@article{kibria_seekamp_xiao_dalyander_eaton_2024, title={Multi-criteria decision approach for climate adaptation of cultural resources along the Atlantic coast of the southeastern United States: Application of AHP method}, volume={43}, ISSN={["2212-0963"]}, url={https://doi.org/10.1016/j.crm.2024.100587}, DOI={10.1016/j.crm.2024.100587}, abstractNote={Prioritizing climate adaptation actions is often made difficult by stakeholders and decision-makers having multiple objectives, some of which may be competing. Transparent, transferable, and objective methods are needed to assess and weight different objectives for complex decisions with multiple interests. In this study, the Analytic Hierarchy Process (AHP) was used to examine priorities in managing cultural resources in the face of climate change at Cape Lookout National Seashore on the Atlantic coast of the southeastern United States. In this process, we conducted facilitated discussion sessions with the selected stakeholder representatives to elicit a comprehensive list of management objectives. Objectives were then merged into three categories: 1) Maximizing Historic Character and Condition Retention (HCC); 2) Fostering Heritage Awareness (HA); and 3) Maximizing Financial Benefits (FB). We facilitated two AHP exercise sessions, both individually and in groups, to seek consensus on the relative importance of the objectives. The AHP process created a space for stakeholders (government agencies and local citizens) to consider and present arguments that we used to contextualize their trade-offs between the objectives. The stakeholders' top priority was to maximize the HCC. This objective was prioritized more than HA and FB in the individual trade-off choices, while HA was given nearly equal priority to FB. The consensus priority vectors of two management objectives (HCC and HA) differ significantly from FB, but the difference between HCC and HA is slight and not statistically different. FB and HA had larger changes in consensus priority vectors among the three objectives relative to individual priority vectors. For HCC, the difference between individual and consensus priority vectors was the smallest and nearly equal. Moreover, very high levels of consistency were found in consensus priority trade-off discussions and AHP application. Our research highlights the advantage of using a two-step AHP process in climate adaptation planning of vulnerable resources to enhance robustness in decision making. Coupling this approach with future efforts to develop management priorities would help estimate indices to determine the order in which adaptation treatments are applied to vulnerable cultural resources.}, journal={CLIMATE RISK MANAGEMENT}, author={Kibria, Abu S. M. G. and Seekamp, Erin and Xiao, Xiao and Dalyander, Soupy and Eaton, Mitchell}, year={2024} }
 @article{martin_richardson_passeri_enwright_yurek_flocks_eaton_zeigler_charkhgard_udell_et al._2023, title={Decision science as a framework for combining geomorphological and ecological modeling for the management of coastal systems}, volume={28}, ISSN={["1708-3087"]}, DOI={10.5751/ES-13696-280150}, abstractNote={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.}, number={1}, journal={ECOLOGY AND SOCIETY}, author={Martin, Julien and Richardson, Matthew S. and Passeri, Davina L. and Enwright, Nicholas M. and Yurek, Simeon and Flocks, James G. and Eaton, Mitchell J. and Zeigler, Sara L. and Charkhgard, Hadi and Udell, Bradley J. and et al.}, year={2023}, month={Mar} }
 @article{yurek_allen_eaton_chagaris_reaver_martin_frederick_dehaven_2023, title={Quantifying uncertainty in coastal salinity regime for biological application using quantile regression}, volume={14}, ISSN={["2150-8925"]}, url={https://doi.org/10.1002/ecs2.4488}, DOI={10.1002/ecs2.4488}, abstractNote={Abstract 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.}, number={4}, journal={ECOSPHERE}, author={Yurek, Simeon and Allen, Micheal and Eaton, Mitchell J. and Chagaris, David and Reaver, Nathan and Martin, Julien and Frederick, Peter and Dehaven, Mark}, year={2023}, month={Apr} }
 @article{miller_eaton_symstad_schuurman_rangwala_travis_2023, title={Scenario-Based Decision Analysis: Integrated scenario planning and structured decision making for resource management under climate change}, volume={286}, ISSN={["1873-2917"]}, url={https://doi.org/10.1016/j.biocon.2023.110275}, DOI={10.1016/j.biocon.2023.110275}, abstractNote={Managing resources under climate change is a high-stakes and daunting task, especially because climate change and associated complex biophysical responses engender sustained directional changes as well as abrupt transformations. This environmental non-stationarity challenges assumptions and expectations among scientists, managers, rights holders, and stakeholders. These challenges are anything but straightforward – a high degree of uncertainty impedes our ability to predict the environmental trajectory with confidence, and affected resources often span multiple governance jurisdictions or are subject to competing management objectives. Fortunately, tools exist to help grapple with such challenges. Two commonly used tools are scenario planning (SP) and structured decision making (SDM). SP is a well-established approach for assessing system response and facilitating decision making under a wide range of conditions that are uncertain and uncontrollable, such as those associated with adapting to climate change. However, SP lacks a defined structure for establishing objectives, quantifying tradeoffs, and evaluating the performance of candidate decisions to meet those objectives. SDM, on the other hand, is rooted in decision theory and focuses on explicit (often quantitative) assessment of the expected outcomes of choosing among a set of decision alternatives. SDM has been criticized for an inability to account for surprises and for imposing an overly narrow framing of problems to increase tractability. We discuss the strengths and limitations of SDM and SP as experienced through their application in various resource-management contexts, and then propose a new generalized framework – Scenario-Based Decision Analysis (SBDA) – that integrates these complementary approaches. SBDA structures resource management problems and solutions while considering uncertainties and surprises to inform resource management decision making.}, journal={BIOLOGICAL CONSERVATION}, author={Miller, Brian W. and Eaton, Mitchell J. and Symstad, Amy J. and Schuurman, Gregor W. and Rangwala, Imtiaz and Travis, William R.}, year={2023}, month={Oct} }
 @book{garcía_eaton_sanchez_keisman_ullman_blackwell_2023, title={Value-aligned planning objectives for restoring North Carolina aquatic resources}, url={https://doi.org/10.3133/ofr20221058}, DOI={10.3133/ofr20221058}, abstractNote={First posted April 11, 2023 For additional information, contact: South Atlantic Water Science CenterU.S. Geological Survey3916 Sunset Ridge RoadRaleigh, NC 27607Contact Pubs Warehouse Rapid population growth and development in the southeastern United States have resulted in substantial impairment to freshwater aquatic ecosystems. National or regional restoration policies strive to address impaired ecosystems but can suffer from inconsistent and opaque processes. The Clean Water Act, for example, establishes reallocation mechanisms to transfer ecosystem services from sites of disturbance to compensation sites to offset aquatic resource functions that are unavoidably lost through land development. However, planning for the prioritization of compensatory mitigation areas is often hampered by unstructured decision-making processes that are narrowly framed because they are not co-produced with stakeholders affected by, or having an interest in, the impacts and mitigation. This summary report represents the collaborative efforts of the U.S. Geological Survey and the North Carolina Department of Environmental Quality, Division of Mitigation Services, to co-develop an applied decision framework following the principles of structured decision-making for prioritizing watershed catchments by their potential for realizing a range of beneficial outcomes from future mitigation projects. The framework focuses on supporting the State’s nationally recognized stream and wetlands compensatory mitigation program by clarifying a discrete decision problem and specifying agency and stakeholder values to formulate fundamental and means objectives for prioritizing restoration sites. The co-development of this decision framework resulted in a number of useful insights from the perspective of the decision maker, including recognition (1) that the problem is a multi-objective decision driven by values beyond restoring lost functionality of ecosystems (that is, biogeophysical goals), (2) that the decision comprises a linked and sequential planning-to-implementation process, and (3) that future risk associated with land-use and climate change must be considered. The outcomes of this collaboration can serve as a systematic and transparent framework to prioritize a wide range of restoration, conservation, and resource-allocation activities in similar environmental contexts across the Nation.}, author={García, Ana María and Eaton, Mitchell and Sanchez, Georgina M. and Keisman, Jennifer L. and Ullman, Kirsten and Blackwell, James}, year={2023} }
 @article{bisbal_eaton_2022, title={Considering science needs to deliver actionable science}, volume={11}, ISSN={["1523-1739"]}, url={https://doi.org/10.1111/cobi.14013}, DOI={10.1111/cobi.14013}, abstractNote={Conservation practitioners, natural resource managers, and environmental stewards often seek out scientific contributions to inform decision‐making. This body of science only becomes actionable when motivated by decision makers considering alternative courses of action. Many in the science community equate addressing stakeholder science needs with delivering actionable science. However, not all efforts to address science needs deliver actionable science, suggesting that the synonymous use of these two constructs (delivering actionable science and addressing science needs) is not trivial. This can be the case when such needs are conveyed by people who neglect decision makers responsible for articulating a priority management concern and for specifying how the anticipated scientific information will aid the decision‐making process. We argue that the actors responsible for articulating these science needs and the process used to identify them are decisive factors in the ability to deliver actionable science, stressing the importance of examining the provenance and the determination of science needs. Guided by a desire to enhance communication and cross‐literacy between scientists and decision makers, we identified categories of actors who may inappropriately declare science needs (e.g., applied scientists with and without regulatory affiliation, external influencers, reluctant decision makers, agents in place of decision makers, and boundary organization representatives). We also emphasize the importance of, and general approach to, undertaking needs assessments or gap analyses as a means to identify priority science needs. We conclude that basic stipulations to legitimize actionable science, such as the declaration of decisions of interest that motivate science needs and using a robust process to identify priority information gaps, are not always satisfied and require verification. To alleviate these shortcomings, we formulated practical suggestions for consideration by applied scientists, decision makers, research funding entities, and boundary organizations to help foster conditions that lead to science output being truly actionable.}, journal={CONSERVATION BIOLOGY}, author={Bisbal, Gustavo A. and Eaton, Mitchell J.}, year={2022}, month={Nov} }
 @article{hyman_courtney_mcneal_bialic-murphy_furiness_eaton_armsworth_2022, title={Distinct pathways to stakeholder use versus academic contribution in climate adaptation research}, volume={6}, ISSN={["1755-263X"]}, DOI={10.1111/conl.12892}, abstractNote={Challenges facing societies around the globe as they plan for and adapt to climate change are so large that usable, research‐driven recommendations to inform management actions are urgently needed. We sought to understand factors that influence the variation of academic contribution and use of collaborative research on climate change. We surveyed researchers (n = 31), program‐leaders (n = 5), and stakeholders (n = 81) from projects supported by a federally funded network across the United States. Our results suggest that peer‐reviewed publications do not lead to use, but frequency of meetings with stakeholders significantly increased use. Overall, the factors needed for projects to have high degrees of academic contributions are distinct from those needed to be useful to stakeholders. Furthermore, leadership perceptions of use of projects were significantly different from users. Our quantitative results can inform future requests for proposals and better enable researchers using collaborative approaches to conduct science that is more often used by stakeholders.}, journal={CONSERVATION LETTERS}, author={Hyman, Amanda A. and Courtney, Steph L. and McNeal, Karen S. and Bialic-Murphy, Lalasia and Furiness, Cari S. and Eaton, Mitchell J. and Armsworth, Paul R.}, year={2022}, month={Jun} }
 @article{sanchez_eaton_garcia_keisman_ullman_blackwell_meentemeyer_2022, title={Integrating principles and tools of decision science into value-driven watershed planning for compensatory mitigation}, volume={12}, ISSN={["1939-5582"]}, url={https://doi.org/10.1002/eap.2766}, DOI={10.1002/eap.2766}, abstractNote={Several environmental policies strive to restore impaired ecosystems and could benefit from a consistent and transparent process - co-developed with key stakeholders - to prioritize impaired ecosystems for restoration activities. The Clean Water Act, for example, establishes reallocation mechanisms to transfer ecosystem services from sites of disturbance to compensation sites to offset aquatic resource functions that are unavoidably lost through land development. However, planning for the prioritization of compensatory mitigation areas is often hampered by decision-making processes that fall into a myopic decision frame because they are not co-produced with stakeholders. In this study, we partnered with domain experts from the North Carolina Division of Mitigation Services (NCDMS) to co-develop a real-world decision framework to prioritize catchments by potential for the development of mitigation projects following principles of a structured decision-making process and knowledge co-production. Following an iterative decision analysis cycle, domain experts revised foundational components of the decision framework and progressively added complexity and realism as they gained additional insights or more information became available. Through the course of facilitated in-person and remote interactions, the co-development of a decision framework produced three main 'breakthroughs' from the perspective of the stakeholder group: a) recognition of the problem as a multi-objective decision driven by several values in addition to biogeophysical goals (e.g., functional uplift; restoring or enhancing lost functionality of ecosystems), b) that the decision comprises a linked and sequential planning-to-implementation process, and c) future risk associated with land-use and climate change must be considered. We also present an interactive tool for 'on-the-fly' assessment of alternatives and tradeoff analysis, allowing domain experts to quickly test, react to, and revise prioritization strategies. The decision framework described in this study is not limited to the prioritization of compensatory mitigation activities across North Carolina, but rather serves as a framework to prioritize a wide range of restoration, conservation, and resource allocation activities in similar environmental contexts across the nation.}, journal={ECOLOGICAL APPLICATIONS}, author={Sanchez, Georgina M. M. and Eaton, Mitchell J. J. and Garcia, Ana M. M. and Keisman, Jennifer and Ullman, Kirsten and Blackwell, James and Meentemeyer, Ross K. K.}, year={2022}, month={Dec} }
 @article{sollmann_eaton_link_mulondo_ayebare_prinsloo_plumptre_johnson_2021, title={A Bayesian Dirichlet process community occupancy model to estimate community structure and species similarity}, volume={31}, ISSN={["1939-5582"]}, url={https://doi.org/10.1002/eap.2249}, DOI={10.1002/eap.2249}, abstractNote={Community occupancy models estimate species-specific parameters while sharing information across species by treating parameters as sampled from a common distribution. When communities consist of discrete groups, shrinkage of estimates towards the community mean can mask differences among groups. Infinite mixture models using a Dirichlet process (DP) distribution, in which the number of latent groups is estimated from the data, have been proposed as a solution. In addition to community structure, these models estimate species similarity, which allows testing hypotheses about whether traits drive species response to environmental conditions. We develop a community occupancy model (COM) using a DP distribution to model species-level parameters. Because clustering algorithms are sensitive to dimensionality and distinctiveness of clusters, we conducted a simulation study to explore performance of the DP-COM with different dimensions (i.e., different numbers of model parameters with species-level DP random effects) and under varying cluster differences. Because the DP-COM is computationally expensive, we compared its estimates to a COM with a normal random species effect. We further applied the DP-COM model to a bird dataset from Uganda. Estimates of the number of clusters and species cluster identity improved with increasing difference among clusters and increasing dimensions of the DP; but the number of clusters was always overestimated. Estimates of number of sites occupied and species and community level covariate coefficients on occupancy probability were generally unbiased with (near-) nominal 95% Bayesian Credible Interval coverage. Accuracy of estimates from the normal and the DP-COM were similar. The DP-COM clustered 166 bird species into 27 clusters regarding their affiliation with open or woodland habitat and distance to oil wells. Estimates of covariate coefficients were similar between a normal and the DP-COM. Except sunbirds, species within a family were not more similar in their response to these covariates than the overall community. Given that estimates were consistent between the normal and the DP-COM, and considering the computational burden for the DP models, we recommend using the DP-COM only when the analysis focuses on community structure and species similarity, as these quantities can only be obtained under the DP-COM.}, number={2}, journal={ECOLOGICAL APPLICATIONS}, author={Sollmann, Rahel and Eaton, Mitchell Joseph and Link, William A. and Mulondo, Paul and Ayebare, Samuel and Prinsloo, Sarah and Plumptre, Andrew J. and Johnson, Devin S.}, year={2021}, month={Mar} }
 @book{eaton_johnson_mikels-carrasco_case_martin_stith_yurek_udell_villegas_taylor_et al._2021, title={Cape Romain partnership for coastal protection}, url={https://doi.org/10.3133/ofr20211021}, DOI={10.3133/ofr20211021}, abstractNote={First posted June 8, 2021 For additional information, contact: Director, Southeast Climate Adaptation Science CenterU.S. Geological Survey127 David Clark LabsRaleigh, NC 27695Contact Pubs Warehouse 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.}, author={Eaton, Mitchell J. and Johnson, Fred A. and Mikels-Carrasco, Jessica and Case, David J. and Martin, Julien and Stith, Bradley and Yurek, Simeon and Udell, Bradley and Villegas, Laura and Taylor, Laura and et al.}, year={2021} }
 @article{eaton_breininger_nichols_fackler_mcgee_smurl_demeyer_baker_zondervan_2021, title={Integrated hierarchical models to inform management of transitional habitat and the recovery of a habitat specialist}, volume={12}, ISSN={["2150-8925"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85099856834&partnerID=MN8TOARS}, DOI={10.1002/ecs2.3306}, abstractNote={. Quantifying the contribution of habitat dynamics relative to intrinsic population processes in regulating species persistence remains an ongoing challenge in ecological and applied conservation. Understanding these drivers and their relationship is essential for managing habitat-dependent species, especially those that specialize in transitional habitats. Limitations in the ability of natural disturbance to mediate transitional habitat dynamics have resulted in a decline in early- and mid-successional vegetation structure and prompted the need for aggressive habitat management to replace natural perturbations and increase habitat structural complexity. We describe a collaborative effort with a group of independent land managers to design an adaptive management program for restoring an imperiled ecosystem and recover-ing declining populations of an endemic habitat specialist. We developed a set of integrated, hierarchical models to estimate management-mediated transition rates among vegetation classes in two dominant scrub communities and the species response (local colonization and extinction probabilities) as a function of habitat state. Models were fi t using a long-term data set of habitat and occupancy observations from 361 Florida scrub-jay territories across two Florida counties. Occupancy model results correspond closely to previous approaches of estimating differential survival and reproductive success associated with habitat conditions, with highest colonization and lowest extinction rates estimated for those habitat states found to have the highest rates of survival and reproduction. In addition to offering an innovative approach for jointly modeling habitat and species population dynamics, the program we describe will also be of interest from a management perspective by providing guidance for developing collaborative, adaptive management frameworks from the ground up. We engaged land managers via workshops to specify objectives and desired state-variable conditions, identify management alternatives, and elicit consensus opinions on model parameters. Treating expert opinions as pseudo-observations to de fi ne Dirichlet priors allowed us to make use of existing management knowledge. Formal learning was then accumulated by updating transition probability estimates as management activities were implemented over the study period. We believe this adaptive management framework provides a useful approach for increasing our understanding of complex ecological relationships and hope that it will be adopted by others who have interest in informing management and conservation efforts.}, number={1}, journal={ECOSPHERE}, author={Eaton, Mitchell J. and Breininger, David R. and Nichols, James D. and Fackler, Paul L. and McGee, Samantha and Smurl, Michelle and DeMeyer, David and Baker, Jonny and Zondervan, Maria B.}, year={2021}, month={Jan} }
 @article{yurek_eaton_lavaud_laney_deangelis_pine_la peyre_martin_frederick_wang_et al._2021, title={Modeling structural mechanics of oyster reef self-organization including environmental constraints and community interactions}, volume={440}, ISSN={["1872-7026"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85098966344&partnerID=MN8TOARS}, DOI={10.1016/j.ecolmodel.2020.109389}, abstractNote={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.}, journal={ECOLOGICAL MODELLING}, author={Yurek, Simeon and Eaton, Mitchell J. and Lavaud, Romain and Laney, R. Wilson and DeAngelis, Donald L. and Pine, William E., III and La Peyre, Megan and Martin, Julien and Frederick, Peter and Wang, Hongqing and et al.}, year={2021}, month={Jan} }
 @article{xiao_seekamp_lu_eaton_burg_2021, title={Optimizing preservation for multiple types of historic structures under climate change}, volume={214}, ISSN={["1872-6062"]}, DOI={10.1016/j.lurbplan.2021.104165}, journal={LANDSCAPE AND URBAN PLANNING}, author={Xiao, Xiao and Seekamp, Erin and Lu, Junyu and Eaton, Mitchell and Burg, Max Post van der}, year={2021}, month={Oct} }
 @article{xiao_seekamp_lu_eaton_burg_2021, title={Optimizing preservation for multiple types of historic structures under climate change}, url={https://doi.org/10.1016/j.landurbplan.2021.104165}, DOI={10.1016/j.landurbplan.2021.104165}, abstractNote={Cultural resources in coastal parks and recreation areas are vulnerable to climate change. The US National Park Service (NPS) is facing the challenge of insufficient budget allocations for both maintenance and climate adaptation of historic structures. Research on adaptation planning for cultural resources has predominately focused on vulnerability assessments of heritage sites; however, few studies integrate multiple factors (e.g., vulnerability, cultural significance, use potential, and costs) that managers should consider when making tradeoff decisions about which cultural resources to prioritize for adaptation. Moreover, heritage sites typically include multiple types of cultural resources, and researchers have yet to examine such complex tradeoffs. This study applies the Optimal Preservation (OptiPres) Model as a decision support framework to evaluate the tradeoffs of adaptation actions among multiple types of historic structures—wooden buildings, masonry and concrete buildings, forts, and batteries—under varying budget scenarios. Results suggest that the resource values of different types of historic structures vary greatly under a range of budget scenarios, and tradeoffs have to be made among different types of historical structures to achieve optimal planning objectives. Moreover, periodic, incremental funding and partial maintenance are identified as optimal funding strategies for preservation needs of cost-intensive historic structures. Also, adaptative use of historical buildings (e.g., building occupancy) can improve the resource values when budgets are constrained. The OptiPres Model provides managers with a unique framework to inform adaptation planning efforts for a broad range of historic structures, which is transferable across coastal parks to enhance historic preservation planning under climate change.}, journal={Landscape and Urban Planning}, author={Xiao, Xiao and Seekamp, Erin and Lu, Junyu and Eaton, Mitchell and Burg, Max Post}, year={2021}, month={Oct} }
 @article{saghand_haider_charkhgard_eaton_martin_yurek_udell_2021, title={SiteOpt: an open-source R-package for site selection and portfolio optimization}, volume={9}, ISSN={["1600-0587"]}, DOI={10.1111/ecog.05717}, abstractNote={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.}, journal={ECOGRAPHY}, author={Saghand, Payman Ghasemi and Haider, Zulqarnain and Charkhgard, Hadi and Eaton, Mitchell and Martin, Julien and Yurek, Simeon and Udell, Bradley J.}, year={2021}, month={Sep} }
 @article{carlson_taylor_cronin_eaton_eckert_kaemingk_reid_trudeau_2020, title={A Social-Ecological Odyssey in Fisheries and Wildlife Management}, volume={45}, ISSN={["1548-8446"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85085133491&partnerID=MN8TOARS}, DOI={10.1002/fsh.10439}, abstractNote={FisheriesVolume 45, Issue 5 p. 238-243 Column: Transitions A Social–Ecological Odyssey in Fisheries and Wildlife Management Andrew K. Carlson, Corresponding Author andrewkc@princeton.edu orcid.org/0000-0002-6681-0853 Princeton University, Princeton Environmental Institute, M30 Guyot Hall, Princeton, NJ, 08544Search for more papers by this authorWilliam W. Taylor, Michigan State University, Center for Systems Integration and Sustainability, Department of Fisheries and Wildlife, East Lansing, MISearch for more papers by this authorMelissa R. Cronin, University of California, Santa Cruz, Department of Ecology and Evolutionary Biology, Santa Cruz, CASearch for more papers by this authorMitchell J. Eaton, orcid.org/0000-0001-7324-6333 U.S. Geological Survey, Southeast Climate Adaptation Science Center, North Carolina State University, Raleigh, NCSearch for more papers by this authorLauren E. Eckert, University of Victoria, Department of Geography, Victoria, BC, CanadaSearch for more papers by this authorMark A. Kaemingk, orcid.org/0000-0001-9588-4563 University of Nebraska–Lincoln, Nebraska Cooperative Fish and Wildlife Research Unit, and School of Natural Resources, Lincoln, NESearch for more papers by this authorAndrea J. Reid, Carleton University, Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Ottawa, ON, CanadaSearch for more papers by this authorAshley Trudeau, orcid.org/0000-0002-3988-9164 Rutgers University, Graduate Program in Ecology and Evolution, Department of Marine and Coastal Sciences, New Brunswick, NJSearch for more papers by this author Andrew K. Carlson, Corresponding Author andrewkc@princeton.edu orcid.org/0000-0002-6681-0853 Princeton University, Princeton Environmental Institute, M30 Guyot Hall, Princeton, NJ, 08544Search for more papers by this authorWilliam W. Taylor, Michigan State University, Center for Systems Integration and Sustainability, Department of Fisheries and Wildlife, East Lansing, MISearch for more papers by this authorMelissa R. Cronin, University of California, Santa Cruz, Department of Ecology and Evolutionary Biology, Santa Cruz, CASearch for more papers by this authorMitchell J. Eaton, orcid.org/0000-0001-7324-6333 U.S. Geological Survey, Southeast Climate Adaptation Science Center, North Carolina State University, Raleigh, NCSearch for more papers by this authorLauren E. Eckert, University of Victoria, Department of Geography, Victoria, BC, CanadaSearch for more papers by this authorMark A. Kaemingk, orcid.org/0000-0001-9588-4563 University of Nebraska–Lincoln, Nebraska Cooperative Fish and Wildlife Research Unit, and School of Natural Resources, Lincoln, NESearch for more papers by this authorAndrea J. Reid, Carleton University, Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Ottawa, ON, CanadaSearch for more papers by this authorAshley Trudeau, orcid.org/0000-0002-3988-9164 Rutgers University, Graduate Program in Ecology and Evolution, Department of Marine and Coastal Sciences, New Brunswick, NJSearch for more papers by this author First published: 07 May 2020 https://doi.org/10.1002/fsh.10439Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinked InRedditWechat Volume45, Issue5May 2020Pages 238-243 RelatedInformation}, number={5}, journal={FISHERIES}, author={Carlson, Andrew K. and Taylor, William W. and Cronin, Melissa R. and Eaton, Mitchell J. and Eckert, Lauren E. and Kaemingk, Mark A. and Reid, Andrea J. and Trudeau, Ashley}, year={2020}, month={May}, pages={238–243} }
 @book{smith_eaton_gannon_smith_derleth_katz_bosma_leduc_2020, title={A decision framework to analyze tide-gate options for restoration of the Herring River Estuary, Massachusetts}, url={https://doi.org/10.3133/ofr20191115}, DOI={10.3133/ofr20191115}, abstractNote={The collective set of decisions involved with the restoration of degraded wetlands is often more complex than considering only ecological responses and outcomes. Restoration is commonly driven by a complex interaction of social, economic, and ecological factors representing the mandate of resource stewards and the values of stakeholders. The authors worked with the Herring River Restoration Committee (HRRC) to develop a decision framework to understand the implications of complex tradeoffs and to guide decision mak ing for the restoration of the 1,100-acre Herring River estuary within Cape Cod National Seashore, which has been restricted from tidal influence for more than 100 years. The HRRC represents decision maker and stakeholder interests in the restoration process. For a 25-year planning horizon, decisions involve the rate at which newly constructed water-control structures allow tidal exchange, and the timing and location of implementing numerous secondary management options. Decisions affect multiple stakeholders, including residents of two adjacent towns who value the watershed for numerous benefits and whose economy relies on seasonal activities and aquaculture. System response to management decisions is characterized by a high degree of uncertainty and risk with positive and negative outcomes possible. Decision policies will affect biophysical (for example, sediment transport, dis charge of fecal coliform bacteria) and ecological (for example, vegetation response, fish passage, effects on shellfish) pro -cesses, as well as socioeconomic interests (for example, effects on property, viewscapes, recreation). The framework provides a structured approach for evaluating tradeoffs among multiple objectives (ecological and social) while appropriately characterizing relevant uncertainties and accounting for levels of risk tolerances and the values of decision makers and stakeholders. Consequences of tide-gate management options are predicted using a range of methods from quantitative physical process models to elicited expert judgement. The decision framework is presented, and the software developed to implement the tradeoff analysis is introduced. The results from an initial prototype analysis using a software application developed for analyses of tradeoffs and of sensitivity of the decision to risk and uncertainty are presented. The next step is to use the decision-support application to analyze options using improved predictions.}, author={Smith, David R. and Eaton, Mitchell J. and Gannon, Jill J. and Smith, Timothy P. and Derleth, Eric L. and Katz, Jonathan and Bosma, Kirk F. and Leduc, Elise}, year={2020} }
 @article{johnson_eaton_mikels-carrasco_case_2020, title={Building adaptive capacity in a coastal region experiencing global change}, volume={25}, ISSN={["1708-3087"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85090611746&partnerID=MN8TOARS}, DOI={10.5751/ES-11700-250309}, abstractNote={Coastal ecosystems in the eastern U.S. have been severely altered by human development, and climate change and other stressors are now further degrading the capacity of those ecological and social systems to remain resilient in the face of such disturbances. We sought to identify potential ways in which local conservation interests in the Lowcountry of South Carolina (USA) could participate in a social process of adaptation planning, and how that process might ultimately be broadened to engage a more diverse set of partners. We engaged participants through a combination of informal meetings, workshops, and other collaborative interactions to explore how the conservation community perceives and pursues its various missions, and how that community might confront the threats and opportunities in its future. Coproduction of knowledge and meaning were facilitated by collaborative scenario planning and strategic planning evaluation, which illuminated how the conservation community is integral to the broader governance of the region and highlighted how responses to forces of change are mediated through local culture, economics, and politics. We suggest an interpretation of conservation in which the fundamental objectives of both social and ecological systems might be prioritized in tandem, rather than narrowly focusing on environmental protection without consideration of the social landscape. Ultimately, adaptive capacity depends on the ability to act collectively, and social capital, trust, and organization greatly influence the capacity to act. Thus, we conclude that the presence of strong social networks, coordination and deliberation among diverse stakeholders, mechanisms for experiential feedback, and emphasis on social learning are key elements needed to build adaptive capacity. Central to the evolving perspective of governance of the commons is recognition that social and ecological systems are coupled; the issues and problems of one cannot be addressed without considering the consequences for the other. Moreover, a dominant theme emerging from our research and that of other scholars is the importance of culture and place attachment, which generates social cohesion and facilitates problem solving. These ideas have important implications for when, where, and how stakeholders are engaged to address the rapid changes being experienced by socialecological systems.}, number={3}, journal={ECOLOGY AND SOCIETY}, author={Johnson, Fred A. and Eaton, Mitchell J. and Mikels-Carrasco, Jessica and Case, David}, year={2020}, month={Sep} }
 @article{rubenstein_weiskopf_carter_eaton_johnson_lynch_miller_morelli_rodriguez_terando_et al._2020, title={Do empirical observations support commonly-held climate change range shift hypotheses? A systematic review protocol}, volume={9}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85085214365&partnerID=MN8TOARS}, DOI={10.1186/s13750-020-00194-9}, abstractNote={Among the most widely anticipated climate-related impacts to biodiversity are geographic range shifts, whereby species shift their spatial distribution in response to changing climate conditions. In particular, a series of commonly articulated hypotheses have emerged: species are expected to shift their distributions to higher latitudes, greater elevations, and deeper depths in response to climate change, reflecting an underlying hypothesis that species will move to cooler locations to track spatial changes in the temperature of their current range. Yet, many species are not demonstrating range shifts consistent with these hypotheses. Resolving this discrepancy and providing effective explanations for the observed variability in species’ range shifts is urgently needed to help support a range of natural resource management decisions. Here, we propose a protocol to review the body of evidence for commonly-held climate change range shift hypotheses at the species level focusing on observed latitudinal, longitudinal, elevational, and depth shifts in response to temperature and precipitation changes. We aim to answer the question: what is the impact of anthropogenic climate change (specifically changes in temperature and precipitation) on species ranges? In this review protocol, we propose to conduct a systematic search of literature from internet databases and search engines in English. Articles will be screened in a two-stage process (title/abstract and full text) to evaluate whether they meet a list of eligibility criteria (e.g., presents species-level data, compares > 1 time period). Initial data coding and extraction will be completed by four reviewers and checked by a secondary reviewer from among our co-authors. We will perform a formal meta-analysis to document estimated effect size using the subset of available range-shift data expressed in distance per time (e.g., km/decade). We will also use multinomial logistic regression models to assess the probability that species are shifting in a direction that supports our hypotheses (i.e. towards higher latitudes, greater elevations, and deeper depths). We will account for study methodology as a potential source of variation.}, number={1}, journal={Environmental Evidence}, author={Rubenstein, M.A. and Weiskopf, S.R. and Carter, S.L. and Eaton, M.J. and Johnson, C. and Lynch, A.J. and Miller, B.W. and Morelli, T.L. and Rodriguez, M.A. and Terando, A. and et al.}, year={2020} }
 @article{sierra-altamiranda_charkhgard_eaton_martin_yurek_udell_2020, title={Spatial conservation planning under uncertainty using modern portfolio theory and Nash bargaining solution}, volume={423}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85081119736&partnerID=MN8TOARS}, DOI={10.1016/j.ecolmodel.2020.109016}, abstractNote={In recent years, researchers from interdisciplinary teams involving ecologists, economists and operations researchers 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 bargaining 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 h 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.}, journal={Ecological Modelling}, author={Sierra-Altamiranda, A. and Charkhgard, H. and Eaton, M. and Martin, J. and Yurek, S. and Udell, B.J.}, year={2020} }
 @article{shea_eaton_mackenzie_2019, title={Implementation of an occupancy-based monitoring protocol for a widespread and cryptic species, the New England cottontail (Sylvilagus transitionalis)}, volume={46}, ISSN={["1448-5494"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85065719162&partnerID=MN8TOARS}, DOI={10.1071/WR18058}, abstractNote={Abstract Context. Designing effective long-term monitoring strategies is essential for managing wildlife populations. Implementing a cost-effective, practical monitoring program is especially challenging for widespread but locally rare species. Early successional habitat preferred by the New England cottontail (NEC) has become increasingly rare and fragmented, resulting in substantial declines from their peak distribution in the mid-1900s. The introduction of a possible competitor species, the eastern cottontail (EC), may also have played a role. Uncertainty surrounding how these factors have contributed to NEC declines has complicated management and necessitated development of an appropriate monitoring framework to understand possible drivers of distribution and dynamics. Aims. Because estimating species abundance is costly, we designed presence–absence surveys to estimate species distributions, test assumptions about competitive interactions, and improve understanding of demographic processes for eastern cottontails (EC) and New England cottontails (NEC). The survey protocol aimed to balance long-term management objectives with practical considerations associated with monitoring a widespread but uncommon species. Modelling data arising from these observations allow for estimation of covariate relationships between species status and environmental conditions including habitat and competition. The framework also allows inference about species status at unsurveyed locations. Methods. We designed a monitoring protocol to collect data across six north-eastern USA states and, using data collected from the first year of monitoring, fit a suite of single-season occupancy models to assess how abiotic and biotic factors influence NEC occurrence, correcting for imperfect detectability. Key results. Models did not provide substantial support for competitive interactions between EC and NEC. NEC occurrence patterns appear to be influenced by several remotely sensed habitat covariates (land-cover classes), a habitat-suitability index, and, to a lesser degree, plot-level habitat covariates (understorey density and canopy cover). Conclusions. We recommend continuing presence–absence monitoring and the development of dynamic occupancy models to provide further evidence regarding hypotheses of competitive interactions and habitat influences on the underlying dynamics of NEC occupancy. Implications. State and federal agencies responsible for conserving this and other threatened species can engage with researchers in thoughtful discussions, based on management objectives, regarding appropriate monitoring design to ensure that the allocation of monitoring efforts provides useful inference on population drivers to inform management intervention.}, number={3}, journal={WILDLIFE RESEARCH}, author={Shea, Colin P. and Eaton, Mitchell J. and MacKenzie, Darryl I.}, year={2019}, month={Mar}, pages={222–235} }
 @article{xiao_seekamp_van der burg_eaton_fatorić_mccreary_2019, title={Optimizing historic preservation under climate change: Decision support for cultural resource adaptation planning in national parks}, volume={83}, ISSN={0264-8377}, url={http://dx.doi.org/10.1016/j.landusepol.2019.02.011}, DOI={10.1016/j.landusepol.2019.02.011}, abstractNote={Climate change poses great challenges for cultural resource management, particularly in coastal areas. Cultural resources, such as historic buildings, in coastal areas are vulnerable to climate impacts including inundation, deterioration, and destruction from sea-level rise and storm-related flooding and erosion. However, research that assesses the trade-offs between actions for protecting vulnerable and valuable cultural resources under budgetary constraints is limited. This study focused on developing a decision support model for managing historic buildings at Cape Lookout National Seashore. We designed the Optimal Preservation Decision Support (OptiPres) model to: (a) identify optimal, annual adaptation actions for historic buildings across a 30-year planning horizon, (b) quantify trade-offs between different actions and the timing of adaptation actions under constrained budgets, and (c) estimate the effectiveness of budget allocations on the resource value of historic buildings. Our analysis of the model suggests that: (1) funding allocation thresholds may exist for national parks to maintain the historical significance and use potential of historic buildings under climate change, (2) the quantitative assessment of trade-offs among alternative adaptation actions provides generalizable guidance for decision makers about the dynamics of their managed system, and (3) the OptiPres model can identify cost-efficient approaches to allocate funding to maintain the historical value of buildings vulnerable to the effects of climate change. Therefore, the OptiPres model, while not designed as a prescriptive decision tool, allows managers to understand the consequences of proposed adaptation actions. The OptiPres model can guide park managers to make cost-effective climate adaptation decisions for historic buildings more transparently and robustly.}, journal={Land Use Policy}, publisher={Elsevier BV}, author={Xiao, Xiao and Seekamp, Erin and van der Burg, Max Post and Eaton, Mitchell and Fatorić, Sandra and McCreary, Allie}, year={2019}, month={Apr}, pages={379–389} }
 @misc{seekamp_post van der burg_fatorić_eaton_xiao_mccreary_2019, title={Optimizing historical preservation under climate change—An overview of the optimal preservation model and pilot testing at Cape Lookout National Seashore}, ISSN={2331-1258}, url={http://dx.doi.org/10.3133/ofr20181180}, DOI={10.3133/ofr20181180}, abstractNote={First posted April 9, 2019 For additional information, contact: National Climate Adaptation Science CenterU.S. Geological Survey12201 Sunrise Valley Drive, Mail Stop 516Reston, VA 20192Email: casc@usgs.gov Adapting cultural resources to climate-change effects challenges traditional cultural resource decision making because some adaptation strategies can negatively affect the integrity of cultural resources. Yet, the inevitability of climate-change effects—even given the uncertain timing of those effects—necessitates that managers begin prioritizing resources for climate-change adaptation. Prioritization imposes an additional management challenge: managers must make difficult tradeoffs to achieve desired management outcomes related to maximizing the resource values. This report provides an overview of a pilot effort to integrate vulnerability (exposure and sensitivity), significance, and use potential metrics in a decision framework—the Optimal Preservation (OptiPres) Model—to inform climate adaptation planning of a subset of buildings in historic districts (listed on the National Register of Historic Places) at Cape Lookout National Seashore. The OptiPres Model uses a numerical optimization algorithm to assess the timing and application of a portfolio of adaptation actions that could most effectively preserve an assortment of buildings associated with different histories, intended uses, and construction design and materials over a 30-year planning horizon. The outputs from the different budget scenarios, though not prescriptive, provide visualizations of and insights to the sequence and type of optimal actions and the changes to individual building resource values and accumulated resource values. Study findings suggest the OptiPres Model has planning utility related to fiscal efficiency by identifying a budget threshold necessary to maintain the historical significance and use potential of historical buildings while reducing vulnerability (collectively, the accumulated resource value). Specifically, findings identify that a minimum of the industry standard ($222,000 annually for the 17 buildings) is needed to maintain the current accumulated resource value. Additionally, results suggest that additional appropriations provided on regular intervals when annual appropriations are at the industry standard are nearly as efficient as annual appropriations at twice the rate of industry standards and increase the amount of accumulated resource values to nearly the same level. However, periodic increases in funding may increase the risks posed to buildings from the probability of a natural hazard (that is, damage or loss from a hurricane). Suggestions for model refinements include developing standardized cost estimations for adaptation actions based on square footage and building materials, developing metrics to quantify the historical integrity of buildings, integrating social values data, including additional objectives (such as public safety) in the model, refining vulnerability data and transforming the data to include risk assessment, and incorporating stochastic events (that is, hurricane and wind effects) into the model.}, journal={Open-File Report}, publisher={US Geological Survey}, author={Seekamp, Erin and Post van der Burg, Max and Fatorić, Sandra and Eaton, Mitchell J. and Xiao, Xiao and McCreary, Allie}, year={2019} }
 @article{eaton_yurek_haider_martin_johnson_udell_charkhgard_kwon_2019, title={Spatial conservation planning under uncertainty: adapting to climate change risks using modern portfolio theory}, volume={29}, ISSN={["1939-5582"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85072848761&partnerID=MN8TOARS}, DOI={10.1002/eap.1962}, abstractNote={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. This article is protected by copyright. All rights reserved.}, number={7}, journal={ECOLOGICAL APPLICATIONS}, author={Eaton, Mitchell J. and Yurek, Simeon and Haider, Zulqarnain and Martin, Julien and Johnson, Fred A. and Udell, Bradley J. and Charkhgard, Hadi and Kwon, Changhyun}, year={2019}, month={Oct} }
 @book{eaton_fuller_johnson_hare_stedman_2017, title={Application of decision science to resilience management in Jamaica Bay}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85008886557&partnerID=MN8TOARS}, DOI={10.5822/978-1-61091-734-6_10}, abstractNote={This book highlights the growing interest in management interventions designed to enhance the resilience of social-ecological systems (SESs) such as the Jamaica Bay watershed. Effective management requires decision makers to anticipate how the managed system will respond to interventions (i.e., via predictions or projections), whether the focus is on managing biological processes or human behavior or (most likely) both. In systems characterized by many interacting components and high uncertainty, however, making even probabilistic predictions is difficult.}, journal={Prospects for Resilience: Insights from New York City's Jamaica Bay}, author={Eaton, M.J. and Fuller, A.K. and Johnson, F.A. and Hare, M.P. and Stedman, R.C.}, year={2017}, pages={217–237} }
 @article{johnson_eaton_mcmahon_nilius_bryant_case_martin_wood_taylor_2015, title={Global change and conservation triage on National Wildlife Refuges}, volume={20}, ISSN={["1708-3087"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84953292871&partnerID=MN8TOARS}, DOI={10.5751/ES-07986-200414}, abstractNote={National Wildlife Refuges (NWRs) in the United States play an important role in the adaptation of social-ecological systems to climate change, land-use change, and other global-change processes. Coastal refuges are already experiencing threats from sea-level rise and other change processes that are largely beyond their ability to influence, while at the same time facing tighter budgets and reduced staff. We engaged in workshops with NWR managers along the U.S. Atlantic coast to understand the problems they face from global-change processes and began a multidisciplinary collaboration to use decision science to help address them. We are applying a values-focused approach to base management decisions on the resource objectives of land managers, as well as those of stakeholders who may benefit from the goods and services produced by a refuge. Two insights that emerged from our workshops were a conspicuous mismatch between the scale at which management can influence outcomes and the scale of environmental processes, and the need to consider objectives related to ecosystem goods and services that traditionally have not been explicitly considered by refuges (e.g., protection from storm surge). The broadening of objectives complicates the decision-making process, but also provides opportunities for collaboration with stakeholders who may have agendas different from those of the refuge, as well as an opportunity for addressing problems across scales. From a practical perspective, we recognized the need to (1) efficiently allocate limited staff time and budgets for short-term management of existing programs and resources under the current refuge design and (2) develop long-term priorities for acquiring or protecting new land/habitat to supplement or replace the existing refuge footprint and thus sustain refuge values as the system evolves over time. Structuring the decision-making problem in this manner facilitated a better understanding of the issues of scale and suggested that a long-term solution will require a significant reassessment of objectives to better reflect the comprehensive values of refuges to society. We discuss some future considerations to integrate these two problems into a single framework by developing novel optimization approaches for dynamic problems that account for uncertainty in future conditions.}, number={4}, journal={ECOLOGY AND SOCIETY}, author={Johnson, Fred A. and Eaton, Mitchell J. and McMahon, Gerard and Nilius, Raye and Bryant, Michael R. and Case, David J. and Martin, Julien and Wood, Nathan J. and Taylor, Laura}, year={2015} }
 @article{johnson_eaton_williams_jensen_madsen_2015, title={Training conservation practitioners to be better decision makers}, volume={7}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84938365635&partnerID=MN8TOARS}, DOI={10.3390/su7078354}, abstractNote={Traditional conservation curricula and training typically emphasizes only one part of systematic decision making ( i.e. , the science), at the expense of preparing conservation practitioners with critical skills in values-setting, working with decision makers and stakeholders, and effective problem framing. In this article we describe how the application of decision science is relevant to conservation problems and suggest how current and future conservation practitioners can be trained to be better decision makers. Though decision-analytic approaches vary considerably, they all involve: (1) properly formulating the decision problem; (2) specifying feasible alternative actions; and (3) selecting criteria for evaluating potential outcomes. Two approaches are available for providing training in decision science, with each serving different needs. Formal education is useful for providing simple, well-defined problems that allow demonstrations of the structure, axioms and general characteristics of a decision-analytic approach. In contrast, practical training can offer complex, realistic decision problems requiring more careful structuring and analysis than those used for formal training purposes. Ultimately, the kinds and degree of training necessary depend on the role conservation practitioners play in a decision-making process. Those attempting to facilitate decision-making processes will need advanced training in both technical aspects of decision science and in facilitation techniques, as well as opportunities to apprentice under decision analysts/consultants. Our primary goal should be an attempt to ingrain a discipline for applying clarity of thought to all decisions.}, number={7}, journal={Sustainability (Switzerland)}, author={Johnson, F.A. and Eaton, M.J. and Williams, J.H. and Jensen, G.H. and Madsen, J.}, year={2015}, pages={8354–8373} }
 @book{eaton_martin_nichols_mcintyre_mccluskie_schmutz_lubow_runge_2014, title={Application of threshold concepts to ecological management problems: Occupancy of Golden Eagles in Denali National Park, Alaska}, volume={9781489980410}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84929886312&partnerID=MN8TOARS}, DOI={10.1007/978-1-4899-8041-0_5}, journal={Application of Threshold Concepts in Natural Resource Decision Making}, author={Eaton, M.J. and Martin, J. and Nichols, J.D. and McIntyre, C. and McCluskie, M.C. and Schmutz, J.A. and Lubow, B.L. and Runge, M.C.}, year={2014}, pages={67–86} }
 @article{breininger_duncan_eaton_johnson_nichols_2014, title={Integrating land cover modeling and adaptive management to conserve endangered species and reduce catastrophic fire risk}, volume={3}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84977845645&partnerID=MN8TOARS}, DOI={10.3390/land3030874}, abstractNote={Land cover modeling is used to inform land management, but most often via a two-step process, where science informs how management alternatives can influence resources, and then, decision makers can use this information to make decisions. A more efficient process is to directly integrate science and decision-making, where science allows us to learn in order to better accomplish management objectives and is developed to address specific decisions. Co-development of management and science is especially productive when decisions are complicated by multiple objectives and impeded by uncertainty. Multiple objectives can be met by the specification of tradeoffs, and relevant uncertainty can be addressed through targeted science ( i.e. , models and monitoring). We describe how to integrate habitat and fuel monitoring with decision-making focused on the dual objectives of managing for endangered species and minimizing catastrophic fire risk. Under certain conditions, both objectives might be achieved by a similar management policy; other conditions require tradeoffs between objectives. Knowledge about system responses to actions can be informed by developing hypotheses based on ideas about fire behavior and then applying competing management actions to different land units in the same system state. Monitoring and management integration is important to optimize state-specific management decisions and to increase knowledge about system responses. We believe this approach has broad utility and identifies a clear role for land cover modeling programs intended to inform decision-making.}, number={3}, journal={Land}, author={Breininger, D. and Duncan, B. and Eaton, M. and Johnson, F. and Nichols, J.}, year={2014}, pages={874–897} }
 @article{eaton_hughes_hines_nichols_2014, title={Testing metapopulation concepts: effects of patch characteristics and neighborhood occupancy on the dynamics of an endangered lagomorph}, volume={123}, ISSN={["1600-0706"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84900429409&partnerID=MN8TOARS}, DOI={10.1111/oik.01008}, abstractNote={Metapopulation ecology is a field that is richer in theory than in empirical results. Many existing empirical studies use an incidence function approach based on spatial patterns and key assumptions about extinction and colonization rates. Here we recast these assumptions as hypotheses to be tested using 18 years of historic detection survey data combined with four years of data from a new monitoring program for the Lower Keys marsh rabbit. We developed a new model to estimate probabilities of local extinction and colonization in the presence of nondetection, while accounting for estimated occupancy levels of neighboring patches. We used model selection to identify important drivers of population turnover and estimate the effective neighborhood size for this system. Several key relationships related to patch size and isolation that are often assumed in metapopulation models were supported: patch size was negatively related to the probability of extinction and positively related to colonization, and estimated occupancy of neighboring patches was positively related to colonization and negatively related to extinction probabilities. This latter relationship suggested the existence of rescue effects. In our study system, we inferred that coastal patches experienced higher probabilities of extinction and colonization than interior patches. Interior patches exhibited higher occupancy probabilities and may serve as refugia, permitting colonization of coastal patches following disturbances such as hurricanes and storm surges. Our modeling approach should be useful for incorporating neighbor occupancy into future metapopulation analyses and in dealing with other historic occupancy surveys that may not include the recommended levels of sampling replication.}, number={6}, journal={OIKOS}, author={Eaton, Mitchell J. and Hughes, Phillip T. and Hines, James E. and Nichols, James D.}, year={2014}, month={Jun}, pages={662–676} }
 @book{nichols_eaton_martin_2014, title={Thresholds for conservation and management: Structured decision making as a conceptual framework}, volume={9781489980410}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84929885334&partnerID=MN8TOARS}, DOI={10.1007/978-1-4899-8041-0_2}, journal={Application of Threshold Concepts in Natural Resource Decision Making}, author={Nichols, J.D. and Eaton, M.J. and Martin, J.}, year={2014}, pages={9–28} }
 @article{laurance_carolina useche_rendeiro_kalka_bradshaw_sloan_laurance_campbell_abernethy_alvarez_et al._2012, title={Averting biodiversity collapse in tropical forest protected areas}, volume={489}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84866154510&partnerID=MN8TOARS}, DOI={10.1038/nature11318}, abstractNote={The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon. With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses. As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world’s major tropical regions. Our analysis reveals great variation in reserve ‘health’: about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.}, number={7415}, journal={Nature}, author={Laurance, W.F. and Carolina Useche, D. and Rendeiro, J. and Kalka, M. and Bradshaw, C.J.A. and Sloan, S.P. and Laurance, S.G. and Campbell, M. and Abernethy, K. and Alvarez, P. and et al.}, year={2012}, pages={290–293} }
 @article{link_eaton_2012, title={On thinning of chains in MCMC}, volume={3}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84867407667&partnerID=MN8TOARS}, DOI={10.1111/j.2041-210X.2011.00131.x}, abstractNote={1. Markov chain Monte Carlo (MCMC) is a simulation technique that has revolutionised the analysis of ecological data, allowing the fitting of complex models in a Bayesian framework. Since 2001, there have been nearly 200 papers using MCMC in publications of the Ecological Society of America and the British Ecological Society, including more than 75 in the journal Ecology and 35 in the Journal of Applied Ecology.}, number={1}, journal={Methods in Ecology and Evolution}, author={Link, W.A. and Eaton, M.J.}, year={2012}, pages={112–115} }
 @article{williams_eaton_breininger_2011, title={Adaptive resource management and the value of information}, volume={222}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80052929991&partnerID=MN8TOARS}, DOI={10.1016/j.ecolmodel.2011.07.003}, abstractNote={The value of information is a general and broadly applicable concept that has been used for several decades to aid in making decisions in the face of uncertainty. Yet there are relatively few examples of its use in ecology and natural resources management, and almost none that are framed in terms of the future impacts of management decisions. In this paper we discuss the value of information in a context of adaptive management, in which actions are taken sequentially over a timeframe and both future resource conditions and residual uncertainties about resource responses are taken into account. Our objective is to derive the value of reducing or eliminating uncertainty in adaptive decision making. We describe several measures of the value of information, with each based on management objectives that are appropriate for adaptive management. We highlight some mathematical properties of these measures, discuss their geometries, and illustrate them with an example in natural resources management. Accounting for the value of information can help to inform decisions about whether and how much to monitor resource conditions through time.}, number={18}, journal={Ecological Modelling}, author={Williams, B.K. and Eaton, M.J. and Breininger, D.R.}, year={2011}, pages={3429–3436} }
 @article{eaton_link_2011, title={Estimating age from recapture data: Integrating incremental growth measures with ancillary data to infer age-at-length}, volume={21}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80053945923&partnerID=MN8TOARS}, DOI={10.1890/10-0626.1}, abstractNote={Estimating the age of individuals in wild populations can be of fundamental importance for answering ecological questions, modeling population demographics, and managing exploited or threatened species. Significant effort has been devoted to determining age through the use of growth annuli, secondary physical characteristics related to age, and growth models. Many species, however, either do not exhibit physical characteristics useful for independent age validation or are too rare to justify sacrificing a large number of individuals to establish the relationship between size and age. Length-at-age models are well represented in the fisheries and other wildlife management literature. Many of these models overlook variation in growth rates of individuals and consider growth parameters as population parameters. More recent models have taken advantage of hierarchical structuring of parameters and Bayesian inference methods to allow for variation among individuals as functions of environmental covariates or individual-specific random effects. Here, we describe hierarchical models in which growth curves vary as individual-specific stochastic processes, and we show how these models can be fit using capture-recapture data for animals of unknown age along with data for animals of known age. We combine these independent data sources in a Bayesian analysis, distinguishing natural variation (among and within individuals) from measurement error. We illustrate using data for African dwarf crocodiles, comparing von Bertalanffy and logistic growth models. The analysis provides the means of predicting crocodile age, given a single measurement of head length. The von Bertalanffy was much better supported than the logistic growth model and predicted that dwarf crocodiles grow from 19.4 cm total length at birth to 32.9 cm in the first year and 45.3 cm by the end of their second year. Based on the minimum size of females observed with hatchlings, reproductive maturity was estimated to be at nine years. These size benchmarks are believed to represent thresholds for important demographic parameters; improved estimates of age, therefore, will increase the precision of population projection models. The modeling approach that we present can be applied to other species and offers significant advantages when multiple sources of data are available and traditional aging techniques are not practical.}, number={7}, journal={Ecological Applications}, author={Eaton, M.J. and Link, W.A.}, year={2011}, pages={2487–2497} }
 @article{eaton_hughes_nichols_morkill_anderson_2011, title={Spatial patch occupancy patterns of the Lower Keys marsh rabbit}, volume={75}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79959722099&partnerID=MN8TOARS}, DOI={10.1002/jwmg.152}, abstractNote={ABSTRACT 
 Reliable estimates of presence or absence of a species can provide substantial information on management questions related to distribution and habitat use but should incorporate the probability of detection to reduce bias. We surveyed for the endangered Lower Keys marsh rabbit (Sylvilagus palustris hefneri) in habitat patches on 5 Florida Key islands, USA, to estimate occupancy and detection probabilities. We derived detection probabilities using spatial replication of plots and evaluated hypotheses that patch location (coastal or interior) and patch size influence occupancy and detection. Results demonstrate that detection probability, given rabbits were present, was <0.5 and suggest that naïve estimates (i.e., estimates without consideration of imperfect detection) of patch occupancy are negatively biased. We found that patch size and location influenced probability of occupancy but not detection. Our findings will be used by Refuge managers to evaluate population trends of Lower Keys marsh rabbits from historical data and to guide management decisions for species recovery. The sampling and analytical methods we used may be useful for researchers and managers of other endangered lagomorphs and cryptic or fossorial animals occupying diverse habitats.}, number={5}, journal={Journal of Wildlife Management}, author={Eaton, M.J. and Hughes, P.T. and Nichols, J.D. and Morkill, A. and Anderson, C.}, year={2011}, pages={1186–1193} }
 @article{martin_fackler_nichols_lubow_eaton_runge_stith_langtimm_2011, title={Structured decision making as a proactive approach to dealing with sea level rise in Florida}, volume={107}, ISSN={["1573-1480"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79958814572&partnerID=MN8TOARS}, DOI={10.1007/s10584-011-0085-x}, number={1-2}, journal={CLIMATIC CHANGE}, author={Martin, Julien and Fackler, Paul L. and Nichols, James D. and Lubow, Bruce C. and Eaton, Mitchell J. and Runge, Michael C. and Stith, Bradley M. and Langtimm, Catherine A.}, year={2011}, month={Jul}, pages={185–202} }
 @article{eaton_meyers_kolokotronis_leslie_martin_amato_2010, title={Barcoding bushmeat: Molecular identification of Central African and South American harvested vertebrates}, volume={11}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77953912978&partnerID=MN8TOARS}, DOI={10.1007/s10592-009-9967-0}, abstractNote={The creation and use of a globally available database of DNA sequences from a standardized gene region has been proposed as a tool for species identification, assessing genetic diversity and monitoring the legal and illegal trade in wildlife species. Here, we contribute to the Barcode of Life Data System and test whether a short region of the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene would reliably distinguish among a suite of commonly hunted African and South American mammal and reptile species. We used universal primers to generate reference barcode sequences of 645 bp for 23 species from five vertebrate families (Crocodilidae, Alligatoridae, Bovidae, Suidae and Cercopithecidae). Primer cocktails yielded high quality barcode sequences for 179 out of 204 samples (87.7%) from all species included in the study. For most taxa, we sequenced multiple individuals to estimate intraspecific sequence variability and document fixed diagnostic characters for species identification. Polymorphism in the COX1 fragment was generally low (mean = 0.24%), while differences between congeneric species averaged 9.77%. Both fixed character differences and tree-based maximum likelihood distance methods unambiguously identified unknown and misidentified samples with a high degree of certainty. Barcode sequences also differentiated among newly identified lineages of African crocodiles and identified unusually high levels of genetic diversity in one species of African duiker. DNA barcoding offers promise as an effective tool for monitoring poaching and commercial trade in endangered species, especially when investigating semi-processed or morphologically indistinguishable wildlife products. We discuss additional benefits of barcoding to ecology and conservation.}, number={4}, journal={Conservation Genetics}, author={Eaton, M.J. and Meyers, G.L. and Kolokotronis, S.-O. and Leslie, M.S. and Martin, A.P. and Amato, G.}, year={2010}, pages={1389–1404} }
 @article{ntie_soto-calderon_eaton_anthony_2010, title={Cross-species amplification of bovid microsatellites in central African duikers (genus Cephalophus) and other sympatric artiodactyls}, volume={10}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-78650489297&partnerID=MN8TOARS}, DOI={10.1111/j.1755-0998.2010.02860.x}, abstractNote={The present study set out to evaluate cross‐species amplification of 34 bovid microsatellites in six central African duikers: Cephalophus callipygus, C. monticola, C. silvicultor, C. nigrifrons, C. dorsalis and C. leucogaster. Of these loci, 16 amplified across all species and appeared polymorphic when initially tested in polyacrylamide gel electrophoresis. Twelve of these loci were subsequently assembled into three multiplex panels of four loci each. These multiplexes successfully amplified across all six duiker species in the present study and the sympatric artiodactyls Tragelaphus spekei and Hyemoschus aquaticus. The only exception was the locus BM848 that did not amplify from C. leucogaster. For species with sufficient sample sizes (C. callipygus and C. monticola), the number of alleles ranged from three to ten and four to fifteen, respectively. Three loci deviated from Hardy–Weinberg equilibrium in C. callipygus and five in C. monticola. We attribute the latter result to possibilities of local population substructuring or to an excess of homozygotes because of null alleles. These multiplex assemblies will greatly facilitate studies of individual identification, parentage analysis, population size estimation and fine‐scale analyses of population genetic structure in central African artiodactyls.}, number={6}, journal={Molecular Ecology Resources}, author={Ntie, S. and Soto-Calderon, I.D. and Eaton, M.J. and Anthony, N.M.}, year={2010}, pages={1059–1065} }
 @article{eaton_martin_thorbjarnarson_amato_2009, title={Species-level diversification of African dwarf crocodiles (Genus Osteolaemus): A geographic and phylogenetic perspective}, volume={50}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-60349100247&partnerID=MN8TOARS}, DOI={10.1016/j.ympev.2008.11.009}, abstractNote={The taxonomy of the African dwarf crocodile (genus Osteolaemus) has been disputed since a novel morphotype was discovered in the early 20th Century. Because this poorly-known reptile is widely hunted throughout the forests of Central and West Africa, resolving the existence and extent of taxonomic units has important management and conservation implications. Lack of molecular data from individuals of known origin and historical disagreement on diagnostic morphological characters have hindered attempts to settle one of the most important taxonomic questions in the Crocodylia. In an effort to clarify the evolutionary relationships among dwarf crocodiles, we sequenced three mitochondrial and two nuclear genes using a large sample of dwarf crocodiles from known localities across major drainage basins of forested Africa. Concordant results from Bayesian, maximum likelihood, maximum parsimony and population aggregation analytical methods support a previously recognized division of the dwarf crocodile into a Congo Basin form (O. osborni) and a West African form (Osteolaemus tetraspis), but also reveal a third diagnosable lineage from West Africa warranting recognition as an separate taxonomic unit. Corrected genetic distances between geographic regions ranged from 0.2% to 0.6% in nuclear fragments and 10.0 to 16.2% in mitochondrial COI. Population aggregation, using fixed and alternate character (nucleotide) states to cluster or divide populations, recovered 232 such molecular characters in 4286 bp of sequence data and unambiguously aggregated populations into their respective geographic clade. Several previously recognized morphological differences coincide with our molecular analysis to distinguish Congo Basin crocodiles from the Ogooué Basin and West Africa. Discrete morphological characters have not yet been documented between the latter two regions, suggesting further work is needed or molecular data may be required to recognize taxonomic divisions in cases where putative species are morphologically cryptic. This study highlights the importance of using widespread taxon sampling and a multiple evidence approach to diagnose species boundaries and reveal cryptic diversity.}, number={3}, journal={Molecular Phylogenetics and Evolution}, author={Eaton, M.J. and Martin, A. and Thorbjarnarson, J. and Amato, G.}, year={2009}, pages={496–506} }