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USGS2024

A guide to environmental DNA extractions for non-molecular trained biologists, ecologists, and conservation scientists

Ecologists, biologists, and conservation scientists are increasingly interested in the use of environmental DNA (eDNA) data for research and potentially decision-making. While commercial DNA extraction kits are typically user-friendly and accessible, they may fail to deliver the desired results with inherently complex eDNA samples, necessitating protocol optimization or educated selection of alternative approaches. To this end, knowledge of the basic steps and principles of DNA extractions is essential, but traditional education tracks in ecology, conservation, and environmental management typically do not include in-depth training in molecular methods. The primary objective of this paper is to enable scientists with an ecological background and limited molecular training to understand the four key steps of eDNA isolations, and to use this expertise to their advantage. We describe the purpose of commonly used reagents and chemicals, point out alternatives for each key step, explain the impact of certain choices regarding isolation approaches on DNA integrity and purity, and highlight the possibility of a tailor-made “mix and match” approach. We anticipate that this paper will enable field ecologists to develop a deeper understanding of the mechanisms and chemistry underlying eDNA extractions, thus allowing them to make informed decisions regarding the best eDNA extraction method for their research goals. Our intention is not to provide comprehensive, step-by-step protocols, but to offer guiding principles while highlighting alternative solutions. Finally, we hope that this paper will act as a useful resource to support knowledge transfer and teaching.

Environmental DNA↗

USGS2016

Are we working towards global research priorities for management and conservation of sea turtles?

In 2010, an international group of 35 sea turtle researchers refined an initial list of more than 200 research questions into 20 metaquestions that were considered key for management and conservation of sea turtles. These were classified under 5 categories: reproductive biology, biogeography, population ecology, threats and conservation strategies. To obtain a picture of how research is being focused towards these key questions, we undertook a systematic review of the peer-reviewed literature (2014 and 2015) attributing papers to the original 20 questions. In total, we reviewed 605 articles in full and from these 355 (59%) were judged to substantively address the 20 key questions, with others focusing on basic science and monitoring. Progress to answering the 20 questions was not uniform, and there were biases regarding focal turtle species, geographic scope and publication outlet. Whilst it offers some meaningful indications as to effort, quantifying peer-reviewed literature output is obviously not the only, and possibly not the best, metric for understanding progress towards informing key conservation and management goals. Along with the literature review, an international group based on the original project consortium was assigned to critically summarise recent progress towards answering each of the 20 questions. We found that significant research is being expended towards global priorities for management and conservation of sea turtles. Although highly variable, there has been significant progress in all the key questions identified in 2010. Undertaking this critical review has highlighted that it may be timely to undertake one or more new prioritizing exercises. For this to have maximal benefit we make a range of recommendations for its execution. These include a far greater engagement with social sciences, widening the pool of contributors and focussing the questions, perhaps disaggregating ecology and conservation.

Endangered Species Research↗

USGS2011

An overview of estrogen-associated endocrine disruption in fishes: Evidence of effects on reproductive and immune physiology

Simply and perhaps intuitively defined, endocrine disruption is the abnormal modulation of normal hormonal physiology by exogenous chemicals. In fish, endocrine disruption of the reproductive system has been observed worldwide in numerous species and is known to affect both males and females. Observations of biologically relevant endocrine disruption most commonly occurs near waste water treatment plant outfalls, pulp and paper mills, and areas of high organic loading sometimes associated with agricultural practices. Estrogenic endocrine disrupting chemicals (EEDCs) have received an overwhelmingly disproportionate amount of scientific attention compared to other EDCs in recent years. In male fishes, exposure to EEDCs can lead to the induction of testicular oocytes (intersex), measurable plasma vitellogenin protein, altered sex steroid profiles, abnormal spawning behavior, skewed population sex ratios, and lessened reproductive success. Interestingly, contemporary research purports that EDCs modulate aspects of non-reproductive physiology including immune function. Here we present an overview of endocrine disruption in fishes associated with estrogenic compounds, implications of this phenomenon, and examples of EDC related research findings by our group in the Potomac River Watershed, USA.

Conference Paper↗

USGS2003

Changing anthropogenic influence on the Santa Monica Bay watershed

Santa Monica Bay is an open coastal embayment located directly seaward of Los Angeles, California. The Bay provides vital economic value through its water-dependent activities, such as swimming, diving, boating, and fishing. An increase from 100,000 residents in 1900 to 10 million in 2000 has imposed numerous environmental stressors on the Bay, including urbanization of the watershed. Pollutant discharges into the Bay increased throughout the early part of the century, but declined following passage of the Clean Water Act in 1972. Since that time, the predominant source of pollutant inputs has changed from point sources to non-point urban runoff. To assess how present-day and historical pollution interact to affect the environmental quality of Santa Monica Bay, three organizations collaborated on a multi-disciplinary study in 1997, towards which this volume is focused. This paper details the temporal patterns of anthropogenic influence on Santa Monica Bay to provide context for the papers that follow.

California↗

USGS2011

The development of an EDSS: Lessons learned and implications for DSS research

The Solar and Wind Energy Resource Assessment (SWERA) project is focused on providing renewable energy (RE) planning resources to the public. Examples include wind, solar, and hydro assessments. SWERA DSS consists of three major components. First, SWERA 'Product Archive' provides for a discovery DSS upon which users can find and access renewable energy data and supporting models. Second, the 'Renewable Resource EXplorer' (RREX) component serves as a web-based, GIS analysis tool for viewing RE resource data available through the SWERA Product Archive. Third, the SWERA web service provides computational access to the data available in the SWERA spatial database through a location based query, and is also utilized in the RREX component. We provide a discussion of various design decisions used in the construction of this EDSS, followed by project experiences and implications for EDSS and broader DSS research.

Conference Paper↗

USGS2009

Supplemental materials for the ICDP-USGS Eyreville A, B, and C core holes, Chesapeake Bay impact structure: Core-box photographs, coring-run tables, and depth-conversion files

During 2005-2006, the International Continental Scientific Drilling Program and the U.S. Geological Survey drilled three continuous core holes into the Chesapeake Bay impact structure to a total depth of 1766.3 m. A collection of supplemental materials that presents a record of the core recovery and measurement data for the Eyreville cores is available on CD-ROM at the end of this volume and in the GSA Data Repository. The supplemental materials on the CD-ROM include digital photographs of each core box from the three core holes, tables of the three coring-run logs, as recorded on site, and a set of depth-conversion programs. In this chapter, the contents, purposes, and basic applications of the supplemental materials are briefly described. With this information, users can quickly decide if the materials will apply to their specific research needs.

Chesapeake Bay↗

USGS2012

Real-time seismic monitoring of the integrated cape girardeau bridge array and recorded earthquake response

This paper introduces the state of the art, real-time and broad-band seismic monitoring network implemented for the 1206 m [3956 ft] long, cable-stayed Bill Emerson Memorial Bridge in Cape Girardeau (MO), a new Mississippi River crossing, approximately 80 km from the epicentral region of the 1811-1812 New Madrid earthquakes. The bridge was designed for a strong earthquake (magnitude 7.5 or greater) during the design life of the bridge. The monitoring network comprises a total of 84 channels of accelerometers deployed on the superstructure, pier foundations and at surface and downhole free-field arrays of the bridge. The paper also presents the high quality response data obtained from the network. Such data is aimed to be used by the owner, researchers and engineers to assess the performance of the bridge, to check design parameters, including the comparison of dynamic characteristics with actual response, and to better design future similar bridges. Preliminary analyses of ambient and low amplitude small earthquake data reveal specific response characteristics of the bridge and the free-field. There is evidence of coherent tower, cable, deck interaction that sometimes results in amplified ambient motions. Motions at the lowest tri-axial downhole accelerometers on both MO and IL sides are practically free from any feedback from the bridge. Motions at the mid-level and surface downhole accelerometers are influenced significantly by feedback due to amplified ambient motions of the bridge. Copyright ASCE 2006.

Conference Paper↗

USGS2017

Cooperative science to inform Lake Ontario management: Research from the 2013 Lake Ontario CSMI program

Since the mid-1970s, successful Lake Ontario management actions including nutrient load and pollution reductions, habitat restoration, and fish stocking have improved Lake Ontario. However, several new obstacles to maintenance and restoration have emerged. This special issue presents management-relevant research from multiple agency surveys in 2011 and 2012 and the 2013 Cooperative Science and Monitoring Initiative (CSMI), that span diverse lake habitats, species, and trophic levels. This research focused on themes of nutrient loading and fate; vertical dynamics of primary and secondary production; fish abundance and behavior; and food web structure. Together these papers identify the status of many of the key drivers of the Lake Ontario ecosystem and contribute to addressing lake-scale questions and management information needs in Lake Ontario and the other Great Lakes and connecting water bodies.

Lake Ontario↗

USGS1995

Fractals in petroleum geology and earth processes

In this unique volume, renowned experts discuss the applications of fractals in petroleum research-offering an excellent introduction to the subject. Contributions cover a broad spectrum of applications from petroleum exploration to production. Papers also illustrate how fractal geometry can quantify the spatial heterogeneity of different aspects of geology and how this information can be used to improve exploration and production results.

Book↗

USGS2008

GSTARS computer models and their applications, part I: theoretical development

GSTARS is a series of computer models developed by the U.S. Bureau of Reclamation for alluvial river and reservoir sedimentation studies while the authors were employed by that agency. The first version of GSTARS was released in 1986 using Fortran IV for mainframe computers. GSTARS 2.0 was released in 1998 for personal computer application with most of the code in the original GSTARS revised, improved, and expanded using Fortran IV/77. GSTARS 2.1 is an improved and revised GSTARS 2.0 with graphical user interface. The unique features of all GSTARS models are the conjunctive use of the stream tube concept and of the minimum stream power theory. The application of minimum stream power theory allows the determination of optimum channel geometry with variable channel width and cross-sectional shape. The use of the stream tube concept enables the simulation of river hydraulics using one-dimensional numerical solutions to obtain a semi-two- dimensional presentation of the hydraulic conditions along and across an alluvial channel. According to the stream tube concept, no water or sediment particles can cross the walls of stream tubes, which is valid for many natural rivers. At and near sharp bends, however, sediment particles may cross the boundaries of stream tubes. GSTARS3, based on FORTRAN 90/95, addresses this phenomenon and further expands the capabilities of GSTARS 2.1 for cohesive and non-cohesive sediment transport in rivers and reservoirs. This paper presents the concepts, methods, and techniques used to develop the GSTARS series of computer models, especially GSTARS3. ?? 2008 International Research and Training Centre on Erosion and Sedimentation and the World Association for Sedimentation and Erosion Research.

International Journal of Sediment Research↗

USGS2018

Classifying physiographic regimes on terrain and hydrologic factors for adaptive generalization of stream networks

Automated generalization software must accommodate multi-scale representations of hydrographic networks across a variety of geographic landscapes, because scale-related hydrography differences are known to vary in different physical conditions. While generalization algorithms have been tailored to specific regions and landscape conditions by several researchers in recent years, the selection and characterization of regional conditions have not been formally defined nor statistically validated. This paper undertakes a systematic classification of landscape types in the conterminous United States to spatially subset the country into workable units, in preparation for systematic tailoring of generalization workflows that preserve hydrographic characteristics. The classification is based upon elevation, standard deviation of elevation, slope, runoff, drainage and bedrock density, soil and bedrock permeability, area of inland surface water, infiltration-excess of overland flow, and a base flow index. A seven class solution shows low misclassification rates except in areas of high landscape diversity such as the Appalachians, Rocky Mountains, and Western coastal regions.

International Journal of Cartography↗

USGS1967

Explorers from space

The statement that a new era in exploration is opening will almost surely bring to mind the venturing of man into space and the ever more imminent exploration of the moon. The reference here, however, is to exploration of earth itself and to the unique capabilities for study of the earth that space technology will provide. Demands for water, minerals, energy, food, and for working, living and recreational space are outrunning our ability to meet them by traditional methods. In order to satisfy these demands, it is necessary now, just as it has been in the past, to look to the activities, the instruments, and the technologies that in part create the pressures for aid in meeting them. Studies being made at the U.S. Geological Survey and elsewhere of the potential applications of remote sensors in space to earth resources research indicate that now, at last, it will be possible to approach solutions on a regional or global basis. This paper discusses the plans for an Earth Resources Observational Satellites Program which will be designed for that purpose.

Journal of Geological Education↗

USGS2022

Attribution of monotonic trends and change points in peak streamflow across the conterminous United States using a multiple working hypotheses framework, 1941–2015 and 1966–2015

The U.S. Geological Survey has a long history of leading flood-frequency analysis studies. These studies play a critical role in the assessment of risk, protection of lives, and planning and design of flood protection infrastructure. Standard flood-frequency analysis is based on the assumption of stationarity—that is, that the distribution of floods at a given site varies around a particular mean within a particular envelope of variance (and skew) and that these parameters of the underlying statistical distribution representative of the floods do not vary over time. Gradual or abrupt changes in one or more of the distributional parameters are called nonstationarities and violate the underlying assumptions of current U.S. Federal Government guidelines for flood-frequency analysis. Uncertainty exists as to what degree of violations calls for the use of a modified method for flood-frequency analysis and what the modified method(s) should be. When deciding whether to perform nonstationary flood-frequency analysis and choosing a method for such analysis, it is important to understand the causes of the nonstationarity. Gradual or abrupt changes in distributional properties of floods may be the result of numerous factors, such as regulation, diversion, land-use change, or climate change. In the interest of developing a cohesive national approach for better understanding the causes of nonstationarities and incorporating potential or observed changes into flood-frequency estimates, subject-matter experts from the U.S. Geological Survey and cooperators worked together to develop a multiple working hypotheses framework for making attributions and a common vocabulary for making provisions of confidence. Seven regional teams of these experts used ancillary datasets and institutional knowledge to evaluate plausible causes for monotonic trends and change points in annual peak-streamflow data for the conterminous United States that had been identified in an earlier phase of the project. The first chapter of this professional paper describes the development of a list of the potential attributions, presents a literature review of the potential attributions, describes the regional approach, summarizes insights obtained from the attribution process, and suggests future research. The other chapters provide the methods used for attribution in the seven regions—Pacific Northwest, Upper Plains, Midwest, Northeast, Southwest, South-Central, and Southeast—and summarize the regional patterns of nonstationarities.

Conterminous United States↗

USGS2015

Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science through data reuse

Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. At the broader scale, national datasets exist for a large number of geospatial features of land, water, and air that are needed to fully understand variation among these ecosystems. However, such datasets originate from different sources and have different spatial and temporal resolutions. By taking an open-science perspective and by combining site-based ecosystem datasets and national geospatial datasets, science gains the ability to ask important research questions related to grand environmental challenges that operate at broad scales. Documentation of such complicated database integration efforts, through peer-reviewed papers, is recommended to foster reproducibility and future use of the integrated database. Here, we describe the major steps, challenges, and considerations in building an integrated database of lake ecosystems, called LAGOS (LAke multi-scaled GeOSpatial and temporal database), that was developed at the sub-continental study extent of 17 US states (1,800,000 km 2 ). LAGOS includes two modules: LAGOS GEO , with geospatial data on every lake with surface area larger than 4 ha in the study extent (~50,000 lakes), including climate, atmospheric deposition, land use/cover, hydrology, geology, and topography measured across a range of spatial and temporal extents; and LAGOS LIMNO , with lake water quality data compiled from ~100 individual datasets for a subset of lakes in the study extent (~10,000 lakes). Procedures for the integration of datasets included: creating a flexible database design; authoring and integrating metadata; documenting data provenance; quantifying spatial measures of geographic data; quality-controlling integrated and derived data; and extensively documenting the database. Our procedures make a large, complex, and integrated database reproducible and extensible, allowing users to ask new research questions with the existing database or through the addition of new data. The largest challenge of this task was the heterogeneity of the data, formats, and metadata. Many steps of data integration need manual input from experts in diverse fields, requiring close collaboration.

Connecticut, Delaware, Illinois, Indiana, Iowa, Ma↗

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↗

USGS2000

Preface paper to the Semi-Arid Land-Surface-Atmosphere (SALSA) Program special issue

The Semi-Arid Land-Surface-Atmosphere Program (SALSA) is a multi-agency, multi-national research effort that seeks to evaluate the consequences of natural and human-induced environmental change in semi-arid regions. The ultimate goal of SALSA is to advance scientific understanding of the semi-arid portion of the hydrosphere-biosphere interface in order to provide reliable information for environmental decision making. SALSA approaches this goal through a program of long-term, integrated observations, process research, modeling, assessment, and information management that is sustained by cooperation among scientists and information users. In this preface to the SALSA special issue, general program background information and the critical nature of semi-arid regions is presented. A brief description of the Upper San Pedro River Basin, the initial location for focused SALSA research follows. Several overarching research objectives under which much of the interdisciplinary research contained in the special issue was undertaken are discussed. Principal methods, primary research sites and data collection used by numerous investigators during 1997-1999 are then presented. Scientists from about 20 US, five European (four French and one Dutch), and three Mexican agencies and institutions have collaborated closely to make the research leading to this special issue a reality. The SALSA Program has served as a model of interagency cooperation by breaking new ground in the approach to large scale interdisciplinary science with relatively limited resources.

Conference Paper↗

USGS2017

Climate change as a long-term stressor for the fisheries of the Laurentian Great Lakes of North America

The Laurentian Great Lakes of North America provide valuable ecosystem services, including fisheries, to the surrounding population. Given the prevalence of other anthropogenic stressors that have historically affected the fisheries of the Great Lakes (e.g., eutrophication, invasive species, overfishing), climate change is often viewed as a long-term stressor and, subsequently, may not always be prioritized by managers and researchers. However, climate change has the potential to negatively affect fish and fisheries in the Great Lakes through its influence on habitat. In this paper, we (1) summarize projected changes in climate and fish habitat in the Great Lakes; (2) summarize fish responses to climate change in the Great Lakes; (3) describe key interactions between climate change and other stressors relevant to Great Lakes fish, and (4) summarize how climate change can be incorporated into fisheries management. In general, fish habitat is projected to be characterized by warmer temperatures throughout the water column, less ice cover, longer periods of stratification, and more frequent and widespread periods of bottom hypoxia in productive areas of the Great Lakes. Based solely on thermal habitat, fish populations theoretically could experience prolonged optimal growth environment within a changing climate, however, models that assess physical habitat influences at specific life stages convey a more complex picture. Looking at specific interactions with other stressors, climate change may exacerbate the negative impacts of both eutrophication and invasive species for fish habitat in the Great Lakes. Although expanding monitoring and research to consider climate change interactions with currently studied stressors, may offer managers the best opportunity to keep the valuable Great Lakes fisheries sustainable, this expansion is globally applicable for large lake ecosystem dealing with multiple stressors in the face of continued human-driven changes.

Great Lakes↗

USGS2024

New developments at the Center for Engineering Strong-Motion Data (CESMD)

The Center for Engineering Strong-Motion Data (CESMD), an internationally utilized joint center of the U.S. Geological Survey (USGS) and the California Geological Survey (CGS), provides a single access point for earthquake strong-motion records and station metadata from the CGS California Strong-Motion Instrumentation Program (CSMIP), the USGS National Strong-Motion Project (NSMP), the USGS Advanced National Seismic System, and other affiliates. The CESMD has been continuously improving its webtools to facilitate the access of strong-motion data and metadata for use in post-earthquake response and for scientific and engineering research applications. The Center provides raw and processed strong-motion data via the Engineering Data Center (EDC) and the Virtual Data Center (VDC) web portals. This paper focuses on the strong-motion products provided by the EDC where more than 48,000 records with peak ground accelerations greater than 0.1% g from over 2400 earthquakes are currently hosted. and on the ongoing efforts to develop data access tools and applications. The new developments and ongoing efforts in the EDC include: 1) enhancements to the CESMD webservices to facilitate access to station metadata, earthquake information, and strong motion records 2) new features to the interactive map interface, improving the visualization and access to earthquake, station, and record information, 3) efforts to develop a new web application tool for data format conversion from a number of data formats, 4) efforts to unify varying waveform data formats into a consistent format, 5) ongoing efforts to compile seismic station site geology, measured or inferred Vs30 values, shear-wave profiles, NEHRP site class, and available structural instrument deployment schematics, and 6) a special studies pages for research topic-specific ground motion datasets that offer uniform processing of records from a variety of sources.

Conference Paper↗