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USGS2011

Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics

Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods’ effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance

International Journal of Molecular Sciences↗

USGS2007

Publications of the Western Earth Surfaces Processes Team 2005

Introduction The Western Earth Surface Processes Team (WESPT) of the U.S. Geological Survey (USGS) conducts geologic mapping, earth-surface process investigations, and related topical earth science studies in the western United States. This work is focused on areas where modern geologic maps and associated earth-science data are needed to address key societal and environmental issues such as ground-water quality, landslides and other potential geologic hazards, and land-use decisions. Areas of primary emphasis in 2005 included southern California, the San Francisco Bay region, the Mojave Desert, the Colorado Plateau region of northern Arizona, and the Pacific Northwest. The team has its headquarters in Menlo Park, California, and maintains smaller field offices at several other locations in the western United States. The results of research conducted by the WESPT are released to the public as a variety of databases, maps, text reports, and abstracts, both through the internal publication system of the USGS and in diverse external publications such as scientific journals and books. This report lists publications of the WESPT released in 2005 as well as additional 2002, 2003, and 2004 publications that were not included in the previous lists (USGS Open-File Reports 03-363, 2004- 1267, 2005-1362). Most of the publications listed were authored or coauthored by WESPT staff. The list also includes some publications authored by non-USGS cooperators with the WESPT, as well as some authored by USGS staff outside the WESPT in cooperation with WESPT projects. Several of the publications listed are available on the World Wide Web; for these, URL addresses are provided. Many of these web publications are USGS Open-File reports that contain large digital databases of geologic map and related information. Information on ordering USGS publications can be found on the World Wide Web at http://www.usgs.gov/pubprod/, or by calling 1-888-ASK-USGS. The U.S. Geological Survey's web server for geologic information in the western United States is located at http://geology.wr.usgs.gov/. More information is available about the WESPT is available on-line at http://geology.wr.usgs.gov/wgmt.

Open-File Report↗

USGS2000

A new approach toward evaluation of fish bioenergetics models

A new approach was used to evaluate the Wisconsin bioenergetics model for lake trout ( Salvelinus namaycush ). Lake trout in laboratory tanks were fed alewife ( Alosa pseudoharengus ) and rainbow smelt ( Osmerus mordax ), prey typical of lake trout in Lake Michigan. Food consumption and growth by lake trout during the experiment were measured. Polychlorinated biphenyl (PCB) concentrations of the alewife and rainbow smelt, as well as of the lake trout at the beginning and end of the experiment, were determined. From these data, we calculated that lake trout retained 81% of the PCBs contained within their food. In an earlier study, application of the Wisconsin lake trout bioenergetics model to growth and diet data for lake trout in Lake Michigan, in conjunction with PCB data for lake trout and prey fish from Lake Michigan, yielded an estimate of PCB assimilation efficiency from food of 81%. This close agreement in the estimates of efficiency with which lake trout retain PCBs from their food indicated that the bioenergetics model was furnishing accurate predictions of food consumption by lake trout in Lake Michigan.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2007

SHRIMP U-Pb evidence for a Late Silurian age of metasedimentary rocks in the Merrimack and Putnam-Nashoba terranes, eastern New England

U-Pb ages of detrital, metamorphic, and magmatic zircon and metamorphic monazite and titanite provide evidence for the ages of deposition and metamorphism of metasedimentary rocks from the Merrimack and Putnam-Nashoba terranes of eastern New England. Rocks from these terranes are interpreted here as having been deposited in the middle Paleozoic above Neoproterozoic basement of the Gander terrane and juxtaposed by Late Paleozoic thrusting in thin, fault-bounded slices. The correlative Hebron and Berwick formations (Merrimack terrane) and Tatnic Hill Formation (Putnam-Nashoba terrane), contain detrital zircons with Mesoproterozoic, Ordovician, and Silurian age populations. On the basis of the age of the youngest detrital zircon population (???425 Ma), the Hebron, Berwick and Tatnic Hill formations are no older than Late Silurian (Wenlockian). The minimum deposition ages of the Hebron and Berwick are constrained by ages of cross-cutting plutons (414 ?? 3 and 418 ?? 2 Ma, respectively). The Tatnic Hill Formation must be older than the oldest metamorphic monazite and zircon (???407 Ma). Thus, all three of these units were deposited between ???425 and 418 Ma, probably in the Ludlovian. Age populations of detrital zircons suggest Laurentian and Ordovician arc provenance to the west. High grade metamorphism of the Tatnic Hill Formation soon after deposition probably requires that sedimentation and burial occurred in a fore-arc environment, whereas time-equivalent calcareous sediments of the Hebron and Berwick formations probably originated in a back-arc setting. In contrast to age data from the Berwick Formation, the Kittery Formation contains primarily Mesoproterozoic detrital zircons; only 2 younger grains were identified. The absence of a significant Ordovician population, in addition to paleocurrent directions from the east and structural data indicating thrusting, suggest that the Kittery was derived from peri-Gondwanan sources and deposited in the Fredericton Sea. Thus, the Kittery should not be considered part of the Laurentian-derived Merrimack terrane; it more likely correlates with the early Silurian Fredericton terrane of northeastern New England and Maritime Canada.

American Journal of Science↗

USGS2002

A pitfall in shallow shear-wave refraction surveying

The shallow shear-wave refraction method works successfully in an area with a series of horizontal layers. However, complex near-surface geology may not fit into the assumption of a series of horizontal layers. That a plane SH-wave undergoes wave-type conversion along an interface in an area of nonhorizontal layers is theoretically inevitable. One real example shows that the shallow shear-wave refraction method provides velocities of a converted wave rather than an SH- wave. Moreover, it is impossible to identify the converted wave by refraction data itself. As most geophysical engineering firms have limited resources, an additional P-wave refraction survey is necessary to verify if velocities calculated from a shear-wave refraction survey are velocities of converted waves. The alternative at this time may be the surface wave method, which can provide reliable S-wave velocities, even in an area of velocity inversion (a higher velocity layer underlain by a lower velocity layer). ?? 2002 Elsevier Science B.V. All rights reserved.

Journal of Applied Geophysics↗

USGS2018

Featured collection introduction: Connectivity of streams and wetlands to downstream waters

Connectivity is a fundamental but highly dynamic property of watersheds. Variability in the types and degrees of aquatic ecosystem connectivity presents challenges for researchers and managers seeking to accurately quantify its effects on critical hydrologic, biogeochemical, and biological processes. However, protecting natural gradients of connectivity is key to protecting the range of ecosystem services that aquatic ecosystems provide. In this featured collection, we review the available evidence on connections and functions by which streams and wetlands affect the integrity of downstream waters such as large rivers, lakes, reservoirs, and estuaries. The reviews in this collection focus on the types of waters whose protections under the U.S. Clean Water Act have been called into question by U.S. Supreme Court cases. We synthesize 40+ years of research on longitudinal, lateral, and vertical fluxes of energy, material, and biota between aquatic ecosystems included within the Act's frame of reference. Many questions about the roles of streams and wetlands in sustaining downstream water integrity can be answered from currently available literature, and emerging research is rapidly closing data gaps with exciting new insights into aquatic connectivity and function at local, watershed, and regional scales. Synthesis of foundational and emerging research is needed to support science‐based efforts to provide safe, reliable sources of fresh water for present and future generations.

Journal of the American Water Resources Associatio↗

USGS2001

Nomad Rover field experiment, Atacama Desert, Chile 1. Science results overview

Nomad was deployed for a 45 day traverse in the Atacama Desert, Chile, during the summer of 1997. During this traverse, 1 week was devoted to science experiments. The goal of the science experiments was to test different planetary surface exploration strategies that included (1) a Mars mission simulation, (2) a science on the fly experiment, where the rover was kept moving 75% of the operation time. (The goal of this operation was to determine whether or not successful interpretation of the environment is related to the time spent on a target. The role of mobility in helping the interpretation was also assessed.) (3) a meteorite search using visual and instrumental methods to remotely identify meteorites in extreme environments, and (4) a time-delay experiment with and without using the panospheric camera. The results were as follow: the remote science team positively identified the main characteristics of the test site geological environment. The science on the fly experiment showed that the selection of appropriate targets might be even more critical than the time spent on a study area to reconstruct the history of a site. During the same operation the science team members identified and sampled a rock from a Jurassic outcrop that they proposed to be a fossil. The presence of paleolife indicators in this rock was confirmed later by laboratory analysis. Both visual and instrumental modes demonstrated the feasibility, in at least some conditions, of carrying out a field search for meteorites by using remote-controlled vehicles. Finally, metrics collected from the observation of the science team operations, and the use team members made of mission data, provided critical information on what operation sequences could be automated on board rovers in future planetary surface explorations.

Atacama Desert↗

USGS2016

Transport of atrazine and dicamba through silt and loam soils

The objectives of this research were to determine the role of preferential flow paths in the transport of atrazine (2-chloro-4-(ethylamino)-6-(isopropylamino)-s-triazine) and dicamba (3-6-dichloro-2-methoxybenzoic acid) through silt and loam soils overlying the High Plains aquifer in Nebraska. In a previous study, 3 of 6 study areas demonstrated high percentages of macropores; those three areas were used in this study for analysis of chemical transport. As a subsequent part of the study, 12 intact soil cores (30-cm diameter by 40-cm height), were excavated sequentially, two from each of the following depths: 0-40cm and 40-80cm. These cores were used to study preferential flow characteristics using dye staining and to determine hydraulic properties. Two undisturbed experimental field plots, each with a 3-m2 surface area, were installed in three study areas in Nebraska. Each was instrumented with suction lysimeters and tensiometers at depths of 10cm to 80cm in 10-cm increments. Additionally, each plot was planted with corn (Zea mays). A neutron probe access tube was installed in each plot to determine soil w ater content at 15-cm intervals. All plots were enclosed w ith a raised frame (of 8-cm height) to prevent surface runoff. All suction lysimeters were purged monthly for three months and were sampled immediately prior to pre-plant herbicide application to obtain background chemical concentrations. Atrazine and dicamba moved rapidly through the soil, but only after a heavy rainfall event, probably owing to the presence of preferential flow paths and lack of microbial degradation in these soil areas. Staining of laboratory cores showed a positive correlation between the percent area stained by depth and the subsequent breakthrough of Br- in the laboratory and leaching of field-applied herbicides owing to large rainfall events. Suction lysimeter samples in the field showed increases in concentrations of herbicides at depths where laboratory data indicated greater percentages of what appeared to be preferential flow paths. Concentrations of atrazine and dicamba exceeding 0.30 and 0.05µg m1-1 were observed at depths of 10-30cm and 50-70cm after two months following heavy rainfall events. It appears from the laboratory experiment that preferential flow paths were a significant factor in transport of atrazine and dicamba.

Nebraska↗

USGS2010

Soil organic carbon stocks in Alaska estimated with spatial and pedon data

Temperatures in high-latitude ecosystems are increasing faster than the average rate of global warming, which may lead to a positive feedback for climate change by increasing the respiration rates of soil organic C. If a positive feedback is confirmed, soil C will represent a source of greenhouse gases that is not currently considered in international protocols to regulate C emissions. We present new estimates of the stocks of soil organic C in Alaska, calculated by linking spatial and field data developed by the USDA NRCS. The spatial data are from the State Soil Geographic database (STATSGO), and the field and laboratory data are from the National Soil Characterization Database, also known as the pedon database. The new estimates range from 32 to 53 Pg of soil organic C for Alaska, formed by linking the spatial and field data using the attributes of Soil Taxonomy. For modelers, we recommend an estimation method based on taxonomic subgroups with interpolation for missing areas, which yields an estimate of 48 Pg. This is a substantial increase over a magnitude of 13 Pg estimated from only the STATSGO data as originally distributed in 1994, but the increase reflects different estimation methods and is not a measure of the change in C on the landscape. Pedon samples were collected between 1952 and 2002, so the results do not represent a single point in time. The linked databases provide an improved basis for modeling the impacts of climate change on net ecosystem exchange.

Soil Science Society of America Journal↗

USGS2003

The saturated zone at Yucca Mountain: An overview of the characterization and assessment of the saturated zone as a barrier to potential radionuclide migration

The US Department of Energy is pursuing Yucca Mountain, Nevada, for the development of a geologic repository for the disposal of spent nuclear fuel and high-level radioactive waste, if the repository is able to meet applicable radiation protection standards established by the US Nuclear Regulatory Commission and the US Environmental Protection Agency (EPA). Effective performance of such a repository would rely on a number of natural and engineered barriers to isolate radioactive waste from the accessible environment. Groundwater beneath Yucca Mountain is the primary medium through which most radionuclides might move away from the potential repository. The saturated zone (SZ) system is expected to act as a natural barrier to this possible movement of radionuclides both by delaying their transport and by reducing their concentration before they reach the accessible environment. Information obtained from Yucca Mountain Site Characterization Project activities is used to estimate groundwater flow rates through the site-scale SZ flow and transport model area and to constrain general conceptual models of groundwater flow in the site-scale area. The site-scale conceptual model is a synthesis of what is known about flow and transport processes at the scale required for total system performance assessment of the site. This knowledge builds on and is consistent with knowledge that has accumulated at the regional scale but is more detailed because more data are available at the site-scale level. The mathematical basis of the site-scale model and the associated numerical approaches are designed to assist in quantifying the uncertainty in the permeability of rocks in the geologic framework model and to represent accurately the flow and transport processes included in the site-scale conceptual model. Confidence in the results of the mathematical model was obtained by comparing calculated to observed hydraulic heads, estimated to measured permeabilities, and lateral flow rates calculated by the site-scale model to those calculated by the regional-scale flow model. In addition, it was confirmed that the flow paths leaving the region of the potential repository are consistent with those inferred from gradients of measured head and those independently inferred from water-chemistry data. The general approach of the site-scale SZ flow and transport model analysis is to calculate unit breakthrough curves for radionuclides at the interface between the SZ and the biosphere using the three-dimensional site-scale SZ flow and transport model. Uncertainties are explicitly incorporated into the site-scale SZ flow and transport abstractions through key parameters and conceptual models. ?? 2002 Elsevier Science B.V. All rights reserved.

Journal of Contaminant Hydrology↗

USGS2006

New insights into the history and origin of the southern Maya block, SE Mexico: U-Pb-SHRIMP zircon geochronology from metamorphic rocks of the Chiapas massif

The histories of the pre-Mesozoic landmasses in southern México and their connections with Laurentia, Gondwana, and among themselves are crucial for the understanding of the Late Paleozoic assembly of Pangea . The Permian igneous and metamorphic rocks from the Chiapas massif as part of the southern Maya block, México, were dated by U–Pb zircon geochronology employing the SHRIMP (sensitive high resolution ion microprobe) facility at Stanford University. The Chiapas massif is composed of deformed granitoids and orthogneisses with inliers of metasedimentary rocks. SHRIMP data from an anatectic orthogneiss demonstrate that the Chiapas massif was part of a Permian (&sim; 272 Ma) active continental margin established on the Pacific margin of Gondwana after the Ouachita orogeny. Latest Permian (252–254 Ma) medium- to high-grade metamorphism and deformation affected the entire Chiapas massif, resulting in anatexis and intrusion of syntectonic granitoids. This unique orogenic event is interpreted as the result of compression due to flat subduction and accretionary tectonics. SHRIMP data of zircon cores from a metapelite from the NE Chiapas massif yielded a single Grenvillian source for sediments. The majority of the zircon cores from a para-amphibolite from the SE part of the massif yielded either 1.0–1.2 or 1.4–1.5 Ga sources, indicating provenance from South American Sunsás and Rondonian-San Ignacio provinces.

Maya block↗

USGS2021

Tide gates form physical and ecological obstacles to river herring (Alosa spp.) spawning migrations

River herring ( Alosa spp.) are anadromous fish that enter North American Atlantic coastal rivers and lakes each spring to spawn. Anthropogenic structures such as dams and tide gates serve as physical obstacles that limit river herring access to spawning habitat. This study examined the physical and ecological components affecting herring passage through a tide gate by applying a time-to-event analysis framework to multiple movement behaviors derived from telemetry data. Herring had higher passage success early in the season (78%) than later (16%). Key behaviors that govern passage varied with diel period, tide, and flow direction through the gates. Furthermore, these behaviors shifted as the season progressed, consistent with the hypothesis that predator avoidance may be driving passage failure late in the spawning season.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2022

Joint-species analysis reveals potential displacement of native fishes by non-native fishes within the Santa Ana River, California

Accurate estimates of abundance are a cornerstone for resource managers to make effective decisions for fish conservation. However, multiple sampling methods often are required to sample fish communities, and ignoring the detection process can create substantial bias in latent state parameter estimation (e.g., abundance, survival). We developed a joint-species N -mixture model that integrated snorkel, seining, and electrofishing surveys to estimate factors affecting native and non-native fish distributions in the Santa Ana River, California. We found through data integration that native Santa Ana sucker ( Catostomus santaanae ) and arroyo chub ( Gila orcuttii ) were most abundant in wide stream channels, and the abundance of both native fishes were negatively correlated with non-native largemouth bass ( Micropterus salmoides ). Our results highlight the power of integrating multiple data sets into a single analysis and incorporating among-species correlation into abundance modeling. Our results also highlight a pattern of native fish declines that coincides with an expanding largemouth bass population, a concern for the management of native aquatic communities within the Santa Ana River.

California↗

USGS1983

Discovery of a Late Triassic basin north of Boston and some implications as to post-Paleozoic tectonics in northeastern Massachusetts (USA)

As deduced from various data the Triassic-Jurassic Middleton basin-trends NE and is probably approx 5.7km in length and no >0.5km in width. Two sets of dikes which have been K/Ar dated as Late Triassic-Early Jurassic have the same NNE strikes as strike-slip faults. There are indications that a tectonic event of some importance may have occurred in Middle Mesozoic time. -from Author

Massachusetts↗

USGS2024

Using open-science workflow tools to produce SCEC CyberShake physics-based probabilistic seismic hazard models

The Statewide (formerly Southern) California Earthquake Center (SCEC) conducts multidisciplinary earthquake system science research that aims to develop predictive models of earthquake processes, and to produce accurate seismic hazard information that can improve societal preparedness and resiliency to earthquake hazards. As part of this program, SCEC has developed the CyberShake platform, which calculates physics-based probabilistic seismic hazard analysis (PSHA) models for regions with high-quality seismic velocity and fault models. The CyberShake platform implements a sophisticated computational workflow that includes over 15 individual codes written by 6 developers. These codes are heterogeneous, ranging from short-running high-throughput serial CPU codes to large, long-running, parallel GPU codes. Additionally, CyberShake simulation campaigns are computationally extensive, typically producing tens of terabytes of meaningful scientific data and metadata over several months of around-the-clock execution on leadership-class supercomputers. To meet the needs of the CyberShake platform, we have developed an extreme-scale workflow stack, including the Pegasus Workflow Management System, HTCondor, Globus, and custom tools. We present this workflow software stack and identify how the CyberShake platform and supporting tools enable us to meet a variety of challenges that come with large-scale simulations, such as automated remote job submission, data management, and verification and validation. This platform enabled us to perform our most recent simulation campaign, CyberShake Study 22.12, from December 2022 to April 2023. During this time, our workflow tools executed approximately 32,000 jobs, and used up to 73% of the Summit system at Oak Ridge Leadership Computing Facility. Our workflow tools managed about 2.5 PB of total temporary and output data, and automatically staged 19 million output files totaling 74 TB back to archival storage on the University of Southern California's Center for Advanced Research Computing systems, including file-based relational data and large binary files to efficiently store millions of simulated seismograms. CyberShake extreme-scale workflows have generated simulation-based probabilistic seismic hazard models that are being used by seismological, engineering, and governmental communities.

Frontiers Earth Science Journal↗

USGS2026

Subsurface water ice mapping on Mars: A probabilistic approach

Subsurface water ice deposits on Mars are an important resource for potential future human exploration. They are also an indicator of the planet’s past climate. However, the distribution of subsurface water ice in Mars’s midlatitudes is uncertain because spacecraft imagery cannot directly observe subsurface ice in most cases. Various spacecraft remote sensing instruments are sensitive to subsurface water ice, including thermal imaging spectrometers, radar sounders, and neutron spectrometers. Geomorphic analyses of images can also implicate subsurface ice. Building upon the data products from the Mars Subsurface Water Ice Mapping project, we provide a probabilistic framework to jointly interpret existing data and estimate the likelihood of subsurface water ice in the Martian midlatitudes between 60 ∘ S and 60 ∘ N with uncertainty. Broadly, we find that near-surface ice is likely present poleward of ∼45 ∘ in both the northern and southern hemispheres. However, closer to the equator, existing remote sensing data cannot uniquely constrain the presence of subsurface water ice. Our probabilistic results provide a framework for quantifying the abundance of ice on Mars, and our uncertainty estimates allow future analysis and exploration to target regions of high uncertainty.

Planetary Science Journal↗

USGS2002

Survival models for harvest management of mourning dove populations

Quantitative models of the relationship between annual survival and harvest rate of migratory game-bird populations are essential to science-based harvest management strategies. I used the best available band-recovery and harvest data for mourning doves (Zenaida macroura) to build a set of models based on different assumptions about compensatory harvest mortality. Although these models suffer from lack of contemporary data, they can be used in development of an initial set of population models that synthesize existing demographic data on a management-unit scale, and serve as a tool for prioritization of population demographic information needs. Credible harvest management plans for mourning dove populations will require a long-term commitment to population monitoring and iterative population analysis.

Journal of Wildlife Management↗

USGS2015

Movement analysis of free-grazing domestic ducks in Poyang Lake, China: A disease connection

Previous work suggests domestic poultry are important contributors to the emergence and transmission of highly pathogenic avian influenza throughout Asia. In Poyang Lake, China, domestic duck production cycles are synchronized with arrival and departure of thousands of migratory wild birds in the area. During these periods, high densities of juvenile domestic ducks are in close proximity to migratory wild ducks, increasing the potential for the virus to be transmitted and subsequently disseminated via migration. In this paper, we use GPS dataloggers and dynamic Brownian bridge models to describe movements and habitat use of free-grazing domestic ducks in the Poyang Lake basin and identify specific areas that may have the highest risk of H5N1 transmission between domestic and wild birds. Specifically, we determine relative use by free-grazing domestic ducks of natural wetlands, which are the most heavily used areas by migratory wild ducks, and of rice paddies, which provide habitat for resident wild ducks and lower densities of migratory wild ducks. To our knowledge, this is the first movement study on domestic ducks, and our data show potential for free-grazing domestic ducks from farms located near natural wetlands to come in contact with wild waterfowl, thereby increasing the risk for disease transmission. This study provides an example of the importance of movement ecology studies in understanding dynamics such as disease transmission on a complicated landscape.

Poyang Lake↗