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USGS2026

Epigenetics in captivity: Restoring wild phenotypes in captive-reared salmonids

Captive rearing is a common practice for the stocking, conservation, and supplementation of fish species worldwide, but captive-reared fish can exhibit altered phenotypes leading to reduced fitness in nature compared to wild conspecifics. In salmonids, certain studies have found limited genetic differentiation between wild and captive-reared fish. However, documented changes in gene expression in hatchery fish have led scientists to investigate epigenetic mechanisms, such as DNA methylation, as a source of these differences. In this binational collaborative piece, we synthesize the knowledge and efforts of academics and government scientists to highlight how interactions between captive rearing and the epigenome elicit parallel phenotypic changes across salmonid species. We examine the known and potential links between DNA methylation and the phenotypic effects of captive rearing including changes in behavior, color, gut microbiomes, and developmental abnormalities. We review efforts to minimize these phenotypic and epigenetic effects including attempts to modify the hatchery environment and rearing protocols. We provide a framework to integrate epigenetic considerations into hatchery rearing protocols by weighing the heritable nature of DNA methylation with the goals of different captive rearing programs and explore whether minimizing the phenotypic and epigenetic effects of captive rearing is worthwhile. We examine heritability and persistence of epigenetic effects, and we propose the exploitation of heritable bet-hedging as an epigenetic buffer to increase post-release survival. We also suggest novel applications of epigenomic biomarkers as a non-lethal method for post-release monitoring. Ultimately, collaborative multi-disciplinary research across species is needed to understand the comprehensive effects of captive rearing, reduce the ecological impacts of captive fish in the wild, and increase population resilience. Integrating epigenetics into fish hatchery management will provide new opportunities for optimizing and improving captive rearing.

Evolutionary Applications↗

USGS2023

Scenario-Based Decision Analysis: Integrated scenario planning and structured decision making for resource management under climate change

Managing resources under climate change is a high-stakes and daunting task, especially because climate change and associated complex biophysical responses engender sustained directional changes as well as abrupt transformations. This environmental non-stationarity challenges assumptions and expectations among scientists, managers, rights holders, and stakeholders. These challenges are anything but straightforward – a high degree of uncertainty impedes our ability to predict the environmental trajectory with confidence, and affected resources often span multiple governance jurisdictions or are subject to competing management objectives. Fortunately, tools exist to help grapple with such challenges. Two commonly used tools are scenario planning (SP) and structured decision making (SDM). SP is a well-established approach for assessing system response and facilitating decision making under a wide range of conditions that are uncertain and uncontrollable, such as those associated with adapting to climate change. However, SP lacks a defined structure for establishing objectives, quantifying tradeoffs, and evaluating the performance of candidate decisions to meet those objectives. SDM, on the other hand, is rooted in decision theory and focuses on explicit (often quantitative) assessment of the expected outcomes of choosing among a set of decision alternatives. SDM has been criticized for an inability to account for surprises and for imposing an overly narrow framing of problems to increase tractability. We discuss the strengths and limitations of SDM and SP as experienced through their application in various resource-management contexts, and then propose a new generalized framework – Scenario-Based Decision Analysis (SBDA) – that integrates these complementary approaches. SBDA structures resource management problems and solutions while considering uncertainties and surprises to inform resource management decision making.

Biological Conservation↗

USGS2010

Geological Impacts and Sedimentary Record of the February 27, 2010, Chile Tsunami-La Trinchera to Concepcion

The February 27, 2010, Chilean tsunami substantially altered the coastal landscape and left a permanent depositional record that may be preserved at many locales along the central coast of Chile. From April 24 to May 2, 2010, a team of U.S. Geological Survey (USGS) and Chilean scientists examined the geological impacts of the tsunami at five sites along a 200-km segment of coast centered on the earthquake epicenter. Significant observations include: (1) substantial tsunami-induced erosion and deposition (+/- 1 m) on the coastal plain; (2) erosion from return flow, inundation scour around the bases of trees, and widespread planation of the land surface; (3) tsunami sand deposits at all sites that extended to near the limit of inundation except at one site; (4) evidence of multiple strong onshore waves that arrived at different times and from different directions; (5) vegetation height and density controlled the thickness of tsunami deposits at one site, (6) the abundance of layers of plane-parallel stratification in some deposits and the presence of large bedforms at one site indicated at least some of the sediment was transported as bed load and not as suspended load; (7) shoreward transport of mud boulders and rock cobbles where they were available; and (8) the maximum tsunami inundation distance (2.35 km) was up an alluvial valley. Most of the tsunami deposits were less than 25 cm thick, which is consistent with tsunami-deposit thicknesses found elsewhere (for example, Papua New Guinea, Peru, Sumatra, Sri Lanka). Exceptions were the thick tsunami deposits near the mouths of Rio Huenchullami (La Trinchera) and Rio Maule (Constitucion), where the sediment supply was abundant. The substantial vertical erosion of the coastal plain at Constitucion

Open-File Report↗

USGS2010

BRIDGES: Evolution of basic and applied linkages in benthic science

Growing awareness of environmental degradation resulted in stricter environmental regulations and laws for aquatic ecosystems. These regulations were followed by an increase in applied research and monitoring beginning in the early 1970s. The number of applied scientists who were members of the North American Benthological Society grew at a commensurate rate. The editors of J-NABS recognized that, despite these increases, submitted manuscripts mostly addressed basic science. In response, the BRIDGES section of J-NABS was created in 1994 to provide a forum for linking basic ecological principles to applied science problems and issues. We examined the emergence of applied science topics in J-NABS and its predecessor, Freshwater Invertebrate Biology , from their beginning in 1982 to 2009. We classified papers among 11 categories that included a basic/applied science linkage. In the 1980s, applied papers were predominantly on effects of eutrophication/pollution and landuse changes. When BRIDGES was established in 1994, papers were solicited by editors and BRIDGES sections usually included >1 paper on a common theme to express complementary or alternate viewpoints. Forty-two papers appeared in BRIDGES between 1994 and 2009, but the number per issue declined after 2001. The total number of applied science papers in J-NABS has increased since ∼1994. Citation analysis of BRIDGES papers illustrates how information is being cited, but applied papers often are used in ways that might not lead to citations. BRIDGES transitioned to a new format in September 2009 to address new types of complex, multifaceted linkages. All new BRIDGES articles will be open access, and authors will be encouraged to produce lay-language fact sheets and to post them on the web.

Journal of the North American Benthological Societ↗

USGS2004

Coastal vulnerability assessment of Fire Island National Seashore to sea-level rise

A coastal vulnerability index (CVI) was used to map the relative vulnerability of the coast to future sea-level rise within Fire Island National Seashore (FIIS), New York. The CVI ranks the following in terms of their physical contribution to sea-level rise-related coastal change: geomorphology, regional coastal slope, rate of relative sea-level rise, shoreline change rates, mean tidal range and mean wave height. The rankings for each variable were combined and an index value calculated for 1-minute grid cells covering the park. The CVI highlights those regions where the physical effects of sea-level rise might be the greatest. This approach combines the coastal system's susceptibility to change with its natural ability to adapt to changing environmental conditions, yielding a quantitative, although relative, measure of the park's natural vulnerability to the effects of sea-level rise. Fire Island consists of stable and washover dominated portions of barrier beach backed by lagoons, tidal wetlands and marsh. The areas most vulnerable to sea-level rise are those with the highest historic occurrence of overwash and the highest rates of shoreline change. Implementation of large-scale beach nourishment and other coastal engineering alternatives being considered for Fire Island could alter the CVI computed here. The CVI provides an objective technique for evaluation and long-term planning by scientists and park managers.

New York↗

USGS2015

U.S. Geological Survey Unmanned Aircraft Systems (UAS) Roadmap 2014

The U.S. Department of the Interior (DOI) is responsible for protecting the natural resources and heritage contained on almost 20 percent of the land in the United States. This responsibility requires acquisition of remotely sensed data throughout vast lands, including areas that are remote and potentially dangerous to access. One promising new technology for data collection is unmanned aircraft systems (UAS), which may be better suited (achieving superior science, safety, and savings) than traditional methods. UAS, regardless of their size, have the same operational components: aircraft, payloads, communications unit, and operator control unit. The aircraft is the platform that flies and carries any required payloads. For Department of the Interior missions these payloads will be either a sensor or set of sensors that can acquire the specific type of remotely sensed data that is needed. The aircraft will also carry the payload that is responsible for transmitting live airborne video images, compass headings, and location information to the operator control unit. The communications unit, which transfers information between the aircraft and the operator control unit, consists of the hardware and software required to establish both uplink and downlink communications. Finally, the operator control unit both controls and monitors the aircraft and can be operated either by a pilot on the ground or autonomously. This Roadmap provides operational procedures and lessons learned from completed proof-of-concept UAS missions in areas such as wildlife management, resource monitoring, and public land inspections. This information provides not only an implementation framework but can also help increase the awareness by resource managers, scientists, and others of the ability of UAS technology to advance data quality, improve personnel safety, and reduce data acquisition costs.

Open-File Report↗

USGS2008

Thiamine Deficiency Complex Workshop final report: November 6-7, 2008, Ann Arbor, MI

Fry mortality which was first observed in the late 1960s in Great Lakes salmonines and in Baltic Sea salmon in 1974 has now been linked to thiamine deficiency (historically referred to as Early Mortality Syndrome, or EMS and M74, respectively). Over the past 14 years significant strides have been made in our understanding of this perplexing problem. It is now known that thiamine deficiency causes embryonic mortality in these salmonids. Both overt mortality and secondary effects of thiamine deficiency are observed in juvenile and adult animals. Collectively the morbidity and mortality (fry and adult mortality, secondary metabolic and behavior affects in juveniles and adult fish) are referred to as Thiamine Deficiency Complex (TDC). A workshop was held in Ann Arbor, MI on 6-7 November 2008 that brought together 38 federal, state, provincial, tribal and university scientists to share information, present data and discuss the latest observations on thiamine status of aquatic animals with thiamine deficiency and the causative agent, thiaminase. Twenty presentations (13 oral and 7 posters) detailed current knowledge. In Lake Huron, low alewife Alosa pseudoharengus abundance has persisted and egg thiamine concentrations in salmonines continue to increase, along with evidence of natural reproduction in lake trout Salvelinus namaycush. Lake Michigan Chinook salmon Oncorhynchus tshawytscha appear to have a lower thiamine requirement than other salmonids in the lake. Lake Ontario American eel Anguilla rostrata foraging on alewife have approximately one third the muscle thiamine compared to eels not feeding on alewife, suggesting that eels may be suffering from thiamine deficiency. Secondary effects of low thiamine exist in Great Lakes salmonines and should not be ignored. Thiaminase activity in dreissenid mussels is extremely high but a connection to TDC has not been made. Thiaminase in net plankton was found more consistently in lakes Michigan and Ontario than other lakes evaluated. The biological role of thiaminase I, associated with thiamine deficiency, remains to be determined whereas thiaminase II has been reported to be part of a salvage pathway leading to thiamine synthesis. The use of gene array technology and 3-dimensional histology is adding new understanding to the affects of thiamine deficiency. Research is needed to determine the thiamine status of species feeding on dreissenids, the environmental sources of thiaminase and the biological role of thiaminase I.

Research Status Report↗

USGS2017

Kīlauea summit eruption—Lava returns to Halemaʻumaʻu

In March 2008, a new volcanic vent opened within Halemaʻumaʻu , a crater at the summit of Kīlauea Volcano in Hawaiʻi Volcanoes National Park on the Island of Hawaiʻi. This new vent is one of two ongoing eruptions on the volcano. The other is on Kīlauea’s East Rift Zone, where vents have been erupting nearly nonstop since 1983. The duration of these simultaneous summit and rift zone eruptions on Kīlauea is unmatched in at least 200 years. Since 2008, Kīlauea’s summit eruption has consisted of continuous degassing, occasional explosive events, and an active, circulating lava lake. Because of ongoing volcanic hazards associated with the summit vent, including the emission of high levels of sulfur dioxide gas and fragments of hot lava and rock explosively hurled onto the crater rim, the area around Halemaʻumaʻu remains closed to the public as of 2017. Through historical photos of past Halemaʻumaʻu eruptions and stunning 4K imagery of the current eruption, this 24-minute program tells the story of Kīlauea Volcano’s summit lava lake—now one of the two largest lava lakes in the world. It begins with a Hawaiian chant that expresses traditional observations of a bubbling lava lake and reflects the connections between science and culture that continue on Kīlauea today. The video briefly recounts the eruptive history of Halemaʻumaʻu and describes the formation and continued growth of the current summit vent and lava lake. It features USGS Hawaiian Volcano Observatory scientists sharing their insights on the summit eruption—how they monitor the lava lake, how and why the lake level rises and falls, why explosive events occur, the connection between Kīlauea’s ongoing summit and East Rift Zone eruptions, and the impacts of the summit eruption on the Island of Hawaiʻi and beyond. The video is also available at the following U.S. Geological Survey Multimedia Gallery link (video hosted on YouTube): Kīlauea summit eruption—Lava returns to Halemaʻumaʻu

Hawai'i↗

USGS2019

Results from the Department of the Interior Strategic Sciences Group Technical Support for the 2018 Kīlauea Eruption

On May 3, 2018 Hawai'i’s Kīlauea volcano erupted, ultimately covering 35 square kilometers (13.5 square miles) of land in lava, destroying over 700 homes in multiple subdivisions, and displacing over 2500 residents in the Puna District on the southeast flank of the volcano. Simultaneously, Kīlauea’s summit experienced its largest collapse in 200 years, with a total of 500 meters (1,640 feet) subsidence and tens of earthquakes each day rattling surrounding communities. These simultaneous events impacted residential, agricultural, business, tourist, and scientific areas. Hawai'i Volcanoes National Park closed, slowing tourism and the local economy. The building housing the United States Geological Survey (USGS) Hawai'ian Volcano Observatory also closed, displacing scientists responsible for monitoring the erupting volcano. The eruption lasted 107 days, one of the longest eruptions in recent history in lower Puna. Throughout the eruption, uncertainty regarding the duration of the event, its extent, and total damage remained high. This uncertainty led to social tensions and fatigue across the affected community, responders, and local officials. At the direction of the USGS Director, serving as the Science Advisor to the Secretary of the of the Interior, the Department of the Interior (DOI, hereafter also referred to as “the Department”) Strategic Sciences Group (SSG) convened a multidisciplinary group of 13 experts in Hilo, Hawai'i, on July 17-19, 2018. The SSG was charged with considering the cascading short- and long-term social, economic, and environmental consequences of the 2018 Kīlauea eruption to DOI resources, employees, and facilities as well as to the surrounding communities. Established in 2012, the SSG is designed to complement ongoing response efforts by providing strategic science to identify potential social, environmental, and economic consequences and potential interventions during a crisis event affecting Departmental resources. This activation of the SSG was funded by the USGS. It was the first official activation of the SSG since it supported Hurricane Sandy recovery in 2013 and provided the unique opportunity to test new methods, including bolstering the social science expertise on the team and interacting directly with stakeholders before, during, and after deployment. The SSG Kīlauea Team developed three scenarios focused on 1) the impacts of continued seismicity and deformation at the summit; 2) vog (volcanic smog); and 3) the eruption in the lower East Rift Zone. Across all scenarios, areas of concern included human health (physical and mental); biosecurity (for example, protecting threatened and endangered species); infrastructure (impacts caused by seismic activity, vog, and lava); communications (internal and public-facing); long-term planning (related to tourism, access, housing); and ongoing needs for community engagement and empowerment. The SSG Kīlauea Team identified 59 potential actions for mitigation. Highlights of these actions were delivered to stakeholders during briefings in August and September 2018. Examples of potential actions included: ● Seize opportunities to develop new partnerships within and outside of DOI to address facilities issues caused by seismic damage and park closure. ● Educate community members and new workers to increase early detection of invasive species and establish new wash stations to address biosecurity threats to the park posed by more frequent commuting from new temporary Hilo locations. ● Create a "vog officer" position to ensure coordination and consistency in communication about vog hazards across federal, state, and county agencies. It is important to note that the potential actions are suggestions and are not intended to be prescriptive. The SSG uses “blue sky thinking” when developing these potential actions to encourage creative approaches to problem solving. In some cases, some of the suggested potential actions derived by the SSG are actions that were already underway, or already under consideration and helped to affirm 3 activities by different stakeholders. In other cases, the actions may be new ideas. Some were applicable to immediate response, while others are more relevant to long-term recovery. This report details the results from the July 2018 activation of the SSG. It includes background on Kīlauea and the 2018 eruption, an overview of SSG methodology, and a complete list of the potential actions to mitigate cascading consequences identified by the SSG. Importantly, Appendix 4 includes several rapidly assembled “issue papers” on a variety of topics for consideration for recovery and future preparedness and response activities. This report is designed to be used by both the Department and more broadly by partners, including the Federal Emergency Management Agency, Hawai'i County, Hawai'i Department of Health, and the Hawai'i Emergency Management Agency.

Hawaii↗

USGS2016

Proceedings of the 12th Biennial Conference of research on the Colorado Plateau

Introduction The Colorado Plateau is a physiographic region that encompasses 330,000 square kilometers in parts of four states in the southwestern United States (Colorado, Utah, New Mexico, and Arizona). Known for its high deserts, the Colorado Plateau also includes isolated mountains, high plateaus, and rugged canyons. Not only is the region topographically diverse, but geologically, biologically, and culturally diverse as well. The landscape is managed by Federal entities including the Bureau of Land Management, the National Park Service, and the U.S. Forest Service; Tribal nations including the Navajo Nation, Kaibab Paiute, Mountain Ute, Southern Ute, Hopi, Zuni, Hualapai, Havasupai, and White Mountain Apache Tribes; State land and wildlife management agencies; and privately owned holdings, creating complex interactions and management challenges. Population growth, increased tourism to Federal and State lands, and energy development have increased water demands and altered land-use patterns, and these changes have emerged as management challenges facing the people working and living in the region. Climate change, particularly the ongoing drought, has exacerbated the effects of population growth, land-use change, and other stressors such as invasive species. As managers seek solutions to the challenges facing the region’s natural and cultural resources, the Biennial Conference of Science and Management of the Colorado Plateau has become an important venue for exchanging information about emerging management concerns and recent scientific research. Each biennial conference has sought to promote discussion, information sharing, and productive communication among the managers, scientists, students, administrators, tribal representatives, and others who attend the conference with the goal of enhancing the use of the best available science to manage the region’s incomparable natural and cultural resources. The publication and dissemination of a conference proceedings series expands the reach of the conference beyond those people in attendance and creates a record on the research presented. The idea of producing a conference proceedings, and its subsequent publication, first occurred in 1993 following the first biennial conference in 1991. A published volume of contributed papers has followed each subsequent biennial conference, including this volume. The venue for publishing proceedings has changed over the years and has included the National Park Service, the Government Printing Office, the U.S. Geological Survey, and University of Arizona Press. Recently, van Riper and others (2015) published a compilation of the abstracts from the 11 previous conference proceedings. Collectively, the proceedings highlight approximately 25 years of natural- and cultural-resources research, promoting the integration of research with resource management across the Colorado Plateau. This volume is freely downloadable by the public, thereby further expanding the influence of this conference beyond the Colorado Plateau. The 12th Biennial Conference held in Flagstaff, Arizona, from September 16 to 19, 2013, covered a range of topics in the physical, biological, and socio-cultural sciences. The conference was organized and hosted by Northern Arizona University’s ( NAU) Merriam-Powell Center for Environmental Research, the Colorado Plateau Cooperative Ecosystem Studies Unit, and the U.S. Geological Survey Southwest Biological Science Center. Financial and in-kind support was provided by a wide range of organizations including the U.S. Forest Service, National Park Service, Bureau of Land Management, Grand Canyon Trust, Colorado Plateau Research Station, and various NAU entities. NAU sponsors include the Landscape Conservation Initiative, School of Forestry, School of Earth Science and Environmental Sustainability, Office of the Provost, and Office of the Vice President of Research. Contributors to these proceedings include researchers and managers from Federal, State, and Tribal governments, universities, private entities, and non-profit organizations. In this regard, this conference has wide-ranging support and participation among private and public entities involved in the science and management of natural resources on the Colorado Plateau.

Arizona, Colorado, New Mexico, Utah↗

USGS2016

The international river interface cooperative: Public domain flow and morphodynamics software for education and applications

This paper describes a new, public-domain interface for modeling flow, sediment transport and morphodynamics in rivers and other geophysical flows. The interface is named after the International River Interface Cooperative (iRIC), the group that constructed the interface and many of the current solvers included in iRIC. The interface is entirely free to any user and currently houses thirteen models ranging from simple one-dimensional models through three-dimensional large-eddy simulation models. Solvers are only loosely coupled to the interface so it is straightforward to modify existing solvers or to introduce other solvers into the system. Six of the most widely-used solvers are described in detail including example calculations to serve as an aid for users choosing what approach might be most appropriate for their own applications. The example calculations range from practical computations of bed evolution in natural rivers to highly detailed predictions of the development of small-scale bedforms on an initially flat bed. The remaining solvers are also briefly described. Although the focus of most solvers is coupled flow and morphodynamics, several of the solvers are also specifically aimed at providing flood inundation predictions over large spatial domains. Potential users can download the application, solvers, manuals, and educational materials including detailed tutorials at www.-i-ric.org . The iRIC development group encourages scientists and engineers to use the tool and to consider adding their own methods to the iRIC suite of tools.

Advances in Water Resources↗

USGS2019

Optimization of salt marsh management at the Chincoteague National Wildlife Refuge, Virginia, through use of structured decision making

Structured decision making is a systematic, transparent process for improving the quality of complex decisions by identifying measurable management objectives and feasible management actions; predicting the potential consequences of management actions relative to the stated objectives; and selecting a course of action that maximizes the total benefit achieved and balances tradeoffs among objectives. The U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service, applied an existing, regional framework for structured decision making to develop a prototype tool for optimizing salt marsh management decisions at the Chincoteague National Wildlife Refuge in Virginia. Refuge biologists, refuge managers, and research scientists identified multiple potential management actions to improve the ecological integrity of 12 salt marsh management units within the refuge and estimated the outcomes of each action in terms of performance metrics associated with each management objective. Value functions previously developed at the regional level were used to transform metric scores to a common utility scale, and utilities were summed to produce a single score representing the total management benefit that would be accrued from each potential management action. Constrained optimization was used to identify the set of management actions, one per salt marsh management unit, that would maximize total management benefits at different cost constraints at the refuge scale. Results indicated that, for the objectives and actions considered here, total management benefits may increase consistently up to approximately $ 2.5 million, but that further expenditures may yield diminishing return on investment. For multiple salt marsh management units, a scenario incorporating managing grazing practices within the marsh was selected to maximize benefits while constraining total costs for the refuge at less than $ 2.5 million. Thin-layer deposition was predicted to increase the total management benefit substantially, but at considerable total costs ( $ 2.5 million to $ 83 million). The prototype presented here provides a framework for decision making at the Chincoteague National Wildlife Refuge that can be updated as new data and information become available. Insights from this process may also be useful to inform future habitat management planning at the refuge.

Virginia↗

USGS2002

CMGTooL user's manual

During the past several years, the sediment transport group in the Coastal and Marine Geology Program (CMGP) of the U. S. Geological Survey has made major revisions to its methodology of processing, analyzing, and maintaining the variety of oceanographic time-series data. First, CMGP completed the transition of the its oceanographic time-series database to a self-documenting NetCDF (Rew et al., 1997) data format. Second, CMGP’s oceanographic data variety and complexity have been greatly expanded from traditional 2-dimensional, single-point time-series measurements (e.g., Electro-magnetic current meters, transmissometers) to more advanced 3-dimensional and profiling time-series measurements due to many new acquisitions of modern instruments such as Acoustic Doppler Current Profiler (RDI, 1996), Acoustic Doppler Velocitimeter, Pulse-Coherence Acoustic Doppler Profiler (SonTek, 2001), Acoustic Bacscatter Sensor (Aquatec, 1001001001001001001). In order to accommodate the NetCDF format of data from the new instruments, a software package of processing, analyzing, and visualizing time-series oceanographic data was developed. It is named CMGTooL. The CMGTooL package contains two basic components: a user-friendly GUI for NetCDF file analysis, processing and manipulation; and a data analyzing program library. Most of the routines in the library are stand-alone programs suitable for batch processing. CMGTooL is written in MATLAB computing language (The Mathworks, 1997), therefore users must have MATLAB installed on their computer in order to use this software package. In addition, MATLAB’s Signal Processing Toolbox is also required by some CMGTooL’s routines. Like most MATLAB programs, all CMGTooL codes are compatible with different computing platforms including PC, MAC, and UNIX machines (Note: CMGTooL has been tested on different platforms that run MATLAB 5.2 (Release 10) or lower versions. Some of the commands related to MAC may not be compatible with later releases of MATLAB). The GUI and some of the library routines call low-level NetCDF file I/O, variable and attribute functions. These NetCDF exclusive functions are supported by a MATLAB toolbox named NetCDF, created by Dr. Charles Denham . This toolbox has to be installed in order to use the CMGTooL GUI. The CMGTooL GUI calls several routines that were initially developed by others. The authors would like to acknowledge the following scientists for their ideas and codes: Dr. Rich Signell (USGS), Dr. Chris Sherwood (USGS), and Dr. Bob Beardsley (WHOI). Many special terms that carry special meanings in either MATLAB or the NetCDF Toolbox are used in this manual. Users are encouraged to read the documents of MATLAB and NetCDF for references.

Open-File Report↗

USGS1992

Crystalline Silica Primer

Crystalline silica is the scientific name for a group of minerals composed of silicon and oxygen. The term crystalline refers to the fact that the oxygen and silicon atoms are arranged in a threedimensional repeating pattern. This group of minerals has shaped human history since the beginning of civilization. From the sand used for making glass to the piezoelectric quartz crystals used in advanced communication systems, crystalline silica has been a part of our technological development. Crystalline silica's pervasiveness in our technology is matched only by its abundance in nature. It's found in samples from every geologic era and from every location around the globe. Scientists have known for decades that prolonged and excessive exposure to crystalline silica dust in mining environments can cause silicosis, a noncancerous lung disease. During the 1980's, studies were conducted that suggested that crystalline silica also was a carcinogen. As a result of these findings, crystalline silica has been regulated under the Occupational Safety and Health Administration's (OSHA) Hazard Communication Standard (HCS). Under HCS, OSHAregulated businesses that use materials containing 0.1% or more crystalline silica must follow Federal guidelines concerning hazard communication and worker training. Although the HCS does not require that samples be analyzed for crystalline silica, mineral suppliers or OSHAregulated businesses may choose to do so if they wish to show that they are exempt from the requirements of HCS. Because crystalline silica is an extremely common mineral and the HCS will affect many mineral commodities, it is important then, that there be as clear an understanding as possible of what is and what is not crystalline silica, and where it is found and used, and how it is qualitatively and quantitatively identified. This primer is an attempt to accomplish this in as nontechnical a manner as possible. This primer will examine crystalline silica. Part I will describe, in nonscientific terms, what crystalline silica is and how we come in contact with it. Part II will discuss the regulatory decisions that have created new interest in this ancient and widespread substance and will present a nontechnical overview of the techniques used to measure crystalline silica. Because this primer is meant to be a starting point for anyone interested in learning more about crystalline silica, a list of selected readings and other resources is included. The detailed glossary, which defines many terms that are beyond the scope of this publication, is designed to help the reader move from this presentation to a more technical one, the inevitable next step.

Special Publication↗

USGS2020

Capturing, preserving and digitizing legacy seismic data from the Montserrat Volcano Observatory analog seismic network, July 1995 – December 2004

An eruption of the Soufrière Hills Volcano (SHV) on the eastern Caribbean island of Montserrat began on 18 July 1995 and continued until February 2010. Within nine days of the eruption onset, an existing four‐station analog seismic network (ASN) was expanded to 10 sites. Telemetered data from this network were recorded, processed, and archived locally using a system developed by scientists from the U.S. Geological Survey (USGS) Volcano Disaster Assistance Program (VDAP). In October 1996, a digital seismic network (DSN) was deployed with the ability to capture larger amplitude signals across a broader frequency range. These two networks operated in parallel until December 2004, with separate telemetry and acquisition systems (analysis systems were merged in March 2001). Although the DSN provided better quality data for research, the ASN featured superior real‐time monitoring tools and captured valuable data including the only seismic data from the first 15 months of the eruption. These successes of the ASN have been rather overlooked. This article documents the evolution of the ASN, the VDAP system, the original data captured, and the recovery and conversion of more than 230,000 seismic events from legacy SUDS, Hypo71, and Seislog formats into Seisan database with waveform data in miniSEED format. No digital catalog existed for these events, but students at the University of South Florida have classified two-thirds of the 40,000 events that were captured between July 1995 and October 1996. Locations and magnitudes were recovered for ~10,000 of these events. Real-time seismic amplitude measurement, seismic spectral amplitude measurement, and tiltmeter data were also captured. The result is that the ASN seismic dataset is now more discoverable, accessible, and reusable, in accordance with FAIR data principles. These efforts could catalyze new research on the 1995–2010 SHV eruption. Furthermore, many observatories have data in these same legacy data formats and might benefit from procedures and codes documented here.

Soufrière Hills Volcano↗

USGS2018

Evolution of the 2015 Cotopaxi eruption revealed by combined geochemical & seismic observations

Through integration of multiple data streams to monitor volcanic unrest scientists are able to make more robust eruption forecast and to obtain a more holistic interpretation of volcanic systems. We examined gas emission and gas geochemistry, seismic and petrologic data recorded during the 2015 unrest of Cotopaxi (Ecuador) in order to decipher the origin and temporal evolution of this eruption. Identification of families of similar seismic events and the use of seismic amplitude ratios reveals temporal changes in volcanic processes. SO2 (300 to 24000 t/d), BrO/SO2 (5-10 x10-5), SO2/HCl (5.8 ± 4.8 and 6.6 ± 3.0) and CO2/SO2 (0.6 to 2.1) measured throughout the eruption indicate a shallow magmatic source. Bulk ash and glass chemistry indicate a homogenous andesitic (SiO2 wt%=56.94 ± 0.25) magma having undergone extensive S-exsolution and degassing during ascent. These data lead us to interpret this eruption as a magma intrusion and ascend to shallow levels. The intrusion progressively interacted with the hydrothermal system, boiled off water, and produced hydromagmatic explosions. A small volume of this intrusion continued to fragment and produced episodic ash emissions until it was sufficiently degassed and rheologically stiff. Based on the 470 kt of measured SO2 we estimate that ~ 65.3 x106 m3 of magma were required to supply the emitted gases. This volume exceeds the volume of erupted juvenile material by a factor of 50. This result emphasizes the importance of careful monitoring of Cotopaxi to identify the intrusion of a new batch of magma, which could rejuvenate the non-erupted material.

Geochemistry, Geophysics, Geosystems↗

USGS2021

Optimization of salt marsh management at the Moosehorn National Wildlife Refuge, Maine, through use of structured decision making

Structured decision making is a systematic, transparent process for improving the quality of complex decisions by identifying measurable management objectives and feasible management actions; predicting the potential consequences of management actions relative to the stated objectives; and selecting a course of action that maximizes the total benefit achieved and balances tradeoffs among objectives. The U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service, applied an existing, regional framework for structured decision making to develop a prototype tool for optimizing tidal marsh management decisions at the Moosehorn National Wildlife Refuge in Maine. Refuge biologists, refuge managers, and research scientists identified multiple potential management actions to improve the ecological integrity of four marsh management units within the refuge, totaling about 13 hectares, and estimated the outcomes of each action in terms of performance metrics associated with each management objective. Value functions previously developed at the regional level were used to transform metric scores to a common utility scale, and utilities were summed to produce a single score representing the total management benefit that could be accrued from each potential management action. Constrained optimization was used to identify the set of management actions, one per marsh management unit, that could maximize total management benefits at different cost constraints at the refuge scale. Results indicated that, for the objectives and actions considered here, total management benefits may increase consistently up to $ 1,000, and may continue to increase at a lower rate with further expenditures. Potential management actions in optimal portfolios at total costs less than or equal to $ 1,000 included improving nesting habitat for Ammodramus nelsoni (Nelson’s sparrow) or restoring hydrologic connections to the upper marsh in one marsh management unit (Hobart Stream West). The potential management benefits were derived from expected increases in the density of nekton and of spiders (as an indicator of trophic health). The prototype presented here does not resolve management decisions; rather, it provides a framework for decision making at the Moosehorn National Wildlife Refuge that can be updated for implementation as new data and information become available. Insights from this process may also be useful to inform future habitat management planning at the refuge.

Maine↗

USGS2011

Nature's Notebook 2010: Data & participant summary

The USA National Phenology Network (USA‐NPN) seeks to engage volunteer observers to collect phenology observations of plants and animals using consistent standards and to contribute to the USANPN National Phenology Database (NPDb). The commencement of 2010 marked the second functional year of Nature’s Notebook , the online phenology observation program developed by the National Coordinating Office (NCO) of the USA‐NPN. The addition of animal species for monitoring was a major enhancement to Nature’s Notebook in 2010. In 2010, with minimal advertising or marketing, 796 new observers registered with Nature’s Notebook and 426 observers reported phenology observations on one or more plants or animals via the online interface. Over 200,000 data records were added to the NPDb. Observations were reported on 179 species of plants and 58 species of animals. The plant species most frequently observed include red maple ( Acer rubrum ), quaking aspen ( Populus tremuloides ), American beech ( Fagus grandifolia ), northern red oak ( Quercus rubra ), and flowering dogwood ( Cornus florida ). The animal species most frequently observed were American robin ( Turdus migratorius ), black‐capped chickadee ( Poecile atricapillus ), American goldfinch ( Carduelis tristis ), bumblebee ( Bombus spp.), and white‐tailed deer ( Odocoileus virginianus ). As in 2009, participants tended to stay involved, reporting most phenophases for an average of nearly ten unique dates during the year. In addition, nearly two hundred participants who submitted observations in previous years continued to participate in 2010. This sustained participation suggests that the Nature’s Notebook interface and the status monitoring protocols inherent in Nature’s Notebook are both conducive to engaging the public and keeping them involved. Data submitted by Nature’s Notebook participants show patterns that follow latitude and elevation. Multiple years of observations now allow for year‐to‐year comparisons within and across species. As such, these data should be useful to a variety of stakeholders interested in the spatial and temporal patterns of plant and animal activity on a national scale; through time, these data should also empower scientists, resource managers, and the public in decision‐making and adapting to variable and changing climates and environments. Data submitted to Nature’s Notebook and supporting metadata are available for download at www.usanpn.org/results/data. Additionally, data visualization tools are available online at www.usanpn.org/results/visualizations.

USA-NPN Technical Series↗