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Acoustic telemetry and fisheries management

This paper reviews the use of acoustic telemetry as a tool for addressing issues in fisheries management, and serves as the lead to the special Feature Issue of Ecological Applications titled “Acoustic Telemetry and Fisheries Management” . Specifically, we provide an overview of the ways in which acoustic telemetry can be used to inform issues central to the ecology, conservation, and management of exploited and/or imperiled fish species. Despite great strides in this area in recent years, there are comparatively few examples where data have been applied directly to influence fisheries management and policy. We review the literature on this issue, identify the strengths and weaknesses of work done to date, and highlight knowledge gaps and difficulties in applying empirical fish telemetry studies to fisheries policy and practice. We then highlight the key areas of management and policy addressed, as well as the challenges that needed to be overcome to do this. We conclude with a set of recommendations about how researchers can, in consultation with stock assessment scientists and managers, formulate testable scientific questions to address and design future studies to generate data that can be used in a meaningful way by fisheries management and conservation practitioners. We also urge the involvement of relevant stakeholders (managers, fishers, conservation societies, etc.) early on in the process (i.e. in the co-creation of research projects), so that all priority questions and issues can be addressed effectively.

Ecological Applications

Do we know how much fluvial sediment reaches the sea? Decreased river monitoring of U.S. coastal rivers

Given the present and future changing climate and human changes to land use and river control, river sediment fluxes to coastal systems are changing and will continue to change in the future. To delineate these changes and their effects, it is increasingly important to document the fluxes of river-borne sediment discharged to the sea. Unfortunately, broad-scale river sediment monitoring programs established more than 50 years ago in the U.S. have diminished substantially and now focus principally on the largest rivers and estuaries. Unless addressed, these data gaps will provide significant challenges in addressing fundamental scientific and management questions about the effects of climate change and sea-level rise in our estuaries and on our coasts.

Hydrological Processes

United States National seismograph network

The USGS National Earthquake Information Center (NEIC) has planned and is developing a broadband digital seismograph network for the United States. The network will consist of approximately 150 seismograph stations distributed across the contiguous 48 states and across Alaska, Hawaii, Puerto Rico and the Virgin Islands. Data transmission will be via two-way satellite telemetry from the network sites to a central recording facility at the NEIC in Golden, Colorado. The design goal for the network is the on-scale recording by at least five well-distributed stations of any seismic event of magnitude 2.5 or greater in all areas of the United States except possibly part of Alaska. All event data from the network will be distributed to the scientific community on compact disc with read-only memory (CD-ROM).

Puerto Rico, U.S. Virgin Islands

The U. S. Geological Survey National Hydrologic Model infrastructure: Rationale, description, and application of a watershed-scale model for the conterminous United States

The ability to effectively manage water resources to meet present and future human and environmental needs is essential. Such an ability necessitates a comprehensive understanding of hydrologic processes that affect streamflow at a watershed scale. In the United States, water-resources management at scales ranging from local to national can benefit from a nationally consistent, process-based watershed modeling capability to provide the requisite understanding. The National Hydrologic Model (NHM) infrastructure, which was developed by the U.S. Geological Survey to support coordinated, comprehensive, and consistent hydrologic modeling at multiple scales for the conterminous United States, provides this essential capability. NHM-based applications provide information to enable more effective water-resources planning and management, fill knowledge gaps in ungaged areas, and support basic scientific inquiry. In the future, as process algorithms and data sets improve, the NHM infrastructure will continue to evolve to better support the nation's water-resources research and management needs.

Conterminous United States

The 2010 explosive eruption of Java's Merapi volcano—A ‘100-year’ event

Merapi volcano (Indonesia) is one of the most active and hazardous volcanoes in the world. It is known for frequent small to moderate eruptions, pyroclastic flows produced by lava dome collapse, and the large population settled on and around the flanks of the volcano that is at risk. Its usual behavior for the last decades abruptly changed in late October and early November 2010, when the volcano produced its largest and most explosive eruptions in more than a century, displacing at least a third of a million people, and claiming nearly 400 lives. Despite the challenges involved in forecasting this ‘hundred year eruption’, we show that the magnitude of precursory signals (seismicity, ground deformation, gas emissions) was proportional to the large size and intensity of the eruption. In addition and for the first time, near-real-time satellite radar imagery played an equal role with seismic, geodetic, and gas observations in monitoring eruptive activity during a major volcanic crisis. The Indonesian Center of Volcanology and Geological Hazard Mitigation (CVGHM) issued timely forecasts of the magnitude of the eruption phases, saving 10,000–20,000 lives. In addition to reporting on aspects of the crisis management, we report the first synthesis of scientific observations of the eruption. Our monitoring and petrologic data show that the 2010 eruption was fed by rapid ascent of magma from depths ranging from 5 to 30 km. Magma reached the surface with variable gas content resulting in alternating explosive and rapid effusive eruptions, and released a total of ~ 0.44 Tg of SO 2 . The eruptive behavior seems also related to the seismicity along a tectonic fault more than 40 km from the volcano, highlighting both the complex stress pattern of the Merapi region of Java and the role of magmatic pressurization in activating regional faults. We suggest a dynamic triggering of the main explosions on 3 and 4 November by the passing seismic waves generated by regional earthquakes on these days.

Merapi volcano

Doctorate time rising sharply: How long should it take?

The period 1967–1987 saw a 20% increase in the time it takes to complete the doctorate. That figure is based on data provided by the National Research Council from 11 scientific and engineering fields, including the Earth, atmospheric and marine sciences. The median time spent earning the degree rose from 5.4 years in 1967 to 6.1 years in 1977 to 6.9 years in 1987—an increase of 1.5 years in a single generation. Completion time still seems to be rising! All graduating doctoral students in 1987 had a median age of 33.6 years; chemistry students were youngest at 29, and education students were the oldsters at 39.8 years.

Eos, Transactions, American Geophysical Union

Cruise report for P1-13-LA, U.S. Geological Survey gas hydrates research cruise, R/V Pelican April 18 to May 3, 2013, deepwater Gulf of Mexico

The U.S. Geological Survey led a seismic acquisition cruise in the Gulf of Mexico from April 18 to May 3, 2013, with the objectives of (1) achieving improved imaging and characterization at two established gas hydrate study sites, and (2) refining geophysical methods for gas hydrate characterization in other locations. We conducted this acquisition aboard the R/V Pelican, and used a pair of 105/105-cubic-inch generator/injector air guns to provide seismic energy that we recorded using a 450-meter 72-channel digital hydrophone streamer and 25 multicomponent ocean-bottom seismometers. In the area of lease block Green Canyon 955, we deployed 21 ocean-bottom seismometers and acquired approximately 400 kilometers of high-resolution two-dimensional streamer seismic data in a grid with line spacing as small as 50 meters and along radial lines that provide source offsets up to 10 kilometers and diverse azimuths for the ocean-bottom seismometers. In the area of lease block Walker Ridge 313, we deployed 25 ocean-bottom seismometers and acquired approximately 450 kilometers of streamer seismic data in a grid pattern with line spacing as small as 250 meters and along radial lines that provide source offsets up to 10 kilometers for the ocean-bottom seismometers. The data acquisition effort was conducted safely and met the scientific objectives.

Open-File Report

Database of potential sources for earthquakes larger than magnitude 6 in Northern California

The Northern California Earthquake Potential (NCEP) working group, composed of many contributors and reviewers in industry, academia and government, has pooled its collective expertise and knowledge of regional tectonics to identify potential sources of large earthquakes in northern California. We have created a map and database of active faults, both surficial and buried, that forms the basis for the northern California portion of the national map of probabilistic seismic hazard. The database contains 62 potential sources, including fault segments and areally distributed zones. The working group has integrated constraints from broadly based plate tectonic and VLBI models with local geologic slip rates, geodetic strain rate, and microseismicity. Our earthquake source database derives from a scientific consensus that accounts for conflict in the diverse data. Our preliminary product, as described in this report brings to light many gaps in the data, including a need for better information on the proportion of deformation in fault systems that is aseismic.

California

Bedrock geologic map of the Uxbridge quadrangle, Worcester County, Massachusetts, and Providence County, Rhode Island

The bedrock geology of the 7.5-minute Uxbridge quadrangle consists of Neoproterozoic metamorphic and igneous rocks of the Avalon zone. In this area, rocks of the Avalon zone lie within the core of the Milford antiform, south and east of the terrane-bounding Bloody Bluff fault zone. Permian pegmatite dikes and quartz veins occur throughout the quadrangle. The oldest metasedimentary rocks include the Blackstone Group, which represents a Neoproterozoic peri-Gondwanan marginal shelf sequence. The metasedimentary rocks are intruded by Neoproterozoic arc-related plutonic rocks of the Rhode Island batholith. This report presents mapping by G.J. Walsh. The complete report consists of a map, text pamphlet, and GIS database. The map and text pamphlet are available only as downloadable files (see frame at right). The GIS database is available for download in ESRI™ shapefile and Google Earth™ formats, and includes contacts of bedrock geologic units, faults, outcrops, structural geologic information, geochemical data, and photographs.

Massachusetts, Rhode Island

Evaluation of the ground-water flow model for northern Utah Valley, Utah, updated to conditions through 2002

This report evaluates the performance of a numerical model of the ground-water system in northern Utah Valley, Utah, that originally simulated ground-water conditions during 1947-1980 and was updated to include conditions estimated for 1981-2002. Estimates of annual recharge to the ground-water system and discharge from wells in the area were added to the original ground-water flow model of the area. The files used in the original transient-state model of the ground-water flow system in northern Utah Valley were imported into MODFLOW-96, an updated version of MODFLOW. The main model input files modified as part of this effort were the well and recharge files. Discharge from pumping wells in northern Utah Valley was estimated on an annual basis for 1981-2002. Although the amount of average annual withdrawals from wells has not changed much since the previous study, there have been changes in the distribution of well discharge in the area. Discharge estimates for flowing wells during 1981-2002 were assumed to be the same as those used in the last stress period of the original model because of a lack of new data. Variations in annual recharge were assumed to be proportional to changes in total surface-water inflow to northern Utah Valley. Recharge specified in the model during the additional stress periods varied from 255,000 acre-feet in 1986 to 137,000 acre-feet in 1992. The ability of the updated transient-state model to match hydrologic conditions determined for 1981-2002 was evaluated by comparing water-level changes measured in wells to those computed by the model. Water-level measurements made in February, March, or April were available for 39 wells in the modeled area during all or part of 1981-2003. In most cases, the magnitude and direction of annual water-level change from 1981 to 2002 simulated by the updated model reasonably matched the measured change. The greater-than-normal precipitation that occurred during 1982-84 resulted in period-of-record high water levels measured in many of the observation wells in March 1984. The model-computed water levels at the end of 1982-84 also are among the highest for the period. Both measured and computed water levels decreased during the period representing ground-water conditions from 1999 to 2002. Precipitation was less than normal during 1999-2002. The ability of the model to adequately simulate climatic extremes such as the wetter-than-normal conditions of 1982-84 and the drier-than-normal conditions of 1999-2002 indicates that the annual variation of recharge to the ground-water system based on streamflow entering the valley, which in turn is primarily dependent upon precipitation, is appropriate but can be improved. The updated transient-state model of the ground-water system in northern Utah Valley can be improved by making revisions on the basis of currently available data and information.

Utah

Geohydrology, geochemistry, and ground-water simulation-optimization of the Central and West Coast Basins, Los Angeles County, California

Historical ground-water development of the Central and West Coast Basins in Los Angeles County, California through the first half of the 20th century caused large water-level declines and induced seawater intrusion. Because of this, the basins were adjudicated and numerous ground-water management activities were implemented, including increased water spreading, construction of injection barriers, increased delivery of imported water, and increased use of reclaimed water. In order to improve the scientific basis for these water management activities, an extensive data collection program was undertaken, geohydrological and geochemical analyses were conducted, and ground-water flow simulation and optimization models were developed. In this project, extensive hydraulic, geologic, and chemical data were collected from new multiple-well monitoring sites. On the basis of these data and data compiled and collected from existing wells, the regional geohydrologic framework was characterized. For the purposes of modeling, the three-dimensional aquifer system was divided into four aquifer systems?the Recent, Lakewood, Upper San Pedro, and Lower San Pedro aquifer systems. Most pumpage in the two basins is from the Upper San Pedro aquifer system. Assessment of the three-dimensional geochemical data provides insight into the sources of recharge and the movement and age of ground water in the study area. Major-ion data indicate the chemical character of water containing less than 500 mg/L dissolved solids generally grades from calcium-bicarbonate/sulfate to sodium bicarbonate. Sodium-chloride water, high in dissolved solids, is present in wells near the coast. Stable isotopes of oxygen and hydrogen provide information on sources of recharge to the basin, including imported water and water originating in the San Fernando Valley, San Gabriel Valley, and the coastal plain and surrounding hills. Tritium and carbon-14 data provide information on relative ground-water ages. Water with abundant tritium (greater than 8 tritium units) is found in and downgradient from the Montebello Forebay and near the seawater barrier projects, indicating recent recharge. Water with less than measurable tritium is present in, and downgradient from, the Los Angeles Forebay and in most wells in the West Coast Basin. Water from several deep wells was analyzed for carbon-14. Uncorrected estimates of age for these samples range from 600 to more than 20,000 years before present. Chemical and isotopic data are combined to evaluate changes in chemical character along flow paths emanating from the Montebello and Los Angeles Forebays. A four-layer ground-water flow model was developed to simulate steady-state ground-water conditions representative of those in 1971 and transient conditions for the period 1971?2000. Model results indicate increases in ground-water storage in all parts of the study area over the simulated thirty-year period. The model was used to develop a three-dimensional ground-water budget and to assess impacts of two alternative future (2001?25) ground-water development scenarios?one that assumes continued pumping at average current rates and a second that assumes increasing pumping from most wells in the Central Basin. The model simulates stable or slightly increasing water levels for the first scenario and declining water levels (25 to 50 ft in the Central Basin) in the second scenario. Model sensitivity to parameter values and to the assumed Orange County boundary condition was evaluated. Particle tracking was applied to simulate advective transport of water from the spreading ponds, the coastline, and the seawater injection barriers. Particle tracking results indicate that most flow within the Upper San Pedro aquifer system occurs within about 20 percent of the total aquifer system thickness and that virtually all water injected into the seawater barrier projects has flowed inland. The simulation model was linked with optimizatio

California

Animal reservoirs and hosts for emerging alphacoronaviruses and betacoronaviruses

The ongoing global pandemic caused by coronavirus disease has once again demonstrated the role of the family Coronaviridae in causing human disease outbreaks. Because severe acute respiratory syndrome coronavirus 2 was first detected in December 2019, information on its tropism, host range, and clinical manifestations in animals is limited. Given the limited information, data from other coronaviruses might be useful for informing scientific inquiry, risk assessment, and decision-making. We reviewed endemic and emerging infections of alphacoronaviruses and betacoronaviruses in wildlife, livestock, and companion animals and provide information on the receptor use, known hosts, and clinical signs associated with each host for 15 coronaviruses detected in humans and animals. This information can be used to guide implementation of a One Health approach that involves human health, animal health, environmental, and other relevant partners in developing strategies for preparedness, response, and control to current and future coronavirus disease threats.

Emerging Infectious Diseases

Composite regional catalogs of earthquakes in the former Soviet Union

Seismological study of the territory of the former Soviet Union developed in the 20th century with the approach of maintaining constant observations with standard instrumentation and methods of data processing, determining standardized parameters describing the seismic sources, and producing regular summary publications. For most of the century, event data were published only in Russian and were generally unavailable to the Western scientific community. Yet for many regions of this vast territory, earthquakes with magnitudes less than 2 were routinely located and characterized, especially since the early 1960s. A great volume of data on the seismicity of the Eurasian land mass is therefore available, although to date only in scattered publications and for incomplete periods of time. To address this problem, we have undertaken a comprehensive compilation, documentation and evaluation of catalogs of seismicity of the former Soviet Union. These include four principal, Soviet-published catalog sources, supplemented by other publications. We view this as the first step in compiling a complete catalog of all known seismic events in this large and important region. Completion of this work will require digitizing the remaining catalogs of the various regional seismological institutes. To make these data more useful for regional seismic investigations, as well as to be consistent with their provenance, we have prepared composite regional catalogs, dividing the territory of the former Soviet Union into 24 regions. For each of these regions, all the data available from the basic catalog sources (see below) have been combined and evaluated. Note that, for regions with low seismicity, the historical (non-instrumental, macro-seismic) data are of increased importance. Such information, if not included in any summary, were taken from various publications and marked as "historical".

Open-File Report

Archive of bathymetry data collected in South Florida from 1995 to 2015

Description Land development and alterations of the ecosystem in south Florida over the past 100 years have decreased freshwater and increased nutrient flows into many of Florida's estuaries, bays, and coastal regions. As a result, there has been a decrease in the water quality in many of these critical habitats, often prompting seagrass die-offs and reduced fish and aquatic life populations. Restoration of water quality in many of these habitats will depend partly upon using numerical-circulation and sediment-transport models to establish water-quality targets and to assess progress toward reaching restoration targets. Application of these models is often complicated because of complex sea floor topography and tidal flow regimes. Consequently, accurate and modern sea-floor or bathymetry maps are critical for numerical modeling research. Modern bathymetry data sets will also permit a comparison to historical data in order to help assess sea-floor changes within these critical habitats. New and detailed data sets also support marine biology studies to help understand migratory and feeding habitats of marine life. This data series is a compilation of 13 mapping projects conducted in south Florida between 1995 and 2015 and archives more than 45 million bathymetric soundings. Data were collected primarily with a single beam sound navigation and ranging (sonar) system called SANDS developed by the U.S. Geological Survey (USGS) in 1993. Bathymetry data for the Estero Bay project were supplemented with the National Aeronautics and Space Administration's (NASA) Experimental Advanced Airborne Research Lidar (EAARL) system. Data from eight rivers in southwest Florida were collected with an interferometric swath bathymetry system. The projects represented in this data series were funded by the USGS Coastal and Marine Geology Program (CMGP), the USGS South Florida Ecosystem Restoration Project- formally named Placed Based Studies, and other non-Federal agencies. The purpose of the data collection for all these projects was to support one or more of the following scientific aspects: numerical model applications, sea floor change analysis, or marine habitat investigations. This report serves as an archive of processed bathymetry sounding data, digital bathymetric contours, digital bathymetric maps, sea floor surface grids, and formal Federal Geographic Data Committee (FGDC) metadata. Refer to the Abbreviations page for explanations of acronyms and abbreviations used in this report. Since 2006, the USGS St. Petersburg Coastal and Marine Science Center (SPCMSC) assigns a unique identifier or Field Activity Number (FAN) for each field data collection. Projects described in this report conducted prior to 2006 do not have a FAN. Data from the 13 projects presented in this report provided critical hydrographic information to support multiple science projects in south Florida. The projects and the types of sounding data collected are: Florida Bay (1995-1999) - single-beam Lake Okeechobee (2001) - single-beam Tampa Bay (2001-2004) - single-beam Caloosahatchee River (2002)- single-beam Estero Bay to Matlacha Pass and offshore to Wiggins Pass (2003) - single-beam and airborne lidar North and Northwest Forks of the Loxahatchee and Lower St. Lucie Rivers (2003) - single-beam South Charlotte Harbor and offshore Sanibel Island (2003-2004) - single-beam Shark River and Trout Creek (2004) - single-beam and interferometric swath Southwest Florida Rivers (2004) - interferometric swath Offshore from Wiggins Pass to Cape Romano (2005) - single-beam Ten Thousand Islands (2009) - single-beam Lemon Bay (2011) - single-beam Southwest Florida Rivers (2015) - interferometric swath

Florida

Measuring suspended sediment

Suspended sediment in streams and rivers can be measured using traditional instruments and techniques and (or) surrogate technologies. The former, as described herein, consists primarily of both manually deployed isokinetic samplers and their deployment protocols developed by the Federal Interagency Sedimentation Project. They are used on all continents other than Antarctica. The reliability of the typically spatially rich but temporally sparse data produced by traditional means is supported by a broad base of scientific literature since 1940. However, the suspended sediment surrogate technologies described herein – based on hydroacoustic, nephelometric, laser, and pressure difference principles – tend to produce temporally rich but in some cases spatially sparse datasets. The value of temporally rich data in the accuracy of continuous sediment-discharge records is hard to overstate, in part because such data can often overcome the shortcomings of poor spatial coverage. Coupled with calibration data produced by traditional means, surrogate technologies show considerable promise toward providing the fluvial sediment data needed to increase and bring more consistency to sediment-discharge measurements worldwide.

Book chapter

Wyoming Landscape Conservation Initiative data management and integration

Six Federal agencies, two State agencies, and two local entities formally support the Wyoming Landscape Conservation Initiative (WLCI) and work together on a landscape scale to manage fragile habitats and wildlife resources amidst growing energy development in southwest Wyoming. The U.S. Geological Survey (USGS) was tasked with implementing targeted research and providing scientific information about southwest Wyoming to inform the development of WLCI habitat enhancement and restoration projects conducted by land management agencies. Many WLCI researchers and decisionmakers representing the Bureau of Land Management, U.S. Fish and Wildlife Service, the State of Wyoming, and others have overwhelmingly expressed the need for a stable, robust infrastructure to promote sharing of data resources produced by multiple entities, including metadata adequately describing the datasets. Descriptive metadata facilitates use of the datasets by users unfamiliar with the data. Agency representatives advocate development of common data handling and distribution practices among WLCI partners to enhance availability of comprehensive and diverse data resources for use in scientific analyses and resource management. The USGS Core Science Informatics (CSI) team is developing and promoting data integration tools and techniques across USGS and partner entity endeavors, including a data management infrastructure to aid WLCI researchers and decisionmakers.

Wyoming

Proceedings of the ocean drilling program: New Jersey continental slope and rise

The Scientific Results volumes of the Proceedings of the Ocean Drilling Program contain specialty papers presenting the results of extensive research in various aspects of scientific ocean drilling. The authors of the papers published in this volume have enabled future investigators to gain ready access to the results of their research, and I acknowledge their contributions with thanks. Each paper submitted to a Scientific Results volume undergoes rigorous peer review by at least two specialists in the author's research field. A paper typically goes through at least one revision cycle before being accepted for publication. We seek to maintain a peer-review system comparable to those of the most highly regarded journals in the geological sciences. Each Scientific Results volume has an Editorial Review Board that is responsible for obtaining peer reviews of papers submitted to the volume. This board usually is made up of the two co-chief scientists for the cruise, the ODP staff scientist for the cruise, and one external specialist who is familiar with the geology of the area investigated. In addition, the volume has an ODP staff editor who assists with manuscripts that require English-language attention and who coordinates volume assembly. Scientific Results volumes may also contain short reports of useful data that are not ready for final interpretation. Papers of this type, which may be found together in a section in the back of the volume, are called Data Reports and include no interpretation of results. Data Report papers are read carefully by at least one specialist to make sure they are well organized, comprehensive, and discuss the techniques or procedures thoroughly. To acknowledge the contributions made by this volume's Editorial Review Board, the Board members are designated Editors of the volume and are so listed on the title page. Reviewers of manuscripts for this volume, whose efforts are so essential to the success of the publication, are listed in the front of the book, without attribution to a particular manuscript. On behalf of the Ocean Drilling Program, I extend sincere appreciation to members of the Editorial Review Boards and to the reviewers for giving their generous contribution of time and effort, which ensures that only papers of high scientific quality are published in the Proceedings .

Book

Creating figures in R that meet the AFS style guide: Standardization and supporting script

Visual display of information in scientific and non‐scientific literature is the most efficient way to summarize large amounts data, focus the readers’ attention on patterns, and substantiate the message in the narrative. Figures often represent years of data collection and substantial monetary investment, and it is worth repeating the cliché “a [figure] is worth a thousand words.” Well‐designed figures are usually simple, yet their ability to relate complex information through simplicity makes them powerful (Tufte 2001 ). Figures are often the focal point of articles when scientists, science communicators, and policy makers are quickly searching for scientific information. Scientists in academia ranked figures and tables as the most important component of research articles (Hubbard and Dunbar 2017 ); moreover, figures quickly become the focus when discussing articles among colleagues or in a classroom setting. If created effectively in combination with a well‐articulated figure caption, figures convey complex information readily for the reader to make a conclusion about results without reading details presented in the narrative. This is especially important as the quantity of research articles continues to increase exponentially in the 21st century, as does the number of journals with specific figure guidelines (Jinha 2010 ).

Fisheries Magazine