Geology Reports⌕ Search

SEARCH · Geology Reports

Results for “Geographical Analysis”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 865 records · Page 48Linked to original sources
USGS2013

Archive of post-Hurricane Isabel coastal oblique aerial photographs collected during U.S. Geological Survey Field Activity 03CCH01 from Ocean City, Maryland, to Fort Caswell, North Carolina and Inland from Waynesboro to Redwood, Virginia, September 21 - 23, 2003

On September 21 - 23, 2003, the United States Geological Survey (USGS) conducted an oblique aerial photographic survey along the Atlantic coast from Ocean City, Md., to Fort Caswell, N.C., and inland oblique aerial photographic survey from Waynesboro to Redwood, Va., aboard a Navajo Piper twin-engine airplane. The coastal survey was conducted at an altitude of 500 feet (ft) and approximately 1,000 ft offshore. For the inland photos, the aircraft tried to stay approximately 500 ft above the terrain. These coastal photos were used to document coastal changes like beach erosion and overwash caused by Hurricane Isabel, while the inland photos looked for potential landslides caused by heavy rains. The photos may also be used as baseline data for future coastal change analysis. The USGS and the National Aeronautics and Space Administration (NASA) surveyed the impact zone of Hurricane Isabel to better understand the changes in vulnerability of the Nation’s coasts to extreme storms (Morgan, 2009). This report serves as an archive of photographs collected during the September 21 - 23, 2003, post-Hurricane Isabel coastal and inland oblique aerial survey along with associated survey maps, KML files, navigation files, digital Field Activity Collection System (FACS) logs, and Federal Geographic Data Committee (FGDC) metadata. Refer to the Acronyms page for expansions of all acronyms and abbreviations used in this report. The USGS St. Petersburg Coastal and Marine Science Center (SPCMSC) assigns a unique identifier to each cruise or field activity. For example, 03CCH01 tells us the data were collected in 2003 for the Coastal Change Hazards (CCH) study and the data were collected during the first field activity for that project in that calendar year. Refer to http://walrus.wr.usgs.gov/infobank/programs/html/definition/activity.html for a detailed description of the method used to assign the ID number. The photographs provided here are Joint Photographic Experts Group (JPEG) scanned images of the analog 35 millimeter (mm) color positive slides. The photograph locations are estimates of the location of the plane (see the Navigation page). The metadata values for photo creation time, GPS latitude, GPS longitude, GPS position (latitude and longitude), keywords, credit, artist, caption, copyright, and contact were added to each photograph's EXIF header using EXIFtool (Subino and others, 2012). Photographs can be opened directly with any JPEG-compatible image viewer by clicking on a thumbnail on the contact sheet, or, when viewing the Google Earth KML file, by clicking on the marker and then clicking on either the thumbnail or the link below the thumbnail. Nathaniel Plant (USGS - St. Petersburg, Fla.), and Ann Marie Ascough (formerly contracted at the USGS - St. Petersburg, Fla.) helped with the creation of KML files. To view the photos and survey maps, proceed to the Photos and Maps page.

Maryland, North Carolina, Virginia↗
USGS2012

Hydrologic and landscape database for the Cache and White River National Wildlife Refuges and contributing watersheds in Arkansas, Missouri, and Oklahoma

A hydrologic and landscape database was developed by the U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service, for the Cache River and White River National Wildlife Refuges and their contributing watersheds in Arkansas, Missouri, and Oklahoma. The database is composed of a set of ASCII files, Microsoft Access® files, Microsoft Excel® files, an Environmental Systems Research Institute (ESRI) ArcGIS® geodatabase, ESRI ArcGRID® raster datasets, and an ESRI ArcReader® published map. The database was developed as an assessment and evaluation tool to use in examining refuge-specific hydrologic patterns and trends as related to water availability for refuge ecosystems, habitats, and target species; and includes hydrologic time-series data, statistics, and hydroecological metrics that can be used to assess refuge hydrologic conditions and the availability of aquatic and riparian habitat. Landscape data that describe the refuge physiographic setting and the locations of hydrologic-data collection stations are also included in the database. Categories of landscape data include land cover, soil hydrologic characteristics, physiographic features, geographic and hydrographic boundaries, hydrographic features, regional runoff estimates, and gaging-station locations. The database geographic extent covers three hydrologic subregions—the Lower Mississippi–St Francis (0802), the Upper White (1101), and the Lower Arkansas (1111)—within which human activities, climatic variation, and hydrologic processes can potentially affect the hydrologic regime of the refuges and adjacent areas. Database construction has been automated to facilitate periodic updates with new data. The database report (1) serves as a user guide for the database, (2) describes the data-collection, data-reduction, and data-analysis methods used to construct the database, (3) provides a statistical and graphical description of the database, and (4) provides detailed information on the development of analytical techniques designed to assess water availability for ecological needs.

Arkansas;Missouri;Oklahoma↗
USGS2009

Groundwater availability of the Central Valley Aquifer, California

California's Central Valley covers about 20,000 square miles and is one of the most productive agricultural regions in the world. More than 250 different crops are grown in the Central Valley with an estimated value of $17 billion per year. This irrigated agriculture relies heavily on surface-water diversions and groundwater pumpage. Approximately one-sixth of the Nation's irrigated land is in the Central Valley, and about one-fifth of the Nation's groundwater demand is supplied from its aquifers. The Central Valley also is rapidly becoming an important area for California's expanding urban population. Since 1980, the population of the Central Valley has nearly doubled from 2 million to 3.8 million people. The Census Bureau projects that the Central Valley's population will increase to 6 million people by 2020. This surge in population has increased the competition for water resources within the Central Valley and statewide, which likely will be exacerbated by anticipated reductions in deliveries of Colorado River water to southern California. In response to this competition for water, a number of water-related issues have gained prominence: conservation of agricultural land, conjunctive use, artificial recharge, hydrologic implications of land-use change, and effects of climate variability. To provide information to stakeholders addressing these issues, the USGS Groundwater Resources Program made a detailed assessment of groundwater availability of the Central Valley aquifer system, that includes: (1) the present status of groundwater resources; (2) how these resources have changed over time; and (3) tools to assess system responses to stresses from future human uses and climate variability and change. This effort builds on previous investigations, such as the USGS Central Valley Regional Aquifer System and Analysis (CV-RASA) project and several other groundwater studies in the Valley completed by Federal, State and local agencies at differing scales. The principal product of this new assessment is a tool referred to as the Central Valley Hydrologic Model (CVHM) that accounts for integrated, variable water supply and demand, and simulates surface-water and groundwater-flow across the entire Central Valley system. The development of the CVHM comprised four major elements: (1) a comprehensive Geographic Information System (GIS) to compile, analyze and visualize data; (2) a texture model to characterize the aquifer system;(3) estimates of water-budget components by numerically modeling the hydrologic system with the Farm Process (FMP); and (4) simulations to assess and quantify hydrologic conditions.

Professional Paper↗
USGS2012

Status and trends of land change in the Western United States--1973 to 2000

Preface U.S. Geological Survey (USGS) Professional Paper 1794–A is the first in a four-volume series on the status and trends of the Nation’s land use and land cover, providing an assessment of the rates and causes of land-use and land-cover change in the Western United States between 1973 and 2000. Volumes B, C, and D provide similar analyses for the Great Plains, the Midwest–South Central United States, and the Eastern United States, respectively. The assessments of land-use and land-cover trends are conducted on an ecoregion-by-ecoregion basis, and each ecoregion assessment is guided by a nationally consistent study design that includes mapping, statistical methods, field studies, and analysis. Individual assessments provide a picture of the characteristics of land change occurring in a given ecoregion; in combination, they provide a framework for understanding the complex national mosaic of change and also the causes and consequences of change. Thus, each volume in this series provides a regional assessment of how (and how fast) land use and land cover are changing, and why. The four volumes together form the first comprehensive picture of land change across the Nation. Geographic understanding of land-use and land-cover change is directly relevant to a wide variety of stakeholders, including land and resource managers, policymakers, and scientists. The chapters in this volume present brief summaries of the patterns and rates of land change observed in each ecoregion in the Western United States, together with field photographs, statistics, and comparisons with other assessments. In addition, a synthesis chapter summarizes the scope of land change observed across the entire Western United States. The studies provide a way of integrating information across the landscape, and they form a critical component in the efforts to understand how land use and land cover affect important issues such as the provision of ecological goods and services and also the determination of risks to, and vulnerabilities of, human communities. Results from this project also are published in peer-reviewed journals, and they are further used to produce maps of change and other tools for land management, as well as to provide inputs for carbon-cycle modeling and other climate change research. This report is only one of the products produced by USGS on land-use and land-cover change in the United States. Other reports and land-cover statistics are available online at http://landcovertrends.usgs.gov .

Professional Paper↗
USGS2015

Status and trends of land change in the Great Plains of the United States--1973 to 2000

Preface U.S. Geological Survey (USGS) Professional Paper 1794–B is the second in a four-volume series on the status and trends of the Nation’s land use and land cover, providing an assessment of the rates and causes of land-use and land-cover change in the Great Plains of the United States between 1973 and 2000. Volumes A, C, and D provide similar analyses for the Western United States, the Midwest–South Central United States, and the Eastern United States, respectively. The assessments of land-use and land-cover trends are conducted on an ecoregion-by-ecoregion basis, and each ecoregion assessment is guided by a nationally consistent study design that includes mapping, statistical methods, field studies, and analysis. Individual assessments provide a picture of the characteristics of land change occurring in a given ecoregion; in combination, they provide a framework for understanding the complex national mosaic of change and also the causes and consequences of change. Thus, each volume in this series provides a regional assessment of how (and how fast) land use and land cover are changing, and why. The four volumes together form the first comprehensive picture of land change across the Nation. Geographic understanding of land-use and land-cover change is directly relevant to a wide variety of stakeholders, including land and resource managers, policymakers, and scientists. The chapters in this volume present brief summaries of the patterns and rates of land change observed in each ecoregion in the Great Plains of the United States, together with field photographs, statistics, and comparisons with other assessments. In addition, a synthesis chapter summarizes the scope of land change observed across the entire Great Plains of the United States. The studies provide a way of integrating information across the landscape, and they form a critical component in the efforts to understand how land use and land cover affect important issues such as the provision of ecological goods and services and also the determination of risks to, and vulnerabilities of, human communities. Results from this project also are published in peer-reviewed journals, and they are further used to produce maps of change and other tools for land management, as well as to provide inputs for carbon-cycle modeling and other climate change research. This report is only one of the products produced by USGS on land-use and land-cover change in the United States. Other reports and land-cover statistics are available online at http://landcovertrends.usgs.gov .

Great Plains↗
USGS2015

Status and trends of land change in the Midwest–South Central United States—1973 to 2000

U.S. Geological Survey (USGS) Professional Paper 1794–C is the third in a four-volume series on the status and trends of the Nation’s land use and land cover, providing an assessment of the rates and causes of land-use and land-cover change in the Midwest–South Central United States between 1973 and 2000. Volumes A, B, and D provide similar analyses for the Western United States, the Great Plains of the United States, and the Eastern United States, respectively. The assessments of land-use and land-cover trends are conducted on an ecoregion-by-ecoregion basis, and each ecoregion assessment is guided by a nationally consistent study design that includes mapping, statistical methods, field studies, and analysis. Individual assessments provide a picture of the characteristics of land change occurring in a given ecoregion; in combination, they provide a framework for understanding the complex national mosaic of change and also the causes and consequences of change. Thus, each volume in this series provides a regional assessment of how (and how fast) land use and land cover are changing, and why. The four volumes together form the first comprehensive picture of land change across the Nation. Geographic understanding of land-use and land-cover change is directly relevant to a wide variety of stakeholders, including land and resource managers, policymakers, and scientists. The chapters in this volume present brief summaries of the patterns and rates of land change observed in each ecoregion in the Midwest–South Central United States, together with field photographs, statistics, and comparisons with other assessments. In addition, a synthesis chapter summarizes the scope of land change observed across the entire Midwest–South Central United States. The studies provide a way of integrating information across the landscape, and they form a critical component in the efforts to understand how land use and land cover affect important issues such as the provision of ecological goods and services and also the determination of risks to, and vulnerabilities of, human communities. Results from this project also are published in peer-reviewed journals, and they are further used to produce maps of change and other tools for land management, as well as to provide inputs for carbon-cycle modeling and other climate change research.

Professional Paper↗
USGS2016

Status and trends of land change in the Eastern United States—1973 to 2000

Preface U.S. Geological Survey (USGS) Professional Paper 1794–D is the fourth in a four-volume series on the status and trends of the Nation’s land use and land cover, providing an assessment of the rates and causes of land-use and land-cover change in the Eastern United States between 1973 and 2000. Volumes A, B, and C provide similar analyses for the Western United States, the Great Plains of the United States, and the Midwest–South Central United States, respectively. The assessments of land-use and land-cover trends are conducted on an ecoregion-by-ecoregion basis, and each ecoregion assessment is guided by a nationally consistent study design that includes mapping, statistical methods, field studies, and analysis. Individual assessments provide a picture of the characteristics of land change occurring in a given ecoregion; in combination, they provide a framework for understanding the complex national mosaic of change and also the causes and consequences of change. Thus, each volume in this series provides a regional assessment of how (and how fast) land use and land cover are changing, and why. The four volumes together form the first comprehensive picture of land change across the Nation. Geographic understanding of land-use and land-cover change is directly relevant to a wide variety of stakeholders, including land and resource managers, policymakers, and scientists. The chapters in this volume present brief summaries of the patterns and rates of land change observed in each ecoregion in the Eastern United States, together with field photographs, statistics, and comparisons with other assessments. In addition, a synthesis chapter summarizes the scope of land change observed across the entire Eastern United States. The studies provide a way of integrating information across the landscape, and they form a critical component in the efforts to understand how land use and land cover affect important issues such as the provision of ecological goods and services and also the determination of risks to, and vulnerabilities of, human communities. Results from this project also are published in peer-reviewed journals, and they are further used to produce maps of change and other tools for land management, as well as to provide inputs for carbon-cycle modeling and other climate change research. This report is only one of the products produced by USGS on land-use and land-cover change in the United States. Other reports and land-cover statistics are available online at http://landcovertrends.usgs.gov .

Professional Paper↗
USGS2011

Geologic map of Big Bend National Park, Texas

The purpose of this map is to provide the National Park Service and the public with an updated digital geologic map of Big Bend National Park (BBNP). The geologic map report of Maxwell and others (1967) provides a fully comprehensive account of the important volcanic, structural, geomorphological, and paleontological features that define BBNP. However, the map is on a geographically distorted planimetric base and lacks topography, which has caused difficulty in conducting GIS-based data analyses and georeferencing the many geologic features investigated and depicted on the map. In addition, the map is outdated, excluding significant data from numerous studies that have been carried out since its publication more than 40 years ago. This report includes a modern digital geologic map that can be utilized with standard GIS applications to aid BBNP researchers in geologic data analysis, natural resource and ecosystem management, monitoring, assessment, inventory activities, and educational and recreational uses. The digital map incorporates new data, many revisions, and greater detail than the original map. Although some geologic issues remain unresolved for BBNP, the updated map serves as a foundation for addressing those issues. Funding for the Big Bend National Park geologic map was provided by the United States Geological Survey (USGS) National Cooperative Geologic Mapping Program and the National Park Service. The Big Bend mapping project was administered by staff in the USGS Geology and Environmental Change Science Center, Denver, Colo. Members of the USGS Mineral and Environmental Resources Science Center completed investigations in parallel with the geologic mapping project. Results of these investigations addressed some significant current issues in BBNP and the U.S.-Mexico border region, including contaminants and human health, ecosystems, and water resources. Funding for the high-resolution aeromagnetic survey in BBNP, and associated data analyses and interpretation, was from the USGS Crustal Geophysics and Geochemistry Science Center. Mapping contributed from university professors and students was mostly funded by independent sources, including academic institutions, private industry, and other agencies.

Texas↗
USGS2021

Applying biodiversity metrics as surrogates to a habitat conservation plan

Unabated urbanization has led to environmental degradation and subsequent biodiversity loss across the globe. As an outcome of unmitigated land use, multi-jurisdictional agencies have developed land use plans that attempt to protect threatened or endangered species across selected areas by which some trade-offs between harm to species and additional conservation approaches are allowed among the partnering organizations. Typical conservation plans can be created to focus on single or multiple species, and although they may protect a species or groups of species, they may not account for biodiversity or its protection across the given area. We applied an approach that clustered deductive habitat models for terrestrial vertebrates into metrics that serve as surrogates for biodiversity and relate to ecosystem services. In order to evaluate this process, we collaborated with the partnering agencies who are creating a Multi-Species Habitat Conservation Plan in southern California and compared it to the entire Mojave Desert Ecoregion. We focused on total terrestrial vertebrate species richness and taxon groupings representing amphibians, birds, mammals, and reptiles, and two special status species using the Normalized Index of Biodiversity (NIB). The conservation planning area had a lower NIB and was less species rich than the Mojave Desert Ecoregion, but the Mojave River riparian corridor had a higher NIB and was more species-rich, and while taxon analysis varied across the geographies, this pattern generally held. Additionally, we analyzed desert tortoise ( Gopherus agassizii ) and desert kit fox ( Vulpes macrotis arsipus ) as umbrella species and determined that both species are associated with increased NIB and large numbers of species for the conservation area. Our process provided the ability to incorporate value-added surrogate information into a formal land use planning process and used a metric, NIB, which allowed comparison of the various planning areas and geographic units. Although this process has been applied to Apple Valley, CA, and other geographies within the U.S., the approach has practical application for other global biodiversity initiatives.

California↗
USGS2007

GIS data for the Seaside, Oregon, Tsunami Pilot Study to modernize FEMA flood hazard maps

A Tsunami Pilot Study was conducted for the area surrounding the coastal town of Seaside, Oregon, as part of the Federal Emergency Management's (FEMA) Flood Insurance Rate Map Modernization Program (Tsunami Pilot Study Working Group, 2006). The Cascadia subduction zone extends from Cape Mendocino, California, to Vancouver Island, Canada. The Seaside area was chosen because it is typical of many coastal communities subject to tsunamis generated by far- and near-field (Cascadia) earthquakes. Two goals of the pilot study were to develop probabilistic 100-year and 500-year tsunami inundation maps using Probabilistic Tsunami Hazard Analysis (PTHA) and to provide recommendations for improving tsunami hazard assessment guidelines for FEMA and state and local agencies. The study was an interagency effort by the National Oceanic and Atmospheric Administration, U.S. Geological Survey, and FEMA, in collaboration with the University of Southern California, Middle East Technical University, Portland State University, Horning Geoscience, Northwest Hydraulics Consultants, and the Oregon Department of Geological and Mineral Industries. The pilot study model data and results are published separately as a geographic information systems (GIS) data report (Wong and others, 2006). The flood maps and GIS data are briefly described here.

Oregon↗
USGS1983

Tectonics and metallogenic provinces

Various theories have been advanced to explain the well-known uneven distribution of metals and ore-deposit types in space and time. Primordial differences in the mantle, preferential concentration of elements in the crust, the prevalence of ore-forming processes at certain times and (or) places, and combinations of one or several of these factors have all been called upon to account for the "metallogenic provinces," which can be defined loosely as regions containing similar deposits of one or a group of metals or minerals. Because many, perhaps most, provinces have complex, multistage origins, the relative importance of inheritance vs. process is still controversial. In recent years the geographic relationship of many geologically young provinces to present-day plate-tectonic positions (accreting or consuming margins, intraplate structures, etc.) has been widely recognized, and the presumption is strong that older provinces had similar relationships to former plates. As most ore deposits resulted from a favorable conjunction of geological processes that are no longer operative, elucidation of their genesis requires reconstruction of the geologic history of the province, with particular emphasis on events coeval with mineralization. Tectonic analysis is an important aspect of this reconstruction; data from orbiting satellites have contributed greatly to this analysis, as the voluminous literature of the past decade testifies. Both the synoptic view of large areas and the ability to emphasize faint contrasts have revealed linear, curvilinear, and circular features not previously recognized from field studies. Some of these undoubtedly reflect basement structures that have contributed to the development, or limit the extent, of metallogenic provinces. Their recognition and delineation will be increasingly valuable to the assessment of resources available and as guides to exploration for the ores needed by future generations. ?? 1983.

Advances in Space Research↗
USGS2022

Multi-hazard risk analysis for the U.S. Department of the Interior: An integration of expert elicitation, planning priorities, and geospatial analysis

An integral part of disaster risk management is identifying and prioritizing hazards and their potential impacts in a meaningful way to support risk-reduction planning. There has been considerable use and subsequent criticism of threat prioritization efforts that simply compare likelihoods and consequences of plausible threats. This article summarizes a new mixed-methods and scalable approach for prioritizing risks in a multi-hazard, multi-objective, and multi-criteria organizational context. This approach integrates (1) hazard characterizations using subject-matter-expert (SME) elicitation, (2) expressed preferences in planning priorities provided by emergency managers, and (3) quantitative estimates of asset exposure to hazards using geospatial data and geographic-information-systems (GIS) software. We demonstrate this approach with a case study designed to support multi-hazard mitigation and response planning done by the U.S. Department of the Interior (DOI) Office of Emergency Management, which required a national understanding of the risks posed by 75 natural, technological, and adversarial hazards to DOI managed and administered lands, facilities, people, revenues, and resources. Results demonstrate that hazard priorities vary depending on the asset, scale, and risk-management context, thereby making the case that “one-size-fits-all” hazard rankings have limited utility or relevance to real-world, risk mitigation and response planning. Our results suggest that recognizing the risk-management context provides greater transparency, flexibility, and relevance in comparing threats than traditional likelihood-threat matrices or the use of hazard SMEs to decide for planners which hazard scenarios are emphasized in risk planning.

International Journal of Disaster Risk Reduction↗
USGS2001

Regional fluid migration in the Illinois basin: Evidence from in situ oxygen isotope analysis of authigenic K-feldspar and quartz from the Mount Simon Sandstone

Oxygen isotope compositions of widespread, authigenic K-feldspar and quartz overgrowths and cements in the Upper Cambrian Mount Simon Sandstone were measured by ion microprobe in 11 samples distributed across the Illinois basin and its periphery. Average K-feldspar δ 18 O values increase systematically from +14‰ ± 1‰ in the southernmost and deepest samples in Illinois to +24‰ ± 2‰ in the northernmost outcrop sample in Wisconsin. A similar trend was observed for quartz overgrowths (22‰ ± 2‰ to 28‰ ± 2‰). Constant homogenization temperatures (100–130 °C) of fluid inclusions associated with quartz overgrowths throughout the basin suggest that the geographic trend in oxygen isotope compositions is a result of diagenetic modification of a south to north migrating basinal fluid.

Illinois, Indiana, Kentucky↗
USGS2008

Genetic analysis of paramyxovirus isolates from pacific salmon reveals two independently co-circulating lineages

Viruses with the morphological and biochemical characteristics of the family Paramyxoviridae (paramyxoviruses) have been isolated from adult salmon returning to rivers along the Pacific coast of North America since 1982. These Pacific salmon paramyxoviruses (PSPV), which have mainly been isolated from Chinook salmon Oncorhynchus tshawytscha, grow slowly in established fish cell lines and have not been associated with disease. Genetic analysis of a 505-base-pair region of the polymerase gene from 47 PsPV isolates produced 17 nucleotide sequence types that could be grouped into two major sublineages, designated A and B. The two independently co-circulating sublineages differed by 12.1-13.9% at the nucleotide level but by only 1.2% at the amino acid level. Isolates of PSPV from adult Pacific salmon returning to rivers from Alaska to California over a 25-year period showed little evidence of geographic or temporal grouping. Phylogenetic analyses revealed that these paramyxoviruses of Pacific salmon were most closely related to the Atlantic salmon paramyxovirus (ASPV) from Norway, having a maximum nucleotide diversity of 26.1 % and an amino acid diversity of 19.0%. When compared with homologous sequences of other paramyxoviruses, PSPV and ASPV were sufficiently distinct to suggest that they are not clearly members of any of the established genera in the family Paramyxoviridae. in the course of this study, a polymerase chain reaction assay was developed that can be used for confirmatory identification of PSPV. ?? Copyright by the American Fisheries Society 2008.

Journal of Aquatic Animal Health↗
USGS1999

Reference intervals and physiologic alterations in hematologic and biochemical values of free-ranging desert tortoises in the Mojave Desert

Desert tortoise ( Gopherus agassizii ) populations have experienced precipitous declines resulting from the cumulative impact of habitat loss, and human and disease-related mortality. Evaluation of hematologic and biochemical responses of desert tortoises to physiologic and environmental factors can facilitate the assessment of stress and disease in tortoises and contribute to management decisions and population recovery. The goal of this study was to obtain and analyze clinical laboratory data from free-ranging desert tortoises at three sites in the Mojave Desert (California, USA) between October 1990 and October 1995, to establish reference intervals, and to develop guidelines for the interpretation of laboratory data under a variety of environmental and physiologic conditions. Body weight, carapace length, and venous blood samples for a complete blood count and clinical chemistry profile were obtained from 98 clinically healthy adult desert tortoises of both sexes at the Desert Tortoise Research Natural area (western Mojave), Goffs (eastern Mojave) and Ivanpah Valley (northeastern Mojave). Samples were obtained four times per year, in winter (February/March), spring (May/June), summer (July/August), and fall (October). Years of near-, above- and below-average rainfall were represented in the 5 yr period. Minimum, maximum and median values, and central 95 percentiles were used as reference intervals and measures of central tendency for tortoises at each site and/or season. Data were analyzed using repeated measures analysis of variance for significant ( P < 0.01) variation on the basis of sex, site, season, and interactions between these variables. Significant sex differences were observed for packed cell volume, hemoglobin concentration, aspartate transaminase activity, and cholesterol, triglyceride, calcium, and phosphorus concentrations. Marked seasonal variation was observed in most parameters in conjunction with reproductive cycle, hibernation, or seasonal rainfall. Year-to-year differences and long-term alterations primarily reflected winter rainfall amounts. Site differences were minimal, and largely reflected geographic differences in precipitation patterns, such that results from these studies can be applied to other tortoise populations in environments with known rainfall and forage availability patterns.

Journal of Wildlife Diseases↗
USGS2013

Population genetic structure of rare and endangered plants using molecular markers

This study was initiated to assess the levels of genetic diversity and differentiation in the remaining populations of Phyllostegia stachyoides and Melicope zahlbruckneri in Hawai`i Volcanoes National Park and determine the extent of gene flow to identify genetically distinct individuals or groups for conservation purposes. Thirty-six Amplified Fragment Length Polymorphic (AFLP) primer combinations generated a total of 3,242 polymorphic deoxyribonucleic acid (DNA) fragments in the P. stachyoides population with a percentage of polymorphic bands (PPB) ranging from 39.3 to 65.7% and 2,780 for the M. zahlbruckneri population with a PPB of 18.8 to 64.6%. Population differentiation (Fst) of AFLP loci between subpopulations of P. stachyoides was low (0.043) across populations. Analysis of molecular variance of P. stachyoides showed that 4% of the observed genetic differentiation occurred between populations in different k ī puka and 96% when individuals were pooled from all k ī puka. Moderate genetic diversity was detected within the M. zahlbruckneri population. Bayesian and multivariate analyses both classified the P. stachyoides and M. zahlbruckneri populations into genetic groups with considerable sub-structuring detected in the P. stachyoides population. The proportion of genetic differentiation among populations explained by geographical distance was estimated by Mantel tests. No spatial correlation was found between genetic and geographic distances in both populations. Finally, a moderate but significant gene flow that could be attributed to insect or bird-mediated dispersal of pollen across the different k ī puka was observed. The results of this study highlight the utility of a multi-allelic DNA-based marker in screening a large number of polymorphic loci in small and closely related endangered populations and revealed the presence of genetically unique groups of individuals in both M. zahlbruckneri and P. stachyoides populations. Based on these findings, approaches that can assist conservation efforts of these species are proposed.

Hawai`i↗
USGS2011

Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis based on 27 polymorphic microsatellite markers

Blastomyces dermatitidis , a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis . We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources ( n =112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and &alpha;-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species.

Applied and Environmental Microbiology↗
USGS2023

Development and application of a qPCR-based genotyping assay for Ophidiomyces ophidiicola to investigate the epidemiology of ophidiomycosis

Ophidiomycosis (snake fungal disease) is an infectious disease caused by the fungus Ophidiomyces ophidiicola to which all snake species appear to be susceptible. Significant variation has been observed in clinical presentation, progression of disease, and response to treatment, which may be due to genetic variation in the causative agent. Recent phylogenetic analysis based on whole-genome sequencing identified that O . ophidiicola strains from the United States formed a clade distinct from European strains, and that multiple clonal lineages of the clade are present in the United States. The purpose of this study was to design a qPCR-based genotyping assay for O . ophidiicola , then apply that assay to swab-extracted DNA samples to investigate whether the multiple O . ophidiicola clades and clonal lineages in the United States have specific geographic, taxonomic, or temporal predilections. To this end, six full genome sequences of O . ophidiicola representing different clades and clonal lineages were aligned to identify genomic areas shared between subsets of the isolates. Eleven hydrolysis-based Taqman primer-probe sets were designed to amplify selected gene segments and produce unique amplification patterns for each isolate, each with a limit of detection of 10 or fewer copies of the target sequence and an amplification efficiency of 90–110%. The qPCR-based approach was validated using samples from strains known to belong to specific clades and applied to swab-extracted O . ophidiicola DNA samples from multiple snake species, states, and years. When compared to full-genome sequencing, the qPCR-based genotyping assay assigned 75% of samples to the same major clade (Cohen’s kappa = 0.360, 95% Confidence Interval = 0.154–0.567) with 67–77% sensitivity and 88–100% specificity, depending on clade/clonal lineage. Swab-extracted O . ophidiicola DNA samples from across the United States were assigned to six different clonal lineages, including four of the six established lineages and two newly defined groups, which likely represent recombinant strains of O . ophidiicola . Using multinomial logistic regression modeling to predict clade based on snake taxonomic group, state of origin, and year of collection, state was the most significant predictor of clonal lineage. Furthermore, clonal lineage was not associated with disease severity in the most intensely sampled species, the Lake Erie watersnake ( Nerodia sipedon insularum ). Overall, this assay represents a rapid, cost-effective genotyping method for O . ophidiicola that can be used to better understand the epidemiology of ophidiomycosis.

PLoS ONE↗