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USGS2011

Integrating science and resource management in Tampa Bay, Florida

Tampa Bay is recognized internationally for its remarkable progress towards recovery since it was pronounced "dead" in the late 1970s. Due to significant efforts by local governments, industries and private citizens throughout the watershed, water clarity in Tampa Bay is now equal to what it was in 1950, when population in the watershed was less than one-quarter of what it is today. Seagrass extent has increased by more than 8,000 acres since the mid-1980s, and fish and wildlife populations are increasing. Central to this successful turn-around has been the Tampa Bay resource management community's long-term commitment to development and implementation of strong science-based management strategies. Research institutions and agencies, including Eckerd College, the Florida Wildlife Commission Fish and Wildlife Research Institute, Mote Marine Laboratory, National Oceanic and Atmospheric Administration, the Southwest Florida Water Management District, University of South Florida, U.S. Environmental Protection Agency, U.S. Geological Survey, local and State governments, and private companies contribute significantly to the scientific basis of our understanding of Tampa Bay's structure and ecological function. Resource management agencies, including the Tampa Bay Regional Planning Council's Agency on Bay Management, the Southwest Florida Water Management District's Surface Water Improvement and Management Program, and the Tampa Bay Estuary Program, depend upon this scientific basis to develop and implement regional adaptive management programs. The importance of integrating science with management has become fully recognized by scientists and managers throughout the region, State and Nation. Scientific studies conducted in Tampa Bay over the past 10–15 years are increasingly diverse and complex, and resource management programs reflect our increased knowledge of geology, hydrology and hydrodynamics, ecology and restoration techniques. However, a synthesis of this research and its integration into resource management has not been prepared for Tampa Bay since the mid-1980s. The need for an up-to-date synthesis of Tampa Bay science and management has resulted in the production of this document. The U.S. Geological Survey recently completed a 5-year Tampa Bay Integrated Science Study, and the Tampa Bay Estuary Program updated the Comprehensive Conservation and Management Plan for Tampa Bay in 2006. These efforts build upon results of the many research and management studies and programs summarized here.

Florida↗

USGS2020

The community code verification exercise for simulating sequences of earthquakes and aseismic slip (SEAS)

Numerical simulations of sequences of earthquakes and aseismic slip (SEAS) have made great progress over past decades to address important questions in earthquake physics. However, significant challenges in SEAS modeling remain in resolving multiscale interactions between earthquake nucleation, dynamic rupture, and aseismic slip, and understanding physical factors controlling observables such as seismicity and ground deformation. The increasing complexity of SEAS modeling calls for extensive efforts to verify codes and advance these simulations with rigor, reproducibility, and broadened impact. In 2018, we initiated a community code-verification exercise for SEAS simulations, supported by the Southern California Earthquake Center. Here, we report the findings from our first two benchmark problems (BP1 and BP2), designed to verify different computational methods in solving a mathematically well-defined, basic faulting problem. We consider a 2D antiplane problem, with a 1D planar vertical strike-slip fault obeying rate-and-state friction, embedded in a 2D homogeneous, linear elastic halfspace. Sequences of quasi-dynamic earthquakes with periodic occurrences (BP1) or bimodal sizes (BP2) and their interactions with aseismic slip are simulated. The comparison of results from 11 groups using different numerical methods show excellent agreements in long-term and coseismic fault behavior. In BP1, we found that truncated domain boundaries influence interseismic stressing, earthquake recurrence, and coseismic rupture, and that model agreement is only achieved with sufficiently large domain sizes. In BP2, we found that complexity of fault behavior depends on how well physical length scales related to spontaneous nucleation and rupture propagation are resolved. Poor numerical resolution can result in artificial complexity, impacting simulation results that are of potential interest for characterizing seismic hazard such as earthquake size distributions, moment release, and recurrence times. These results inform the development of more advanced SEAS models, contributing to our further understanding of earthquake system dynamics.

Seismological Research Letters↗

USGS2006

2005 annual progress report: Elk and bison grazing ecology in the Great Sand Dunes complex of lands

In 2000 the U.S. Congress authorized the expansion of the former Great Sand Dunes National Monument by establishing a new Great Sand Dunes National Park and Preserve in its place, and establishing the Baca National Wildlife Refuge. The establishment of Great Sand Dunes National Park and Preserve and the new Baca National Wildlife Refuge in the San Luis Valley (SLV), Colorado was one of the most significant land conservation actions in the western U.S. in recent years. The action was a result of cooperation between the National Park Service (NPS), U.S. Fish and Wildlife Service (USFWS), Bureau of Land Management (BLM), U.S. Forest Service (USDA-FS), and The Nature Conservancy (TNC). The new national park, when fully implemented, will consist of 107,265 acres, the new national preserve 41,872 acres, and the new national wildlife refuge (USFWS lands) 92,180 acres (fig. 1). The area encompassed by this designation protects a number of natural wonders and features including a unique ecosystem of natural sand dunes, the entire watershed of surface and groundwaters that are necessary to preserve and recharge the dunes and adjacent wetlands, a unique stunted forest, and other valuable riparian vegetation communities that support a host of associated wildlife and bird species. When the National Park was initially established, there were concerns about overconcentrations and impacts on native plant communities of the unhunted segments of a large and possibly growing elk (Cervus elaphus) population. This led to the designation of the Preserve as a compromise solution, where the elk could be harvested. The Preserve Unit, however, will not address all the ungulate management challenges. In order to reduce the current elk population, harvests of elk may need to be aggressive. But aggressive special hunts of elk to achieve population reductions can result in elk avoidance of certain areas or elk seeking refuge in areas where they cannot be hunted, while removals of whole herd segments and abandonment or alterations of migration routes can occur (Smith and Robbins, 1994; Boyce and others, 1991). Elk may seek refuge from hunting in the newly expanded Park Unit and TNC lands where they might overconcentrate and impact unique vegetation communities. In these sites of refugia, or preferred loafing sites, elk and bison could accelerate a decline in woody riparian shrubs and trees. This decline may also be due to changes in hydrology, climatic, or dunal processes, but ungulate herbivory might exacerbate the effects of those processes. To address the questions and needs of local resource managers, a multi-agency research project was initiated in 2005 to study the ecology, forage relations, and habitat relations of elk and bison in the Great Sand Dunes–Sangre de Cristo–Baca complex of lands. Meetings and discussions of what this research should include were started in 2001 with representatives from NPS, USFWS, TNC, the Colorado Division of Wildlife (CDOW), and USDA-FS/BLM. The final study plan was successfully funded in 2004 with research scheduled to start in 2005. The research was designed to encompass three major study elements: (1) animal movements and population dynamics, (2) vegetation and nutrient effects from ungulate herbivory, and (3) development of ecological models, using empirical data collected from the first two components, that will include estimates of elk carrying capacity and management scenarios for resource managers.

Colorado↗

USGS2017

Application of paleoflood surveys for the southern Black Hills of South Dakota

Flood-frequency analyses for the Black Hills area have especially large uncertainties and are especially important for planning purposes because of a history of extremely large and damaging floods, such as the extreme floods of June 9–10, 1972. Geology, topography, and climatology are additional complicating factors for flood-frequency characterization for the area. Two previous paleoflood studies for the Black Hills area indicated good potential for improving flood-frequency analyses through implementation of paleoflood investigations. The objectives of this study (SD2010-04) for the southern Black Hills were to (1) develop long-term flood chronologies and associated peak-flow frequency analyses for selected stream reaches by applying paleoflood hydrology approaches; and (2) develop flood-frequency information regarding “high-elevation” stream reaches to help address questions regarding differential potential for generation of exceptionally strong rain-producing thunderstorms across elevation gradients in the area. Neither objective was accomplished because the study was terminated before planned completion. Substantial efforts could be applied for only 2 of the 12 research tasks prior to study termination. These were task 3 (preliminary reconnaissance) and task 4 (activities associated with Section 106 of the National Historic Preservation Act). Field reconnaissance conducted along 10 candidate streams indicated that conditions in the southern Black Hills appear quite favorable for conducting paleoflood investigations. All 10 candidate streams had moderate to good potential for favorable paleoflood evidence, and in general are well constrained in relatively narrow canyon reaches, which provides good sensitivity for changes in stage, relative to discharge. Task 4 (Section 106 activities) was needed because alcoves and rock shelters that are well suited for deposition and preservation of paleoflood evidence may have been used as shelters or cache locations by indigenous inhabitants and thus may be eligible for consideration as historic properties because of possible archaeological or cultural materials. The complexity of the Section 106 concerns and issues became progressively more apparent as the study evolved. The study eventually was terminated when it became apparent that the resources needed to address the Section 106 issues would overwhelm the resources available for study implementation. In the event of consideration of future re-implementation, approaches that might help expedite Section 106 issues could include (1) a partnership with another Federal agency that has substantial experience with the Section 106 process; (2) securing assistance from a consultant that could help with both the Section 106 process and the required archaeological component; and (3) partnering with a tribal college with archaeological or earth science/hydrology programs, which could help make this study become part of a learning exercise.

South Dakota↗

USGS2022

Science mission requirements for a globally ranging, riserless drilling vessel for U.S. Scientific Ocean Drilling

Through the collection and analysis of shallow and deep subseafloor sediments, rocks, fluids, and life, scientific ocean drilling has enriched our understanding of the complex Earth system. Among other achievements, scientific ocean drilling has documented the history of Earth’s climate, the waxing and waning of polar ice sheets, the past changes in ocean and atmospheric circulation, the existence and function of microbial life in the subseafloor, the compositional variations in Earth’s crust and underlying mantle, and the physical and chemical processes acting at subduction zones, including those associated with tsunamigenic earthquakes. Over the decades, more than 12,000 articles that depend on analyses of scientific ocean drilling samples and geophysical data have been published, many detailing breakthrough contributions to global knowledge about the Earth system. Approximately 45% of these publications were led by U.S.-affiliated authors (International Ocean Discovery Program Publication Services, 2021). Since the mid-1980s, the workhorse of this multidisciplinary, international research effort has been the riserless D/V JOIDES Resolution, operated by Texas A&M University with funding from the U.S. National Science Foundation (NSF). D/V JOIDES Resolution has conducted the vast majority of scientific ocean drilling expeditions and collected most of the scientific cores over that period, including 82% of the expeditions and 93% of the cores in the last decade alone, despite being one of three platforms that is operated within the International Ocean Discovery Program. However, D/V JOIDES Resolution is approaching the end of its useful life. With a strong commitment to continue scientific ocean drilling beyond the end of the current phase, the community developed a document outlining the research frontiers that should be pursued. Exploring Earth by Scientific Ocean Drilling: 2050 Science Framework (Koppers and Coggon, 2020) describes seven scientific strategic objectives that focus on understanding interconnections within the Earth system and five flagship initiatives that integrate these objectives into long-term research efforts that address issues facing society. Additional elements in the 2050 Science Framework, including STEM education, workforce development, technology development, and innovative applications of data analytics, will advance the goals of scientific ocean drilling. Addressing the 2050 Science Framework also requires building partnerships with allied U.S. and international science programs and strengthening existing ones. To implement a significant portion of the 2050 Science Framework, the U.S. scientific community seeks to lease or acquire a newly built, globally ranging, state-of-the art, riserless drilling vessel. The many and varied technical and human resources requirements for successful accomplishment of scientific and educational goals summarized in this document and described in detail in the 2050 Science Framework require broad community input and careful consideration. Following receipt of NSF’s formal Request for Assistance to the United States Science Support Program (USSSP), the U.S. scientific ocean drilling community conducted a one-year exercise to identify its national scientific needs and priorities in order to determine the Science Mission Requirements (SMRs) presented here. This community effort included: (1) a U.S. community-wide survey to identify the specific operational and technical capabilities critical to addressing science in the 2050 Science Framework; (2) a series of online workshops focusing on critical capabilities identified by the survey; and (3) a large in-person workshop to synthesize the results of the survey and the virtual workshops (Appendix 1). The approach was designed to reach as many participants as possible. Overall, 278 survey responses were received from U.S. community members, representing 104 unique institutions from 39 states and the District of Columbia, and 137 unique individuals participated in the workshops (Appendix 2). The results of this effort comprise two classes of SMRs: Foundational Science Mission Requirements and Primary Science Mission Requirements. Foundational SMRs define minimum criteria for a new riserless drilling vessel that can address significant portions of the 2050 Science Framework. Primary SMRs build upon the Foundational SMRs and will create more robust science opportunities and data collection capabilities, will increase progress in addressing the 2050 Science Framework objectives, and will provide more real-time ship-to-shore interaction to improve science productivity, engagement, and outreach. Modern safety and environmental standards, including meeting standards to access protected waters such as exclusive economic zones, extended continental shelves, or high latitudes, while being cognizant of the vessel’s environmental footprint. Safe and efficient operations in global locations and in water depths from 70 m to 6000+ m, with total drill string length of at least 7000 m. High-quality core and data collection from a range of key subseafloor environments. Advanced heave compensation, dynamic positioning, and drill pipe stability. Modern mud and cement/casing systems. Critical onboard measurements for safety, operational decision-making, documentation of ephemeral properties, mission-specific science, and long-term science goals that extend beyond a single expedition. Designated and appropriate space for sample and data preservation. Highly skilled onboard personnel, including technical staff for curation and core handling; support for safety, time-sensitive, and critical shipboard measurements; computer support; equipment and instrument repair; application support; and data assurance. Primary Science Mission Requirements include: Flexible shipboard space for laboratories and on deck to ensure safe, successful implementation of diverse science objectives and operations. Minimizing contamination of recovered samples. Over-the-side capabilities for science-supporting technology (e.g., remotely operated vehicles, water- column sampling, sediment-water interface sampling). Downhole logging and measurements. Expanded borehole observatory capabilities. Reliable and consistent ship-to-shore communications. NSF’s investment in a new globally ranging, riserless drilling vessel will have a powerful economic multiplier effect, including the infusion of additional science support funds in the United States for training and research, the development of new technologies and tools, and the associated scientific and technical workforce development. The skills and knowledge gained through scientific ocean drilling are translatable to careers in fields such as sustainable energy development (e.g., geothermal and offshore wind), carbon sequestration, data management and cyberinfrastructure, biotechnology, communications, science education, policy, hazard mitigation, and environmental management. The United States is a leader in a well-established and internationally collaborative scientific ocean drilling community. A modern, globally ranging, riserless drilling vessel will allow the United States to expand its leadership position, address broad scientific questions that current capabilities preclude, and cultivate equitable international, multidisciplinary collaborations that will ensure scientific ocean drilling’s future success.

Report↗

USGS2024

Incorporating climate data into emergency planning and exercises: A primer for emergency management practioners and data developers

Climate change has and will continue to sharpen climate-related risks to communities and natural resources in California and elsewhere, as the probabilities of more extreme weather, floods, and fires continue to increase. This poses a problem of novel situations for emergency management. Progress has been made in terms of formally incorporating climate projections, data, and research on expected changes in climate-driven hazards into long-term hazard mitigation and climate adaptation strategies at both state and national levels. However, there are fewer examples of how climate change considerations have, or could be, incorporated into shorter-term emergency preparedness and response strategies. This is an important gap to fill, as climate resilience depends not only on mitigation and prevention measures, but also on the ability of agencies to coordinate and effectively minimize impacts when prevention measures fall short. The goal of this primer is to provide guidance on how to incorporate the best available information on climate variability and change into emergency management planning, with a focus on the development and use of extreme weather event scenarios for use in exercises. The first section is aimed toward a broad audience, including emergency management practitioners who use extreme weather event scenarios. It provides an overview of available data and tools that can inform scenario design as well as techniques for scenario design based on the hazard of interest, the audience and application, and the technical skills and resources required to develop, summarize, and/or visualize the data. This section concludes with an overview of approaches and lessons learned related to extreme event response planning and exercise design. Overall, this section highlights the advantages of developing quantitative scenarios based on spatial data, which allows visualizations and interactive data explorations that can provide greater specificity in discussions related to preparedness and response strategies. It further highlights the advantages of developing a core expert working group to guide planning, holding pre-exercise workshops to engage diverse communities outside of the emergency management sector, and engaging decisionmakers post-exercise to communicate key issues and outcomes as well as potential approaches for mitigating consequences that were identified by participants. The second section is aimed toward the scientific community and data developers involved in the creation of extreme weather event scenarios. This section provides technical guidance and detailed descriptions of four types of data resources and five analytical approaches that can be used to create extreme weather event scenarios based on the design considerations highlighted in section one. The computational resources and expertise required varies substantially across the options presented and is a primary consideration. These requirements, in addition to considerations related to audience and application, may determine the novelty and detail of the event, the detail of weather forecast information that can be provided, and the spatial extent across which the event can reasonably be modeled. The importance of, and approaches for, delivering information in a form that is accessible to emergency management practitioners is also discussed.

Report↗

USGS2013

U.S. Department of the Interior South Central Climate Science Center strategic science plan, 2013--18

The Department of the Interior (DOI) recognizes and embraces the unprecedented challenges of maintaining our Nation’s rich natural and cultural resources in the 21st century. The magnitude of these challenges demands that the conservation community work together to develop integrated adaptation and mitigation strategies that collectively address the impacts of climate change and other landscape-scale stressors. On September 14, 2009, DOI Secretary Ken Salazar signed Secretarial Order 3289 (amended February 22, 2010) entitled, “Addressing the Impacts of Climate Change on America’s Water, Land, and Other Natural and Cultural Resources.” The Order establishes the foundation for two partner-based conservation science entities to address these unprecedented challenges: Climate Science Centers (CSCs and Landscape Conservation Cooperatives (LCCs). CSCs and LCCs are the Department-wide approach for applying scientific tools to increase understanding of climate change and to coordinate an effective response to its impacts on tribes and the land, water, ocean, fish and wildlife, and cultural-heritage resources that DOI manages. Eight CSCs have been established and are managed through the U.S. Geological Survey (USGS) National Climate Change and Wildlife Science Center (NCCWSC); each CSC works in close collaboration with their neighboring CSCs, as well as those across the Nation, to ensure the best and most efficient science is produced. The South Central CSC was established in 2012 through a cooperative agreement with the University of Oklahoma, Texas Tech University, Louisiana State University, the Chickasaw Nation, the Choctaw Nation of Oklahoma, Oklahoma State University, and NOAA’s Geophysical Fluid Dynamics Lab; hereafter termed the ”Consortium” of the South Central CSC. The Consortium has a broad expertise in the physical, biological, natural, and social sciences to address impacts of climate change on land, water, fish and wildlife, ocean, coastal, and cultural resources. The South Central CSC will provide scientific information, tools, and techniques that managers and other parties interested in land, water, wildlife, and cultural resources can use to anticipate, monitor, and adapt to climate change, actively engaging LCCs and other partners in translating science into management decisions. This document is the first Strategic Science Plan for the South Central CSC (2013-18). Using the January 2011 DOI guidance as a model, this document (1) describes the role and interactions of the South Central CSC among partners and stakeholders including Federal, State, and non-governmental organizations throughout the region; (2) describes a concept of what the center will provide to its partners; (3) defines a context for climate impacts in the south central United States; and (4) establishes the science priorities the center will address through research. Science priorities are currently organized as immediate or future research needs; however, this document is intended to be reevaluated and modified as partner needs change and as scientific work progresses.

Open-File Report↗

USGS2013

Ecological thresholds as a basis for defining management triggers for National Park Service vital signs: case studies for dryland ecosystems

Threshold concepts are used in research and management of ecological systems to describe and interpret abrupt and persistent reorganization of ecosystem properties (Walker and Meyers, 2004; Groffman and others, 2006). Abrupt change, referred to as a threshold crossing, and the progression of reorganization can be triggered by one or more interactive disturbances such as land-use activities and climatic events (Paine and others, 1998). Threshold crossings occur when feedback mechanisms that typically absorb forces of change are replaced with those that promote development of alternative equilibria or states (Suding and others, 2004; Walker and Meyers, 2004; Briske and others, 2008). The alternative states that emerge from a threshold crossing vary and often exhibit reduced ecological integrity and value in terms of management goals relative to the original or reference system. Alternative stable states with some limited residual properties of the original system may develop along the progression after a crossing; an eventual outcome may be the complete loss of pre-threshold properties of the original ecosystem. Reverting to the more desirable reference state through ecological restoration becomes increasingly difficult and expensive along the progression gradient and may eventually become impossible. Ecological threshold concepts have been applied as a heuristic framework and to aid in the management of rangelands (Bestelmeyer, 2006; Briske and others, 2006, 2008), aquatic (Scheffer and others, 1993; Rapport and Whitford 1999), riparian (Stringham and others, 2001; Scott and others, 2005), and forested ecosystems (Allen and others, 2002; Digiovinazzo and others, 2010). These concepts are also topical in ecological restoration (Hobbs and Norton 1996; Whisenant 1999; Suding and others, 2004; King and Hobbs, 2006) and ecosystem sustainability (Herrick, 2000; Chapin and others, 1996; Davenport and others, 1998). Achieving conservation management goals requires the protection of resources within the range of desired conditions (Cook and others, 2010). The goal of conservation management for natural resources in the U.S. National Park System is to maintain native species and habitat unimpaired for the enjoyment of future generations. Achieving this goal requires, in part, early detection of system change and timely implementation of remediation. The recent National Park Service Inventory and Monitoring program (NPS I&M) was established to provide early warning of declining ecosystem conditions relative to a desired native or reference system (Fancy and others, 2009). To be an effective tool for resource protection, monitoring must be designed to alert managers of impending thresholds so that preventive actions can be taken. This requires an understanding of the ecosystem attributes and processes associated with threshold-type behavior; how these attributes and processes become degraded; and how risks of degradation vary among ecosystems and in relation to environmental factors such as soil properties, climatic conditions, and exposure to stressors. In general, the utility of the threshold concept for long-term monitoring depends on the ability of scientists and managers to detect, predict, and prevent the occurrence of threshold crossings associated with persistent, undesirable shifts among ecosystem states (Briske and others, 2006). Because of the scientific challenges associated with understanding these factors, the application of threshold concepts to monitoring designs has been very limited to date (Groffman and others, 2006). As a case in point, the monitoring efforts across the 32 NPS I&M networks were largely designed with the knowledge that they would not be used to their full potential until the development of a systematic method for understanding threshold dynamics and methods for estimating key attributes of threshold crossings. This report describes and demonstrates a generalized approach that we implemented to formalize understanding and estimating of threshold dynamics for terrestrial dryland ecosystems in national parks of the Colorado Plateau. We provide a structured approach to identify and describe degradation processes associated with threshold behavior and to estimate indicator levels that characterize the point at which a threshold crossing has occurred or is imminent (tipping points) or points where investigative or preventive management action should be triggered (assessment points). We illustrate this method for several case studies in national parks included in the Northern and Southern Colorado Plateau NPS I&M networks, where historical livestock grazing, climatic change, and invasive species are key agents of change. The approaches developed in these case studies are intended to enhance the design, effectiveness, and management-relevance of monitoring efforts in support of conservation management in dryland systems. They specifically enhance National Park Service (NPS) capacity for protecting park resources on the Colorado Plateau but have applicability to monitoring and conservation management of dryland ecosystems worldwide.

Colorado Plateau↗

USGS2010

Geology, geochemistry, and genesis of the Greens Creek massive sulfide deposit, Admiralty Island, southeastern Alaska

In 1996, a memorandum of understanding was signed by representatives of the U.S. Geological Survey and Kennecott Greens Creek Mining Company to initiate a cooperative applied research project focused on the Greens Creek massive sulfide deposit in southeastern Alaska. The goals of the project were consistent with the mandate of the U.S. Geological Survey Mineral Resources Program to maintain a leading role in national mineral deposits research and with the need of Kennecott Greens Creek Mining Company to further development of the Greens Creek deposit and similar deposits in Alaska and elsewhere. The memorandum enumerated four main research priorities: (1) characterization of protoliths for the wall rocks, and elucidation of their alteration histories, (2) determination of the ore mineralogy and paragenesis, including metal residences and metal zonation within the deposit, (3) determination of the ages of events important to ore formation using both geochronology and paleontology, and (4) development of computer models that would allow the deposit and its host rocks to be examined in detail in three dimensions. The work was carried out by numerous scientists of diverse expertise over a period of several years. The written results, which are contained in this Professional Paper, are presented by 21 authors: 13 from the U.S. Geological Survey, 4 from Kennecott Greens Creek Mining Company, 2 from academia, and 2 from consultants. The Greens Creek deposit (global resource of 24.2 million tons at an average grade of 13.9 percent zinc, 5.1 percent lead, 0.15 troy ounce per ton gold, and 19.2 troy ounces per ton silver at zero cutoff) formed in latest Triassic time during a brief period of rifting of the Alexander terrane. The deposit exhibits a range of syngenetic, diagenetic, and epigenetic features that are typical of volcanogenic (VMS), sedimentary exhalative (SEDEX), and Mississippi Valley-type (MVT) genetic models. In the earliest stages of rifting, formation of precious-metal-rich silica-barite-carbonate white ores began at low temperature in a shallow, subaqueous setting, probably a thin carbonate shelf on the flanks of the Alexander landmass. Epigenetic carbonate replacement textures in the footwall dolostones are overlain by stratiform silica-carbonate-barite-rich ores and indicate that early mineralization formed at and just beneath the paleo sea floor by mixing of a reduced, precious-metal-rich, base-metal-poor hydrothermal fluid with oxygenated seawater. As rifting intensified, the shelf was downfaulted and isolated as a graben. Isolation of the basin and onset of starved-basin shale sedimentation was concurrent with emplacement of mafic-ultramafic intrusives at shallow levels in the rift, resulting in an increasingly higher temperature and progressively more anoxic ore-forming environment. The formation of the main stage of massive sulfide ores began as the supply of bacterially reduced sulfur increased in the accumulating shales. As the main-stage mineralization intensified, shale sedimentation inundated the hydrothermal system, eventually forming a cap. Biogenic sulfate reduction supplied reduced sulfur to the base of the shales where mixing occurred with hot, base-metal-rich hydrothermal fluids. Ore deposition continued by destruction and epigenetic replacement of the early white ores in proximal areas and by inflation and diagenetic replacement of unlithified shale at the interface between the white ores and the base of the shale cap. Ore deposition waned as the shales became lithified and as the supply of bacterially reduced sulfur to the site of ore deposition ceased. The final stages of rifting resulted in the emplacement of mafic-ultramafic intrusive rocks into the Greens Creek system and extrusion of voluminous basaltic flows at the top of the Triassic section. Greenschist facies metamorphism during the Jurassic-Cretaceous accretion of the Alexander terrane to the continental margin resulted in recrystalli

Professional Paper↗

USGS2024

Analysis and review of fishery-dependent data for Hawaiian nearshore noncommercial fisheries

Noncommercial, shore-based fisheries provide economic, social, and cultural services to communities throughout the Hawaiian Islands. The State of Hawai‘i Department of Land and Natural Resources (DLNR), Division of Aquatic Resources (DAR) routinely conducts surveys to monitor noncommercial fisheries such that estimates of fishing effort and catch by gear type can be generated and used to implement more sustainable management practices. DAR executes both the Hawai‘i Marine Recreational Fishery Survey (HMRFS), a nationally standardized survey that focuses on intercepting fishers at access points (i.e., boat ramps) across the main Hawaiian Islands, and a set of roving creel surveys on O‘ahu, Maui Nui, and Kaua‘i that observe and intercept fishers at locations along the shoreline outside of those targeted by HMRFS. The latter set of creel surveys were designed to complement HMRFS by expanding its geographic coverage and thus providing a more representative picture of noncommercial fishing in Hawai‘i. Sustainable management priorities set by DAR rely on the availability of statewide, fishery- dependent data. Thus, we collate information from island-based roving creel surveys into a cohesive Statewide Creel Survey Database. Further, we provide preliminary analyses and describe ways that surveys could be streamlined to improve future data collection, analysis, and utility. In so doing, we synthesize the most detailed information to-date about noncommercial shore-based fisheries of Hawai‘i. The unprecedented spatial and temporal coverage of DAR’s dataset reveals the value of their survey efforts over the last decade to address fishery management needs. Our primary objectives, results, and conclusions are summarized below: 1) Integrate DAR roving creel survey data from different islands into a single Statewide Creel Survey Dataset (Chapter II). We describe the collation of creel survey data from O‘ahu, Maui Nui, and Kaua‘i into a statewide dataset. We also offer ways in which these surveys could be streamlined to meet the needs of managers and decision makers. Briefly, these are to create a statewide strategic plan, standardize the execution of standard operating procedures, centralize the creel survey database and associated metadata, and consider using technology that improves the data pipeline, including transitioning from paper-based to electronic systems for data entry and processing. 2) Assess whether the new Statewide Creel Survey Dataset can provide inputs for length-based stock assessments (Chapter III). Only on Maui were interviews conducted with associated catch data. There was reasonably high taxonomic coverage (42 species from 186 interviews with 310 fishers), but low sample sizes for nearly all species precluded the development of length-based stock assessments. We provide summary statistics from the existing data and briefly discuss how technologies could be used to automate analysis of images of noncommercial catch. 3) Analyze the Statewide Creel Survey Dataset for spatial and temporal patterns in fishing effort (Chapter IV): a. Visualizing noncommercial fishing pressure . We found that fishing effort (mean number of fishers observed per survey event at a site) on O'ahu was over three times greater than that recorded during similar surveys conducted on Maui or Kaua'i. We create maps that display the distribution of angling and spearfishing effort around each of the three islands. b. Factors that predict fishing “hotspots” around Maui . Fishing effort on Maui was associated with areas with more wave power and less parking availability. There were half as many fishers in areas with parking lots than in areas with parking on the road shoulder only. c. Changes in fishing effort during the COVID-19 pandemic . There was no change in fishing effort on O‘ahu during the first year of the pandemic, but there was a 20% decline in year 2 and a 33% decline in year 3, both in comparison to pre-pandemic levels. Pre-pandemic creel survey data were unavailable for Maui and Kaua‘i, but fishing effort on these islands also declined as the pandemic progressed at similar or greater rates than those observed on O‘ahu. 4) Quantify potential bias in survey methods by experimentally deriving fisher detection probabilities of shore-based and drone-based surveys (Chapter V): a. Shore-based surveys . We conducted roving creel surveys for four months at three locations around Hilo Bay, designed to emulate and estimate the efficacy of DAR standard operating procedures. There was high agreement between paired observers in counting fishers, leading to near-perfect detection probabilities of both anglers (94%) and spearfishers (97%), but relatively low agreement and detection probabilities of other fishers (throw net, ‘opihi picking, etc.) (52%). b. Drone-based surveys . We used an unmanned aerial vehicle (UAV; operated by DAR staff) to collect imagery of fishers along the Hilo Bay shoreline. We used still images and video clips (with known fishing activity) to build an online survey that was distributed to DAR and HCFRU personnel, asking them to count and categorize resource users as a snorkeler, spearfisher, angler, or other fisher. Only 40.0% of the responses correctly counted and categorized resource users in the image. Anglers were correctly identified and enumerated in 90.0% of the responses, but the correct response rates of the other three user categories ranged from 67.8% – 79.4%. Snorkelers and anglers tended to be undercounted while spearfishers and other fishers were overcounted. 5) Review the potential for incorporating emerging technologies that will improve, augment, and evolve creel survey data collection, especially for spearfishing (Chapter VI). Within the context of monitoring shore-based noncommercial fishing, we review the use of electronic data entry/processing systems with geospatial and image capabilities, field cameras, drones, smart buoys, citizen science apps, data mining social media, artificial intelligence and machine learning. We highlight several of the challenges and considerations when implementing these technologies into creel surveys and provide a synthesis of options that could be used to better estimate spearfishing. The general conclusion of this assessment is that the DAR roving creel survey program is collecting valuable data that supplement the existing HMRFS efforts. However, there are a number of areas that could be improved to make these efforts a more effective tool for decision-making processes in resource management and conservation: 1) Establishment of clear statewide and island objectives for the Statewide Creel Survey Dataset. Currently, data collection efforts are focused towards addressing a very broad purpose – supplementing the HMRFS data collection efforts. However, the results of the preliminary analyses conducted as part of this project suggest that the data could be used to address other areas of need if these objectives were clearly defined. Further, the design of the creel survey would benefit from greater standardization of survey protocols between islands and an effort to define a) the acceptable margins of error associated with the estimates generated by these data and b) the minimum level of change that the surveys would need to detect to be useful to managers. 2) Centralization of data entry, data quality assessment, and data accessibility. Currently, each DAR office manages data entry, checks the data for errors, and is responsible for managing and storing the data. Instituting a centralized data entry system, particularly an online database that can receive survey data from tablets or smartphones running a standardized data collection application would improve efficiency, reduce data entry errors, and accelerate the availability of data to managers. A substantial amount of time and effort from the project described in this report was devoted to checking the dataset for errors. The development and application of data quality assurance protocols would ensure that the data are reliable and available in a timely fashion to support management decisions. 3) Address lingering questions regarding the efficacy of current survey protocols to capture and characterize the spearfishing component of the noncommercial fishery. The results presented in the report suggest that the current creel survey protocols do a good job detecting spearfishers when present but are not capturing sufficient data about their catch or total effort. There are also questions remaining as to whether the survey times and sites are sufficiently capturing the behavior of spearfishers in Hawai‘i. A more thorough assessment – whether through additional research, alteration of survey design, or review of data by representatives of the spearfishing community – would provide insight on how to use the Statewide Creel Survey Database to inform management of spearfishing. 4) Investigate the integration of technological advancements into the creel survey methods. As priorities and needs are developed and formalized, it would be valuable to consider how various technological advancements might enhance and streamline data collection or open new avenues of inquiry.

Hawaii↗

USGS2010

Biosecurity Plan for Palmyra Atoll

This Biosecurity Plan for Palmyra Atoll was developed for The Nature Conservancy (TNC) Palmyra Program to refine and expand goals and objectives developed through the Conservation Action Plan process. The Biosecurity Plan is one in a series of adaptive management plans designed to achieve TNC's mission toward the protection and enhancement of native wildlife and habitat. The Biosecurity Plan focuses on ecosystem security, and specifically identifies and addresses issues related to non-native and potentially invasive species. The Plan attempts to identify pathways of invasion and strategies for preventing or reducing new introductions. Overall, the Biosecurity Plan provides a framework to implement and track the progress of conservation and restoration goals related to non-native species on Palmyra Atoll. Palmyra Atoll is one of the Northern Line Islands in the Pacific Ocean southwest of the Hawai`ian Islands. It consists of many heavily vegetated islets arranged in a horseshoe pattern around four lagoons and surrounded by a coral reef. At present, Palmyra Atoll harbors various non-native or invasive species in the terrestrial and marine ecosystems. The most notable examples of terrestrial invasive species include coconut trees (Cocos nucifera) and black rats (Rattus rattus). Although it is unclear whether they are non-native, coconut trees are currently the most dominant plant across Palmyra Atoll. They compete with native plant species for space and resources, and are potentially detrimental to seabirds dependent on native vegetation. Black rats are known to predate ground-nesting seabirds and are likely responsible for the lack of burrowing seabird reproduction on Palmyra Atoll. The most notable example of a marine invasive species is the corallimorph (Rhodactis howsei). Although Rhodactis howsei is a native species, it can take advantage of human-altered habitat and significantly change the natural habitat by aggressively outcompeting native corals. Although the extent and impacts of these and other non-native and (or) invasive species are not fully understood, they are clearly a threat to the native species and overall ecosystem integrity of Palmyra Atoll. In fact, non-native invasive species have been considered the most important threat to ecosystems in Hawai`i and the second most important threat to biodiversity world-wide. Palmyra Atoll is somewhat protected because of its remote location, but there are still potential pathways for the introduction of non-native and possibly invasive species. With the continued influx of aircraft and ocean vessels and their contents to and around Palmyra Atoll, we anticipate many more concerns related to the import and spread of non-native invasive species in the future. In terms of ecosystem security, prevention is the most effective and efficient tool for managing invasive species. There are various potential pathways for introduction and spread of non-native species within Palmyra Atoll's terrestrial and marine ecosystems. Identification of these pathways provides a first step in preventing introductions. We also recommend establishing, enhancing, and enforcing quarantine protocols to prevent future non-native species invasions. Other critical steps to minimize the impacts and spread of invasive species include early detection through inventory and monitoring, as well as containment, control, and management of non-native species already established at Palmyra Atoll. These efforts in combination with research and education will serve to inform management decisions related to ecosystem integrity. Along with reinstating ecosystem security, this Biosecurity Plan aims to evaluate new risk factors related to non-native and potentially invasive species. To that end, an adaptive management process of audit and review is highly recommended to ensure the implementation and efficacy of the management practices outlined above. In addition, it will be important to identify high r

Open-File Report↗

USGS1987

Geologic map of the east part of the San Francisco Volcanic Field, north-central Arizona

The geologic map of the east part of the San Francisco volcanic field (called the East map area) is one of five adjoining geologic maps (fig. 1) prepared under the Geothermal Research Program of the U.S. Geological Survey as a basis for interpreting the history of magmatic activity in the volcanic field. This map is a revision of an earlier one (Moore and Wolfe, 1976). Detail of pyroclastic and alluvial deposits has been reduced for clarity on this uncolored version, and eolian deposits, represented by numerous active dunes of basaltic ash, have been completely omitted. Small cinder cones developed over rootless vents on the basalt flow (Qbb) of = vent 2019 have also been omitted. In addition, a few changes have been made in correlations of flows and vents. The stratigraphic classification has been modified because magnetic-polarity determinations and new K-Ar ages indicate that the physiographically defined Tappan and Woodhouse age groups (Moore and others, 1976) overlap significantly in age, and the rocks of those age groups are now assigned to the Brunhes or Matuyama Polarity Chronozones (Mankinen and Dalrymple, 1979). The San Francisco field, which is largely Pliocene and Pleistocene in age, is in northern Arizona, just north of the broad transition zone between the Colorado Plateau and the Basin and Range province. It is one of several dominantly basaltic volcanic fields of late Cenozoic age situated near the southern margin of the Colorado Plateau. The East map area encompasses approximately 1,220 km 2 . The volcanic field contains rocks ranging in composition from basalt to rhyolite--the products of eruption through Precambrian basement rocks and approximately a kilometer of overlying, nearly horizontal, Paleozoic and Mesozoic sedimentary rocks. About 500 km 3 of erupted rocks cover about 5,000 km 2 of predominantly Permian and locally preserved Triassic sedimentary rocks that form the erosionally stripped surface of the Colorado Plateau in northern Arizona. In the East map area, basalt, basaltic andesite and locally associated small dacite domes, and, in a few cases, andesite were extruded from numerous individual vents, each of which presumably erupted briefly and then became inactive. Such short-lived vents, represented mainly by cinder cones or tuff rings, are widely distributed over the map area, and their flows cover much of its surface. However, repeated eruption of andesite, dacite, and rhyolite domes and flows formed the O'Leary Peak eruptive center in the northwest part of the map area, and flows of andesite (Qa 1 and Qa 2 ) from the San Francisco Mountain stratovolcano entered the East map area from the west. A northeastward progression of volcanism during the past 15 m.y., from central Arizona into the San Francisco volcanic field, is shown by the compilation of Luedke and Smith (1978). Although complicated in detail, a general northeastward to eastward progression of volcanic activity is also apparent within the San Francisco volcanic field. Thus, much of the eruptive activity of the East map area occurred late in the development of the San Francisco field, and the East map area includes the youngest volcanic rocks of the field. These youngest rocks were formed during the Sunset Crater eruption, which occurred within the past 1,000 years (Smiley, 1958). A northeast-trending, faulted monocline occurs near Doney Mountain in the north-central part of the East map area, and a broad north- to northwest-trending anticline occurs at the east edge of the map area. Nearby volcanic rocks are not folded or faulted by either structure. Northwest-trending normal faults of small throw occur in the southern and northwestern parts of the map area. The faults in the northwestern part transect basalt flows of Matuyama and Brunhes ages (Tmb, Qmb, and Qbb). The volcanic rocks are not faulted elsewhere in the East map area. However, local northwestward elongation and alignment of vent deposits, as shown for example by the fissure deposits of the Sunset Crater eruption (Qbsbf), indicate the presence of a northwest-trending fracture system that apparently localized some of the eruptive feeders.

Arizona↗

USGS2008

Mapping of Florida's coastal and marine resources: Setting priorities workshop

The importance of mapping habitats and bioregions as a means to improve resource management has become increasingly clear. Large areas of the waters surrounding Florida are unmapped or incompletely mapped, possibly hindering proper management and good decisionmaking. Mapping of these ecosystems is among the top priorities identified by the Florida Oceans and Coastal Council in their Annual Science Research Plan. However, lack of prioritization among the coastal and marine areas and lack of coordination of agency efforts impede efficient, cost–effective mapping. A workshop on Mapping of Florida’s Coastal and Marine Resources was sponsored by the U.S. Geological Survey (USGS), Florida Department of Environmental Protection (FDEP), and Southeastern Regional Partnership for Planning and Sustainability (SERPPAS). The workshop was held at the USGS Florida Integrated Science Center (FISC) in St. Petersburg, FL, on February 7-8, 2007. The workshop was designed to provide State, Federal, university, and non-governmental organizations (NGOs) the opportunity to discuss their existing data coverage and create a prioritization of areas for new mapping data in Florida. Specific goals of the workshop were multifold, including to: provide information to agencies on state-of-the-art technology for collecting data; inform participants of the ongoing mapping programs in waters off Florida; present the mapping needs and priorities of the State and Federal agencies and entities operating in Florida; work with State of Florida agencies to establish an overall priority for areas needing mapping; initiate discussion of a unified classification of habitat and bioregions; discuss and examine the need to standardize terminology and data collection/storage so that data, in particular habitat data, can be shared; identify opportunities for partnering and leveraging mapping efforts among agencies and entities; identify impediments and organizational gaps that hinder collection of data for mapping; seek innovative solutions to the primary obstacles identified; identify the steps needed to move mapping of Florida’s oceans and coasts forward, in preparation for a better coordinated, more cost-effective mapping program to allow State and Federal agencies to make better decisions on coastal-resource issues. Over 90 invited participants representing more than 30 State and Federal agencies, universities, NGOs, and private industries played a large role in the success of this two-day workshop. State of Florida agency participants created a ranked priority order for mapping 13 different regions around Florida. The data needed for each of the 13 priority regions were outlined. A matrix considering State and Federal priorities was created, utilizing input from all agencies. The matrix showed overlapping interests of the entities and will allow for partnering and leveraging of resources. The five most basic mapping needs were determined to be bathymetry, high-vertical resolution coastline for sea-level rise scenarios, shoreline change, subsurface geology, and benthic habitats at sufficient scale. There was a clear convergence on the need to coordinate mapping activities around the state. Suggestions for coordination included: creating a glossary of terms: a standard for specifying agency data-mapping needs; creating a geographic information officer (GIO) position or permanent organizing group to maintain communications established at this workshop and to maintain progress on the issues identified during the workshop. The person or group could develop a website, maintain a project-status matrix, develop a list of contacts, create links to legislative updates and links to funding sources; developing a web portal and one-stop/clearinghouse of data. There was general consensus on the need to adopt a single habitat classification system and a strategy to accommodate existing systems smoothly. Unresolved aspects of the systems warrant that a separate workshop would be needed to work out details. Participants recognized that the State priority list would necessarily be updated periodically. An annual review of priorities would facilitate information exchange, mapping activities updates, and re-allocation of funding among changing priorities. It was recognized that mapping of State waters would take billions of dollars and in light of tightening budgets there was need for processes that could be used to appropriate or leverage monies for mapping and reduce data-collection costs. Fourteen different avenues were explored. There was a clear consensus that the linking of public to private partnerships to support mapping was imperative, and ways to achieve this were discussed.

Florida↗

USGS2025

Insights and strategic opportunities from the USGS 2024 Per- and Polyfluoroalkyl Substances (PFAS) Interagency Workshop

Introduction In 2021, the U.S. Geological Survey (USGS) published Circular 1490 titled, “Integrated Science for the Study of Perfluoroalkyl and Polyfluoroalkyl Substances (PFAS) in the Environment: A Strategic Science Vision for the U.S. Geological Survey” (Tokranov and others, 2021). Circular 1490 was created to be a resource for USGS scientists prioritizing and planning research related to per- and polyfluoroalkyl substances (PFAS) and to be a guide for developing partnerships with other scientists, State and Federal agencies, and stakeholders engaged in PFAS research and management and mitigation of the environmental and human-health effects of PFAS. This USGS PFAS Strategic Science Vision document was intended to be the foundation for a “living strategic vision,” periodically providing updates on the state of USGS PFAS research, emerging PFAS data gaps and needs, and progress on interagency and stakeholder PFAS partnerships and priorities. To meet this objective, the USGS planned to host an Interagency and Stakeholder PFAS Workshop every 2–3 years. During September 10–12, 2024, the USGS hosted the first Interagency and Stakeholder PFAS Workshop in Reston, Virginia. The Workshop brought together experts from other Federal agencies (U.S. Environmental Protection Agency, National Institute of Environmental Health Sciences, Food and Drug Administration, Department of Defense [Air Force, Army]), State agencies (Washington Fish and Wildlife, Virginia Department of Transportation), and academia (Harvard University, University of Maryland) to address key challenges relating to the measurement and modeling of PFAS and the implications for environmental health. Participants engaged in in-depth discussions centered around six pivotal topics related to PFAS: (1) sampling protocols, methods and interpretation; (2) environmental sources, source apportionment, and occurrence; (3) environmental fate and transport; (4) human and wildlife exposure routes and risk; (5) bioconcentration, bioaccumulation, and biomagnification; and (6) ecotoxicology and effects. Each topic had three breakout sessions. A recurrent theme of workshop discussions was how data on a nationwide scale for PFAS occurrence in various environmental matrices, including air, water, food crops, biota, soil, and streambed sediment could help to advance scientific understanding. Participants noted significant geospatial data gaps, particularly in the midwestern and southern United States and the Pacific Northwest. PFAS data collection tends to be more robust along the eastern seaboard and in California. Participants stressed how enhancing the integration of large and small datasets across various agencies could help to support national scale understanding of PFAS. To address these gaps, attendees suggested leveraging datasets from Federal entities like the USGS and the U.S. Department of Defense, State agencies, and municipal utility services to develop predictive contaminant detection and transport models. Improved coordination between water quality programs and USGS research could help to facilitate access to valuable data, leading to comprehensive databases that inform PFAS point (wastewater treatment plants and landfills) and nonpoint (runoff from land, atmospheric deposition, food packaging) sources, environmental transport mechanisms, environmental detection and concentrations, potential exposure routes, and health effects on different biota, including humans. A specific request was made to develop a map demarking the depth of modern (1953 or later) groundwater, which is susceptible to surface-derived anthropogenic (that is, human-made) contamination, based on tritium-age dating. Emphasis was placed on incorporation of hydrology, groundwater flow paths, groundwater–surface water interactions, and landscape factors in predictive statistical models as a step to improve contaminant source identification and tracking. Molecular fingerprinting approaches garnered attention as techniques to link specific PFAS mixtures detected in a sample to environmental sources and levels in biota (Dávila-Santiago and others, 2022). Integrating data from abiotic (that is, water, soil, and air) and biotic (that is, living organisms) systems identified as a research opportunity. For example, understanding the composition of soils and sediments, which include a mixture of mineral, plant, and animal components, could advance understanding of exposure pathways. The discussions highlighted opportunities to explore and understand the potential redistribution and biotic exposures of PFAS from biosolid and wastewater treatment plant effluent land application practices, in addition to atmospheric releases and discharges from landfill and wastewater treatment plants. Participants identified research gaps surrounding how these sources may contribute to contamination and may affect surrounding ecosystems, including a better definition of anthropogenic background concentrations. Moving forward, the collection of co-occurrence data was noted as a means to improve understanding of complex mixtures and to leverage companion modeling efforts focused on areas with high and low contamination levels to identify areas of concern and unaffected resources. Participants emphasized how centralized USGS databases and the establishment of sample-metadata archives can help to ensure that samples are preserved and accessible for future research. In conclusion, the workshop participants identified opportunities to bridge data gaps and improve measurement techniques, modeling frameworks, databases, and communication, to enhance the understanding of PFAS and their effects on environmental and human health. Upon completion of the workshop, participants indicated an interest in developing strategic data collection, modeling, and analytical approaches to address these challenges.

Open-File Report↗

USGS2015

U.S. Geological Survey science for the Wyoming Landscape Conservation Initiative—2014 annual report

This is the seventh report produced by the U.S. Geological Survey (USGS) for the Wyoming Landscape Conservation Initiative (WLCI) to detail annual activities conducted by the USGS for addressing specific management needs identified by WLCI partners. In FY2014, there were 26 projects, including a new one that was completed, two others that were also completed, and several that entered new phases or directions. The 26 projects fall into several categories: (1) synthesizing and analyzing existing data to identify current conditions on the landscape and using the data to develop models for projecting past and future landscape conditions; (2) monitoring indicators of ecosystem conditions and the effectiveness of on-the-ground habitat projects; (3) conducting research to elucidate the mechanisms underlying wildlife and habitat responses to changing land uses; (4) managing and making accessible the large number of databases, maps, and other products being developed; and (5) coordinating efforts among WLCI partners, helping them use USGS-developed decision-support tools, and integrating WLCI outcomes with future habitat enhancement and research projects. The new (completed) project was the development and publication of a public outreach piece for visitors of Fossil Butte National Monument. The final product was a USGS Fact Sheet that capitalized on previously collected elk-monitoring data to interpret the ecology of the Monument’s elk population and the importance of the Monument’s habitats to this highly visible wildlife species. One of the completed projects entailed developing and evaluating a synthetic approach to high-resolution satellite imagery for use in effectiveness monitoring, which culminated in a journal article. The other completed project was a coalescing of two similar tasks under data and information management that pertain to Web application development and the development of outreach and graphic products into a single integrated project that focuses on developing and maintaining/upgrading Web applications and other tools for visualizing, mapping, and using geospatial data. Major accomplishments for FY2014 included several publications, including Part B of an energy resources map that (with Part A) depicts coal, wind, oil, gas, oil shale, uranium, and solar energy production in the WLCI region. Two published works associated with sage-grouse included a Wildlife Monograph on prioritizing species’ habitats across large landscapes, multiple seasons, and novel areas (using sage-grouse in Wyoming as an example), and a USGS Data Series report that includes both the data used in the habitat-prioritization models and the habitat prioritization models developed for sage-grouse. Our Science Team also published a framework for conducting large, collaborative projects that rely on geospatial data, and a paper that describes the efficacy of fusing satellite data collected at various resolutions for measuring and monitoring vegetation changes. These products are all invaluable tools for maximizing the efficiency and effectiveness of managing species of concern, conducting future landscape-scale assessments, and monitoring status and trends of landscape conditions. Other highlights of FY2014 included a renewed effort to gather and analyze wildlife and habitat status and trend data for the WLCI Interagency Monitoring Database (IAMD) to assess long-term trends and cumulative effects associated with land-use and climate changes. Water-monitoring efforts included drilling four new groundwater-monitoring wells in the Green and New Fork River basins near the proposed Normally Pressured Lance Formation energy development, and continued data collection at established water-monitoring sites. Three additional wells were sampled as part of the Wyoming Groundwater Monitoring Network, bringing the total to 19 Network wells sampled in the WLCI region since 2010. Combined, these water-monitoring efforts can help to identify potential changes in water quality or levels that may result from land-use changes. Major terrestrial monitoring accomplishments included processing satellite imagery from 1985−2010 to develop a historical perspective of long-term vegetation changes, which can serve as a basis for monitoring current and future trends in sagebrush steppe. Such data are crucial tools for agencies tasked with sage-grouse management and conservation. The USGS WLCI Science Team also continued monitoring and testing methods for evaluating WLCI habitat treatments designed to promote aspen regeneration and enhance sage-grouse habitat, and to assess how those treatments influence invasive species distributions and ungulate herbivory. Highlights included analyzing field data collected to elucidate the relationships between sage-grouse habitat use and the proximity of energy infrastructure, and using new instruments to measure productivity responses of aspen woodlands to various factors. Numerous FY2014 accomplishments specifically addressed agency needs to manage and conserve Wyoming’s wildlife species of concern. A pygmy rabbit habitat model and Wyoming distribution map were completed to identify factors associated with rabbit habitat occupancy. Previous work on sage-grouse population dynamics was expanded to better understand the factors that drive long-term viability of sage-grouse populations and to develop a tool that helps to identify key factors limiting sage-grouse persistence in Wyoming. Field work and data analyses continued for elucidating the relationships between sagebrush songbird abundance and productivity, the intensity of energy development, and community dynamics of nest predators. For the mule deer study, mixed mountain shrublands important to migrating and wintering mule deer were mapped and delivered to WLCI partners. Additionally, the relationships between energy development and crucial winter habitat for mule deer were evaluated, and a new phase of work was implemented to better understand relationships between plant phenology and mule deer migration movements. Finally, initial analyses of data collected to evaluate fish-community composition in relation to habitat quality indicate that water quality, as measured by concentrations of hydrocarbons, water temperature, and others parameters, has been diminished in subwatersheds with higher levels of energy development. Overall, the outcomes and products of these wildlife studies contribute significantly to the information and tools needed for addressing effects of land-use changes on Wyoming’s species of concern. Finally, capabilities of the WLCI Web site and the USGS ScienceBase infrastructure were maintained and upgraded to help ensure access to and efficient use of all the WLCI data, products, assessment tools, and outreach materials that have been developed. Of particular note is the completion of three Web applications developed for mapping (1) the 1900−2008 progression of oil and gas development;(2) the predicted distributions of Wyoming’s Species of Greatest Conservation Need; and (3) the locations of coal and wind energy production, sage-grouse distribution and core management areas, and alternative routes for transmission lines within the WLCI region. Collectively, these applications tools provide WLCI planners and managers with powerful tools for better understanding the distributions of wildlife species and potential alternatives for energy development.

Wyoming↗

USGS2020

Recent planform changes in the Upper Mississippi River

Geomorphic changes in the Upper Mississippi River (UMR) have long been a concern of river agencies charged with maintaining and restoring river habitat (GREAT 1980; Jackson et al. 1981; USFWS 1992). Large meandering alluvial rivers like the UMR are expected to constantly change and adjust their fluvial landforms within their riparian corridors as a result of the natural interaction of hydrologic processes, sediment movement, and vegetation over time. However, present geomorphic changes in the UMR reflect altered hydrologic, hydraulic, and sediment conditions caused by regulated flows, constructed agricultural levees and navigation dams, altered land use in the watershed, and climate change. Levees reduce lateral hydrologic and sediment connectivity between channels and floodplains on many tributaries and on the Mississippi River downstream of Pool 13. Between each of the dams are a repeating series of landforms associated with tailwater, intermediate, and impounded conditions. The dams maintain a minimum water level, thus creating many off-channel areas that act as sediment traps. Whereas high-head dams cut off sedimentological connectivity longitudinally through the river corridor (Skalak et al., 2013), low head dams on the UMR only slightly altered transport longitudinally. Deltaic-like sedimentation can be common in the impounded sections of dammed rivers. Erosion of relict land surfaces that remained above the raised impounded water levels has been the dominant change in UMR impounded sections due to increased wind fetch leading to increased wave action. Even though upland sources of sediment from tributaries have decreased over the middle to late 20th century, increased annual precipitation, the interplay of increased variability in flood magnitudes from year to year, and more fall and winter flooding have likely changed erosion and sedimentation patterns in the UMR (Belby, et al., 2019). Paradoxically, monitoring and research indicates that the concentration of some water column constituents like total suspended solids and phosphorous has decreased during the 1991 to 2014 time period (Kreiling and Houser, 2016). In areas prone to increased sedimentation, bed elevations rise and thereby water depths are reduced at a given discharge, resulting in loss of fish habitat. Sediment deposition or erosion further influences water exchange rates between main channel and off-channel areas in the river by increasing resistance in connecting channels or enlarging existing connecting channels. Water depth and water exchange rates are the most prominent features describing habitat quality in the UMR (De Jager et al. 2018), and in some cases, the trajectory of planform change from heightened deposition promises to threaten deep backwater habitats particularly important for overwintering fish. Although information on the rate of vertical change in bed elevation is needed for a complete assessment of geomorphic change associated with the loss of deep backwater habitats, mapping planform changes over time (i.e., lateral changes between the land-water boundary) provide needed information on the location, potential cause, and progressive direction of deposition, especially in the mid sections between dams where deltaic processes are the most pronounced. Several types of planform changes have been observed and identified as concerns. For example, island loss in the large impounded areas of the upper part of the UMR was one of the concerns identified by river managers in the 1980s and 90s, and subsequently island construction became a common form of restoration implemented by the Upper Mississippi River Restoration (UMRR) Program (USACE 2012). Other subtler planform changes, such as channel bank erosion and delta formation in backwaters, are perceived to be important, but have largely gone unquantified. A systemwide reconnaissance of the UMR and IWW conducted in 1998 concluded that 14-percent of the river banks were eroding (Nakato and Anderson 1998). However, stabilization of existing river banks has never been widely pursued as a restoration measure, due to the high cost and uncertain benefits. Delta formation reduces the amount of backwater habitat; however, the deltas maintain and create a mix of riparian and aquatic habitats, and that is generally considered to be beneficial for wildlife and fish. If recent hydrologic trends of more frequent and longer duration flood events continue, a better understanding of planform changes can help in describing past changes, and then be used to forecast potential future trajectories of change. If UMR resource managers determine that past and forecasted conditions are undesirable, then UMRR projects could be identified and prioritized to address those concerns. Vegetative cover associations with landform changes have been used to detect and quantify planform changes in many rivers (Johnson 1985; Hiatt 2015; Volte et al. 2015). Freyer and Jefferson (2013) completed such a study in Pool 6 of the UMR using the landcover data from 12 dates over a 115-yr period, including the 1989, 2000, and 2010/2011 landcover/use (LCU) data from the UMRR Program. Planform change detected over the last 20 years represented by the UMRR Program data best reflect present-day geomorphic patterns, rates and processes. Changes occurring prior to dam construction and changes occurring soon after dam construction are likely not the same as those happening now, 50-70 years after dam construction and creation of the impoundments (McHenry et al., 1984; Bhowmik and Adams, 1986; WEST Consultants, 2000). The LCU data from each of the 1989, 2000, and 2010/2011 imagery was developed using similar methods and is available in a Geographical Information System (GIS) for the entire UMR and therefore provides the opportunity for a more comprehensive planform change analysis. This study used GIS overlays of LCU classes to map and quantify changes in planform features over two periods, looking specifically for depositional areas where terrestrial and wetland vegetation expanded at the expense of open water. The land expansion was grouped into four possible process-based types common in large floodplain rivers, some following that used by Lewin et al. (2017). The four types include: crevasse deltas emanating from a breach from a main channel through a natural levee or narrow floodplain into backwaters (crevasse deltas), tributary deltas expanding into backwaters (tributary deltas), deltaic bars at the upstream end of impoundments (impounded deltas), and linear-like bars extending from the downstream ends of narrow levees and remnant floodplains (bar-tail limbs). The methods deployed for change detection addressed possible errors from a variety of sources.

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗

USGS2020

Using advanced population genomics to better understand the relationship between offshore and spawning habitat use for Atlantic Sturgeon

Atlantic Sturgeon ( Acipenser oxyrinchus oxyrinchus ) are a large-bodied anadromous fish that historically supported important fisheries along the east coast of the United States. Following years of overharvest and habitat degradation, populations experienced severe declines. In 2012, the National Marine Fisheries Service listed Atlantic Sturgeon under the Endangered Species Act (ESA; 61 FR 4722). Their listing named five Distinct Population Segments (DPSs), predicated on genetic groups composed of geographically proximate populations. Federal management of Atlantic Sturgeon presents challenges, as sturgeon from each of the five DPSs mix extensively in coastal and marine habitats yet take and recovery progress must be evaluated separately for each unit. Genetic assignment testing based on mitochondrial and microsatellite markers allows individuals to be assigned back to their natal river and DPS. However, this approach is not perfect and some individuals may be incorrectly assigned. Recent advances in genomics offer the potential of a higher resolution approach to genetic assignment testing, and thus may reduce uncertainty associated with assignment testing. In addition, genomics allows a greater number of markers to be examined from across a broader portion of the sturgeon genome, thus may provide an enhanced perspective of population structure for the species, and potentially allow other previously intractable questions to be addressed (Bernatchez et al. 2017, Supple and Shapiro 2018). We used next-generation sequencing to develop a draft genome for Atlantic Sturgeon and identify single nucleotide polymorphisms (SNPs) that could be used to resolve the natal river and DPS of individual Atlantic Sturgeon. We identified 1,210 candidate SNPs within the nuclear genome as well as 49 SNPs within the mitochondrial genome. After filtering and review, we selected 161 nuclear SNPs and 39 mitochondrial SNPs for further testing and evaluation. We used genotyping-in-thousands by sequencing (GT-seq) to simultaneously sequence nuclear SNP loci, mitochondrial SNP loci, and the existing panel of twelve microsatellite loci. This effort required a pilot sequencing run on a single sturgeon sample to test marker amplification and refine primer strengths, followed by a series of sequencing runs to generate baseline data for 288 individuals representing nine populations of Atlantic Sturgeon in four DPSs. Using baseline data from the nine populations, we ran a series of genomic analyses to characterize diversity within and among populations, providing a benchmark for this species using the new SNP markers. Allelic richness was similar for all populations, although there was a general trend of more northern population containing greater levels of allelic richness. Interestingly, we observed linkage disequilibrium among many pairs of loci within many populations. This might be the result of physical linkage but could also suggest these populations are recovering from genetic bottlenecks and/or are effectively small, leading to specific haplotypes to be favored by chance. Pairwise differentiation among populations varied among the populations ( F ST range: 0.010-0.098) and was significantly correlated ( r = 0.771; P < 0.001) to pairwise F ST observed using microsatellite markers). Population clustering and ordination techniques using the new genomic data both support an overall population structure that is similar to the current DPS management units (which were developed primarily based on microsatellite genetic data). Overall, this suggests that existing microsatellite markers and the panel of SNP markers developed in this study provide similar information about the populations structure and ecology of Atlantic Sturgeon. Given the observed differences in allele frequencies among populations, our genomic baseline supports previous assertations that Atlantic Sturgeon show natal homing, despite mixing extensively in marine waters during non-breeding periods. Lower levels of differentiation between populations in the South Atlantic DPS suggest that populations in this region may have greater levels of gene flow relative to their more northerly conspecifics, which has also previously been suggested based on microsatellite data. The observed differentiation among populations provides the necessary foundation for determining the natal river and DPS of Atlantic Sturgeon using assignment testing. We tested the utility of our new genomic baseline for resolving the population and DPS of Atlantic Sturgeon. Our nuclear SNP markers showed utility for identifying the origin of unknown Atlantic Sturgeon samples, as 86.5% were assigned to the correct DPS and 66.3% were assigned to the correct natal river. However, since this study was funded the Conservation Genetics and Genomics Laboratory at Leetown Science Center has made significant improvements to their microsatellite genetic baseline, which now performs more effectively than our new genomic approach (the genetic baseline includes 12 populations and 5 DPSs, and correctly assigns 95.8% of individuals to DPS and 84.9% of individuals to their natal population using 12 microsatellite loci). We conducted an ad hoc exploration of how additional microsatellite or nuclear SNP loci may further improve the accuracy of assignment testing. We found that additional microsatellite markers are likely to result in greater improvements in assignment efficiency than additional nuclear SNPs. However, a much larger number of SNP loci (which if identified could be sequenced using other methods that are now available; e.g., the RAD-capture approach published by Ali et al. 2016) could produce assignment efficiencies that are greater than what is currently feasible using microsatellites. In the absence of further research and development of additional SNP markers for Atlantic Sturgeon (possibly using an approach other than GT-seq), the existing microsatellite loci are the most effective means available to determine the natal river and DPS of Atlantic Sturgeon encountered in offshore waters. Because our new genomic markers were less effective than the existing panel of 12 microsatellite markers, we chose to use the existing microsatellite markers to assign Atlantic Sturgeon captured in another BOEM-funded study (cooperative agreement M16AC00003; Monitoring endangered Atlantic Sturgeon and commercial finfish habitat use offshore New York) following consultation with our project officer. Using this approach, we genotyped and assigned 186 Atlantic Sturgeon captured in coastal waters off the Rockaway Peninsula, New York. The vast majority of these sturgeon were assigned to the New York Bight DPS (94.62%), and most appear to belong to the Hudson River population (87.10%) with smaller contributions from the Delaware River population (7.53%). Smaller contributions (2.15%) were observed from six other populations, including those from the James, York, Kennebec, Ogeechee, and Edisto rivers. Although most of the fish we assigned were assigned to the nearest spawning rivers (Hudson and Delaware), the contributions from distant rivers is consistent with the propensity of this species to move long distances and form mixed stock aggregations along the continental shelf. This finding indicates that spawning populations (and their corresponding DPS) from distant locations may potentially be impacted by offshore activities. In fact, activities in this region of the New York Bight could negatively impact Atlantic Sturgeon population from at least four different DPSs. Genetic or genomic assignment testing remains an essential tool to characterize potential impacts to Atlantic Sturgeon populations and should be applied more broadly to better characterize potential impacts of activities in other locations.

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