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USGS2018

Leveraging geodetic data to reduce losses from earthquakes

Seismic hazard assessments that are based on a variety of data and the best available science, coupled with rapid synthesis of real-time information from continuous monitoring networks to guide post-earthquake response, form a solid foundation for effective earthquake loss reduction. With this in mind, the Earthquake Hazards Program (EHP) of the U.S. Geological Survey (USGS) Natural Hazards Mission Area (NHMA) engages in a variety of undertakings, both established and emergent, in order to provide high quality products that enable stakeholders to take action in advance of and in response to earthquakes. Examples include the National Seismic Hazard Model (NSHM), development of tools for improved situational awareness such as earthquake early warning (EEW) and operational earthquake forecasting (OEF), research about induced seismicity, and new efforts to advance comprehensive subduction zone science and monitoring. Geodetic observations provide unique and complementary information directly relevant to advancing many aspects of these efforts (fig. 1). EHP scientists have long leveraged geodetic data for a range of influential studies, and they continue to develop innovative observation and analysis methods that push the boundaries of the field of geodesy as applied to natural hazards research. Given the ongoing, rapid improvement in availability, variety, and precision of geodetic measurements, considering ways to fully utilize this observational resource for earthquake loss reduction is timely and essential. This report presents strategies, and the underlying scientific rationale, by which the EHP could achieve the following outcomes: The EHP is an authoritative source for the interpretation of geodetic data and its use for earthquake loss reduction throughout the United States and its territories. The USGS consistently provides timely, high quality geodetic data to stakeholders. Significant earthquakes are better characterized by incorporating geodetic data into USGS event response products and by expanded use of geodetic imaging data to assess fault rupture and source parameters. Uncertainties in the NSHM, and in regional earthquake models, are reduced by fully incorporating geodetic data into earthquake probability calculations. Geodetic networks and data are integrated into the operations and earthquake information products of the Advanced National Seismic System (ANSS). Earthquake early warnings are improved by more rapidly assessing ground displacement and the dynamic faulting process for the largest earthquakes using real-time geodetic data. Methodology for probabilistic earthquake forecasting is refined by including geodetic data when calculating evolving moment release during aftershock sequences and by better understanding the implications of transient deformation for earthquake likelihood. A geodesy program that encompasses a balanced mix of activities to sustain missioncritical capabilities, grows new competencies through the continuum of fundamental to applied research, and ensures sufficient resources for these endeavors provides a foundation by which the EHP can be a leader in the application of geodesy to earthquake science. With this in mind the following objectives provide a framework to guide EHP efforts: Fully utilize geodetic information to improve key products, such as the NSHM and EEW, and to address new ventures like the USGS Subduction Zone Science Plan. Expand the variety, accuracy, and timeliness of post-earthquake information products, such as PAGER (Prompt Assessment of Global Earthquakes for Response), through incorporation of geodetic observations. Determine if geodetic measurements of transient deformation can significantly improve estimates of earthquake probability. Maintain an observational strategy aligned with the target outcomes of this document that includes continuous monitoring, recording of ephemeral observations, focused data collection for use in research, and application-driven data processing and analysis systems. Collaborate on research, development, and operation of affordable, high-precision seafloor geodetic methods that improve earthquake forecasting and event response. Advance computational techniques and instrumentation to enable use of strategies like repeat-pass imagery and low-cost geodetic sensors for earthquake response, monitoring, and research. Engage stakeholders and collaborate with partner institutions to foster operational and research objectives and to safeguard the continued health of geodetic infrastructure upon which we mutually depend. Maintaining a vibrant internal research program provides the foundation by which the EHP can remain an effective and trusted source for earthquake science. Exploiting abundant new data sources, evaluating and assimilating the latest science, and pursuing novel avenues of investigation are means to fulfilling the EHP’s core responsibilities and realizing the important scientific advances envisioned by its scientists. Central to the success of such a research program is engaging personnel with a breadth of competencies and a willingness and ability to adapt these to the program’s evolving priorities, enabling current staff to expand their skills and responsibilities, and planning holistically to meet shared workforce needs. In parallel, collaboration with external partners to support scientific investigations that complement ongoing internal research enables the EHP to strengthen earthquake information products by incorporating alternative perspectives and approaches and to study topics and geographic regions that cannot be adequately covered internally. With commensurate support from technical staff who possess diverse skills, including engineering, information technology, and proficiency in quantitative analysis combined with basic geophysical knowledge, the EHP can achieve the geodetic outcomes identified in this document.

Open-File Report↗

USGS2002

Occurrence and status of volatile organic compounds in ground water from rural, untreated, self-supplied domestic wells in the United States, 1986-99

Samples of untreated ground water from 1,926 rural, self-supplied domestic wells were analyzed for volatile organic compounds (VOCs) during 1986-99. This information was used to characterize the occurrence and status of VOCs in domestic well water. The samples were either collected as part of the U.S. Geological Survey?s National Water-Quality Assessment (NAWQA) Program occurrence-assessment studies or were compiled by NAWQA from existing ambient ground-water or source-water-quality monitoring programs conducted by local, State, and other Federal agencies. Water samples were collected at the wellhead prior to treatment or storage. In most samples, 55 target VOCs were analyzed, and occurrence and status information generally was computed at an assessment level of 0.2 mg/L (microgram per liter). At least one VOC was detected in 12 percent of samples (232 samples) at an assessment level of 0.2 mg/L. This detection frequency is relatively low compared to the 26 percent detection frequency of at least one VOC in public sup-ply wells sampled by NAWQA, and the difference may be due, in part, to the higher pumping rates, pumping stress factors, and larger contributing areas of public supply wells. Samples with detections of at least one VOC were collected from wells located in 31 of 39 States. Solvents were the most frequently detected VOC group with detections in 4.6 percent of samples (89 samples) at an assessment level of 0.2 mg/L. The geographic distribution of detections of some VOC groups, such as fumigants and oxygenates, relates to the use pattern of com-pounds in that group. With the exception of com-pounds used in organic synthesis, detection frequencies of VOCs by group are proportional to the average half-life of compounds in the group. When the organic synthesis group is excluded from the analysis, a good correlation exists between the detection frequency of VOCs by group and average half-life of compounds in the group. Individually, VOCs were not commonly detected at an assessment level of 0.2 mg/L, with the seven most frequently detected VOCs found in only 1 to 5 percent of samples. Mixtures (two or more compounds) were a common mode of occurrence for VOCs when no assessment level was applied, and mixtures occurred in one-half of all samples that contained at least one VOC. Only 1.4 percent of samples (27 samples) had one or more VOC concentrations that exceeded a federally established drinking-water standard or health criterion. Only 0.1 percent of samples (2 samples) had one or more VOC concentrations that exceeded a taste/odor threshold. Potential point sources of VOCs near domestic wells are numerous. Leaks from under-ground storage tanks and aboveground storage tanks that hold gasoline, diesel fuel, or heating oil have the potential to be major point sources of contaminants to domestic wells. Shock chlorination may be a source of trichloromethane and other trihalomethanes in some domestic wells. Septic systems are believed to be an important source of contaminants to domestic wells, but extensive research on this subject does not exist. VOCs frequently are ingredients in household products such as cleansers and insecticides, and some VOCs have been found in septic systems.

Water-Resources Investigations Report↗

USGS2012

Archive of single beam and swath bathymetry data collected nearshore of the Gulf Islands National Seashore, Mississippi, from West Ship Island, Mississippi, to Dauphin Island, Alabama: Methods and data report for USGS Cruises 08CCT01 and 08CCT02, July 2008, and 09CCT03 and 09CCT04, June 2009

During the summers of 2008 and 2009 the USGS conducted bathymetric surveys from West Ship Island, Miss., to Dauphin Island, Ala., as part of the Northern Gulf of Mexico (NGOM) Ecosystem Change and Hazard Susceptibility project. The survey area extended from the shoreline out to approximately 2 kilometers and included the adjacent passes (fig. 1). The bathymetry was primarily used to create a topo-bathymetric map and provide a base-level assessment of the seafloor following the 2005 hurricane season. Additionally, these data will be used in conjunction with other geophysical data (chirp and side scan sonar) to construct a comprehensive geological framework of the Mississippi Barrier Island Complex. The culmination of the geophysical surveys will provide baseline bathymetry necessary for scientists to define and interpret seafloor habitat for this area and for scientists to predict future geomorpholocial changes of the islands with respect to climate change, storm impact, and sea-level rise. Furthermore, these data provide information for feasibility of barrier island restoration, particularly in Camille Cut, and for the preservation of historical Fort Massachusetts. For more information refer to http://ngom.usgs.gov/gomsc/mscip/index.html. Since bathymetric surveys have often been conducted for navigational purposes, soundings have traditionally been referenced to a water level datum using tide gages and tide models. Bathymetric measurements referenced to a Global Positioning System (GPS) is a more accurate way of representing water depth and has been implemented in the acquisition and processing procedures for these datasets. Previous single-beam bathymetric studies performed at the USGS Center for Coastal and Marine Science have successfully referenced bathymetric measurements to GPS (DeWitt and others, 2007; Hansen 2008 and 2009). The 2008-2009 bathymetry surveys were conducted as a test to (1) develop acquisition and processing technology utilizing both single beam and swath bathymetry survey methods together, (2) reference both types of measurements to GPS rather than water level, and (3) compare the differences between methods in acquisition and processing. Results of the survey are explained in greater detail within this report. To acquire suitable coverage of the study area in a limited time frame, the seafloor-elevation survey was conducted using three techniques: single-beam bathymetry, interferometric swath bathymetry, and a walking kinematic survey of the island shorelines. All three techniques utilized GPS measurements. Implementation of these techniques was executed concurrently yet independently aboard two research vessels: the RV Survey Cat , a 26-foot (ft) shallow-draft Glacier Bay Coastal Runner, and the 50-ft RV G.K. Gilbert . A portable push buggy with a rigid antenna mount served as the platform for the kinematic shoreline survey. Data from each survey technique was post-processed and edited independently with proper inclusion of the differentially processed external navigation files. The x,y,z components from each method were then combined and the two survey years (2008 and 2009) were merged into one dataset. The 2008 bathymetry data were processed at the USGS Center for Coastal and Marine Science in St. Petersburg, Fla., and the 2009 bathymetry data were processed at the USGS Coastal and Marine Science Center located in Woods Hole, Mass. This report serves as an archive of the processed single beam and interferometric swath bathymetry, outlines the methodology, and reports the results. Data products herein include gridded and interpolated digital depth surfaces, and x,y,z data products for both single beam and interferometric swath bathymetry. Additional files include trackline maps, navigation files, geographic information system (GIS) files, Field Activity Collection System (FACS) logs, and formal Federal Geographic Data Committee (FGDC) metadata. Scanned images of the handwritten FACS logs and digital FACS logs are also provided as PDF files. Refer to the Acronyms page for description of acronyms and abbreviations used in this report or hold the cursor over an acronym for a pop-up explanation. The USGS St. Petersburg Coastal and Marine Science Center assigns a unique identifier to each cruise or field activity. For example, 08CCT01 indicates that the data were collected in 2008 for the Coastal Change and Transport (CCT) study and the data were collected during the first (01) field activity for that project in that calendar year. Refer to http://walrus.wr.usgs.gov/infobank/programs/html/definition/activity.html for a detailed description of the method used to assign the field activity ID. See the digital FACS equipment log for details about the acquisition equipment used. Raw datasets are stored digitally at the USGS St. Petersburg Coastal and Marine Science Center and processed systematically using Novatel's GrafNav version 7.6, SANDS version 3.7, SEA SWATH plus version 3.06.04.03, CARIS HIPS AND SIPS version 3.6, and ESRI ArcGIS version 9.3.1. For more information on processing refer to the Equipment and Processing page. Chirp seismic data were also collected during these surveys and are archived separately.

Mississippi;Alabama↗

USGS1987

Results of a workshop concerning ecological zonation in bottomland hardwoods

Under Section 404 of the Clean Water Act, the U.S. Environmental Protection Agency (EPA) has regulatory responsibilities concerning the discharge of dredged or fill material into the Nation's waters. In addition to its advisory role in the U.S. Army Corps of Engineers' permit program, EPA has a number of specific authorities, including formulation of the Section 404(b)(1) Guidelines, use of Section 404(c) to prohibit disposal at particular sites, and enforcement actions for unauthorized discharges. A number of recent court cases focus on the geographic scope of Section 404 jurisdiction in potential bottomland hardwood (BLH) wetlands and the nature of landclearing activities in these areas that require a permit under Section 404. Accordingly, EPA needs to establish the scientific basis for implementing its responsibilities under Section 404 in bottomland hardwoods. EPA is approaching this task through a series of workshops designed to provide current scientific information on bottomland hardwoods and to organize that information in a manner pertinent to key questions, including the following. What are the characteristics of bottomland hardwoods (in terms of hydrology, soils, vegetation, fish, wildlife, agricultural potential, and the like) and how can the functions (e.g., flood storage, water quality maintenance, detrital export) that they perform best be quantified? How do perturbations like landclearing, levee construction, and drainage impact the functions that bottomland hardwoods perform and how can these effects best be quantified? And finally, how significant are the impacts and how is their significance likely to change under various management scenarios? The first workshop in this series was held December 3-7, 1984, in St. Francisville, Louisiana. The workshop was attended by over 40 scientists and regulators (see ACKNOWLEDGMENTS section) and facilitated by the editors of this report under an Interagency Agreement between EPA and the U.S. Fish and Wildlife Service. The general objective of the workshop was to examine ways in which the structure and function of BLH ecosystems can be characterized and, in particular, to investigate the utility of a conceptual framework developed at a workshop held in Lake Lanier, Georgia, in 1980. In this framework, the transition from aquatic habitats to upland habitats through a BLH ecosystem is divided into six zones based on concomitant variation in the soil moisture regime and associated vegetation (Table 1). The zonation concept is of particular interest to EPA from at least two perspectives. The first is simply as a framework for organizing information. If the zones are discernible in the field, have recognizable characteristics, and perform identifiable functions, they might form a useful basis for tasks such as assessing the impacts of a particular site-specific activity. The second is the potential utility of the zonation concept in identifying the wetland portions of BLH communities. If the zones can be recognized in the field, and if one or more of them can be shown consistently to have wetland characteristics (i.e., perform functions, such as detrital export, often attributed to wetlands), while others do not, then the zones might have utility in identifying areas that fall under the jurisdiction of Section 404. The workshop itself was divided into two parts. The first was a series of papers in which authors described current research and data-synthesis activities in the context of the zonation concept. The second was a series of six workgroups in which participants discussed the zonation concept from the perspective of hydrology, soils, vegetation, fish, wildlife, and ecosystem processes. This report is a compilation of the written material from those workgroups, much of which was produced at the workshop. The formal papers presented in the first part of the workshop have been distributed to participants under separate cover, but are referenced in this report by citations such as: (Jones, workshop presentation).

Report↗

USGS1985

Environmental systems and management activities on the Kennedy Space Center, Merritt Island, Florida: results of a modeling workshop

In the early 1960's, the National Aeronautics and Space Administration (NASA) began purchasing 140,000 acres on Merritt Island, Florida, in order to develop a center for space exploration. Most of this land was acquired to provide a safety and security buffer around NASA facilities. NASA, as the managing agency for the Kennedy Space Center (KSC), is responsible for preventing or controlling environmental pollution from the Federal facilities and activities at the Space Center and is committed to use all practicable means to protect and enhance the quality of the surrounding environment. The Merritt Island National Wildlife Refuge was established in 1963 when management authority for undeveloped lands at KSC was transferred to the U.S. Fish and Wildlife Service. In addition to manage for 11 Federally-listed threatened and endangered species and other resident and migratory fish and wildlife populations, the Refuge has comanagement responsibility for 19,000 acres of mosquito control impoundments and 2,500 acres of citrus groves. The Canaveral National Seashore was developed in 1975 when management of a portion of the coastal lands was transferred from NASA to the National Park Service. This multiagency jurisdiction on Merritt Island has resulted in a complex management environment. The modeling workshop described in this report was conducted May 21-25, 1984, at the Kennedy Space Center to: (1) enhance communication among the agencies with management responsibilities on Merritt Island; (2) integrate available information concerning the development, management, and ecology of Merritt Island; and (3) identify key research and monitoring needs associated with the management and use of the island's resources. The workshop was structured around the formulation of a model that would simulate primary management and use activities on Merritt Island and their effects on upland, impoundment, and estuarine vegetation and associated wildlife. The simulation model is composed of four connected submodels. The Uplands submodel calculates changes in acres and structural components of vegetation communities resulting from succession, fire, facilities development, and shuttle launch depositions, as well as the quantity and quality of surface runoff and aquifer input to an impoundment and an estuary. The Impoundment submodel next determines water quality and quantity and changes in vegetation resulting from water level manipulation and prescribed burning. The Estuary submodel than determines water quality parameters and acres of seagrass beds. Finally, the Wildlife submodel calculates habitat suitability indices for key species of interest, based on vegetation conditions in the uplands and impoundments and on several hydrologic parameters. The model represents a hypothetical management unit with 2,500 acres of uplands, a 600-acre impoundment, and a 1,500-acre section of estuary. Two management scenarios were run to analyze model behavior. The scenarios differ in the frequency of shuttle launches and prescribed burning, the extent of facilities development, the amount of land disposed waste material applied, and the nature and timing of impoundment water level control. Early in a model development project, the process of building the model is usually of greater benefit than the model itself. The model building process stimulates interaction among agencies, assists in integrating existing information, and helps identify research needs. These benefits usually accrue even in the absence of real predictive power in the resulting model. Open communication occurs among the Federal, State, and local agencies involved with activities on Merritt Island and the agencies have a cooperative working relationship. The workshop provided an opportunity for all of these agencies to meet at one time and have focused discussions on the key environmental and multiagency resource management issues. The workshop framework helped to integrate information and assumptions from a number of disciplines and agencies. This integration occurred in the computer simulation model and among workshop participants as submodel linkages were developed and scenario results discussed. A number of research needs were identified at the workshop during the model building and testing exercises and associated discussions. These needs were based on the informed judgement of researchers and managers familiar with Merritt Island or similar areas, rather than on a comprehensive literature review of sensitivity analysis of the preliminary model developed at the workshop. Some of the needs can be addressed by interpreting the results of completed studies from similar geographic areas as they relate to Merritt Island, while other will require additional research studies on Merritt Island. Major research needs associated with the Upland submodel include behavior of the near-surface aquifer, factors limiting slash pine regeneration, frequency and effects of natural fire on various cover types, cumulative effects of shuttle launches, and fate in upland soils of nitrogen and phosphorous from land applied waste material. Key Impoundment submodel needs include documentation of vegetation changes in response to altered water depth, salinity, and nutrient concentrations and better specification of the functional characteristics of impoundments as chemical filters. Important information gaps identified in the Estuary submodel include a more complete analysis of factors contributing to phytoplankton abundance, evaluation of sources of turbidity other than phytoplankton, and identification and quantification of factors limiting seagrass distribution. Primary research needs associated with the Wildlife submodel include a survey of breeding habitat, production data, and harvest data for mottled ducks; data on the emigration and immigration of juvenile mullet (and other transient fish) in the impoundment; the contribution of various seagrasses to habitat requirements of sea trout; and the effects of dissolved oxygen on survival of juvenile sea trout. Ideally, the modeling workshop process is iterative in nature. Periods between workshops are used for research, data collection, and model refinement. Each workshop integrates information collected since the last workshop and produces a more credible model that is more useful in evaluating management alternatives. Participants felt that continued application of this process would help provide ongoing integration and communication among agencies and would allow each agency's planning and management activities to be viewed within the context of an overall assessment.

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USGS2001

U.S. Geological Survey Activities Related to American Indians and Alaska Natives Fiscal Year 2001

Information is a resource that can help Native American governments and their people. The U.S. Geological Survey (USGS) makes available technical expertise, reports, and other impartial information sources that can benefit Native Americans interested in subsistence issues, water, land use, and the health of many parts of the environment. The USGS works in cooperation with American Indian and Alaska Native governments, conducting research on water and mineral resources, animals and plants of environmental, economic, or subsistence importance, natural hazards, and geologic resources. Digital data on cartography, mineral resources, stream flow, biota, and other topics are available to American Indian and Alaska Native individuals and institutions. The USGS recognizes the need to learn from and share knowledge with Native peoples. This report describes most of the activities that the USGS conducted with American Indian and Alaska Native governments, educational institutions, and individuals during Federal fiscal year 2001. Some of these USGS activities were carried out in concert with the Bureau of Indian Affairs (BIA). Others were conducted by Tribes and the USGS. In 2001, the USGS began examining its activities related to American Indians and Alaska Natives to determine how it can better serve these customers within its mandates. A growing number of Tribal governments, educational institutions, and other Tribal organizations have begun using geographic information systems and other digital technologies in recent years. As Tribes become more interested in and more adept at managing digital information, they are seeking relevant data from the USGS more frequently. Using digital technologies provides Tribal governments with additional means of managing lands and resources for the benefit of current and future generations. The USGS recognizes the need to make its information available to Tribal governments, and to work with those governments and other institutions to advance data management capabilities. The USGS is responding to this need by increasing the transfer of scientific information to American Indian and Alaska Native governments and by training employees of those governments to conduct and improve scientific studies. The USGS is also encouraging American Indians and Alaska Natives to pursue careers in science, and seeking ways to hire Indian and Native students. By identifying, improving, and disseminating information about available hiring mechanisms, the USGS is working to make hiring such students easier, and therefore more likely, for USGS managers. The U.S. Geological Survey is the Federal science bureau within the Department of the Interior (DoI). The USGS is non-regulatory and is not a significant manager of Federal or Trust lands or assets. However, there are two types of USGS activities that do involve American Indians, Alaska Natives, and their lands. The first type of activity is the course of formal studies, conducted through existing USGS programs, that involves collection of specific types of data as well as investigative and research projects. These projects typically last 2 or 3 years, although a few are parts of longer-term activities. Some projects are funded through cooperative agreements, from monies provided to the USGS by individual Tribal governments or by the BIA. The USGS provides matching funds for cooperative projects. These formal projects may also receive funding from the U.S. Environmental Protection Agency, the Indian Health Service (part of the Department of Health and Human Services), or other Federal agencies. The USGS routinely works with its sister bureaus in the Department of the Interior to provide the scientific information and expertise needed to meet the Department's science priorities. Within this context, the USGS and the BIA are cooperating to use USGS information resources to benefit American Indian and Alaska Native peoples and their lands. The second type of USGS activity is less formal, based on initiatives designed and conducted by USGS employees. Frequently involving educational activities, these endeavors are prompted by employee interests, often as collateral issues, that result from one or more USGS employees identifying and responding to an observed need. In these activities, USGS employees help fulfill a mission of the USGS-to make science relevant-while helping their fellow citizens. USGS employees have also taken the initiative in assisting American Indians and Alaska Natives through participation in several organizations that were created to foster awareness of science among Native peoples and to help build support and communication networks. One such group is the American Indian Science and Engineering Society (AISES). This group sponsors an annual national meeting in which USGS employees participate. USGS employees join this organization on a voluntary basis, bringing the benefits of this expanded network to the USGS, as many employees do with other professional organizations. Each part of the USGS has identified an American Indian/Alaska Native liaison. Furthermore, the USGS has instituted a regional organizational structure, with Western, Central, and Eastern Regions. The regions work in concert with specific scientific disciplines to conduct the scientific mission of the USGS. The regional structure is intended to bring us closer to our customers; we hope that Native Americans and Alaska Natives will use the contacts listed at the end of this report.

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USGS2000

U.S. Geological Survey Activities Related to American Indians and Alaska Natives Fiscal Year 2000

The U.S. Geological Survey (USGS) is an impartial scientific organization that strives to produce scientific results that are relevant to the people of the United States and their land and resource managers. USGS does not improve the quality of its customers' lives; it provides the informational tools for American Indians, Alaska Natives, and other customers to understand and improve their own lives. In cooperation with American Indian and Alaska Native governments, the USGS conducts research on water and mineral resources, animals and plants of environmental, economic, or subsistence importance, natural hazards, and geologic resources. Digital data on cartography, mineral resources, stream flows, biota, and other data sets are available to American Indian and Alaska Native institutions. The USGS recognizes the need to learn from and share knowledge with Native peoples. This report describes most of the activities that the USGS conducted with American Indian and Alaska Native governments, educational institutions, and individuals during Federal Fiscal Year 2000. Some of these USGS activities were conducted in concert with the Bureau of Indian Affairs. Others were conducted by Tribes and the USGS. In the year 2000, the USGS began examining its activities related to American Indians and Native Alaskans to determine how it can better serve these customers within its mandates. More Tribal governments, educational institutions, and other Tribal organizations are using geographic information systems and other digital technologies in recent years. As Tribes become more interested and more adept at managing digital information, they are seeking such data from the USGS with greater frequency. The increasing use of such technologies allows Tribal governments additional means of managing lands and resources for the benefit of current and future generations. The USGS recognizes the need to make its information available to Tribal governments, and to work with those governments and other institutions to advance data management capabilities. The USGS is responding to this need by increasing the transfer of scientific information to American Indian and Alaska Native governments and by training employees of these governments to conduct and improve scientific studies. The USGS is also encouraging American Indians and Alaska Natives to pursue careers in science, and seeking ways to hire Indian and Native students. By identifying, improving, and disseminating information about available hiring mechanisms, the USGS is working to make hiring such students easier, and therefore more likely, for USGS managers. The U.S. Geological Survey is the Federal science bureau within the Department of the Interior (DoI). The USGS is non-regulatory and is not a significant manager of Federal or Trust lands or assets. However, there are two types of USGS activities that do involve American Indians, Alaska Natives, and their lands. The first type of activity is the course of formal studies, conducted through existing USGS programs, that involve collection of specific types of data as well as investigative and research projects. These projects have a duration of two or three years, although a few are parts of longer-term activities. Some are funded through cooperative agreements or reimbursable accounts, from monies provided to the USGS by individual Tribal governments or by the Bureau of Indian Affairs (BIA). The USGS provides matching funds for cooperative projects. These formal projects may also receive funding from the U.S. Environmental Protection Agency, the Indian Health Service (part of the Department of Health and Human Services), or other Federal agencies. The USGS routinely works with its sister bureaus in the Department of the Interior to provide the scientific information and expertise needed to meet the Department's science priorities. Within this context, the USGS and the Bureau of Indian Affairs are cooperating to use USGS knowledge for the benefit of American Indian and Native peoples and their lands. The second type of USGS activity is less formal, based on initiatives designed and conducted by USGS employees. Frequently involving educational activities, these endeavors are prompted by employee interests, often as collateral issues, that result from an individual or group of USGS employees identifying and responding to an observed need. In these activities, USGS employees help us fulfill a mission of the USGS, to make science relevant, while helping their fellow citizens. USGS employees have also taken the initiative to assist American Indians and Alaska Natives through participation in several organizations that were created to foster knowledge of science among Native peoples and to help build support and communication networks. One such group is the American Indian Science and Engineering Society (AISES). This group sponsors an annual national meeting in which USGS employees participate. USGS employees join this organization on a voluntary basis, paying the costs themselves, yet bringing the benefits of this expanded network to the USGS, as many employees do with other professional organizations. Each part of the USGS has identified an American Indian/Alaska Native liaison. As USGS moves to a more regional organizational structure, it will establish contacts in the Western, Central, and Eastern Regions. Within the USGS, this report will help in developing outreach, educational, and program documents for use in future years. It is hoped that USGS employees, American Indians, and Alaska Natives will adapt these activities in new areas and will use the USGS contacts to expand the relevance of the USGS to more Americans.

Report↗

USGS2020

Mapping, exploration, and characterization of the California continental margin and associated features from the California-Oregon border to Ensenada, Mexico

Priority Geographic Area: Both within and outside US Exclusive Economic Zone (EEZ). California continental margin. This area includes and continues south of the geographic area captured in the Watt et al. white paper. Description of Priority Area: The California continental margin, from the narrow shelf to abyssal depths, contains diverse seafloor features that influence benthic community types, biological connectivity, and is associated with significant seafloor geohazards. These complex features include marginal basins, depositional slopes, submarine canyons, ridges, and seamounts, and seep environments as a result of fluid seeps along active faults. Water column characteristics are variable, with steep gradients in current velocities, which influence sediment transport, from depositional fans (slow flow, muddy) to submarine canyons and seamounts (high currents, rocky, rugged terrain). These features and associated environments can influence the distribution of deep-sea habitats, including coral and sponge communities. South of the region described in the Watt et al. and Demopoulos et al. white papers, plentiful seeps occur from northern California down to the southern California Borderland. However, the underlying foundational geology associated with these seeps varies along the margin, changing with contrasting tectonic settings, from convergent tectonics to regions dominated by strike-slip faulting (Barry et al. 1996; Paull et al. 2008; Bernardo and Smith 2010; Maloney et al. 2015). For seeps located off southern California, the relationship to strike-slip fault systems may influence the distribution of seep fluid expulsion sites and associated seep habitats (Maloney et al. 2015; Grupe et al. 2015; Conrad et al., 2017), where transpression plays a key role in formation and localization of fluid seeps. Further exploration is required in order to understand these connections. Several submarine canyons intersect the shelf within this region, serving as important channels of energy and transport of sediment from shelf to slope depths. Canyons are typically associated with high currents, turbidity flows, steep and rugged terrain, and high food availability, all of which structures canyon communities and supports hotspots of biodiversity. Specific canyons along the California margin that have been well studied include Scripps and La Jolla Canyons off San Diego, and Monterey Canyon off Monterey, but many more remain relatively unexplored. Commercially important species of fish and invertebrates have been found associated with canyons, as well as deep-sea corals and sponges (e.g., Barry et al. 1996). However, in contrast to their Atlantic counterparts (e.g., through ACUMEN and ASPIRE campaigns) there has been a dearth of exploration and characterization of canyons along the California margin. A number of questions remain regarding canyon and slope wall stability and associated geohazards, plus, how the canyons connect and influence the broader regional biogeography of benthic communities is unknown. Due to their topography, seamounts along the California margin are characterized by steep slopes, large areas of rocky substrate, and high currents. Hydrological complexity is associated with seamounts given they impinge different watermasses, depending on depth range. This heterogeneity yields complex and diverse benthic communities, including commercially important fishes (e.g., Tracey et al., 2012). The geology of Davidson, Pioneer, San Juan, and Rodriquez Seamounts has received considerable study (e.g., Davis et al., 2010) but other seamounts are less known, including how they are biologically and ecologically connected. For example, research comparing the benthic communities associated with Rodriguez and San Juan Seamounts, located outside of the Channel Islands National Marine Sanctuary and within the proposed Chumash Heritage National Marine Sanctuary, to communities found within the sanctuary is critical for managing and protecting resources within the sanctuary and modifying sanctuary boundaries. Exploration would yield the data needed to delineate and characterize essential fish habitats, and deep-sea coral and sponge communities, thus directly connecting the utility of exploration and discovery to decision making. The southern California Borderland is a geomorphologically heterogeneous area created by a complex network of faults, containing deep basins separated by shallow ridges and islands. Persistent fault-related deformation has created complex features, such as exposure of scarps and uplift rocks/ridges, seeps, erosional terraces, hydrate mounds, and mud volcanoes that provide support for thriving benthic communities. That said, significant oxygen minimum zones and low aragonite saturation states persist within several of the basin environments, influencing energy flow, community ecology, and calcification. For example, the combined effects of hypoxia and acidification pose serious threats to marine organisms and biological resources along the California margin. Mapping and exploration of the extensive faults and fault scarps can help constrain historical earthquake activity. But many questions remain regarding how the underlying geology and geological processes have shaped the biological communities.

California↗

USGS2011

Geographic distribution of the mid-continent population of sandhill cranes and related management applications

The Mid-continent Population (MCP) of sandhill cranes ( Grus canadensis ) is widely hunted in North America and is separated into the Gulf Coast Subpopulation and Western Subpopulation for management purposes. Effective harvest management of the MCP requires detailed knowledge of breeding distribution of subspecies and subpopulations, chronology of their use of fall staging areas and wintering grounds, and exposure to and harvest from hunting. To address these information needs, we tagged 153 sandhill cranes with Platform Transmitting Terminals (PTTs) during 22 February–12 April 1998–2003 in the Central and North Platte River valleys of south-central Nebraska. We monitored PTT-tagged sandhill cranes, hereafter tagged cranes, from their arrival to departure from breeding grounds, during their fall migration, and throughout winter using the Argos satellite tracking system. The tracking effort yielded 74,041 useable locations over 49,350 tag days; median duration of tracking of individual cranes was 352 days and 73 cranes were tracked >12 months. Genetic sequencing of mitochondrial DNA (mtDNA) from blood samples taken from each of our random sample of tagged cranes indicated 64% were G. c. canadensis and 34% were Grus canadensis tabida . Tagged cranes during the breeding season settled in northern temperate, subarctic, and arctic North America (U.S. [23%, n = 35], Canada [57%, n = 87]) and arctic regions of northeast Asia (Russia [20%, n = 31]). Distribution of tagged cranes by breeding affiliation was as follows: Western Alaska–Siberia (WA–S, 42 ± 4% [SE]), northern Canada–Nunavut (NC–N, 21 ± 4%), west-central Canada–Alaska (WC–A, 23 ± 4%) and East-central Canada–Minnesota (EC–M, 14 ± 3%). All tagged cranes returned to the same breeding affiliation used during the previous year with a median distance of 1.60 km (range: 0.08–7.7 km, n = 53) separating sites used in year 1 and year 2. Fall staging occurred primarily in central and western Saskatchewan (69%), North Dakota (16%), southwestern Manitoba (10%), and northwestern Minnesota (3%). Space-use sharing indices showed that except for NC–N and WC–A birds, probability of finding a crane from one breeding affiliation within the home range of another breeding affiliation was low during fall staging. Tagged cranes from WC–A and EC–M breeding affiliations, on average, spent 25 and 20 days, respectively, longer on fall staging areas in the northern plains than did WA–S and NC–N birds. Cranes in the NC–N, WA–S, and WC–A affiliations spent 99%, 74%, and 64%, respectively, of winter in western Texas in Hunting Zone A; EC–M cranes spent 83% of winter along the Texas Gulf Coast in Hunting Zone C. Tagged cranes that settled within the breeding range of the Gulf Coast Subpopulation spent 28% and 42% of fall staging and winter within the range of the Western Subpopulation, indicating sufficient exchange of birds to potentially limit effectiveness of MCP harvest management. Harvests of EC–M and WC–A cranes during 1998–2003 were disproportionately high to their estimated numbers in the MCP, suggesting more conservative harvest strategies may be required for these subpopulations in the future, and for sandhill cranes to occupy major parts of their historical breeding range in the Prairie Pothole Region. Exceptionally high philopatry of MCP cranes of all 4 subpopulations to breeding sites coupled with strong linkages between crane breeding distribution, and fall staging areas and wintering grounds, provide managers guidance for targeting MCP crane harvest to meet management goals. Sufficient temporal or spatial separation exists among the 4 subpopulations on fall staging areas and wintering grounds to allow harvest to be targeted at the subpopulation level in all states and provinces (and most hunting zones within states and provinces) when conditions warrant. Knowledge gained from our study provides decision-makers in the United States, Canada, Mexico, and Russia with improved guidance for developing sound harvest regulations, focusing conservation efforts, and generating collaborative efforts among these nations on sandhill crane research and management to meet mutually important goals.

Nebraska↗

USGS2005

Vascular Plant and Vertebrate Inventory of Tumacacori National Historical Park

Executive Summary This report summarizes the results of the first comprehensive biological inventory of Tumacacori National Historical Park (NHP) in southern Arizona. These surveys were part of a larger effort to inventory vascular plants and vertebrates in eight National Park Service units in Arizona and New Mexico. From 2000 to 2003 we surveyed for vascular plants and vertebrates (fish, amphibians, reptiles, birds, and mammals) at Tumacacori NHP to document presence of species within the administrative boundaries of the park's three units. Because we used repeatable study designs and standardized field techniques, these inventories can serve as the first step in a long-term monitoring program. We recorded 591 species at Tumacacori NHP, significantly increasing the number of known species for the park (Table 1). Species of note in each taxonomic group include: * Plants: second record in Arizona of muster John Henry, a non-native species that is ranked a 'Class A noxious weed' in California; * Amphibian: Great Plains narrow-mouthed toad; * Reptiles: eastern fence lizard and Sonoran mud turtle; * Birds: yellow-billed cuckoo, green kingfisher, and one observation of the endangered southwestern willow flycatcher; * Fishes: four native species including an important population of the endangered Gila topminnow in the Tumacacori Channel; * Mammals: black bear and all four species of skunk known to occur in Arizona. We recorded 79 non-native species (Table E.S.1), many of which are of management concern, including: Bermudagrass, tamarisk, western mosquitofish, largemouth bass, bluegill, sunfish, American bullfrog, feral cats and dogs, and cattle. We also noted an abundance of crayfish (a non-native invertebrate). We review some of the important non-native species and make recommendations to remove them or to minimize their impacts on the native biota of the park. Based on the observed species richness, Tumacacori NHP possesses high biological diversity of plants, fish, and birds for a park of its size. This richness is due in part to the ecotone between ecological provinces (Madrean and Sonoran), the geographic distribution of the three units (23 km separates the most distant units), and their close proximity to the Santa Cruz River. The mesic life zone along the river, including rare cottonwood/willow forests and adjacent mesquite bosque at the Tumacacori unit, is representative of areas that have been destroyed or degraded in many other locations in the region. Additional elements such as the semi-desert grassland vegetation community are also related to high species richness for some taxonomic groups. This report includes lists of species recorded by us (or likely to be recorded with additional effort) and maps of study sites. We also suggest management implications and ways to maintain or enhance the unique biological resources of Tumacacori NHP: limit development adjacent to the park, exclude cattle and off-road vehicles, develop an eradication plan for non-native species, and hire a natural resource specialist. These recommendations are intended to assist park staff with addressing many of the goals set out in their most recent natural resources management plan. This study is the first step in a long-term process of compiling information on the biological resources of Tumacacori NHP and its surrounding areas, and our findings should not be viewed as the final authority on the plants and animals of the park. Therefore, we also recommend additional inventory and monitoring studies and identify components of our effort that could be improved upon, either through the application of new techniques (e.g., use of genetic markers) or by extending the temporal and/or spatial scope of our research.

Open-File Report↗

USGS2002

U.S. Geological Survey Activities Related to American Indians and Alaska Natives Fiscal Year 2002

Information is a resource for Native American governments, communities, organizations, and people. The U.S. Geological Survey (USGS) provides technical expertise, reports, and other impartial information sources that benefit Native Americans interested in subsistence issues, water, land use, and the health of many parts of the environment. Native self-sufficiency, economic development, and conservation are cultivated through Native decisions informed with USGS data and analyses. The USGS works in cooperation with American Indian and Alaska Native governments, conducting research on water and mineral resources, animals and plants of environmental, economic, or subsistence importance, natural hazards, and geologic resources. Digital data on cartography, mineral resources, streamflow, biota, and other topics are available to American Indian and Alaska Native individuals and institutions. The USGS recognizes the need to learn from and share knowledge with Native peoples. This report describes most of the activities that the USGS conducted with American Indian and Alaska Native governments, educational institutions, and individuals during Federal Fiscal Year 2002. Some of these USGS activities were carried out in concert with the Bureau of Indian Affairs (BIA). Others were conducted by Tribes, Tribal organizations, professional societies, and the USGS. A growing number of Tribal governments, educational institutions, and other Tribal organizations have begun using geographic information systems and other digital technologies in recent years. As Tribes become more interested in and more adept at managing digital information, they are seeking relevant data from the USGS more frequently. Using digital technologies provides Tribal governments with additional means of managing lands and resources for the benefit of current and future generations. The USGS recognizes the need to make its information available to Tribal governments, and to work with those governments and other institutions to advance data management capabilities. The USGS also recognizes that Tribal institutions have varying needs, interests, and capacities. The USGS strives to be sensitive to the unique circumstances of each of these institutions while supporting their self-driven evolution. The USGS is responding to these needs by increasing the transfer of scientific information to American Indian and Alaska Native governments and by training employees of those governments to conduct scientific studies and improve scientific data management. The USGS is also encouraging American Indians and Alaska Natives to pursue careers in science and seeking ways to hire Indian and Native students. By identifying, improving, and disseminating information about available hiring mechanisms, the USGS is working to make hiring such students easier, and, therefore, more likely, for USGS managers. The U.S. Geological Survey is the Federal science bureau within the Department of the Interior (DoI). The USGS is non-regulatory and is not a significant manager of Federal or Trust lands or assets. However, as described in this report, there are several types of USGS activities that involve American Indians, Alaska Natives, and their lands. One type of activity is the course of formal studies, conducted through existing USGS programs, that involves collection of specific types of data as well as investigative and research projects. These projects typically last 2 or 3 years, although a few are parts of longer-term activities. Some projects are funded through cooperative agreements, from monies provided to the USGS by individual Tribal governments, or by the BIA. The USGS provides matching funds for cooperative projects. These formal projects may also receive funding from the U.S. Environmental Protection Agency, the Indian Health Service (part of the Department of Health and Human Services), or other Federal agencies. The USGS routinely works with its sister bureaus in the Department of the Interior to provide the scientific information and expertise needed to meet the Department's science priorities. Within this context, the USGS and the BIA are cooperating to use USGS information resources to benefit American Indian and Alaska Native peoples and their lands. The second type of USGS activity is less formal, based on initiatives designed and conducted by USGS employees. Frequently involving educational activities, these endeavors are prompted by employee interests, often as collateral issues, that result from one or more USGS employees identifying and responding to an observed need. In these activities, USGS employees help fulfill a mission of the USGS--to prove scientific relevance--while helping their fellow citizens. Increasingly, some of the educational activities are becoming parts of formal USGS projects. USGS employees have also taken the initiative in assisting American Indians and Alaska Natives through participation in several organizations that were created to foster awareness of science among Native peoples and to help build support and communication networks. One such group is the American Indian Science and Engineering Society (AISES). This group sponsors an annual national meeting in which USGS employees participate. USGS employees join this organization on a voluntary basis, bringing the benefits of this expanded network to the USGS, as many employees do with other professional organizations. Each part of the USGS has identified an American Indian/Alaska Native liaison. The USGS has a regional organizational structure, with Western, Central, and Eastern Regions. The regions work in concert with specific scientific disciplines to conduct the scientific mission of the USGS. The regional structure is intended to bring us closer to our customers; we hope that Native Americans and Alaska Natives will use the contacts listed at the end of this report.

Report↗

USGS1985

Effects of flood control alternatives on fish and wildlife resources of the Malheur-Harney lakes basin

Malheur Lake is the largest freshwater marsh in the western contiguous United States and is one of the main management units of the Malheur National Wildlife Refuge in southeastern Oregon. The marsh provides excellent waterfowl production habitat as well as vital migration habitats for birds in the Pacific flyway. Water shortages have typically been a problem in this semiarid area; however, record snowfalls and cool summers have recently caused Malheur Lake to rise to its highest level in recorded history. This has resulted in the loss of approximately 57,000 acres of important wildlife habitat as well as extensive flooding of local ranches, roads, and railroad lines. Because of the importance of the Refuge, any water management plan for the Malheur-Harney Lakes Basin needs to consider the impact of management alternatives on the hydrology of Malheur Lake. The facilitated modeling workshop described in this report was conducted January 14-18, 1985, under the joint sponsorship of the Portland Ecological Services Field Office and the Malheur National Wildlife Refuge, Region 1, U.S. Fish and Wildlife Service (FWS). The Portland Field Office is responsible for FWS reporting requirements on Federal water resource projects while the Refuge staff has management responsibility for much of the land affected by high water levels in the Malheur-Harney Lakes Basin. The primary objective of the workshop was to begin gathering and analyzing information concerning potential fish and wildlife impacts, needs, and opportunities associated with proposed U.S. Army Corps of Engineers (COE) flood control alternatives for Malheur Lake. The workshop was structured around the formulation of a computer model that would simulate the hydrologic effects of the various alternatives and any concommitant changes in vegetation communities and wildlife use patterns. The simulation model is composed of three connected submodels. The Hydrology submodel calculates changes in lake volume, elevation, and surface area, as well as changes in water quality, that result from the proposed water management projects (upstream storage, upstream diversions, drainage canals) and the no action alternative. The Vegetation submodel determines associated changes in the areal extent of wetland and upland vegetation communities. Finally, the Wildlife submodel calculates indices of abundance or habitat suitability for colonial nesting birds (great egret, double-crested cormorant, white-faced ibis), greater sandhill crane, diving ducks, tundra swan, dabbling ducks, and Canada goose based on hydrologic and vegetation conditions. The model represents the Malheur-Harney Lakes Basin, but provides water quantity and quality indicators associated with additional flows that might occur in the Malheur River Basin. Several management scenarios, representing various flood control alternatives and assumptions concerning future runoff, were run to analyze model behavior. Scenario results are not intended as an analysis of all potential management actions or assumptions concerning future runoff. Rather, they demonstrate the type of analysis that could be conducted if the model was sufficiently refined and tested. Early in a model development project, the process of building the model is usually of greater benefit than the model itself. The model building process stimulates interaction among agencies, assists in integrating existing information, and helps identify research needs. These benefits usually accrue even in the absence of real predictive power in the resulting model. This workshop initiated interaction among the primary State and Federal resource and development agencies in a nonadversarial forum. The exchange of information and expertise among agencies provided the FWS with the best information currently available for use in the Planning Aid Letter it will develop at the Reconnaissance state of the COE study. If the COE subsequently initiates a Feasability Study, this information will be refined further and will aid the FWS in preparing its Coordination Act Report on any flood control alternative proposed by the COE. The model building and testing process also helped identify model limitations and more general information needs that should be evaluated for further study prior to preparation of an FWS Coordination Act Report. Major needs associated with the Hydrology submodel include a more detailed representation of hydrologic units (separately consider Harney Lake, Mud Lake, and Malheur Lake or the three hydrological units within Malheur Lake, rather than a combined lake system) and explicitly representation of groundwater storage and discharge in water budget calculations. A better representation of the hydrological units will require more detailed topographic data for the basin, capacity-elevation and elevation-surface area curves for each unit, and better water flow data between the units. Additional water quality parameters and constraints on proposed canal operation due to conditions in the Malheur River might also be added. Key Vegetation submodel needs include fine-tuning existing vegetation relationships in the model and adding relationships to address the influence of historical conditions on vegetation development, effects of very rapid changes in lake level, effects of wildlife populations (e.g., carp, muskrat), responses of vegetation to habitat management actions (e.g, haying, grazing, burning), and better representation of sago pondweed dynamics. A complementary geographic information system might also be developed for spatial analyses. Major needs that should be evaluated for the Wildlife submodel include addition of other wildlife species that have important effects on habitat on the Refuge (e.g., carp, muskrat) and consideration of additional life-cycle requisites and controlling variable for species presently in the model. Some of these limitations could perhaps be overcome if historical data on habitat conditions were developed to use with historical data on wildlife populations.

Oregon↗

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.

Atlantic Coast↗

USGS2015

Southern Salish Sea Habitat Map Series: Admiralty Inlet

In 2010 the Environmental Protection Agency, Region 10 initiated the Puget Sound Scientific Studies and Technical Investigations Assistance Program, designed to support research in support of implementing the Puget Sound Action Agenda. The Action Agenda was created in response to Puget Sound having been designated as one of 28 estuaries of national significance under section 320 of the U.S. Clean Water Act, and its overall goal is to restore the Puget Sound Estuary's environment by 2020. The Southern Salish Sea Mapping Project was funded by the Assistance Program request for proposals process, which also supports a large number of coastal-zone- and ocean-management issues. The issues include the recommendations of the Marine Protected Areas Work Group to the Washington State Legislature (Van Cleve and others, 2009), which endorses a Puget Sound and coast-wide marine conservation needs assessment, gap analysis of existing Marine Protected Areas (MPA) and recommendations for action. This publication is the first of four U.S. Geological Survey Scientific Investigation Maps that make up the Southern Salish Sea Mapping Project. The remaining three map blocks to be published in the future, located south of Admiralty Inlet, are shown in figure 1. Puget Sound is a deep, fjord-type estuary covering an area of 2,330 km 2 in the Pacific Northwest region of the United States (fig. 1). It is connected to the ocean by the Strait of Juan de Fuca, a turbulent passage approximately 160 km in length and 22 km wide at its west end, expanding to over 40 km wide at its east end (Thomson, 1994). During the Pleistocene, the area was occupied several times by lobes of continental ice, resulting in a complex basin-fill of glacial and interglacial deposits that are locally as thick as 1100 m (Johnson and others, 2001). The last glaciation, called the Fraser glaciation, began after 28,800±740 14 C yr B.P. when ice started a slow expansion (Clague, 1981). At peak advance the westward Juan de Fuca lobe reached the edge of the continental shelf through the Juan de Fuca Strait shortly before 14,460±200 14 C yr B.P. (Herzer and Bornhold, 1982). The southward Puget lobe advanced to its terminal position in Puget Sound by around 14,150 14 C yr B.P. (Porter and Swanson, 1998). Ice retreated from its maximum to northern Whidbey Island by 13,650±350 14 C yr B.P. (Dethier and others, 1995). Retreating glaciers resulted in a thick sequence of ice-contact, glacial-marine sediment, and early post-glacial sediments (Linden and Schurrer, 1988). These deposits have experienced the effects of a marine transgression followed by regression, resulting in a sea-level several tens of meters lower than the present day (Linden and Schurrer, 1988). A second transgression brought sea level to about the present level by around 5,470±120 14 C yr B.P. (Clague and others, 1982) establishing the present oceanographic and geologic environment Puget Sound is separated into four interconnected basins; Whidbey, Central (Main), Hood Canal, and South (Thomson, 1994). The Whidbey, Central, and Hood Canal basins are the three main branches of the Puget Sound estuary and are separated from the Strait of Juan de Fuca by a double sill at Admiralty Inlet. The Admiralty Inlet map area includes the Inlet and a portion of the Whidbey Basin (fig. 1). The shallower South Basin is separated by a sill at Tacoma Narrows and is highly branched with numerous finger inlets. Flow within Puget Sound is dominated by tidal currents of as much as 1 m/s at Admiralty Inlet, reducing to approximately 0.5 m/s in the Central Basin (Lavelle and others, 1988). The lack of silt and clay-sized sediments in the Admiralty Inlet map area is likely a result of the strong currents (see Ground-Truth Studies for the Admiralty Inlet Map Area, sheet 3). The subtidal component of flow reaches approximately 0.1 m/s and is driven by density gradients arising from the contrast in salty ocean water at the entrance and freshwater inputs from stream flow (Lavelle and others, 1988). The total freshwater input to Puget Sound is approximately 3.4 x 10 6 m 3 /day, primarily from the Skagit River (Cannon, 1983). The subtidal circulation mostly consists of a two-layered flow in the basins with fresher water exiting at the surface and saltier water entering at depth (Ebbesmeyer and Cannon, 2001). In general, surface waters flow north and deeper waters flow south; variations arise from wind effects that can drive a surface current in the same direction as the wind, and a baroclinic response in the lower layer to about 100-m depth (Matsuura and Cannon, 1997). Oceanographic properties are influenced by temporal forcing parameters such as reduced stream flow during the 2000-01 drought that increased surface salinity and decreased differences between surface and bottom waters (Newton and others, 2003). On offshore seismic-reflection profiles, Pleistocene strata (excluding latest Pleistocene glacial and post-glacial deposits) form a distinct seismic unit, bounded below by pre-Tertiary or Tertiary basement and above by typically flat-lying latest Pleistocene to Holocene deposits that fill in erosional or depositional relief (Johnson and others, 2001). Cores from central Puget Sound have accumulation rates that range from 85 to 1200 mg/cm 2 /yr, or 0.12 to 2.4 cm/yr; the highest accumulation rates are near the southern end of central Puget Sound (Carpenter and others, 1985). Carpenter and others (1985) un-weighted arithmetic mean of accumulation rates for central Puget Sound deeper stations is 480±340 (± one standard deviation) mg/cm 2 /yr. Lavelle and others (1985) also found rates as high as 1200 mg/cm 2 /yr over the past approximately 70 years in cores in the Central Basin off of and north and south of Elliott Bay. Puget Sound basin rates are comparable to rates in midshelf silt deposits on the Washington coast north of the Columbia River (Nittrouer and others, 1979). The deep subtidal (in other words, below SCUBA depths) habitats of Puget Sound are relatively poorly known. A few subtidal surveys exist for several habitat types from the 1960s and 1970s (reviewed in Dethier, 1990), using grab and box core data. The Dethier (1990) review divides habitat up into Coast and Marine Ecological Classification Standard (CMECS) substrate, water column energy, and depth zones but does not attempt to map these habitats, rather it is an inventory of habitats found in the area and the flora and fauna associated with each habitat. The approach of the Southern Salish Sea Mapping project is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data (the undersea equivalent of satellite remote-sensing data in terrestrial mapping), acoustic backscatter, seafloor video, seafloor photography, and bottom-sediment sampling data. This approach is based in part on methods presented and data collection and product needs identified at the Washington State Seafloor Mapping Workshop (Washington State Seafloor Mapping Workshop Steering Committee, 2008), attended by coastal and marine managers and scientists. The map products display seafloor geomorphology and substrate, and identify potential marine benthic habitats. It is emphasized that the more interpretive habitat and geology maps rely on the integration of multiple, new high-resolution datasets and that mapping at small scales would not be possible without such data. Oceanographic current and wave data is not included in this analysis, however, the accompanying geographic information system (GIS) data set is designed and intended to be combined with oceanographic and biologic data sets assembled by others in the future and some of the GIS data has already been incorporated in the unpublished Nature Conservancy Benthic Habitats of Puget Sound database. This publication includes four map sheets, explanatory text, and a descriptive pamphlet. Each map sheet is published as a portable document format (PDF) file. ESRI ArcGIS compatible geotiffs (for example, bathymetry) and shapefiles (for example video observation points) will be available for download in the data catalog associated with this publication (Cochrane, 2015). An ArcGIS Project File with the symbology used to generate the map sheets is also provided. For those who do not own the full suite of ESRI GIS and mapping software, the data can be read using ESRI ArcReader, a free viewer that is available at http://www.esri.com/software/arcgis/arcreader/index.html .

Washington↗

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.

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