey pulsing dynamics that were robust across modeled assumptions. The first included a homogeneous landscape described by simple geometry, and implicit fish movement as wetland volume contracts. The second modeled transverse movement across a heterogeneous landscape, with isolated drying patches. Results Both models produced rapid fish prey concentrations as the wetland dried to shallow water depths. These conditions are critical for making prey available to wading birds. Fish were also rapidly depleted by birds, representing daily caloric intake supporting birds. Model 1 provided average estimates across the modeled domain. Model 2 mapped locations of emerging prey hotspots on the landscape through time. Conclusions Our models tracked predator, prey, and landscape dynamics in parallel, inducing systems dynamics from empirical observations. Explicit inclusion of dynamic wetland hydrologic connectivity, a key landscape mechanism, allowed for a comprehensive picture of links between landscape dynamics and the adapted predator–prey system.

Landscape Ecology

Spatially explicit modeling in ecology: A review

The use of spatially explicit models (SEMs) in ecology has grown enormously in the past two decades. One major advancement has been that fine-scale details of landscapes, and of spatially dependent biological processes, such as dispersal and invasion, can now be simulated with great precision, due to improvements in computer technology. Many areas of modeling have shifted toward a focus on capturing these fine-scale details, to improve mechanistic understanding of ecosystems. However, spatially implicit models (SIMs) have played a dominant role in ecology, and arguments have been made that SIMs, which account for the effects of space without specifying spatial positions, have an advantage of being simpler and more broadly applicable, perhaps contributing more to understanding. We address this debate by comparing SEMs and SIMs in examples from the past few decades of modeling research. We argue that, although SIMs have been the dominant approach in the incorporation of space in theoretical ecology, SEMs have unique advantages for addressing pragmatic questions concerning species populations or communities in specific places, because local conditions, such as spatial heterogeneities, organism behaviors, and other contingencies, produce dynamics and patterns that usually cannot be incorporated into simpler SIMs. SEMs are also able to describe mechanisms at the local scale that can create amplifying positive feedbacks at that scale, creating emergent patterns at larger scales, and therefore are important to basic ecological theory. We review the use of SEMs at the level of populations, interacting populations, food webs, and ecosystems and argue that SEMs are not only essential in pragmatic issues, but must play a role in the understanding of causal relationships on landscapes.

Ecosystems

Persistence and diversity of directional landscape connectivity improves biomass pulsing in expanding and contracting wetlands

In flood-pulsed ecosystems, hydrology and landscape structure mediate transfers of energy up the food chain by expanding and contracting in area, enabling spatial expansion and growth of fish populations during rising water levels, and subsequent concentration during the drying phase. Connectivity of flooded areas is dynamic as waters rise and fall, and is largely determined by landscape geomorphology and anisotropy. We developed a methodology for simulating fish dispersal and concentration on spatially-explicit, dynamic floodplain wetlands with pulsed food web dynamics, to evaluate how changes in connectivity through time contribute to the concentration of fish biomass that is essential for higher trophic levels. The model also tracks a connectivity index (DCI) over different compass directions to see if fish biomass dynamics can be related in a simple way to topographic pattern. We demonstrate the model for a seasonally flood-pulsed, oligotrophic system, the Everglades, where flow regimes have been greatly altered. Three dispersing populations of functional fish groups were simulated with empirically-based dispersal rules on two landscapes, and two twelve-year time series of managed water levels for those areas were applied. The topographies of the simulations represented intact and degraded ridge-and-slough landscapes (RSL). Simulation results showed large pulses of biomass concentration forming during the onset of the drying phase, when water levels were falling and fish began to converge into the sloughs. As water levels fell below the ridges, DCI declined over different directions, closing down dispersal lanes, and fish density spiked. Persistence of intermediate levels of connectivity on the intact RSL enabled persistent concentration events throughout the drying phase. The intact landscape also buffered effects of wet season population growth. Water level reversals on both landscapes negatively affected fish densities by depleting fish populations without allowing enough time for them to regenerate. Testable, spatiotemporal predictions of the timing, location, duration, and magnitude of fish concentration pulses were produced by the model, and can be applied to restoration planning.

Ecological Complexity