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Reference manual for generation and analysis of Habitat Time Series: version II
The selection of an instream flow requirement for water resource management often requires the review of how the physical habitat changes through time. This review is referred to as 'Time Series Analysis." The Tune Series Library (fSLIB) is a group of programs to enter, transform, analyze, and display time series data for use in stream habitat assessment. A time series may be defined as a sequence of data recorded or calculated over time. Examples might be historical monthly flow, predicted monthly weighted usable area, daily electrical power generation, annual irrigation diversion, and so forth. The time series can be analyzed, both descriptively and analytically, to understand the importance of the variation in the events over time. This is especially useful in the development of instream flow needs based on habitat availability. The TSLIB group of programs assumes that you have an adequate study plan to guide you in your analysis. You need to already have knowledge about such things as time period and time step, species and life stages to consider, and appropriate comparisons or statistics to be produced and displayed or tabulated. Knowing your destination, you must first evaluate whether TSLIB can get you there. Remember, data are not answers . This publication is a reference manual to TSLIB and is intended to be a guide to the process of using the various programs in TSLIB. This manual is essentially limited to the hands-on use of the various programs. a TSLIB use interface program (called RTSM) has been developed to provide an integrated working environment where the use has a brief on-line description of each TSLIB program with the capability to run the TSLIB program while in the user interface. For information on the RTSM program, refer to Appendix F. Before applying the computer models described herein, it is recommended that the user enroll in the short course "Problem Solving with the Instream Flow Incremental Methodology (IFIM)." This course is offered by the Aquatic Systems Branch of the National Ecology Research Center. For more information about the TSLIB software, refer to the Memorandum of Understanding. Chapter 1 provides a brief introduction to the Instream Flow Incremental Methodology and TSLIB. Other chapters in this manual provide information on the different aspects of using the models. The information contained in the other chapters includes (2) acquisition, entry, manipulation, and listing of streamflow data; (3) entry, manipulation, and listing of the habitat-versus-streamflow function; (4) transferring streamflow data; (5) water resources systems analysis; (6) generation and analysis of daily streamflow and habitat values; (7) generation of the time series of monthly habitats; (8) manipulation, analysis, and display of month time series data; and (9) generation, analysis, and display of annual time series data. Each section includes documentation for the programs therein with at least one page of information for each program, including a program description, instructions for running the program, and sample output. The Appendixes contain the following: (A) sample file formats; (B) descriptions of default filenames; (C) alphabetical summary of batch-procedure files; (D) installing and running TSLIB on a microcomputer; (E) running TSLIB on a CDC Cyber computer; (F) using the TSLIB user interface program (RTSM); and (G) running WATSTORE on the USGS Amdahl mainframe computer. The number for this version of TSLIB--Version II-- is somewhat arbitrary, as the TSLIB programs were collected into a library some time ago; but operators tended to use and manage them as individual programs. Therefore, we will consider the group of programs from the past that were only on the CDC Cyber computer as Version 0; the programs from the past that were on both the Cyber and the IBM-compatible microcomputer as Version I; and the programs contained in this reference manual as Version II.
The confluences of ideas leading to, and the flow of ideas emerging from, individual-based modeling of riverine fishes
In this review article, we trace the history of events leading to the development of individual-based models (IBMs) to represent aquatic organisms in rivers and streams. As a metaphor, we present this history as a series of confluences between individual scientists (tributaries) sharing ideas. We describe contributions of these models to science and management. One iconic feature of river IBMs is the linkage between flow and the physical habitat experienced by individual animals, and the first model that focused on this linkage is briefly described. We continue by reviewing the contributions of riverine IBMs to eight broad areas of scientific inquiry. The first four areas include research to understand 1) the effects of flow regimes on fish populations, 2) species interactions (e.g., size-mediated competition and predation), 3) fish movement and habitat selection, and 4) contaminant and water quality impacts on populations. Next, we review research using IBMs 5) to guide conservation biology of imperiled taxa through population viability analysis, including research 6) to understand river fragmentation by dams and reconnection, 7) to understand genetic outcomes for riverine metapopulations, and 8) to anticipate the future effects of temperature and climate change. This rich body of literature has contributed to both theoretical insights (e.g., about animal behavior and life history) and applied insights (e.g., population-level effects of flow regimes, temperature, and the effects of hydropower and other industries that share rivers with aquatic biota). We finish by exploring promising branches that lie ahead in the braided, downstream channel that represents future river modeling research.
Book review: Rare earth elements—A new approach to the nexus of supply, demand and use: exemplified along the use of neodymium in permanent magnets
This book is part of the “Springer Theses” published by Springer, a book series designed to highlight and share outstanding Ph.D. research. As explained by Springer (on the second page), this series “brings together a selection of the very best Ph.D. theses from around the world and across the physical sciences.” I admire Springer for this endeavor because a large number of exceptional theses are never published, and thus are difficult to obtain, while most of those that are published are presented only in highly condensed form as journal articles. Review info: Rare Earth Elements—A New Approach to the Nexus of Supply, Demand and Use: Exemplified Along the Use of Neodymium in Permanent Magnets . By Volker Zerf. 2013. ISBN 978-3-642-35457-1. 157 pp.
Geomorphic consequences of volcanic eruptions in Alaska: A review
Eruptions of Alaska volcanoes have significant and sometimes profound geomorphic consequences on surrounding landscapes and ecosystems. The effects of eruptions on the landscape can range from complete burial of surface vegetation and preexisting topography to subtle, short-term perturbations of geomorphic and ecological systems. In some cases, an eruption will allow for new landscapes to form in response to the accumulation and erosion of recently deposited volcaniclastic material. In other cases, the geomorphic response to a major eruptive event may set in motion a series of landscape changes that could take centuries to millennia to be realized. The effects of volcanic eruptions on the landscape and how these effects influence surface processes has not been a specific focus of most studies concerned with the physical volcanology of Alaska volcanoes. Thus, what is needed is a review of eruptive activity in Alaska in the context of how this activity influences the geomorphology of affected areas. To illustrate the relationship between geomorphology and volcanic activity in Alaska, several eruptions and their geomorphic impacts will be reviewed. These eruptions include the 1912 Novarupta–Katmai eruption, the 1989–1990 and 2009 eruptions of Redoubt volcano, the 2008 eruption of Kasatochi volcano, and the recent historical eruptions of Pavlof volcano. The geomorphic consequences of eruptive activity associated with these eruptions are described, and where possible, information about surface processes, rates of landscape change, and the temporal and spatial scale of impacts are discussed. A common feature of volcanoes in Alaska is their extensive cover of glacier ice, seasonal snow, or both. As a result, the generation of meltwater and a variety of sediment–water mass flows, including debris-flow lahars, hyperconcentrated-flow lahars, and sediment-laden water floods, are typical outcomes of most types of eruptive activity. Occasionally, such flows can be quite large, with flow volumes in the range of 10 7 –10 9 m 3 . A review of the lahars generated during the 2009 eruption of Redoubt volcano will illustrate the geomorphic impacts of lahars on stream channels and riparian habitat. Although much work is needed to develop a comprehensive understanding of the geomorphic consequences of volcanic activity in Alaska, this review provides a synthesis of some of the best-studied eruptions and perhaps will serve as a starting point for future work on this topic.
Observing systems, modeling, and forecasting
Predicting harmful algal blooms (HABs) requires integrating physical, chemical, and biological data collected from observing networks and then assimilating these data into models, which are used to generate forecasts. In 2005, the Harmful Algal Research and Response: A National Environmental Science Strategy 2005-2015 (HARRNESS, 2005) made recommendations on how to improve HAB modeling and forecasting over the next decade. Key HARRNESS recommendations related to sensing, networking, and modeling HABs included: ● Support the development and validation of new and improved technologies for remote cell and toxin detection, and for modeling and forecasting, ● Improve coordination of monitoring/ and modeling efforts, both at national and regional levels, ● Improve the use of networking technologies for monitoring and modeling efforts, ● Conduct sustained time series measurements of the biotic, chemical, and physical environments impacted by HABs, ● Develop food web models on the ecosystem fate and effects of toxins, ● Develop and improve species-specific models that link to physical-biological models. Here we review HAB observing, modeling, and forecasting advances and technologies and recommend research and management priorities for the next decade and beyond. Our report encompasses sensing technologies, sensor networking and data management, models and forecasts, and the paths to operationalize forecasts. Continued improvements of deployable sensors are foundational to improving early warning indicators, models, and forecasts, which are only as good as the underlying data. Sensing technology has advanced considerably in the last decade; for example, more capable fluorometric pigment sensors can track changes in bloom biomass in real-time. Additionally, automated imaging/classifying systems to identify and quantify key harmful algal (HA) taxa are being routinely deployed. However, deployable toxin sensors are available for only some HAB toxins and continue to be identified as a critical need by researchers and managers. As more and improved sensors and technologies become available, the data quality associated with each sensor needs to be assessed. Data quality encompasses the reliability, accuracy, and uncertainty associated with sensor-generated data. These data need to be of known quality so that researchers, managers, and end-users can reliably determine if the information is appropriate for their intended applications. Many of the data quality recommendations from HARRNESS (2005) are still relevant and have been reiterated within the management community. Understanding and documenting data quality, and when applicable, standardizing best practices for sensor use, continue to be recommended.
Detecting sea-level hazards: Simple regression-based methods for calculating the acceleration of sea level
This report documents the development of statistical tools used to quantify the hazard presented by the response of sea-level elevation to natural or anthropogenic changes in climate and ocean circulation. A hazard is a physical process (or processes) that, when combined with vulnerability (or susceptibility to the hazard), results in risk. This study presents the development and comparison of new and existing sea-level analysis methods, exploration of the strengths and weaknesses of the methods using synthetic time series, and when appropriate, synthesis of the application of the method to observed sea-level time series. These reports are intended to enhance material presented in peer-reviewed journal articles where it is not always possible to provide the level of detail that might be necessary to fully support or recreate published results. The purpose of this report is to document and compare three simple methodologies that have previously been used to provide estimates with associated errors of the acceleration of sea-level elevation. These techniques have been used by coastal scientists and planners in assessing coastal risk over a wide range of spatial and temporal scales. Because relative sea-level (SL) elevation time series contain energetic fluctuations at many time scales, extracting what can be relatively small rate and acceleration signals (along with estimates of the error) from much larger “noise” has proven to be both difficult and controversial. Acceleration is a preferred measure of SL response to recent changes in the Earth’s climate because over time scales of 100 years or less slow vertical land motions (such as glacial isostatic adjustment) contribute only to the linear signal and not to acceleration, thus reducing the complexity of the analysis. Hence acceleration is useful if the goal of a study is to characterize and quantify the hazard associated with the changing relative elevation of water with respect to land on decadal time scales. Although in some cases it may be necessary to determine the cause of relative sea level rise, as a first step, it is important to accurately estimate the magnitude of the threat. Most researchers agree that global sea level (GSL) rose persistently through much of the 20th century at about 1.5–2.0 millimeters per year (mm/yr). There is far less agreement about whether the rate of sea-level rise (SLR) is increasing (that is, an acceleration in SL). Recent studies, and most of their predecessors, use tide gage data to quantify SL acceleration, A SL (t). In the current study, three techniques were used to calculate acceleration from tide gage data, and of those examined, it was determined that the two techniques based on sliding a regression window through the time series are more robust compared to the technique that fits a single quadratic form to the entire time series, particularly if there is temporal variation in the magnitude of the acceleration. The single-fit quadratic regression method has been the most commonly used technique in determining acceleration in tide gage data. The inability of the single-fit method to account for time-varying acceleration may explain some of the inconsistent findings between investigators. Properly quantifying A SL (t) from field measurements is of particular importance in evaluating numerical models of past, present, and future SLR resulting from anticipated climate change.
The role of giant impacts in planet formation
Planets are expected to conclude their growth through a series of giant impacts: energetic, global events that significantly alter planetary composition and evolution. Computer models and theory have elucidated the diverse outcomes of giant impacts in detail, improving our ability to interpret collision conditions from observations of their remnants. However, many open questions remain, as even the formation of the Moon—a widely suspected giant-impact product for which we have the most information—is still debated. We review giant-impact theory, the diverse nature of giant-impact outcomes, and the governing physical processes. We discuss the importance of computer simulations, informed by experiments, for accurately modeling the impact process. Finally, we outline how the application of probability theory and computational advancements can assist in inferring collision histories from observations, and we identify promising opportunities for advancing giant-impact theory in the future. Giant impacts exhibit diverse possible outcomes leading to changes in planetary mass, composition, and thermal history depending on the conditions. Improvements to computer simulation methodologies and new laboratory experiments provide critical insights into the detailed outcomes of giant impacts. When colliding planets are similar in size, they can merge or escape one another with roughly equal probability, but with different effects on their resulting masses, densities, and orbits. Different sequences of giant impacts can produce similar planets, encouraging the use of probability theory to evaluate distinct formation hypothesis.
Climate variability and change in high elevation regions: Past, present & future
This special issue of Climatic Change contains a series of research and review articles, arising from papers that were presented and discussed at a workshop held in Davos, Switzerland on 25–28 June 2001. The workshop was titled ‘Climate Change at High Elevation Sites: Emerging Impacts’, and was convened to reprise an earlier conference on the same subject that was held in Wengen, Switzerland in 1995 (Diaz et al., 1997). The Davos meeting had as its main goals, a discussion of the following key issues: (1) reviewing recent climatic trends in high elevation regions of the world, (2) assessing the reliability of various biological indicators as indicators of climatic change, and (3) assessing whether physical impacts of climatic change in high elevation areas are becoming evident, and to discuss a range of monitoring strategies needed to observe and to understand the nature of any changes.
Model structure of the stream salmonid simulator (S3)—A dynamic model for simulating growth, movement, and survival of juvenile salmonids
Fisheries and water managers often use population models to aid in understanding the effect of alternative water management or restoration actions on anadromous fish populations. We developed the Stream Salmonid Simulator (S3) to help resource managers evaluate the effect of management alternatives on juvenile salmonid populations. S3 is a deterministic stage-structured population model that tracks daily growth, movement, and survival of juvenile salmon. A key theme of the model is that river flow affects habitat availability and capacity, which in turn drives density dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily time series of discharge, water temperature, and usable habitat area or carrying capacity. The physical characteristics of each habitat unit and the number of fish occupying each unit, in turn, drive survival and growth within each habitat unit and movement of fish among habitat units. The purpose of this report is to outline the underlying general structure of the S3 model that is common among different applications of the model. We have developed applications of the S3 model for juvenile fall Chinook salmon ( Oncorhynchus tshawytscha ) in the lower Klamath River. Thus, this report is a companion to current application of the S3 model to the Trinity River (in review). The general S3 model structure provides a biological and physical framework for the salmonid freshwater life cycle. This framework captures important demographics of juvenile salmonids aimed at translating management alternatives into simulated population responses. Although the S3 model is built on this common framework, the model has been constructed to allow much flexibility in application of the model to specific river systems. The ability for practitioners to include system-specific information for the physical stream structure, survival, growth, and movement processes ensures that simulations provide results that are relevant to the questions asked about the population under study.
Contaminant Hazard Reviews. [Reports No. 1-28 on CD-ROM.]
This compact disc (CD) contains the first 28 reports in the Contaminant Hazard Reviews (CHR) that were published originally between 1985 and 1994 in the U.S. Department of the Interior Biological Report series. The CD was produced because printed supplies of these reviews--a total of 84,000--became exhausted and demand remained high. Each review was prepared at the request of environmental specialists of the U.S. Fish and Wildlife Service and each contained specific information on mirex, cadmium, carbofuran, toxaphene, selenium, chromium, polychlorinated biphenyls, dioxins, diazinon, mercury, polycyclic aromatic hydrocarbons, arsenic, chlorpyrifos, lead, tin, index issue, pentachlorophenol, atrazine, molybdenum, boron, chlordane, paraquat, cyanide, fenvalerate, diflubenzuron, zinc, famphur, or acrolein. Each report reviewed and synthesized the technical literature on a single contaminant and its effects on terrestrial plants and invertebrates, aquatic plants and animals, avian and mammalian wildlife, and other natural resources. The subtopics include contaminant sources and uses; physical, chemical, and metabolic properties; concentrations in field collections of abiotic materials and living organisms; deficiency effects, where appropriate; lethal and sublethal effects, including effects on survival, growth, reproduction, metabolism, mutagenicity, teratogenicity, and carcinogenicity; proposed criteria for the protection of human health and sensitive natural resources; and recommendations for additional research.
Contaminant Hazard Reviews (compilation)
This compact disc (CD) contains the 35 reports in the Contaminant Hazard Reviews (CHR) that were published originally between 1985 and 1999 in the U.S. Department of the Interior Biological Report series. The CD was produced because printed supplies of these reviews--a total of 105,000--became exhausted and demand remained high. Each review was prepared at the request of environmental specialists of the U.S. Fish and Wildlife Service and each contained specific information on the following: mirex, cadmium, carbofuran, toxaphene, selenium, chromium, polychlorinated biphenyls, dioxins, diazinon, mercury, polycyclic aromatic hydrocarbons, arsenic, chlorpyrifos, lead, tin, index issue, pentachlorophenol, atrazine, molybdenum, boron, chlordane, paraquat, cyanide, fenvalerate, diflubenzuron, zinc, famphur, acrolein, radiation, sodium monofluoroacetate, planar PCBs, silver, copper, nickel, and a cumulative index to chemicals and species. Each report reviewed and synthesized the technical literature on a single contaminant and its effects on terrestrial plants and invertebrates, aquatic plants and animals, avian and mammalian wildlife, and other natural resources. The subtopics include contaminant sources and uses; physical, chemical, and metabolic properties; concentrations in field collections of abiotic materials and living organisms; deficiency effects, where appropriate; lethal and sublethal effects, including effects on survival, growth, reproduction, metabolism, mutagenicity, teratogenicity, and carcinogenicity; proposed criteria for the protection of human health and sensitive natural resources; and recommendations for additional research.
Volcanological applications of unoccupied aircraft systems (UAS): Developments, strategies, and future challenges
Unoccupied aircraft systems (UAS) are developing into fundamental tools for tackling the grand challenges in volcanology; here, we review the systems used and their diverse applications. UAS can typically provide image and topographic data at two orders of magnitude better spatial resolution than space-based remote sensing, and close-range observations at temporal resolutions down to those of video frame rates. Responsive deployments facilitate dense time-series measurements, unique opportunities for geophysical surveys, sample collection from hostile environments such as volcanic plumes and crater lakes, and emergency deployment of ground-based sensors (and robots) into hazardous regions. UAS have already been used to support hazard management and decision-makers during eruptive crises. As technologies advance, increased system capabilities, autonomy and availability, supported by more diverse and lighter-weight sensors, will offer unparalleled potential for hazard monitoring. UAS are expected to provide opportunities for pivotal advances in our understanding of complex physical and chemical volcanic processes.
Phytoplankton primary production in the world's estuarine-coastal ecosystems
Estuaries are biogeochemical hot spots because they receive large inputs of nutrients and organic carbon from land and oceans to support high rates of metabolism and primary production. We synthesize published rates of annual phytoplankton primary production (APPP) in marine ecosystems influenced by connectivity to land – estuaries, bays, lagoons, fjords and inland seas. Review of the scientific literature produced a compilation of 1148 values of APPP derived from monthly incubation assays to measure carbon assimilation or oxygen production. The median value of median APPP measurements in 131 ecosystems is 185 and the mean is 252 g C m −2 yr −1 , but the range is large: from −105 (net pelagic production in the Scheldt Estuary) to 1890 g C m −2 yr −1 (net phytoplankton production in Tamagawa Estuary). APPP varies up to 10-fold within ecosystems and 5-fold from year to year (but we only found eight APPP series longer than a decade so our knowledge of decadal-scale variability is limited). We use studies of individual places to build a conceptual model that integrates the mechanisms generating this large variability: nutrient supply, light limitation by turbidity, grazing by consumers, and physical processes (river inflow, ocean exchange, and inputs of heat, light and wind energy). We consider method as another source of variability because the compilation includes values derived from widely differing protocols. A simulation model shows that different methods reported in the literature can yield up to 3-fold variability depending on incubation protocols and methods for integrating measured rates over time and depth. Although attempts have been made to upscale measures of estuarine-coastal APPP, the empirical record is inadequate for yielding reliable global estimates. The record is deficient in three ways. First, it is highly biased by the large number of measurements made in northern Europe (particularly the Baltic region) and North America. Of the 1148 reported values of APPP, 958 come from sites between 30 and 60° N; we found only 36 for sites south of 20° N. Second, of the 131 ecosystems where APPP has been reported, 37% are based on measurements at only one location during 1 year. The accuracy of these values is unknown but probably low, given the large interannual and spatial variability within ecosystems. Finally, global assessments are confounded by measurements that are not intercomparable because they were made with different methods. Phytoplankton primary production along the continental margins is tightly linked to variability of water quality, biogeochemical processes including ocean–atmosphere CO 2 exchange, and production at higher trophic levels including species we harvest as food. The empirical record has deficiencies that preclude reliable global assessment of this key Earth system process. We face two grand challenges to resolve these deficiencies: (1) organize and fund an international effort to use a common method and measure APPP regularly across a network of coastal sites that are globally representative and sustained over time, and (2) integrate data into a unifying model to explain the wide range of variability across ecosystems and to project responses of APPP to regional manifestations of global change as it continues to unfold.
Using advanced population genomics to better understand the relationship between offshore and spawning habitat use for Atlantic Sturgeon
Atlantic Sturgeon ( Acipenser oxyrinchus oxyrinchus ) are a large-bodied anadromous fish that historically supported important fisheries along the east coast of the United States. Following years of overharvest and habitat degradation, populations experienced severe declines. In 2012, the National Marine Fisheries Service listed Atlantic Sturgeon under the Endangered Species Act (ESA; 61 FR 4722). Their listing named five Distinct Population Segments (DPSs), predicated on genetic groups composed of geographically proximate populations. Federal management of Atlantic Sturgeon presents challenges, as sturgeon from each of the five DPSs mix extensively in coastal and marine habitats yet take and recovery progress must be evaluated separately for each unit. Genetic assignment testing based on mitochondrial and microsatellite markers allows individuals to be assigned back to their natal river and DPS. However, this approach is not perfect and some individuals may be incorrectly assigned. Recent advances in genomics offer the potential of a higher resolution approach to genetic assignment testing, and thus may reduce uncertainty associated with assignment testing. In addition, genomics allows a greater number of markers to be examined from across a broader portion of the sturgeon genome, thus may provide an enhanced perspective of population structure for the species, and potentially allow other previously intractable questions to be addressed (Bernatchez et al. 2017, Supple and Shapiro 2018). We used next-generation sequencing to develop a draft genome for Atlantic Sturgeon and identify single nucleotide polymorphisms (SNPs) that could be used to resolve the natal river and DPS of individual Atlantic Sturgeon. We identified 1,210 candidate SNPs within the nuclear genome as well as 49 SNPs within the mitochondrial genome. After filtering and review, we selected 161 nuclear SNPs and 39 mitochondrial SNPs for further testing and evaluation. We used genotyping-in-thousands by sequencing (GT-seq) to simultaneously sequence nuclear SNP loci, mitochondrial SNP loci, and the existing panel of twelve microsatellite loci. This effort required a pilot sequencing run on a single sturgeon sample to test marker amplification and refine primer strengths, followed by a series of sequencing runs to generate baseline data for 288 individuals representing nine populations of Atlantic Sturgeon in four DPSs. Using baseline data from the nine populations, we ran a series of genomic analyses to characterize diversity within and among populations, providing a benchmark for this species using the new SNP markers. Allelic richness was similar for all populations, although there was a general trend of more northern population containing greater levels of allelic richness. Interestingly, we observed linkage disequilibrium among many pairs of loci within many populations. This might be the result of physical linkage but could also suggest these populations are recovering from genetic bottlenecks and/or are effectively small, leading to specific haplotypes to be favored by chance. Pairwise differentiation among populations varied among the populations ( F ST range: 0.010-0.098) and was significantly correlated ( r = 0.771; P < 0.001) to pairwise F ST observed using microsatellite markers). Population clustering and ordination techniques using the new genomic data both support an overall population structure that is similar to the current DPS management units (which were developed primarily based on microsatellite genetic data). Overall, this suggests that existing microsatellite markers and the panel of SNP markers developed in this study provide similar information about the populations structure and ecology of Atlantic Sturgeon. Given the observed differences in allele frequencies among populations, our genomic baseline supports previous assertations that Atlantic Sturgeon show natal homing, despite mixing extensively in marine waters during non-breeding periods. Lower levels of differentiation between populations in the South Atlantic DPS suggest that populations in this region may have greater levels of gene flow relative to their more northerly conspecifics, which has also previously been suggested based on microsatellite data. The observed differentiation among populations provides the necessary foundation for determining the natal river and DPS of Atlantic Sturgeon using assignment testing. We tested the utility of our new genomic baseline for resolving the population and DPS of Atlantic Sturgeon. Our nuclear SNP markers showed utility for identifying the origin of unknown Atlantic Sturgeon samples, as 86.5% were assigned to the correct DPS and 66.3% were assigned to the correct natal river. However, since this study was funded the Conservation Genetics and Genomics Laboratory at Leetown Science Center has made significant improvements to their microsatellite genetic baseline, which now performs more effectively than our new genomic approach (the genetic baseline includes 12 populations and 5 DPSs, and correctly assigns 95.8% of individuals to DPS and 84.9% of individuals to their natal population using 12 microsatellite loci). We conducted an ad hoc exploration of how additional microsatellite or nuclear SNP loci may further improve the accuracy of assignment testing. We found that additional microsatellite markers are likely to result in greater improvements in assignment efficiency than additional nuclear SNPs. However, a much larger number of SNP loci (which if identified could be sequenced using other methods that are now available; e.g., the RAD-capture approach published by Ali et al. 2016) could produce assignment efficiencies that are greater than what is currently feasible using microsatellites. In the absence of further research and development of additional SNP markers for Atlantic Sturgeon (possibly using an approach other than GT-seq), the existing microsatellite loci are the most effective means available to determine the natal river and DPS of Atlantic Sturgeon encountered in offshore waters. Because our new genomic markers were less effective than the existing panel of 12 microsatellite markers, we chose to use the existing microsatellite markers to assign Atlantic Sturgeon captured in another BOEM-funded study (cooperative agreement M16AC00003; Monitoring endangered Atlantic Sturgeon and commercial finfish habitat use offshore New York) following consultation with our project officer. Using this approach, we genotyped and assigned 186 Atlantic Sturgeon captured in coastal waters off the Rockaway Peninsula, New York. The vast majority of these sturgeon were assigned to the New York Bight DPS (94.62%), and most appear to belong to the Hudson River population (87.10%) with smaller contributions from the Delaware River population (7.53%). Smaller contributions (2.15%) were observed from six other populations, including those from the James, York, Kennebec, Ogeechee, and Edisto rivers. Although most of the fish we assigned were assigned to the nearest spawning rivers (Hudson and Delaware), the contributions from distant rivers is consistent with the propensity of this species to move long distances and form mixed stock aggregations along the continental shelf. This finding indicates that spawning populations (and their corresponding DPS) from distant locations may potentially be impacted by offshore activities. In fact, activities in this region of the New York Bight could negatively impact Atlantic Sturgeon population from at least four different DPSs. Genetic or genomic assignment testing remains an essential tool to characterize potential impacts to Atlantic Sturgeon populations and should be applied more broadly to better characterize potential impacts of activities in other locations.
Rockslides on the Terminus of "Jokulsargilsjokull", Southern Iceland
On 10 November 1976, a 1.5 km × 0.5 km rockslide deposit on the surface of an unnamed outlet glacier of Mýrdalsjökull ice cap, southern Iceland, was observed from an aircraft. Deposits from two different rockslides, including the larger one observed on 10 November 1976, were visible on a 10 September 1978 aerial photograph of the unnamed outlet glacier. An analysis of vertical and oblique aerial photographs, Landsat images, and seismological records was used to establish the time of occurrence of the larger rockslide to a 30-day period between 9 September 1972 and 9 October 1972. The trigger mechanisms for the rockslide activity appear to have been heavy precipitation prior to the event and the decrease of buttressing mass at the base of the valley wall resulting from recession of the glacier (decrease in width and thickness). The recession led to instability of highly altered hyaloclastite bedrock, talus, and morainal materials on an oversteepened slope. An earthquake as a trigger mechanism was considered to be unlikely from a thorough review of seismic records. Measurements of the downglacier movement of the larger rockslide deposit give an average speed of the glacier as 30±3 m a-1 between September/October 1972 and 10 September 1978. From measurements of aerial photographs taken on 10 September 1978 and 4 September 1984, the average speed of the glacier increased to 45 m a-1 during this 6-year interval. Although the terminus of the unnamed outlet glacier had not yet begun to advance in 1986, it had undergone thickening since 1978.
The Novarupta-Katmai eruption of 1912 - largest eruption of the twentieth century; centennial perspectives
The explosive outburst at Novarupta (Alaska) in June 1912 was the 20th century's most voluminous volcanic eruption. Marking its centennial, we illustrate and document the complex eruptive sequence, which was long misattributed to nearby Mount Katmai, and how its deposits have provided key insights about volcanic and magmatic processes. It was one of the few historical eruptions to produce a collapsed caldera, voluminous high-silica rhyolite, wide compositional zonation (51-78 percent SiO 2 ), banded pumice, welded tuff, and an aerosol/dust veil that depressed global temperature measurably. It emplaced a series of ash flows that filled what became the Valley of Ten Thousand Smokes, sustaining high-temperature metal-transporting fumaroles for a decade. Three explosive episodes spanned ~60 hours, depositing ~17 km 3 of fallout and 11±2 km 3 of ignimbrite, together representing ~13.5 km 3 of zoned magma. No observers were nearby and no aircraft were in Alaska, and so the eruption narrative was assembled from scattered villages and ship reports. Because volcanology was in its infancy and the early investigations (1915-23) were conducted under arduous expeditionary conditions, many provocative misapprehensions attended reports based on those studies. Fieldwork at Katmai was not resumed until 1953, but, since then, global advances in physical volcanology and chemical petrology have gone hand in hand with studies of the 1912 deposits, clarifying the sequence of events and processes and turning the eruption into one of the best studied in the world. To provide perspective on this century-long evolution, we describe the geologic and geographic setting of the eruption - in a remote, sparsely inhabited wilderness; we review the cultural and scientific contexts at the time of the eruption and early expeditions; and we compile a chronology of the many Katmai investigations since 1912. Products of the eruption are described in detail, including eight layers of regionwide fallout, nine packages of ash flows, and three lava domes that followed the explosive pyroclastic episodes. Changes in the proportions of coerupting rhyolite, dacite, and andesite pumice documented for the fallout and ash-flow successions, which are locally interbedded, permit close correlation of those synchronously emplaced sequences and their varied facies. Petrological correlation of the sequence of deposits near Novarupta with ash layers at Kodiak village, 170 km downwind, where three episodes of ashfall were recorded (to the hour), provides key constraints on timing of the eruptive events. Syneruptive collapse of a kilometer-deep caldera took place atop Mount Katmai, a stratovolcano centered 10 km east of the eruption site at Novarupta, owing to drainage of magma from beneath the Katmai edifice. Correlation of ~50 earthquakes recorded at distant seismic stations (including 14 shocks of magnitude 6.0 to 7.0) to fitful caldera collapse provides further constraints on eruption timing, because layers of nonjuvenile breccia and mud ejected from Mount Katmai during collapse pulses are intercalated with the pumice-fall layers from Novarupta. Structure of the Novarupta vent, a 2-km-wide depression backfilled by welded tuff and inferred to be funnel-shaped at depth, is described in detail, as is the 4-km-wide caldera at Mount Katmai. Discussions are also provided concerning: (1) the impact on global climate of the great mass of sulfur-poor but halogen-rich aerosol ejected into the atmosphere by the rhyolite-dominated eruption; (2) chemical and mineralogical effects of the fumarolic acid gases; and (3) the timing of several syneruptive landslide deposits sandwiched within the pumice-fall sequence. Secondary posteruption phenomena characterized include impounded lakes, ash-rich debris flows, phreatic craters on the ignimbrite sheet, responses of glaciers to the fallout blanket and to beheading by caldera collapse, growth of new glaciers inside the caldera, and gradual filling of the caldera lake. Structure, composition, and ages of the several andesite-dacite stratovolcanoes, closely clustered near Novarupta, all of which remain fumarolically and seismically active, are summarized. But among them only Mount Katmai extends compositionally to include basalt and rhyolite. The petrological affinities of 1912 magmas erupted at Novarupta with pre-1912 Katmai lavas are outlined, and various chemical, mineralogical, isotopic, and experimental data are assembled to construct a model of preeruptive magma storage beneath Mount Katmai. The monograph concludes by comparing the 1912 eruption with several other well-studied large explosive eruptions, 14 of them historical and 9 prehistoric. Finally, we retrospectively review the historical difficulties in understanding what had actually taken place at Katmai in 1912 and the century of progress in volcano science that has allowed most of it to be figured out.
Integrating remote sensing and ground methods to estimate evapotranspiration
Evapotranspiraton (ET) is the second largest term in the terrestrial water budget after precipitation, and ET is expected to increase with global warming. ET studies are relevant to the plant sciences because over 80% of terrestrial ET is due to transpiration by plants. Remote sensing is the only feasible means for projecting ET over large landscape units. In the past decade or so, new ground and remote sensing tools have dramatically increased our ability to measure ET at the plot scale and to scale it over larger regions. Moisture flux towers and micrometeorological stations have been deployed in numerous natural and agricultural biomes and provide continuous measurements of actual ET or potential ET with an accuracy or uncertainty of 10–30%. These measurements can be scaled to larger landscape units using remotely-sensed vegetation indices (VIs), Land Surface Temperature (LST), and other satellite data. Two types of methods have been developed. Empirical methods use time-series VIs and micrometeorological data to project ET measured on the ground to larger landscape units. Physically-based methods use remote sensing data to determine the components of the surface energy balance, including latent heat flux, which determines ET. Errors in predicting ET by both types of methods are within the error bounds of the flux towers by which they are calibrated or validated. However, the error bounds need to be reduced to 10% or less for applications that require precise wide-area ET estimates. The high fidelity between ET and VIs over agricultural fields and natural ecosystems where precise ground estimates of ET are available suggests that this might be an achievable goal if ground methods for measuring ET continue to improve.