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At least 1,765 records · Page 98Linked to original sources

A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves)

The birds in the family Parulidae-commonly termed the New World warblers or wood-warblers-are a classic model radiation for studies of ecological and behavioral differentiation. Although the monophyly of a 'core' wood-warbler clade is well established, no phylogenetic hypothesis for this group has included a full sampling of wood-warbler species diversity. We used parsimony, maximum likelihood, and Bayesian methods to reconstruct relationships among all genera and nearly all wood-warbler species, based on a matrix of mitochondrial DNA (5840 nucleotides) and nuclear DNA (6 loci, 4602 nucleotides) characters. The resulting phylogenetic hypotheses provide a highly congruent picture of wood-warbler relationships, and indicate that the traditional generic classification of these birds recognizes many non-monophyletic groups. We recommend a revised taxonomy in which each of 14 genera (Seiurus, Helmitheros, Mniotilta, Limnothlypis, Protonotaria, Parkesia, Vermivora, Oreothlypis, Geothlypis, Setophaga, Myioborus, Cardellina, Basileuterus, Myiothlypis) corresponds to a well-supported clade; these nomenclatural changes also involve subsuming a number of well-known, traditional wood-warbler genera (Catharopeza, Dendroica, Ergaticus, Euthlypis, Leucopeza, Oporornis, Parula, Phaeothlypis, Wilsonia). We provide a summary phylogenetic hypothesis that will be broadly applicable to investigations of the historical biogeography, processes of diversification, and evolution of trait variation in this well studied avian group. ?? 2010 Elsevier Inc.

Molecular Phylogenetics and Evolution↗

Vascular Plant and Vertebrate Inventory of Chiricahua National Monument

This report summarizes the results of the first comprehensive inventory of vascular plants and vertebrates at Chiricahua National Monument (NM) in Arizona. This project was part of a larger effort to inventory vascular plants and vertebrates in eight National Park Service units in the Sonoran Desert Network of parks in Arizona and New Mexico. In 2002, 2003, and 2004 we surveyed for plants and vertebrates (amphibians, reptiles, birds, and mammals) at Chiricahua NM to document the presence of species within the boundaries of the monument. Because we used repeatable study designs and standardized field methods, these inventories can serve as the first step in a biological monitoring program for the monument. This report is also the first summary of previous research from the monument and therefore it provides an important overview of survey efforts to date. We used data from our inventory and previous research to compile complete species lists for the monument and to assess inventory completeness. We recorded a total of 424 species, including 37 not previously found at the monument (Table 1). We found 10 species of non-native plants and one non-native mammal. Most non-native plants were found along the western boundary of the monument. Based on a review of our inventory and past research at the monument, there have been a total of 1,137 species of plants and vertebrates found at the monument. We believe the inventories of vascular plants and vertebrates are nearly complete and that the monument has one of the most complete inventories of any unit in the Sonoran Desert Network. The mammal community at the monument had the highest species richness (69 species) and the amphibian and reptile community was among the lowest species richness (33 species) of any park in the Sonoran Desert Network. Species richness of the plant and bird communities was intermediate. Among the important determinants of species richness for all groups is the geographic location of the monument at the intergrades between the Chihuahuan and Sonoran deserts with influences from the Great Plains and Madrean ecological provinces. The diversity of plants results from a wide variety of soil types and aspects (from cool, moist canyons to semi-desert grasslands to pine forests). In turn, the vertebrate communities respond to this diversity of vegetation, topography, and microsites. For example, for each taxonomic group we found that some species were only associated with a single community type, most often the riparian areas or semi-desert grasslands. The area of highest species richness for most groups was the western-most portion of Bonita Canyon. The low species richness observed in the amphibian and reptile community was likely because the monument is at the elevational edge of the more species-rich semi-desert grasslands. This report includes management implications from our work and suggestions for how the monument staff might better maintain or enhance the unique biological resources of the monument. We suggest additional inventory, monitoring, and research studies and we identify components of our effort that could be improved upon, either through the application of new techniques (e.g., establishment of vegetation monitoring plots) or by extending the temporal and/or spatial scope of our work.

Open-File Report↗

Weed-suppressive bacteria applied as a spray or seed mixture did not control Bromus tectorum

We conducted two case studies testing effectiveness of a soil-borne bacteria, Pseudomonas fluorescens strain D7, in controlling Bromus tectorum (cheatgrass) and in affecting the density of sown desirable seedlings. We conducted two case studies testing D7’s ability to control of B. tectorum (cover, biomass and density) when mixed with native seeds sown after a fire and when sprayed on a native community with high abundances of B. tectorum. Each case study area (162 ha) compared treatments with D7 present and absent and was replicated four times (20.3 ha each) in a completely randomized design. Response variables (foliar cover, aboveground biomass, and density of B. tectorum; density of sown native plants) were measured pretreatment for the sprayed area and each year for three years after treatment at both study areas and were evaluated as a repeated measures analysis. Foliar cover, biomass, and density of B. tectorum with sprayed or seed mixture applications did not differ between D7-treated and untreated areas at any time within the study (F1,6 ≤ 1.42; p ≥ 0.28). D7 as a seed mixture did not significantly impact densities of native seedlings (F1,6 = 1.27; p = 0.30) at any time during the study. Results contrasted with previous D7 studies that showed effective control of B. tectorum within three years of treatment. Since bioherbicidal methods are being commonly applied, we believe that reporting negative results are important for future meta-analytical studies that provide managers with information on the likelihood for weed suppressive bacteria to effectively control weeds.

Rangeland Ecology and Management↗

Museum genomics provide evidence for persistent genetic differentiation in a threatened seabird species in the Western Atlantic

Connectivity among wildlife populations facilitates exchange of genetic material between groups. Changes to historical connectivity patterns resulting from anthropogenic activities can therefore have negative consequences for genetic diversity, particularly for small or isolated populations. DNA obtained from museum specimens can enable direct comparison of temporal changes in connectivity among populations, which can aid in conservation planning and contribute to understanding of population declines. However, museum DNA can be degraded and only available in low quantities, rendering it challenging for use in population genomic analyses. Applications of genomic methodologies such as targeted sequencing address this issue by enabling capture of shared variable sites, increasing quantity and quality of recovered genomic information. We used targeted sequencing of Ultra-conserved Elements (UCEs) to evaluate potential changes in connectivity and genetic diversity of roseate terns ( Sterna dougallii ) with a breeding distribution in the Northwestern Atlantic and the Caribbean. Both populations experienced range contractions and population declines due to anthropogenic activity in the 20 th century, which has the potential to alter historical connectivity regimes. Instead, we found that the two populations were differentiated historically as well as contemporaneously, with little evidence of migration between them for either time period. We also found no evidence for temporal changes in genetic diversity, although these interpretations may have been limited due to sequencing artifacts caused by the degraded nature of the museum samples. Population structuring in migratory seabirds is typically reflective of low rates of divergence and high connectivity among geographically segregated subpopulations. Our contrasting results suggest the potential presence of ecological mechanisms driving population differentiation, and highlight the value of targeted sequencing on DNA derived from museum specimens to uncover long-term patterns of genetic differentiation in wildlife populations.

Integrative and Comparative Biology↗

Using mark-recapture distance sampling methods on line transect surveys

Mark–recapture distance sampling (MRDS) methods are widely used for density and abundance estimation when the conventional DS assumption of certain detection at distance zero fails, as they allow detection at distance zero to be estimated and incorporated into the overall probability of detection to better estimate density and abundance. However, incorporating MR data in DS models raises survey and analysis issues not present in conventional DS. Conversely, incorporating DS assumptions in MR models raises issues not present in conventional MR. As a result, being familiar with either conventional DS methods or conventional MR methods does not on its own put practitioners in good a position to apply MRDS methods appropriately. This study explains the sometimes subtly different varieties of MRDS survey methods and the associated concepts underlying MRDS models. This is done as far as possible without giving mathematical details – in the hope that this will make the key concepts underlying the methods accessible to a wider audience than if we were to present the concepts via equations. We illustrate use of the two main types of MRDS model by using data collected on two different types of survey: a survey of ungulate faecal pellets where two observers searched independently of each other; and a cetacean survey that used a search protocol that could accommodate responsive movement, with only one observer searching independently and the other being aware of all detections. Synthesis and applications . Mark–recapture DS is a widely used method for estimating animal density and abundance when detection of animals at distance zero is not certain. Two observer configurations and three statistical models are described, and it is important to choose the most appropriate model for the observer configuration and target species in question. By way of making the methods more accessible to practicing ecologists, we describe the key ideas underlying MRDS methods, the sometimes subtle differences between them, and we illustrate these by applying different kinds of MRDS method to surveys of two different target species using different survey configurations.

Methods in Ecology and Evolution↗

A database of lotic invertebrate traits for North America

The assessment and study of stream communities may be enhanced if functional characteristics such as life-history, habitat preference, and reproductive strategy were more widely available for specific taxa. Species traits can be used to develop these functional indicators because many traits directly link functional roles of organisms with controlling environmental factors (for example, flow, substratum, temperature). In addition, some functional traits may not be constrained by taxonomy and are thus applicable at multiple spatial scales. Unfortunately, a comprehensive summary of traits for North American invertebrate taxa does not exist. Consequently, the U.S. Geological Survey's National Water-Quality Assessment Program in cooperation with Colorado State University compiled a database of traits for North American invertebrates. A total of 14,127 records for over 2,200 species, 1,165 genera, and 249 families have been entered into the database from 967 publications, texts and reports. Quality-assurance procedures indicated error rates of less than 3 percent in the data entry process. Species trait information was most complete for insect taxa. Traits describing resource acquisition and habitat preferences were most frequently reported, whereas those describing physiological tolerances and reproductive biology were the least frequently reported in the literature. The database is not exhaustive of the literature for North American invertebrates and is biased towards aquatic insects, but it represents a first attempt to compile traits in a web-accessible database. This report describes the database and discusses important decisions necessary for identifying ecologically relevant, environmentally sensitive, non-redundant, and statistically tractable traits for use in bioassessment programs.

Data Series↗

Shifting currents: Progress, setbacks, and shifts in policy and practice

The Wisconsin Academy’s initial Waters of Wisconsin project (WOW I) facilitated a statewide conversation between 2000 and 2003 around one main question: How can we ensure healthy aquatic ecosystems and clean, abundant water supplies for tomorrow’s Wisconsin? Robust participation in this conversation underscored the important role citizens have in the stewardship of our waters, and we found enthusiastic support for farsighted policies—based on sound science—to manage our water legacy. Overall, we found that Wisconsinites cherish water and see our waters as essential to our way of life in Wisconsin. Nationally, our state ranks 25th in land area but has the fourth-highest area covered by water. Wisconsin is 20th in population but is second only to Florida in the number of fishing licenses sold each year. Clean water supports billions of dollars’ worth of economic activity through tourism, agriculture, and industry. From the Northwoods cabin to the Port of Milwaukee to the Wisconsin Dells, water shapes our state’s identity. Our tradition of safeguarding Wisconsin’s waters is grounded in values such as responsibility to family and future generations, respect for land and wildlife, protecting public health and safety, and caring for water as a common good, as articulated in the state’s Public Trust Doctrine (see page 9). These deeply held values have also shaped a conservation ethic, and its legacy has served many generations who depend upon and enjoy the waters of the state. Through WOW I, we identified the need to overcome the institutional and disciplinary separation of science, policy, and management protocols through a more integrated approach to water management. WOW also affirmed that the Wisconsin Department of Natural Resources (DNR) and other public agencies play a critical role in sound scientific application, citizen participation, and the practical implementation of policy while balancing public and private interests toward the goal of a clean water future. More than a decade has passed since our first statewide WOW conversation and the report that captured recommendations from its participants: Waters of Wisconsin: The Future of Our Aquatic Ecosystems and Resources. Drawing from a diverse and growing set of stakeholders from across the state, the Wisconsin Academy initiated a new conversation in 2012 (known as WOW II) to assess progress in regard to our 2003 recommendations. We also sought to review the status of waters in Wisconsin today. The result of this renewed conversation is Shifting Currents: Progress, Setbacks, and Shifts in Policy and Practice. The new report assesses progress in brief, and explores in greater depth the continuing and emerging challenges to water quality, supply, and aquatic ecosystems in Wisconsin. In this report, we first review the context and frameworks for public decision-making about water and then examine some of the root causes—or “drivers”—and ecological stressors that underlie many of the symptoms we see in the form of pollution or ecosystem degradation in Wisconsin. This is followed by a summary of current water issues, many of which had been identified in the 2003 report and remain relevant today. We examine progress since 2003 but also setbacks, and discuss issues that we are likely to continue to face in the coming decades, including controlling agricultural runoff, mitigating climate change and grappling with its effects on the state’s waters, protecting groundwater from bacterial contamination and other pollutants, and preventing groundwater depletion. We also attempt to anticipate issues on the horizon. We offer a deeper look at some particular challenges, such as phosphorus pollution and groundwater contamination. We then consider the current decision-making framework and how it is shaping our capacity to respond to water challenges in Wisconsin. Finally, we offer recommendations and identify opportunities to safeguard Wisconsin’s waters in the decades ahead. From its inception, the Wisconsin Academy’s Waters of Wisconsin Initiative has brought together a diverse community of experts from across the state and from varied fields and areas of interest, to address challenges and seize opportunities related to our precious waters. We have done so as a matter of both principle and practical reality: the state of our waters reflects the ways we interact not only with them, but also with one another and our institutions. The WOW Initiative has aimed to provide guidance for Wisconsin citizens in sustaining the health of our aquatic ecosystems and the resilience of our water supplies over the long term.

Report↗

Using a network modularity analysis to inform management of a rare endemic plant in the northern Great Plains, USA

1. Analyses of flower-visitor interaction networks allow application of community-level information to conservation problems, but management recommendations that ensue from such analyses are not well characterized. Results of modularity analyses, which detect groups of species (modules) that interact more with each other than with species outside their module, may be particularly applicable to management concerns. 2. We conducted modularity analyses of networks surrounding a rare endemic annual plant, Eriogonum visheri , at Badlands National Park, USA, in 2010 and 2011. Plant species visited were determined by pollen on insect bodies and by flower species upon which insects were captured. Roles within modules (network hub, module hub, connector and peripheral, in decreasing order of network structural importance) were determined for each species. 3. Relationships demonstrated by the modularity analysis, in concert with knowledge of pollen species carried by insects, allowed us to infer effects of two invasive species on E. visheri . Sharing a module increased risk of interspecific pollen transfer to E. visheri . Control of invasive Salsola tragus , which shared a module with E. visheri , is therefore a prudent management objective, but lack of control of invasive Melilotus officinalis , which occupied a different module, is unlikely to negatively affect pollination of E. visheri . Eriogonum pauciflorum may occupy a key position in this network, supporting insects from the E. visheri module when E. visheri is less abundant. 4. Year-to-year variation in species' roles suggests management decisions must be based on observations over several years. Information on pollen deposition on stigmas would greatly strengthen inferences made from the modularity analysis. 5. Synthesis and applications: Assessing the consequences of pollination, whether at the community or individual level, is inherently time-consuming. A trade-off exists: rather than an estimate of fitness effects, the network approach provides a broad understanding of the relationships among insect visitors and other plant species that may affect the focal rare plant. Knowledge of such relationships allows managers to detect, target and prioritize control of only the important subset of invasive species present and identify other species that may augment a rare species' population stability, such as E. pauciflorum in our study.

South Dakota↗

Capture versus tagging impacts on chum salmon freshwater spawning migration travel times

The spawning migration travel times of chum salmon, Oncorhynchus keta (Walbaum), fitted with gastrically implanted radio tags vs external spaghetti tags were tested for a short [≈60 river km (rkm)] and long migration route (≈730 rkm) on the Koyukuk River, Alaska, USA. Using a novel application of statistical arrival curve models to infer travel times for uncaptured fish, migrations by chum salmon not directly handled during the study were also assessed. Results demonstrated negligible differences in travel times within migration routes between fish fitted only with spaghetti tags and fish fitted with radio tags, indicating low impacts on migration travel behaviour associated with gastric tags once deployed. Conversely, travel times for unhandled fish as inferred by statistical arrival models may have been 12%–24% shorter than those for fish captured with gillnets for tagging. These results suggest that, if present, chum salmon migration behaviour impacts may be more strongly associated with fish capture than tag deployment.

Fisheries Management and Ecology↗

Dynamic occupancy models for explicit colonization processes

The dynamic, multi-season occupancy model framework has become a popular tool for modeling open populations with occupancies that change over time through local colonizations and extinctions. However, few versions of the model relate these probabilities to the occupancies of neighboring sites or patches. We present a modeling framework that incorporates this information and is capable of describing a wide variety of spatiotemporal colonization and extinction processes. A key feature of the model is that it is based on a simple set of small-scale rules describing how the process evolves. The result is a dynamic process that can account for complicated large-scale features. In our model, a site is more likely to be colonized if more of its neighbors were previously occupied and if it provides more appealing environmental characteristics than its neighboring sites. Additionally, a site without occupied neighbors may also become colonized through the inclusion of a long-distance dispersal process. Although similar model specifications have been developed for epidemiological applications, ours formally accounts for detectability using the well-known occupancy modeling framework. After demonstrating the viability and potential of this new form of dynamic occupancy model in a simulation study, we use it to obtain inference for the ongoing Common Myna ( Acridotheres tristis ) invasion in South Africa. Our results suggest that the Common Myna continues to enlarge its distribution and its spread via short distance movement, rather than long-distance dispersal. Overall, this new modeling framework provides a powerful tool for managers examining the drivers of colonization including short- vs. long-distance dispersal, habitat quality, and distance from source populations.

Ecology↗

Cape Romain partnership for coastal protection

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

South Carolina↗

Oregon OCS seafloor mapping: Selected lease blocks relevant to renewable energy

In 2014 the U.S. Geological Survey (USGS) and the Bureau of Ocean Energy Management (BOEM) entered into Intra-agency agreement M13PG00037 to map an area of the Oregon Outer Continental Shelf (OCS) off of Coos Bay, Oregon, under consideration for development of a floating wind energy farm. The BOEM requires seafloor mapping and site characterization studies in order to evaluate the impact of seafloor and sub-seafloor conditions on the installation, operation, and structural integrity of proposed renewable energy projects, as well as to assess the potential effects of construction and operations on archaeological resources. The mission of the USGS is to provide geologic, topographic, and hydrologic information that contributes to the wise management of the Nation's natural resources and that promotes the health, safety, and well being of the people. This information consists of maps, databases, and descriptions and analyses of the water, energy, and mineral resources, land surface, underlying geologic structure, and dynamic processes of the earth. For the Oregon OCS study, the USGS acquired multibeam echo sounder and seafloor video data surrounding the proposed development site, which is 95 km2 in area and 15 miles offshore from Coos Bay. The development site had been surveyed by Solmar Hydro Inc. in 2013 under a contract with WindFloat Pacific. The USGS subsequently produced a bathymetry digital elevation model and a backscatter intensity grid that were merged with existing data collected by the contractor. The merged grids were published along with visual observations of benthic geo-habitat from the video data in an associated USGS data release (Cochrane and others, 2015). This report includes the results of analysis of the video data conducted by Oregon State University and the geo-habitat interpretation of the multibeam echo sounder (MBES) data conducted by the USGS. MBES data was published in Cochrane and others (2015). Interpretive data associated with this publication is published in Cochrane (2017). All the data is provided as geographic information system (GIS) files that contain both Esri ArcGIS geotiffs or shapefiles. For those who do not own the full suite of Esri GIS and mapping software, the data can be read using Esri ArcReader, a free viewer that is available at http://www.esri.com/software/arcgis/arcreader/index.html (last accessed August 29, 2016). Web services, which consist of standard implementations of ArcGIS representational state transfer (REST) Service and Open Geospatial Consortium (OGC) GIS web map service (WMS), also are available for all published GIS data. Web services were created using an ArcGIS service definition file, resulting in data layers that are symbolized as shown on the associated report figures. Both the ArcGIS REST Service and OGC WMS Service include all the individual GIS layers. Data layers are bundled together in a map-area web service; however, each layer can be symbolized and accessed individually after the web service is ingested into a desktop application or web map. Web services enable users to download and view data, as well as to easily add data to their own workflows, using any browser-enabled, standalone or mobile device. Though the surficial substrate is dominated by combinations of mud and sand substrate, a diverse assortment of geomorphologic features are related to geologic processes—one anticlinal ridge where bedrock is exposed, a slump and associated scarps, and pockmarks. Pockmarks are seen in the form of fields of small pockmarks, a lineation of large pockmarks with methanogenic carbonates, and areas of large pockmarks that have merged into larger variously shaped depressions. The slump appears to have originated at the pockmark lineation. Video-supervised numerical analysis of the MBES backscatter intensity data and vector ruggedness derived from the MBES bathymetry data was used to produce a substrate model called a seafloor character raster for the study area. The seafloor character raster consists of three substrate classes: soft-flat areas, hard-flat areas, and hard-rugged areas. A Coastal and Marine Ecological Classification Standard (CMECS) geoform and substrate map was also produced using depth, slope, and benthic position index classes to delineate geoform boundaries. Seven geoforms were identified in this process, including ridges, slump scars, slump deposits, basins, and pockmarks. Statistical analysis of the video data for correlations between substrate, depth, and invertebrate assemblages resulted in the identification of seven biomes: three hard-bottom biomes and four softbottom biomes. A similar analysis of vertebrate observations produces a similar set of biomes. The biome between-group dissimilarity was very high or high. Invertebrates alone represent most of the structure of the whole benthic community into different assemblages. A biotope map was generated using the seafloor character raster and the substrate and depth values of the biomes. Hard substrate biotopes were small in size and were located primarily on the ridge and in pockmarks along the pockmark lineation. The soft-bottom bitopes consisted of large contiguous areas delimited by isobaths.

Open-File Report↗

Hierarchical spatial capture-recapture models: Modeling population density from stratified populations

Capture–recapture studies are often conducted on populations that are stratified by space, time or other factors. In this paper, we develop a Bayesian spatial capture–recapture (SCR) modelling framework for stratified populations – when sampling occurs within multiple distinct spatial and temporal strata. We describe a hierarchical model that integrates distinct models for both the spatial encounter history data from capture–recapture sampling, and also for modelling variation in density among strata. We use an implementation of data augmentation to parameterize the model in terms of a latent categorical stratum or group membership variable, which provides a convenient implementation in popular BUGS software packages. We provide an example application to an experimental study involving small-mammal sampling on multiple trapping grids over multiple years, where the main interest is in modelling a treatment effect on population density among the trapping grids. Many capture–recapture studies involve some aspect of spatial or temporal replication that requires some attention to modelling variation among groups or strata. We propose a hierarchical model that allows explicit modelling of group or strata effects. Because the model is formulated for individual encounter histories and is easily implemented in the BUGS language and other free software, it also provides a general framework for modelling individual effects, such as are present in SCR models.

Methods in Ecology and Evolution↗

Editorial: Subsurface microbiology within hydrocarbon resources or stored gases

A Research Topic on the microbiology of hydrocarbon and gas storage reservoirs has far reaching industrial applications. In recent decades, there has been a growing interest in understanding microbial communities in subsurface energy reservoirs, such as coal, oil, and shale beds. This area of research has broadened to include gas storage reservoirs for hydrogen and CO 2 . Scientists are beginning to unravel the unexpected impact microorganisms have on these systems, through changing the fluid geochemistry, the gas content, and even the permeability. By recognizing the influence of these tiny organisms on our engineered environments, we can develop better risk assessments, target mitigation strategies, expand energy production, and refine operational guidance, ultimately contributing to a more sustainable energy future.

Frontiers in Ecology and Evolution↗

Recognizing political influences in participatory social-ecological systems modeling

Stakeholder participation in social-ecological systems (SES) modeling is increasingly considered a desirable way to elicit diverse sources of knowledge about SES behavior and to promote inclusive decision-making in SES. Understanding how participatory modeling processes function in the context of long-term adaptive management of SES may allow for better design of participatory processes to achieve the intended outcomes of inclusionary knowledge, representativeness, and social learning, while avoiding unintended outcomes. Long-term adaptive management contexts often include political influences -- attempts to shift or preserve power structures and authority, and efforts to represent the political and economic interests of stakeholders -- in the computer models that are used to shape policy making and implementation. In this research, we examine a period that included a major transition in the watershed model used for management of the Chesapeake Bay in the United States. The Chesapeake Bay watershed model has been in development since the 1980s, and is considered by many to be an exemplary case of participatory modeling. We use documentary analysis and interviews with participants involved in the model application and development transition to reveal a variety of ways in which participatory modeling may be subject to different kinds of political influences, some of which resulted in unintended outcomes, including: perceptions of difficulty updating the model in substantive ways, “gaming” of the model/participatory process by stakeholders, and increasing resistance against considering uncertainty in the system not captured by the model. This research suggests unintended or negative outcomes may be associated with both participatory decision-making and stakeholder learning even though they are so often touted as the benefits of participatory modeling. We end with a hypothesis that further development of a theory of computer model governance to bridge model impact and broader theories of environmental governance at the science-policy interface may result in improved SES modeling outcomes.

Maryland, Virginia↗

Legacy data for a northern prairie grassland: Woodworth Study Area, North Dakota, 1963-89

Ecological data commonly become more valuable through time. Such legacy data provide baseline records of past biological, physical, and social information that provide historical perspective and are necessary for assessment of stasis or change. Legacy data collected at the Woodworth Study Area (WSA), a contiguous block of grasslands, croplands, and wetlands covering more than 1,000 hectares of the Prairie Pothole Region of North Dakota, are cataloged and summarized in this study. The WSA is one of the longest researched grassland sites in the Upper Midwest. It has an extensive history of settlement, land use, and management that provides a deeper context for future research. The WSA data include long-term vegetation transect records, land use history, habitat management records, geologic information, wetland hydrology and chemistry information, and spatial images. Substantial parts of these data have not been previously reported. The WSA is representative of many other lands purchased by the U.S. Fish and Wildlife Service in the Prairie Pothole Region from the 1930s to the 1970s; therefore, synthesized data from the WSA are broadly applicable to topics of concern in northern grasslands, such as increases in non-native plants, managing for biodiversity, and long-term effects of habitat management. New techniques are also described that were used to preserve these data for future analyses. The data preservation techniques are applicable to any project with data that should be preserved for 100 years or more.

North Dakota↗

Relative energy production determines effect of repowering on wildlife mortality at wind energy facilities

Reduction in wildlife mortality is often cited as a potential advantage to repowering wind facilities, that is, replacing smaller, lower capacity, closely spaced turbines, with larger, higher capacity ones, more widely spaced. Wildlife mortality rates, however, are affected by more than just size and spacing of turbines, varying with turbine operation, seasonal and daily weather and habitat, all of which can confound our ability to accurately measure the effect of repowering on wildlife mortality rates. We investigated the effect of repowering on wildlife mortality rates in a study conducted near Palm Springs, CA. We controlled for confounding effects of weather and habitat by measuring turbine‐caused wildlife mortality rates over a range of turbine sizes and spacing, all within the same time period, habitat and local weather conditions. We controlled for differences in turbine operation by standardizing mortality rate per unit energy produced. We found that avian and bat mortality rate was constant per unit of energy produced, across all sizes and spacings of turbines. Synthesis and applications . In the context of repowering a wind facility, our results suggest that the relative amount of energy produced, rather than simply the size, spacing or nameplate capacity of the replacement turbines, determines the relative rate of mortality prior to and after repowering. Consequently, in a given location, newer turbines would be expected to be less harmful to wildlife only if they produced less energy than the older models they replace. The implications are far‐reaching as 18% of US and 8% of world‐wide wind power capacity will likely be considered for repowering within ~5 years.

California↗

Reconstructing relative abundance indices for Atlantic sturgeon using hierarchical ecological models

Objective The Atlantic Sturgeon Acipenser oxyrinchus is a wide-ranging, long-lived diadromous fish that is endangered in most of its range. Our objective was to develop and apply long-term, detection-corrected indices of relative abundance for juvenile and adult Atlantic Sturgeon in the Hudson River, New York, United States, to support population monitoring and stock assessment. Methods We used long-term gill-net catches to estimate relative abundances of juvenile and adult Atlantic Sturgeon while accounting for imperfect detection within an N- mixture modeling framework. We validated the model framework using a simulation–estimation framework based on mean parameter estimates from the adult Atlantic Sturgeon relative abundance index. Results Simulation testing indicated that absolute abundance estimates may be biased low due to poor characterization of detection probabilities. However, model estimates of relative abundance tracked simulated abundance trends well. Juvenile relative abundance estimates followed similar trends as raw gill-net catches but were less variable among years when corrected for detection probability. Relative abundance of juveniles increased from 2004 to 2015 prior to declining through 2022, with little evidence for change between the start and end of the survey. Detection-corrected indices for adult sturgeon indicated a consistent increase in relative abundance that was not readily apparent in raw catch indices. Conclusions Detection-corrected catch indices can provide improved characterization of Atlantic Sturgeon relative abundance dynamics over raw gill-net catches through use of N- mixture models. The approach has broad applicability to data types that are commonly collected for understanding population trends in stock assessment. Estimation of absolute abundance and other population demographics germane to management would benefit from alternative or auxiliary data collected through approaches such as side-scan sonar or acoustic telemetry, which are increasingly common for monitoring sturgeon populations.

New York↗