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USGS1999

Computer Program for Point Location And Calculation of ERror (PLACER)

A program designed for point location and calculation of error (PLACER) was developed as part of the Quality Assurance Program of the Federal Highway Administration/U.S. Geological Survey (USGS) National Data and Methodology Synthesis (NDAMS) review process. The program provides a standard method to derive study-site locations from site maps in highwayrunoff, urban-runoff, and other research reports. This report provides a guide for using PLACER, documents methods used to estimate study-site locations, documents the NDAMS Study-Site Locator Form, and documents the FORTRAN code used to implement the method. PLACER is a simple program that calculates the latitude and longitude coordinates of one or more study sites plotted on a published map and estimates the uncertainty of these calculated coordinates. PLACER calculates the latitude and longitude of each study site by interpolating between the coordinates of known features and the locations of study sites using any consistent, linear, user-defined coordinate system. This program will read data entered from the computer keyboard and(or) from a formatted text file, and will write the results to the computer screen and to a text file. PLACER is readily transferable to different computers and operating systems with few (if any) modifications because it is written in standard FORTRAN. PLACER can be used to calculate study site locations in latitude and longitude, using known map coordinates or features that are identifiable in geographic information data bases such as USGS Geographic Names Information System, which is available on the World Wide Web.

Open-File Report↗

USGS2010

Seismology of the continental crust and upper mantle

More seismological studies of the continental crust and sub‐crustal lithosphere of the United States have been completed in the past four years than at any other similar period, and a continued growth in activity is likely to continue for years to come. Several trends account for this phenomenon. First, the interest in seismic reflection studies generated initially by COCORP results in this country [ Brown and others , 1986], and later by the British BIRPS results [ Matthews and Gheadie , 1986], has led to the development of several other seismic reflection programs. Among the most active of these research programs are those of the University of Wyoming [ Smithson and others , 1986], Virginia Polytechnic Institute, CALCRUST [ Henyey , 1986], and the U.S. Geological Survey (USGS) [ Hamilton , 1986]. In Canada, the Lithoprobe program has achieved remarkable results in a variety of geographic locations [ Green et al. , 1986]. A second trend is the resurgence of interest in seismic‐refraction/wide‐angle reflection profiling. The year 1978 marked the beginning of this increased activity when several large projects were conducted in the western U.S., such as the Yellowstone‐Snake River Plain experiment organized by the University of Utah. Since 1979, a large amount of refraction/wide‐angle reflection data has been collected by the USGS and by university groups utilizing large numbers of state‐of‐the‐art industry seismographs in cooperative experiments. A third trend is the increased sophistication of other seismic methods such as teleseismic delay‐time methods, tomography, and receiver‐transfer functions. In these studies, permanent or temporary recording arrays have been used to determine local and regional crustal and upper‐mantle structure with impressive resolution.

Reviews of Geophysics↗

USGS2020

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.

Atlantic Coast↗

USGS2009

A historical perspective on the "fish tumors or other deformities" beneficial use impairment at Great Lakes Areas of Concern

The Great Lakes Water Quality Agreement defines Areas of Concern as geographic areas that fail to meet the general or specific objectives of the agreement where such failure has caused or is likely to cause impairment of beneficial use of the area's ability to support aquatic life. One of the beneficial use impairments, fish tumors or other deformities, is defined by the International Joint Commission to occur when the incidence rate of fish tumors and other deformities exceeds rates at unimpacted or control sites, or when survey data confirm the presence of neoplastic or preneoplastic liver tumors in bullhead or suckers. Brown bullhead, a benthic species with a limited home range, have frequently been used as indicator species in U.S. Areas of Concern. While there is strong field evidence for an association between PAH exposure and hepatic neoplasia in brown bullhead, laboratory investigations would strengthen the association. There is less evidence linking specific classes of chemicals in the environment to orocutaneous neoplasia in brown bullhead. Studies on orocutaneous neoplasia of brown bullhead should focus on assessing the presence or absence of viruses and on epidermal exposure to specific chemicals and chemical mixtures. Lastly, the effects of covariates such as length, age, and gender on the prevalence of liver and skin neoplasms should be investigated. This paper reviews the state of science on the fish tumors or other deformities beneficial use impairment. Subsequent papers address specific issues related to this impairment and provide recommendations for standardized criteria.

Journal of Great Lakes Research↗

USGS2019

On the eruption age and provenance of the Old Crow tephra

Tephrochronology is used to correlate and reconstruct geographically disparate sedimentary records of changing environment, climate, and landscape throughout geologic time. Single tephra layers represent isochronous markers across broad regions, thus accurate and precise radiometric constraints on the timing of eruption are critical to their utility. The Old Crow tephra is found throughout eastern Beringia and represents the largest preserved Pleistocene ashfall event in the region. Despite its volume and significance as a stratigraphic marker, the provenance of this tephra is debated, and the interpreted eruption age of marine isotope stage (MIS) 5 at ∼125 ka has vacillated. To investigate provenance and eruption age, we develop a geochemical fingerprint for the Old Crow tephra via titanomagnetite geochemistry, and zircon crystallization/cooling age via coupled U/Pb, U/Th, and (U Th)/He zircon geochronology. Our results indicate that Old Crow oxides are geochemically distinct from the commonly assumed source-caldera system at the Emmons Lake Volcanic Center (ELVC). Zircon crystals from the Old Crow tephra range in age from Proterozoic to Pleistocene, with concordant zircon U/Pb, U/Th, and (U Th)/He dates on the youngest population of grains suggesting crystallization in their parent magma, and in turn eruption, at 202.9 ± 9.5 ka. We discuss strengths and shortcomings of our radiogenic datasets in light of this result and review the far-reaching implications of a change in Old Crow eruption age.

Alaska↗

USGS2015

Final project memorandum: sea-level rise modeling handbook: resource guide for resource managers, engineers, and scientists

Coastal wetlands of the Southeastern United States are undergoing retreat and migration from increasing tidal inundation and saltwater intrusion attributed to climate variability and sea-level rise. Much of the literature describing potential sea-level rise projections and modeling predictions are found in peer-reviewed academic journals or government technical reports largely suited to reading by other Ph.D. scientists who are more familiar or engaged in the climate change debate. Various sea-level rise and coastal wetland models have been developed and applied of different designs and scales of spatial and temporal complexity for predicting habitat and environmental change that have not heretofore been synthesized to aid natural resource managers of their utility and limitations. Training sessions were conducted with Federal land managers with U.S. Fish and Wildlife Service, National Park Service, and NOAA National Estuarine Research Reserves as well as state partners and nongovernmental organizations across the northern Gulf Coast from Florida to Texas to educate and to evaluate user needs and understanding of concepts, data, and modeling tools for projecting sea-level rise and its impact on coastal habitats and wildlife. As a result, this handbook was constructed from these training and feedback sessions with coastal managers and biologists of published decision-support tools and simulation models for sea-level rise and climate change assessments. A simplified tabular context was developed listing the various kinds of decision-support tools and ecological models along with criteria to distinguish the source, scale, and quality of information input and geographic data sets, physical and biological constraints and relationships, datum characteristics of water and land elevation components, utility options for setting sea-level rise and climate change scenarios, and ease or difficulty of storing, displaying, or interpreting model output. The handbook is designed to be a primer to understanding sea-level rise and a practical synthesis of the current state of knowledge and modeling tools as a resource guide for DOl land management needs and facilitating Landscape Conservation Cooperative (LCC) research and conservation initiatives.

Conference Paper↗

USGS2012

User’s guide and metada for the PICES Nonindigenous Species Information System

Introduction Welcome to the PICES Nonindigenous Species Information System, a Microsoft Access database that displays the biogeographic distributions, invasion status, vectors, and key life history attributes of the approximately 740 reported nonindigenous species (NIS) in the estuarine and near-coastal habitats of the North Pacific and Hawaii. This database was developed by the U.S. Environmental Protection Agency and the U.S. Geological Survey under the auspices of Working Group 21 (Invasive Species) of the North Pacific Marine Science Organization (PCIES). The PICES database contains the data used to generate the “Atlas of Nonindigenous Marine and Estuarine Species in the North Pacific” (Lee and Reusser, 2012; herein referred to as the “Atlas”). The User’s Guide provides instructions on how to use the PICES database as well as metadata for the database and the Atlas. We note that for most users, the Atlas provides a simpler approach to accessing key information on NIS in the PICES countries than the database, though the database does provide additional information on species and sources as well as allowing users to extract information on specific taxa and/or locations (see Section 4). The PICES database also includes species reported from the PICES Rapid Assessment Surveys (RAS). PICES sponsored four rapid assessment surveys with the objective of quickly characterizing the native, non-native, and cryptogenic species present in different locations. Surveys were sponsored in Dalian, China in 2008, Jeju, Korea in 2009, Newport, Oregon, USA in 2010, and Peter the Great Bay, near Vladivostok and Nakhodka, Russia in 2011 ( http://www.pices.int/publications/pices_press/volume19/v19_n1/pp_30-31_Kobe-WS_f.pdf , http://www.pices.int/publications/pices_press/volume20/v20_n1/pp_26-29_RAS-2011.pdf ). The PICES database contains the RAS species that were made available in time for inclusion. Thus, the database does not capture all the species found in these surveys. In addition, much of the information on the RAS species was provided by the experts conducting the survey, and their distributions, environmental requirements, and life history attributes were not evaluated to the same level of detail by the PICES authors as the North Pacific NIS. In lieu of the more extensive review as conduced with the Atlas species, the information on the RAS species needs to be considered preliminary. Additionally, it is important to use the “Map All Distributions” option (see Section 3.6.6) when mapping their distribution or conducting a query. The general reference for the RAS surveys in the PICES database is “PICES Working Group 21, YEAR SURVEY”. The overall goal of both the database and Atlas was to simplify and standardize the dissemination of distributional, habitat, and life history characteristics of near-coastal and estuarine nonindigenous species. This database provides a means of querying these data and displaying the information in a consistent format. The specific classes of information the database captures include: Regional and global ranges of native and nonindigenous near-coastal and estuarine species at different hierarchical spatial scales. Habitat and physiological requirements of near-coastal and estuarine species. Life history characteristics of near-coastal and estuarine species. Invasion history and vectors for nonindigenous species. This standardized and synthesized data in the database and the Atlas provide the basic information needed to address a number of managerial and scientific needs. Thus, users will be able to: Create a baseline on the extent of invasion by region in order to assess new invasions. Use existing geographical patterns of invasion to gain some insights into potential new invaders. Use existing geographical patters of invasion to gain some insights into mechanisms affecting relative invasibility of different areas. Use life history attributes and environmental requirements of the reported nonindigenous species to evaluate traits of invaders. Understand the potential spread of invaders based on their habitat and environmental requirements. Understand importance of different vectors of introduction of nonindigenous species by region. The data in the Atlas of Nonindigenous Marine and Estuarine Species in the North Pacific (Lee and Reusser, 2012) are up-to-date as of June 2012. Updates to the PICES database were made in September 2012.

Report↗

USGS2015

U.S. Geological Survey National Water Census: Colorado River Basin Geographic Focus Area Study

Introduction The U.S. Geological Survey’s (USGS) concept of a national census (or accounting) of water resources has evolved over the last several decades as the Nation has experienced increasing concern over water availability for multiple competing uses. The implementation of a USGS National Water Census was described in the USGS 2007 science strategy document that identified the highest priority science topics for the decade 2007–17. In 2009, the SECURE Water Act (Public Law 111–11, subtitle F) authorized the USGS to create a Water Availability and Use Assessment Program for the Nation, and in 2012, the Department of the Interior WaterSMART initiative provided funding to begin implementation of the USGS National Water Census (NWC). Generally, the USGS NWC approaches water-availability assessment in terms of a “water budget.” The water-budget approach seeks to better quantify the inflows and outflows of water, as well as the change in storage volume, both nationally and at a regional scale and, by doing so, provides critical information to managers and stakeholders responsible for making water-availability decisions. The NWC has two primary components: Topical Studies and Geographic Focus Area Studies. Topical Studies do research on methods that can provide nationwide estimates of particular water-budget components at the subwatershed scale. Some examples of NWC Topical Studies include estimation of streamflow at ungaged locations; periodic quantification of evapotranspiration; and water use related to development of unconventional oil and gas. These efforts are planned to include additional topics in the future. Geographic Focus Area Studies (FASs) assess water availability and use within a defined geographic area, typically a surface-water drainage basin, to increase the understanding of factors affecting water availability in the region. In the FASs, local stakeholder input helps the USGS identify what components of the water budget are in most need of additional understanding or quantification. Focus Area Studies are planned as 3-year efforts and, typically, three FASs are ongoing in different parts of the country at any given time. The Colorado River Basin (CRB) and the Delaware and Apalachicola-Chattahoochee-Flint (ACF) River Basins were selected by the Department of the Interior for the first round of FASs because of the perceived water shortages in the basins and potential conflicts over water supply and allocations. After gathering input from numerous stakeholders in the CRB, the USGS determined that surface-water resources in the basin were already being closely monitored and that the most important scientific contribution could be made by helping to improve estimates of four water-budget components: evapotranspiration losses, snowpack hydrodynamics, water-use information, and the relative importance of groundwater discharge in supporting streamflow across the basin. The purpose of this fact sheet is to provide a brief summary of the CRB FAS results as the study nears completion. Although some project results are still in the later stages of review and publication, this fact sheet provides an overall description of the work completed and cites the publications in which additional information can be found.

Arizona, California, Colorado, Nevada, New Mexico,↗

USGS2017

The role of the North American Breeding Bird Survey in conservation

The North American Breeding Bird Survey (BBS) was established in 1966 in response to a lack of quantitative data on changes in the populations of many bird species at a continental scale, especially songbirds. The BBS now provides the most reliable regional and continental trends and annual indices of abundance available for >500 bird species. This paper reviews some of the ways in which BBS data have contributed to bird conservation in North America over the past 50 yr, and highlights future program enhancement opportunities. BBS data have contributed to the listing of species under the Canadian Species at Risk Act and, in a few cases, have informed species assessments under the U.S. Endangered Species Act. By raising awareness of population changes, the BBS has helped to motivate bird conservation efforts through the creation of Partners in Flight. BBS data have been used to determine priority species and locations for conservation action at regional and national scales through Bird Conservation Region strategies and Joint Ventures. Data from the BBS have provided the quantitative foundation for North American State of the Birds reports, and have informed the public with regard to environmental health through multiple indicators, such as the Canadian Environmental Sustainability Indicators and the U.S. Environmental Protection Agency's Report on the Environment. BBS data have been analyzed with other data (e.g., environmental, land cover, and demographic) to evaluate potential drivers of population change, which have then informed conservation actions. In a few cases, BBS data have contributed to the evaluation of management actions, including informing the management of Mourning Doves ( Zenaida macroura ), Wood Ducks ( Aix sponsa ), and Golden Eagles ( Aquila chrysaetos ). Improving geographic coverage in northern Canada and in Mexico, improving the analytical approaches required to integrate data from other sources and to address variation in detectability, and completing the database, by adding historical bird data at each point count location and pinpointing the current point count locations would further enhance the survey's value.

Condor↗

USGS1998

Digital Geologic Map of the Rosalia 1:100,000 Quadrangle, Washington and Idaho: A Digital Database for the 1990 S.Z. Waggoner Map

The geologic map of the Rosalia 1:100,000-scale quadrangle was compiled in 1990 by S.Z. Waggoner of the Washington state Division of Geology and Earth Resources. This data was entered into a geographic information system (GIS) as part of a larger effort to create regional digital geology for the Pacific Northwest. The intent was to provide a digital geospatial database for a previously published black and white paper geologic map. This database can be queried in many ways to produce a variety of geologic maps. Digital base map data files are not included: they may be obtained from a variety of commercial and government sources. This database is not meant to be used or displayed at any scale larger than 1:100,000 (e.g., 1:62,500 or 1:24,000) as it has been somewhat generalized to fit the 1:100,000 scale map. The map area is located in eastern Washington and extends across the state border into western Idaho. This open-file report describes the methods used to convert the geologic map data into a digital format, documents the file structures, and explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet. We wish to thank J. Eric Schuster of the Washington Division of Geology and Earth Resources for providing the original stable-base mylar and the funding for it to be scanned. We also thank Dick Blank and Barry Moring of the U.S. Geological Survey for reviewing the manuscript and digital files, respectively.

Open-File Report↗

USGS1999

Digital Geologic Map of the Wallace 1:100,000 Quadrangle, Idaho

The geology of the Wallace 1:100,000 quadrangle, Idaho was compiled by Reed S. Lewis in 1997 primarily from published materials including 1983 data from Foster, Harrison's unpublished mapping done from 1975 to 1985, Hietenan's 1963, 1967, 1968, and 1984 mapping, Hobbs and others 1965 mapping, and Vance's 1981 mapping, supplemented by eight weeks of field mapping by Reed S. Lewis, Russell F. Burmester, and Mark D. McFaddan in 1997 and 1998. This geologic map information was inked onto a 1:100,000-scale greenline mylar of the topographic base map for input into a geographic information system (GIS). The resulting digital geologic map GIS can be queried in many ways to produce a variety of geologic maps. Digital base map data files (topography, roads, towns, rivers and lakes, etc.) are not included: they may be obtained from a variety of commercial and government sources. This database is not meant to be used or displayed at any scale larger than 1:100,000 (e.g., 1:62,500 or 1:24,000). The map area is located in north Idaho. The primary sources of map data are shown in figure 2 and additional sources are shown in figure 3. This open-file report describes the geologic map units, the methods used to convert the geologic map data into a digital format, the Arc/Info GIS file structures and relationships, and explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet. Mapping and compilation was completed by the Idaho Geological Survey under contract with the U.S. Geological Survey (USGS) office in Spokane, Washington. The authors would like to acknowledge the help of the following field assistants: Josh Goodman, Yvonne Issak, Jeremy Johnson and Kevin Myer. Don Winston provided help with our ongoing study of Belt stratigraphy, and Tom Frost assisted with logistical problems and sample collection. Manuscript reviews by Steve Box, Tom Frost, and Brian White are greatly appreciated. We wish to thank Karen S. Bolm of the USGS for reviewing the digital files.

Open-File Report↗

USGS2007

Design and implementation of estimation-based monitoring programs for flora and fauna: A case study on the Cherokee National Forest

Science-based monitoring of biological resources is important for a greater understanding of ecological systems and for assessment of the target population using theoretic-based management approaches. When selecting variables to monitor, managers first need to carefully consider their objectives, the geographic and temporal scale at which they will operate, and the effort needed to implement the program. Generally, monitoring can be divided into two categories: index and inferential. Although index monitoring is usually easier to implement, analysis of index data requires strong assumptions about consistency in detection rates over time and space, and parameters are often biasednot accounting for detectability and spatial variation. In most cases, individuals are not always available for detection during sampling periods, and the entire area of interest cannot be sampled. Conversely, inferential monitoring is more rigorous because it is based on nearly unbiased estimators of spatial distribution. Thus, we recommend that detectability and spatial variation be considered for all monitoring programs that intend to make inferences about the target population or the area of interest. Application of these techniques is especially important for the monitoring of Threatened and Endangered (T&E) species because it is critical to determine if population size is increasing or decreasing with some level of certainty. Use of estimation-based methods and probability sampling will reduce many of the biases inherently associated with index data and provide meaningful information with respect to changes that occur in target populations. We incorporated inferential monitoring into protocols for T&E species spanning a wide range of taxa on the Cherokee National Forest in the Southern Appalachian Mountains. We review the various approaches employed for different taxa and discuss design issues, sampling strategies, data analysis, and the details of estimating detectability using site occupancy. These techniques provide a science-based approach for monitoring and can be of value to all resource managers responsible for management of T&E species.

Proceedings of the Annual Conference of the Southe↗

USGS2017

Risk assessment for the reintroduction of anadromous salmonids upstream of Chief Joseph and Grand Coulee Dams, Northeastern Washington

The Upper Columbia United Tribes (UCUT; Spokane, Colville, Kootenai, Coeur d’Alene, and Kalispel Tribes) and Washington Department of Fish and Wildlife want to reintroduce anadromous salmonids to their historical range to restore ecosystem function and lost cultural and spiritual relationships in the upper Columbia River, northeastern Washington. The UCUT contracted with the U.S. Geological Survey to assess risks to resident taxa (existing fish populations in the reintroduction area upstream of Chief Joseph and Grand Coulee Dams) and reintroduced salmon associated with reintroduction. We developed a risk assessment framework for reintroduction of anadromous salmonids upstream of Chief Joseph and Grand Coulee Dams. To accomplish this goal, we applied strategies identified in previous risk assessment frameworks for reintroduction. The risk assessment is an initial step towards an anadromous reintroduction strategy. An initial list of potential donor sources for reintroduction species was developed from previous published sources for Chinook Salmon ( Oncorhynchus tshawytscha ) donors in the Transboundary Reach of the Columbia River, British Columbia; an ecological risk assessment of upper Columbia River hatchery programs on non-target taxa of concern; and a review of existing hatchery programs During two workshops, we further identified and ranked potential donor sources of anadromous Redband Trout (steelhead; O. mykiss ), Chinook Salmon, Sockeye Salmon ( O. nerka ), and Coho Salmon ( O. kisutch ). We also identified resident fish populations of interest and their primary habitat, location, status, and pathogen concerns to determine the potential risks of reintroduction. Species were deemed of interest based on resource management and potential interactions (that is, genetics, competition, and predation) with introduced species. We developed tables of potential donors by species and characterized potential sources (hatchery and natural origins), populations (individual runs), broodstock management and history, and potential constraints (that is, Endangered Species Act [ESA] listing, Evolutionarily Significant Unit concerns, pathogens, and availability). During the workshops, a group of regional fisheries and topic experts subjectively ranked the relative risks of pathogens, genetic effects, predation, and competition to resident fish and reintroduced salmonids. We assessed the pathogen risk of each potential donor for introducing new pathogens and the increased burden to existing pathogens for resident species upstream of the dams. We considered genetic risks to resident and downstream conspecifics and ecological impacts, including competition for food and space, predator-prey interactions, and ecosystem benefits/impacts. Each reintroduced species donor source was ranked based on abundance/viability (demographic risk to source and feasibility of collection), ancestral/genetic similarity (evolutionary similarity to historical populations), local adaptation (geographic proximity/similarity of source conditions to reintroduction conditions), and life history compatibility (including migration; spawn timing; and relative usage of reservoir, main-stem, or tributary habitats) with environmental conditions in the reintroduction area. We synthesized this information by species for all potential donors, in which an overall score and ranking system was established for decision support in donor selection for reintroduction into the upper Columbia River. We also provided information outside the ranking process by: Identifying predator-prey interactions and competition for food and space among species, Developing a decision support framework for donor selection, and Providing decision support for reintroduction strategies.

Washington↗

USGS2015

Geographic distribution: Boiga irregularis (Brown treesnake)

Rota: Rota Seaport (14.136502°N, 145.135351°E; WGS84). 3 September 2014. Shelwyn Taisacan, Robert Ulloa. Verified by G. Zug. USNM 581745. Snake (42 g, 810 mm SVL, 1020 mm total length) captured in a mouse-baited trap hung on the fence perimeter of the Rota Seaport. Because the Northern Marianas Islands are historically snake-free, these traps are used around ports and airports for early detection of snakes that may stow away in vessels or aircraft from Guam (60 km to the south), possibly evading quarantine detections. Necropsy revealed no prey items in stomach or gas- trointestinal tract. Dissection at USNM confirmed the snake was female. To our knowledge, this is the first incursion of a live Boiga irregularis on Rota. Brown Treesnakes previously observed on the island (N = 3) arrived in cargo already dead. The USGS Brown Treesnake Rapid Response Team mobilized 4 September–20 Oc- tober 2014 to search the focal and surrounding areas for evidence of a possible incipient population; no additional snakes were found during this search effort.

Herpetological Review↗

USGS2025

Peak streamflow trends in Montana and northern Wyoming and their relation to changes in climate, water years 1921–2020

Frequency analysis on annual peak streamflow (hereinafter, peak flow) is essential to water-resources management applications, including critical structure design (for example, bridges and culverts) and floodplain mapping. Nonstationarity is a statistical property of a peak-flow series such that the distributional properties (the mean, variance, or skew) change either gradually (monotonic trend) or abruptly (shift, step change or change point) through time. Not incorporating or accounting for observed nonstationarity into peak-flow frequency analysis might result in a poor representation of the true probability of large floods and thus misrepresent the actual flood risks to life and property. This report summarizes how hydroclimatic variability might affect the temporal and spatial distributions of peak-flow data in the State of Montana (and northern Wyoming) and is part of a larger study to document peak-flow nonstationarity and hydroclimatic changes across a nine-State region consisting of Illinois, Iowa, Michigan, Minnesota, Missouri, Montana, North Dakota, South Dakota, and Wisconsin. A wide range of analyses and statistical approaches are applied to document the primary mechanisms controlling floods and characterize temporal changes in hydroclimatic variables and peak flows. This study was completed in cooperation with the Montana Department of Natural Resources and Conservation. The purpose of this report is to characterize temporal and spatial patterns of nonstationarity in peak flows and hydroclimatology in Montana and northern Wyoming. In this evaluation, peak-flow, daily streamflow, and model-simulated gridded climatic data were examined for monotonic trends, change points, and other statistical properties that might indicate changing climatic and environmental conditions. This report includes background information on the study area, the history of U.S. Geological Survey peak-flow data collection and frequency analysis in Montana, and the review of research relating to hydroclimatic variability and change in Montana. This study might help provide a framework for addressing potential nonstationarity issues in peak-flow frequency updates that commonly are completed by the U.S. Geological Survey in cooperation with other agencies throughout the Nation. The analytical structure of this study includes analyses of monotonic trends and change points in numerous hydroclimatic variables in assigned 30-, 50-, 75-, and 100-year analysis periods. For Montana and part of Wyoming, the 30-, 50-, 75, and 100-year analyses included 157, 70, 48, and 12 streamgages, respectively. For those streamgages, nonstationarities were analyzed in the following variables: (1) climatic variables, including annual and seasonal (winter, spring, summer, and fall) temperature and precipitation; (2) daily streamflow variables, including the annual center of volume duration, annual center of volume median, and peaks over threshold with a mean of four events per year; and (3) annual peak-flow variables, including peak-flow timing and magnitude. A likelihood approach was used to express statistical confidence and assign the nonstationarity results as likely upward or downward (highest statistical confidence), somewhat likely upward or downward (less statistical confidence), or about as likely as not (little statistical confidence; hereinafter, neutral). For the nonstationarity analyses of the climatic, daily streamflow, and peak-flow variables, the results are presented in detail and discussed with respect to statewide patterns and geographic variability. For each of the 30-, 50-, and 75-year analyses, peak-flow change-point and monotonic trend analyses were compiled for streamgages classified with likely downward or likely upward trends. For those streamgages, the associated basin characteristics and nonstationarity results for peak-flow timing, daily streamflow, and climatic variables were investigated and statistically compared to discern associations among other variables that might contribute to the peak-flow nonstationarity results. The 50- and 75-year peak-flow nonstationarities identified in this study are mostly downward, in association with mostly upward temperature and potential evapotranspiration:precipitation monotonic trends. For the 50-, 75-, and 100-year analyses, the peak-flow change points are predominantly downward and are concentrated in the 1970s and 1980s, which indicates general consistency among the longer trend periods. These findings are in association with substantial research documenting globally rising temperature and atmospheric greenhouse gas concentrations that might be largely attributed to anthropogenic activities. Anthropogenic effects might represent long-term (on the order of several decades to more than a century) climate changes that might happen within highly variable natural climate fluctuations. Several paleo studies in the north-central United States have indicated that hydroclimatic extremes (that is, low- and high-streamflow conditions) before European settlement have been outside of extremes since the 1900s. Depending on the interactions of anthropogenic effects and natural climate variability, extreme high-streamflow conditions might occur in the future, even in the presence of long-term downward peak-flow trends.

Montana, Wyoming↗

USGS2006

Predicting woodrat ( Neotoma ) responses to anthropogenic warming from studies of the palaeomidden record

Aim The influence of anthropogenic climate change on organisms is an area of great scientific concern. Increasingly there is recognition that abrupt climate transitions have occurred over the late Quaternary; studies of these shifts may yield insights into likely biotic responses to contemporary warming. Here, we review research undertaken over the past decade investigating the response of Neotoma (woodrats) body size and distribution to climate change over the late Quaternary (the last 40,000 years). By integrating information from woodrat palaeomiddens, historical museum specimens and field studies of modern populations, we identify potential evolutionary responses to climate change occurring over a variety of temporal and spatial scales. Specifically, we characterize climatic thresholds in the past that led to local species extirpation and/or range alterations rather than in situ adaptation, and apply them to anticipate potential biotic responses to anthropogenic climate change. Location Middens were collected at about 55 sites scattered across the western United States, ranging from about 34 to 46° N and about 104 to 116° W, respectively. Data for modern populations were drawn from studies conducted in Death Valley, California, Missoula, Montana and the Sevilleta LTER site in central New Mexico. Methods We analysed faecal pellets from midden series collected at numerous cave sites across the western United States. From these we estimated body mass using techniques validated in earlier studies. We compared body size fluctuations at different elevations in different regions and integrated these results with studies investigating temperature–body size tradeoffs in modern animals. We also quantify the rapidity of the size changes over the late Quaternary to estimate the evolutionary capacity of woodrats to deal with predicted rates of anthropogenic climate change over the next century. Results We find remarkable similarities across the geographical range to late Quaternary climate change. In the middle of the geographical range woodrats respond in accordance to Bergmann's rule: colder climatic conditions select for larger body size and warmer conditions select for smaller body size. Patterns are more complicated at range boundaries, and local environmental conditions influence the observed response. In general, woodrat body size fluctuates with approximately the same amplitude and frequency as climate; there is a significant and positive correlation between woodrat body size and generalized climate proxies (such as ice core records). Woodrats have achieved evolutionary rates of change equal to or greater than those needed to adapt in situ to anthropogenic climate change. Main conclusions In situ body size evolution is a likely outcome of climate change, and such shifts are part of a normal spectrum of adaptation. Woodrats appear to be subject to ongoing body size selection in response to fluctuating environmental conditions. Allometric considerations suggest that these shifts in body size lead to substantial changes in the physiology, life history and ecology of woodrats, and on their direct and indirect interactions with other organisms in the ecosystem. Our work highlights the importance of a finely resolved and long-term record in understanding biotic responses to climatic shifts.

Journal of Biogeography↗

USGS2007

Crust and lithospheric structure – Global crustal structure

The Earth’s crust has played an important role in all aspects of this planet’s evolution. This chapter presents a review of our current understanding of the physical properties of the crust on a global basis. This understanding comes from extensive seismic measurements using many techniques, as well as nonseismic geophysics, including gravity, magnetic, geoelectric, and heat flow measurements. Seismic measurements include those that employ active (man-made) sources and those that use passive (naturally occurring) sources. Deep seismic reflection profiles provide a seismic image of the crust in twodimensions with a high (50–100m) resolution. Local earthquake tomography can provide three-dimensional (3-D) seismic images at moderate (500–1000m) resolution and higher, depending on the number and spacing of seismographs. Nonseismic methods provide estimates of crustal density, magnetic properties, conductivity and geotherms (temperature vs depth). The crust in deep ocean basins is 6–7km thick and has a relatively uniform seismic velocity structure, but there are numerous oceanic regions with anomalous crustal structure, including mid-ocean ridges, trenches, volcanic islands, and oceanic plateaux. Ocean–continent passive margins are also highly variable in structure, and may be classified as volcanic versus nonvolcanic margins. Continental crust ranges in thickness from 16 to 80km, and has a highly variable seismic velocity and density structure. The proportions of continental crust, by area, are 69% shield and platform (cratons), 15% old and young orogens, 9% extended (stretched) crust, 6 % magmatic arc, and 1% rifts. The weighted mean continental crustal thickness and average crustal velocity are 41km (SD 6.2km) and 6.45kms−1 (SD 0.21kms−1), respectively. A global geographic distribution of seismic data has made it possible to create global crustal models with cell sizes as small as 2°×2°. These models provide a complete description of seismic velocities and density within the crust and uppermost mantle, including, where present, ice, water, and sedimentary layers and the crystalline crust (parameterized in three layers, upper, middle and lower crust), and sub-Moho properties. The crust is the most intensely studied region of the Earth’s interior and consequently is the best understood in terms of its structure, composition, and evolution. © 2007 Elsevier B.V. All rights reserved.

Book chapter↗

USGS2005

Modern pollen data from North America and Greenland for multi-scale paleoenvironmental applications

The modern pollen network in North America and Greenland is presented as a database for use in quantitative calibration studies and paleoenvironmental reconstructions. The georeferenced database includes 4634 samples from all regions of the continent and 134 pollen taxa that range from ubiquitous to regionally diagnostic taxa. Climate data and vegetation characteristics were assigned to every site. Automated and manual procedures were used to verify the accuracy of geographic coordinates and identify duplicate records among datasets, incomplete pollen sums, and other potential errors. Data are currently available for almost all of North America, with variable density. Pollen taxonomic diversity, as measured by the Shannon-Weiner coefficient, varies as a function of location, as some vegetation regions are dominated by one or two major pollen producers, while other regions have a more even composition of pollen taxa. Squared-chord distances computed between samples show that most modern pollen samples find analogues within their own vegetation zone. Both temperature and precipitation inferred from best analogues are highly correlated with observed values but temperature exhibits the strongest relation. Maps of the contemporary distribution of several pollen types in relation to the range of the plant taxon illustrate the correspondence between plant and pollen ranges. ?? 2005 Elsevier Ltd. All rights reserved.

Quaternary Science Reviews↗