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USGS2025

A framework tool that applies weight-of-evidence integration to the analysis of existing datasets to guide freshwater conservation

The overarching issue we address here is how to extract clear and actionable ecological and management insights from real-world field data that often do not satisfy traditional statistical assumptions. Toward this goal, we developed a general 12+6 step adaptive management framework tool. We applied this framework tool to existing biodiversity monitoring data to create a proof-of-concept result that addresses the overarching question of “ why might a specific native stream fish taxon be present or absent at specific locations? ” Our multi-step framework tool links established steps and steps that are unique to our framework through weight-of evidence (WOE) integration, an approach that combines quantitative results from multiple visualization and statistical procedures. The systematic use of all steps in our framework can provide improved conservation outcomes compared to a single analysis. Advantages accrue from our approach because our framework tool refines the overarching goal into related sub-questions, applies a specific quantitative procedure to each sub-step, combines results from all sub-questions using a WOE integration, identifies testable questions that elucidate ambiguities and gaps revealed through WOE integration, and proposes practical field methods for obtaining this clarifying information through future research and data collections. The process of considering multiple visualizations and analyses as individual pieces of a shared puzzle offers a new way to approach the use of existing data. Our team-based approach transforms the collection and analysis of existing data into a series of field tests that can guide future actions (e.g., data collection-analysis events, restoration initiatives, research). Habitat and impact regressors will vary with taxa and system, but our structured process tool has broad generality for a range of conservation issues in which freshwater systems are threatened by human impacts.

Kansas↗
USGS2003

Comparing marine and terrestrial ecosystems: Implications for the design of coastal marine reserves

Concepts and theory for the design and application of terrestrial reserves is based on our understanding of environmental, ecological, and evolutionary processes responsible for biological diversity and sustainability of terrestrial ecosystems and how humans have influenced these processes. How well this terrestrial -based theory can be applied toward the design and application of reserves in the coastal marine environment depends, in part, on the degree of similarity between these systems. Several marked differences in ecological and evolutionary processes exist between marine and terrestrial ecosystems as ramifications of fundamental differences in their physical environments (i.e., the relative prevalence of air and water) and contemporary patterns of human impacts. Most notably, the great extent and rate of dispersal of nutrients, materials, holoplanktonic organisms, and reproductive propagules of benthic organisms expand scales of connectivity among near-shore communities and ecosystems . Consequently, the "openness" of marine populations, communities, and ecosystems probably has marked influences on their spatial, genetic, and trophic structures and dynamics in ways experienced by only some terrestrial species. Such differences appear to be particularly significant for the kinds of organisms most exploited and targeted for protection in coastal marine ecosystems (fishes and macroinvertebrates). These and other differences imply some unique design criteria and application of reserves in the marine environment. In explaining the implications of these differences for marine reserve design and application, we identify many of the environmental and ecological processes and design criteria necessary for consideration in the development of the analytical approaches developed elsewhere in this Special Issue.

Ecological Applications↗
USGS2014

Competitive interactions and resource partitioning between northern spotted owls and barred owls in western Oregon

The federally threatened northern spotted owl ( Strix occidentalis caurina ) is the focus of intensive conservation efforts that have led to much forested land being reserved as habitat for the owl and associated wildlife species throughout the Pacific Northwest of the United States. Recently, however, a relatively new threat to spotted owls has emerged in the form of an invasive competitor: the congeneric barred owl ( S. varia ). As barred owls have rapidly expanded their populations into the entire range of the northern spotted owl, mounting evidence indicates that they are displacing, hybridizing with, and even killing spotted owls. The range expansion by barred owls into western North America has made an already complex conservation issue even more contentious, and a lack of information on the ecological relationships between the 2 species has hampered recovery efforts for northern spotted owls. We investigated spatial relationships, habitat use, diets, survival, and reproduction of sympatric spotted owls and barred owls in western Oregon, USA, during 2007–2009. Our overall objective was to determine the potential for and possible consequences of competition for space, habitat, and food between these previously allopatric owl species. Our study included 29 spotted owls and 28 barred owls that were radio-marked in 36 neighboring territories and monitored over a 24-month period. Based on repeated surveys of both species, the number of territories occupied by pairs of barred owls in the 745-km 2 study area (82) greatly outnumbered those occupied by pairs of spotted owls (15). Estimates of mean size of home ranges and core-use areas of spotted owls (1,843 ha and 305 ha, respectively) were 2–4 times larger than those of barred owls (581 ha and 188 ha, respectively). Individual spotted and barred owls in adjacent territories often had overlapping home ranges, but interspecific space sharing was largely restricted to broader foraging areas in the home range with minimal spatial overlap among core-use areas. We used an information-theoretic approach to rank discrete-choice models representing alternative hypotheses about the influence of forest conditions, topography, and interspecific interactions on species-specific patterns of nighttime resource selection. Spotted owls spent a disproportionate amount of time foraging on steep slopes in ravines dominated by old (>120 yr) conifer trees. Barred owls used available forest types more evenly than spotted owls, and were most strongly associated with patches of large hardwood and conifer trees that occupied relatively flat areas along streams. Spotted and barred owls differed in the relative use of old conifer forest (greater for spotted owls) and slope conditions (steeper slopes for spotted owls), but we found no evidence that the 2 species differed in their use of young, mature, and riparian-hardwood forest types. Mean overlap in proportional use of different forest types between individual spotted owls and barred owls in adjacent territories was 81% (range = 30–99%). The best model of habitat use for spotted owls indicated that the relative probability of a location being used was substantially reduced if the location was within or in close proximity to a core-use area of a barred owl. We used pellet analysis and measures of food-niche overlap to determine the potential for dietary competition between spatially associated pairs of spotted owls and barred owls. We identified 1,223 prey items from 15 territories occupied by spotted owls and 4,299 prey items from 24 territories occupied by barred owls. Diets of both species were dominated by nocturnal mammals, but diets of barred owls included many terrestrial, aquatic, and diurnal prey species that were rare or absent in diets of spotted owls. Northern flying squirrels ( Glaucomys sabrinus ), woodrats ( Neotoma fuscipes , N. cinerea ), and lagomorphs ( Lepus americanus , Sylvilagus bachmani ) were primary prey for both owl species, accounting for 81% and 49% of total dietary biomass for spotted owls and barred owls, respectively. Mean dietary overlap between pairs of spotted and barred owls in adjacent territories was moderate (42%; range = 28–70%). Barred owls displayed demographic superiority over spotted owls; annual survival probability of spotted owls from known-fate analyses (0.81, SE = 0.05) was lower than that of barred owls (0.92, SE = 0.04), and pairs of barred owls produced an average of 4.4 times more young than pairs of spotted owls over a 3-year period. We found a strong, positive relationship between seasonal (6-month) survival probabilities of both species and the proportion of old (>120 yr) conifer forest within individual home ranges, which suggested that availability of old forest was a potential limiting factor in the competitive relationship between these 2 species. The annual number of young produced by spotted owls increased linearly with increasing distance from a territory center of a pair of barred owls, and all spotted owls that attempted to nest within 1.5 km of a nest used by barred owls failed to successfully produce young. We identified strong associations between the presence of barred owls and the behavior and fitness potential of spotted owls, as shown by changes in movements, habitat use, and reproductive output of spotted owls exposed to different levels of spatial overlap with territorial barred owls. When viewed collectively, our results support the hypothesis that interference competition with barred owls for territorial space can constrain the availability of critical resources required for successful recruitment and reproduction of spotted owls. Availability of old forests and associated prey species appeared to be the most strongly limiting factors in the competitive relationship between these species, indicating that further loss of these conditions can lead to increases in competitive pressure. Our findings have broad implications for the conservation of spotted owls, as they suggest that spatial heterogeneity in vital rates may not arise solely because of differences among territories in the quality or abundance of forest habitat, but also because of the spatial distribution of a newly established competitor. Experimental removal of barred owls could be used to test this hypothesis and determine whether localized control of barred owl numbers is an ecologically practical and socio-politically acceptable management tool to consider in conservation strategies for spotted owls.

Oregon↗
USGS2012

Developing a broader scientific foundation for river restoration: Columbia River food webs

Well-functioning food webs are fundamental for sustaining rivers as ecosystems and maintaining associated aquatic and terrestrial communities. The current emphasis on restoring habitat structure—without explicitly considering food webs—has been less successful than hoped in terms of enhancing the status of targeted species and often overlooks important constraints on ecologically effective restoration. We identify three priority food web-related issues that potentially impede successful river restoration: uncertainty about habitat carrying capacity, proliferation of chemicals and contaminants, and emergence of hybrid food webs containing a mixture of native and invasive species. Additionally, there is the need to place these food web considerations in a broad temporal and spatial framework by understanding the consequences of altered nutrient, organic matter (energy), water, and thermal sources and flows, reconnecting critical habitats and their food webs, and restoring for changing environments. As an illustration, we discuss how the Columbia River Basin, site of one of the largest aquatic/riparian restoration programs in the United States, would benefit from implementing a food web perspective. A food web perspective for the Columbia River would complement ongoing approaches and enhance the ability to meet the vision and legal obligations of the US Endangered Species Act, the Northwest Power Act (Fish and Wildlife Program), and federal treaties with Northwest Indian Tribes while meeting fundamental needs for improved river management.

Proceedings of the National Academy of Sciences of↗
USGS2015

Sediment conditions in the San Antonio River Basin downstream from San Antonio, Texas, 2000-13

Sediment plays an important role in the ecological health of rivers and estuaries and consequently is an important issue for water-resource managers. To better understand sediment characteristics in the San Antonio River Basin, the U.S. Geological Survey, in cooperation with the San Antonio River Authority, completed a two-part study in the San Antonio River Basin downstream from San Antonio, Texas, to (1) collect and analyze sediment data to characterize sediment conditions and (2) develop and calibrate a watershed model to simulate hydrologic conditions and suspended-sediment loads during 2000–12.

Texas↗
USGS2014

Resource manager information needs regarding hydrologic regime shifts for the North Pacific Landscape Conservation

Landscape Conservation Cooperatives (LCCs) are a network of 22 public-private partnerships, defined by ecoregion, that share and provide science to ensure the sustainability of land, water, wildlife, and cultural resources in North America. LCCs were established by the U.S. Department of the Interior (DOI) in recognition of the fact that response to climate change must be coordinated on a landscape-level basis because important resources, ecosystem processes, and resource management challenges extend beyond most of the boundaries considered in current natural resource management. The North Pacific LCC (NPLCC) covers the range of the Pacific coastal temperate rainforest, including an area of 528,360 km 2 spanning 22 degrees of latitude from the Kenai Peninsula, Alaska, to Bodega Bay, California. The coverage area includes parts of four States, two Canadian provinces, and more than 100 Tribes and First Nation language groups. It extends from alpine areas at the crest of coastal mountains across subalpine, montane, and lowland forests to the nearshore marine environment. This wide range of latitudes and elevation zones; terrestrial, freshwater, and marine habitats; and complex jurisdictional boundaries hosts a diversity of natural resources and their corresponding management issues are equally diverse. As evidenced by the Science and Traditional Ecological Knowledge (S-TEK) Strategy guiding principles, identifying and responding to the needs of resource managers is key to the success of the NPLCC. To help achieve this goal of the NPLCC, the U.S. Geological Survey (USGS) has organized several workshops with resource managers and resource scientists to identify management information needs relevant to the priority topics identified in the S-TEK Strategy. Here, we detail the results from a first workshop to address the effects of changes in hydrologic regime on rivers, streams, and riparian corridors. The workshop focused on a subset of the full NPLCC geography and was structured to answer the following questions: What are the valued resources and services that may be affected by hydrologic regime changes in the region? What are the management goals for those resources? How is climate change anticipated to affect valued resources and goals? What adaptation strategies may managers use in response to anticipated changes in resources due to climate-related hydrologic change? What information is needed to inform and use management responses?

Open-File Report↗
USGS2014

Simulation of hydrologic conditions and suspended-sediment loads in the San Antonio River Basin downstream from San Antonio, Texas, 2000-12

Suspended sediment in rivers and streams can play an important role in ecological health of rivers and estuaries and consequently is an important issue for water-resource managers. To better understand suspended-sediment loads and transport in a watershed, the U.S. Geological Survey (USGS), in cooperation with the San Antonio River Authority, developed a Hydrological Simulation Program—FORTRAN model to simulate hydrologic conditions and suspended-sediment loads during 2000–12 for four watersheds, which comprise the overall study area in the San Antonio River Basin (hereinafter referred to as the “USGS–2014 model”). The study area consists of approximately 2,150 square miles encompassing parts of Bexar, Guadalupe, Wilson, Karnes, DeWitt, Goliad, Victoria, and Refugio Counties. The USGS–2014 model was calibrated for hydrology and suspended sediment for 2006–12. Overall, model-fit statistics and graphic evaluations from the calibration and testing periods provided multiple lines of evidence indicating that the USGS–2014 model simulations of hydrologic and suspended-sediment conditions were mostly “good” to “very good.” Model simulation results indicated that approximately 1,230 tons per day of suspended sediment exited the study area and were delivered to the Guadalupe River during 2006–12, of which approximately 62 percent originated upstream from the study area. Sample data and simulated model results indicate that most of the suspended-sediment load in the study area consisted of silt- and clay-sized particles (less than 0.0625 millimeters). The Cibolo Creek watershed was the largest contributor of suspended sediment from the study area. For the entire study area, open/developed land and cropland exhibited the highest simulated soil erosion rates; however, the largest contributions of sediment (by land-cover type) were pasture and forest/rangeland/shrubland, which together composed approximately 80 percent of the land cover of the study area and generated about 70 percent of the suspended-sediment load from the study area.

Texas↗
USGS1995

[Book review] The Eastern Screech Owl: Life History, Ecology and Behavior in the Suburbs and Countryside, by Frederick Gehlback

Review of: Eastern Screech Owl: Life History, Ecology, and Behavior in the Suburbs and Countryside. Frederick R. Gehlbach. Issue 16; Issue 2008 of W. L. Moody Jr. Natural History Series. Texas A&M University Press; 1st edition (November 1994). ISBN: 0890966095. For ornithologists and ecologists alike, Fred Gehlbach's book promises to hold both interest and information value as a comprehensive study of the eastern screech owl (Otus asio hasbroucki). Gehlbach was intrigued with screech owls as a boy and encouraged as an undergraduate by William Hamilton, who underscored that in-depth studies of familiar backyard species can be as fascinating as those in exotic sites. Correspondence with another owl-aficionado, the late H. N. Southern, inspired the author's long-term study of screech owls in a woodland landscape in central Texas and led him to provide nest boxes to enhance his access and sample size. This book is based on observations over a 25-year period-beginning in 1967, with intensive study during an 11-year period (1976-1987) in Texas south of Waco, where Gehlbach teaches at Baylor University. The study represents observations on 659 screech owls, covering several generations of birds and entire lives of many individuals. Gehlbach compares screech owl nesting behavior in a rural versus suburban setting and includes chapters on food supplies and predation tactics; egg-laying, incubation, and parental behavior; vocalizations; and population structure and flux. He discusses why screech owls are widespread across the eastern half of North America and why they succeed among people in suburban environments, where they adapt as easily to mailboxes and porch columns as to natural tree cavities. The book mixes two approaches: on the one hand the dense style of a technical book in which the professional biologist can find information on many aspects of screech owl behavior, life history, and population, including tables, figures, summary statistics, results of statistical comparisons, and experimental tests of hypotheses. On the other hand, each chapter begins with and includes vivid visual images, personal experiences, and thoughtful reflections to draw in the general reader, bridging the interesting topic to the technical details and making the information accessible to a wider audience. The reader is impressed with Dr. Gehlbach's love of his subject, his devotion to long-term study, and his care in presenting the work to his fellow ornithologists, ecologists, and all those interested in wildlife and conservation. It will be a useful reference because of its wealth of information on all aspects of screech owl life history. It is well documented and, in addition to its 10 chapters, includes 10 appendices with information on types of food supplies, bird species that mob screech owls, a daily chronology of nestling development, and a selection of edited field notes to provide background for each chapter. The book is thoroughly referenced and indexed. The Eastern Screech Owl will be read with interest by those with an interest in long-term, in-depth studies and those who love charming stories about remarkable birds with strong personalities and interesting behavior.

Wildlife Review↗
USGS2015

Characterizing and simulating sediment loads and transport in the lower part of the San Antonio River Basin

This extended abstract is based on the U.S. Geological Survey Scientific Investigations Reports by Crow et al. (2013) and Banta and Ockerman (2014). Suspended sediment in rivers and streams can play an important role in ecological health of rivers and estuaries and consequently is an important issue for water-resource managers. The quantity and type of suspended sediment can affect the biological communities (Wood and Armitage, 1997), the concentration and movement of natural constituents and anthropogenic contaminants (Moran and others, 2012), and the amount of sediment deposition in coastal environments (Milliman and Meade, 1983). To better understand suspended-sediment characteristics in the San Antonio River Basin, the U.S. Geological Survey (USGS), in cooperation with the San Antonio River Authority and Texas Water Development Board, conducted a two-phase study to (1) collect and analyze sediment data to characterize sediment conditions in the San Antonio River downstream of San Antonio, Texas, and (2) develop and calibrate a watershed model to simulate hydrologic conditions and suspended-sediment loads for four watersheds in the San Antonio River Basin, downstream from San Antonio, Texas.

Texas↗
USGS2015

Blackbrush ( Coleogyne ramosissima Torr. ): State of our knowledge and future challenges

Covering 130,000 square miles and a wide range of elevations from desert to alpine in Arizona, Utah, Colorado, and New Mexico, the Colorado Plateau has long fascinated researchers. The Colorado Plateau VI provides readers with a plethora of updates and insights into land conservation and management questions currently surrounding the region. The Colorado Plateau VI’s contributors show how new technologies for monitoring, spatial analysis, restoration, and collaboration improve our understanding, management, and conservation of outcomes at the appropriate landscape scale for the Colorado Plateau. The volume’s chapters fall into five major themes: monitoring as a key tool for addressing management challenges, restoration approaches to improving ecosystem condition and function, collaboration and organizational innovations to achieve conservation and management objectives, landscape-scale approaches to understanding, and managing key species and ecological communities. Focusing on the integration of science into resource management issues over the Colorado Plateau, this volume includes contributions from dozens of leading scholars of the region. The Colorado Plateau VI proves a valuable resource to all interested in the conservation management, natural history, and cultural biological resources of the Colorado Plateau.

Arizona, Colorado, New Mexico, Utah↗
USGS2013

Fort Collins Science Center Ecosystem Dynamics branch--interdisciplinary research for addressing complex natural resource issues across landscapes and time

The Ecosystem Dynamics Branch of the Fort Collins Science Center offers an interdisciplinary team of talented and creative scientists with expertise in biology, botany, ecology, geology, biogeochemistry, physical sciences, geographic information systems, and remote-sensing, for tackling complex questions about natural resources. As demand for natural resources increases, the issues facing natural resource managers, planners, policy makers, industry, and private landowners are increasing in spatial and temporal scope, often involving entire regions, multiple jurisdictions, and long timeframes. Needs for addressing these issues include (1) a better understanding of biotic and abiotic ecosystem components and their complex interactions; (2) the ability to easily monitor, assess, and visualize the spatially complex movements of animals, plants, water, and elements across highly variable landscapes; and (3) the techniques for accurately predicting both immediate and long-term responses of system components to natural and human-caused change. The overall objectives of our research are to provide the knowledge, tools, and techniques needed by the U.S. Department of the Interior, state agencies, and other stakeholders in their endeavors to meet the demand for natural resources while conserving biodiversity and ecosystem services. Ecosystem Dynamics scientists use field and laboratory research, data assimilation, and ecological modeling to understand ecosystem patterns, trends, and mechanistic processes. This information is used to predict the outcomes of changes imposed on species, habitats, landscapes, and climate across spatiotemporal scales. The products we develop include conceptual models to illustrate system structure and processes; regional baseline and integrated assessments; predictive spatial and mathematical models; literature syntheses; and frameworks or protocols for improved ecosystem monitoring, adaptive management, and program evaluation. The descriptions in this fact sheet provide snapshots of our three research emphases, followed by descriptions of select current projects.

Fact Sheet↗
USGS2007

A watershed approach to ecosystem monitoring in Denali National Park and preserve, Alaska

The National Park Service and the National Biological Service initiated research in Denali National Park and Preserve, a 2.4 million-hectare park in southcentral Alaska, to develop ecological monitoring protocols for national parks in the Arctic/Subarctic biogeographic area. We are focusing pilot studies on design questions, on scaling issues and regionalization, ecosystem structure and function, indicator selection and evaluation, and monitoring technologies. Rock Creek, a headwater stream near Denali headquarters, is the ecological scale for initial testing of a watershed ecosystem approach. Our conceptual model embraces principles of the hydrological cycle, hypotheses of global climate change, and biological interactions of organisms occupying intermediate, but poorly studied, positions in Alaskan food webs. The field approach includes hydrological and depositional considerations and a suite of integrated measures linking key aquatic and terrestrial biota, environmental variables, or defined ecological processes, in order to establish ecological conditions and detect, track, and understand mechanisms of environmental change. Our sampling activities include corresponding measures of physical, chemical, and biological attributes in four Rock Creek habitats believed characteristic of the greater system diversity of Denali. This paper gives examples of data sets, program integration and scaling, and research needs.

Journal of the American Water Resources Associatio↗
USGS2016

The conservation genetics juggling act: Integrating genetics and ecology, science and policy

The field of conservation genetics, when properly implemented, is a constant juggling act integrating molecular genetics, ecology, and demography with applied aspects concerning managing declining species or implementing conservation laws and policies. This young field has grown substantially since the 1980’s following development of the polymerase chain reaction and now into the genomics era. Our lab has “grown up” with the field, having worked on these issues for over three decades. Our multi-disciplinary approach entails understanding the behavior and ecology of species as well as the underlying processes that contribute to genetic viability. Taking this holistic approach provides a comprehensive understanding of factors that influence species persistence and evolutionary potential while considering annual challenges that occur throughout their life cycle. As a federal lab, we are often addressing the needs of the U.S. Fish and Wildlife Service in their efforts to list, de-list or recover species. Nevertheless, there remains an overall communication gap between research geneticists and biologists who are charged with implementing their results. Therefore, we outline the need for a National Center for Small Population Biology to ameliorate this problem and provide organizations charged with making status decisions firmer ground from which to make their critical decisions.

Evolutionary Applications↗
USGS2013

Invasive species in southern Nevada

Southern Nevada contains a wide range of topographies, elevations, and climactic zones emblematic of its position at the ecotone between the Mojave Desert, Great Basin, and Colorado Plateau ecoregions. These varied environmental conditions support a high degree of biological diversity (Chapter 1), but they also provide opportunities for a wide range of invasive species. In addition, the population center of the Las Vegas valley, and the agricultural area scattered throughout Clark, Lincoln, and Nye counties, all connected by a network of roads and highways, plus ephemeral and perennial watercourses, provide abundant opportunities for new invaders to be transported into and within southern Nevada (Brooks 2009; Brookes and Lair 2009). Invasive species are a concern for land managers because they can compete directly with native species (Brooks 2000; Chambers and others 2007; DeFlaco and others 2003, 2007; Mazzola and others 2010), change habitat conditions (Brooks and Esque 2002; Esque and others 2010; Miller and others 2011), and alter ecosystems properties (Brooks and Matchett 2006; Brooks and Pyke 2001; Evans and others 2001). Many invasive species have already established and spread to the point that they are now considered to pose significant problems in southern Nevada. However, there are likely many more than have wither not been transported to or colonized the region, or have established by for various reasons not spread or increased in abundance to the point where they have a significant impact. Land managers must understand both current and potential future problems posed by invasive species to appropriately prioritize management actions. This chapter addressed Sub-goal 1.2 in the SNAP Science Research Strategy (table 1.3; Turner and others 2009), which is to protect southern Nevada's ecosystems from the adverse impacts of invasive species. It provides a brief overview of the key concepts associated with the ecology and management of invasive species, and includes information relevant to all five strategic goals identified by the National Invasive Species Council: prevention, early detection and rapid response, control and management, restoration, and organization collaboration (National Invasive Species Council 2001, 2008). Restoration also is discussed in a broader context in Chapter 5 and 7. This chapter does not present a comprehensive review of all invasive species associated land management issues in southern Nevada, but rather uses key species of concern to illustrate invasion ecology concepts and management strategies. It is focused on terrestrial and aquatic plants and animals, and does not address potential invasive taxa from the other Kingdoms. The information presented herein is intended to provide a foundation upon which land management plans can be developed and project-level decisions can be made relative to the management of invasive species in southern Nevada.

Nevada↗
USGS2022

Diatoms.org: Supporting taxonomists, connecting communities

Consistent identification of diatoms is a prerequisite for studying their ecology, biogeography, and successful application as environmental indicators. However, taxonomic consistency among observers has been difficult to achieve because taxonomic information is scattered across numerous literature sources, presenting challenges to the diatomist. Firstly, literature is often inaccessible because of cost or its location in journals that are not widely circulated. Secondly, taxonomic revisions of diatoms are taking place faster than floras can be updated. Finally, taxonomic information is often contradictory across literature sources. These issues can be addressed by developing a content creation community dedicated to making taxonomic, ecological, and image-based data freely available for diatom researchers. Diatoms.org represents such a content curation community, providing open, online access to a vast amount of recent and historical information on North American diatom taxonomy and ecology. The content curation community aggregates existing taxonomic information, creates new content, and provides feedback in the form of corrections and notices of literature with nomenclatural changes. The website not only addresses the needs of experienced diatom scientists for consistent identification but is also designed to meet users at their level of expertise, including engaging the lay public in the importance of diatom science. The website now contains over 1000 species pages contributed by over 100 content contributors, from students to established scientists. The project began with the intent to provide accurate information on diatom identification, ecology, and distribution using an approach that incorporates engaging design, user feedback, and advanced data access technology. In retrospect, the project that began as an ‘extended electronic book’ has emerged not only as a means to support taxonomists, but for practitioners to communicate and collaborate, expanding the size of and benefits to the content curation community. In this paper, we outline the development of diatoms.org , document key elements of the project, examine ongoing challenges and consider the unexpected emergent properties, including the value of diatoms.org as a source of data. Ultimately, if the field of diatom taxonomy, ecology, and biodiversity is to be relevant, a new generation of taxonomists needs to be trained and employed using new tools. We propose that diatoms.org is in a key position to serve as a hub of training and continuity for the study of diatom biodiversity and aquatic conditions.

Diatom Research↗
USGS2019

Sampling and analysis frameworks for inference in ecology

1. Reliable statistical inference is central to ecological research, much of which seeks to estimate population attributes and their interactions. The issue of sampling design and its relationship to inference has become increasingly important due to rapid proliferation of modeling methodology (line transect modeling, capture-recapture, estimation of occurrence, model selection procedures, hierarchical modeling) and new sampling approaches (adaptive sampling, other specialized designs). It is important for ecologists using these advanced methods to be aware of how the linkages between sample selection and data analysis can potentially affect inference. 2. We examine design-based and model-based inference frameworks for ecological data collected randomly, purposively, or opportunistically. We elucidate differences in the probability structures for data arising from these frameworks, clarify the assumptions that underlie them, and demonstrate their differences. 3. Design-based inference builds on a probability structure inherited from randomized data collection, whereas model-based inference relies on an assumed stochastic model of the data. By itself, a design-based approach is of limited value for inferences about causal hypotheses. In contrast, model-based inference is dependent on a conditionality principle that can seldom be shown to be met for an ecological system. We describe the conditions under which one can safely ignore sampling design in model-based analysis, along with inferential implications if these conditions are not met. The special case of opportunistic sampling is discussed. 4. We present a combined framework that takes advantage of both approaches to inference, and provides a robust methodology that can deal with the modeling of sampling problems such as nondetection and misclassification, as well as the exploration of causal hypotheses. The combined framework can be useful for identifying optimal sampling strategies. 5. Each approach to inference has its strengths and weaknesses, and practitioners should be aware of these in order to tailor designs and analyses to specific questions. We use the approaches and their underlying rationales to provide guidelines for choosing designs and estimators for reliable inference.

Methods in Ecology and Evolution↗
USGS2024

Best practices for genetic and genomic data archiving

Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible and FAIR (findable, accessible, interoperable and reusable) compliant, they could be reused for many additional purposes. We discuss the main challenges with existing genetic and genomic data archives, and suggest best practices for archiving genetic and genomic data. Recognizing that this is a longstanding issue due to little formal data management training within the fields of ecology and evolution, we highlight steps that research institutions and publishers could take to improve data archiving.

Nature, Ecology and Evolution↗
USGS2004

Urban growth in American cities : glimpses of U.S. urbanization

The Earth's surface is changing rapidly. Changes are local, regional, national, and even global in scope. Some changes have natural causes, such as earthquakes or drought. Other changes, such as urban expansion, agricultural intensification, resource extraction, and water resources development, are examples of human-induced change that have significant impact upon people, the economy, and resources. The consequences that result from these changes are often dramatic and widespread (Buchanan, Acevedo, and Zirbes, 2002) It is the role of the U.S. Geological Survey (USGS) to provide useful and relevant scientific information both to the agencies within the Department of the Interior and to the Nation in general. In an effort to comply with this task, USGS scientists are assessing the status of, and the trends in, the Nation's land surface. This assessment provides useful information for regional and national land use decisionmaking. This knowledge can be used to deal with issues of significance to the Nation, such as quality-of-life, ecology of urban environments, ecosystem health, ecological integrity, water quality and quantity concerns, resource availability, vulnerability to natural hazards, safeguards to human health, air and land quality, and accessibility to scientific information. Results of these assessments can also be analyzed to reveal rates and trends in land use change. Results from urban growth studies provide a firm foundation for continuing research that explores the consequences of human modification of the landscape. The USGS seeks to illustrate and explain the spatial history of urban growth and corresponding land use change. Scientists are studying urban environments from a regional perspective and a time scale of decades to measure the changes that have occurred in order to help understand the impact of anticipated changes in the future. Within this booklet are pairs of images of selected urbanized regions from across the Nation. These image pairs illustrate the transformation that these areas have undergone over two decades. Specifically, they depict changes in the extent of urban land. Each change pair is composed of one image from the 1970s and one image from the 1990s. Accompanying each image pair is a brief historical geography of factors that helped facilitate major changes that have occurred since the founding of the main city and the consequences and challenges of regional urban growth. The goal of this publication is to provide an illustration of urban change that is easily understood by a broad audience. The images used throughout this booklet were generated from land cover data developed by the USGS. The data sources include the Geographic Information Retrieval and Analysis System (GIRAS) for the 1970s images and the National Land Cover Dataset (NLCD) for the 1990s images. GIRAS digital maps are based on photointerpretations completed in the mid-1970s. The NLCD is a land cover dataset for the conterminous United States based on 1992 Landsat thematic mapper (TM) satellite imagery and supplemental data (fig. 1a and fig. 1b). The USGS distributes both of these land use and land cover digital datasets. The images were developed by using a geographic information system (GIS). The GIRAS and NLCD datasets were used to identify urban land within each region. In the final images all urban areas are shown in red. A shaded-relief map of each region was used to display the topographic context of the red polygon coverage. For all of these images, urban land is defined as areas transformed into a built-up environment for human use. It includes residential areas, commercial and industrial developments, transportation features, and institutions.

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