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The U.S. Geological Survey, Western Ecological Research Center (USGS-WERC) was requested by the Bureau of Ocean Energy Management (BOEM) to create a database for marine birds of the California Current System (CCS) that would allow quantification and species ranking regarding vulnerability to offshore wind energy infrastructure (OWEI). This was needed so that resource managers could evaluate potential impacts associated with siting and construction of OWEI within the California Current System section of the Pacific Offshore Continental Shelf, including California, Oregon, and Washington. Along with its accompanying Open File Report (OFR), this comprehensive database can be used (and modified or updated) to quantify...
(i) This dataset presents macroscopic and microscopic pathological findings and bacteriology of 178 tadpoles diagnosed with Severe Perkinsea Infections. (ii) Specimen were collected and submitted to the NWHC as part of mortality investigations and collection of specimen from apparently healthy populations as part of ongoing amphibian health monitoring. (iii) Necropsies and gross evaluation of carcasses were carried out under a dissecting microscope. (iv) Severe Perkinsea Infection was confirmed in each specimen by histological observation of pathological changes in tissues with presence of Perkinsea-like organisms in at least one organ, including brain, eyes, gastrointestinal tract, gills, heart, liver, lungs, kidney,...
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These data were collected as part of a field trial to test the effectiveness of a sylvatic plague vaccine (see Rocke et al., 2017 for details). Vaccine and control plots were selected randomly from the available pairs at each location. Baits containing Rhodamine B, a biomarker, were distributed at each plot. At least 1 week and no more than 2 months post-baiting each year, local collaborators captured, marked, and sampled prairie dogs. Hair and whisker samples were collected from up to 50 unique prairie dogs from each plot each year. Sex, age, weight, and the identity of all current-year and prior-year recaptures were recorded for each captured animal. In the laboratory, hair/whiskers were assessed for the presence...
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This dataset was used to summarize and analyze the mortality factors recorderd on dead trees in the Sierra Nevada Forest Dynamics Plot Network, which is managed by the Sequoia and Kings Canyon Field station of the U.S. Geological Survey's Western Ecological Research Center. Each row of the dataset represents an individual dead tree. These are dead trees that were recorded in the network from 1998 to 2010 for the subset of plots as described in the associated manuscript; These data support the following: Das, A.J., Stephenson, N.L., Davis, K.P. 2016. Why do trees die? Characterizing the drivers of background tree mortality. Ecology. 97(10): 2616-2627, https://doi.org/10.1002/ecy.1497
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This data set consists of monthly averages of soil and litter properties. Rows are grouped in the following order: year, month, vegetation type, plot ID. Within a single month five plots were sampled within each of the 2 vegetation types (10 plots total). Columns F+ represent individual measurements.
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A site in north eastern MI, Oscoda Township, has some of the highest recorded exposure in birds to perfluorinated substances (PFASs) in the U.S. Some egg and plasma concentrations at that location exceeded the lowest reproductive effect threshold established for two avian laboratory species. The objectives of this study were to determine whether there were reproductive effects or physiological responses in a model bird species, the tree swallow (Tachycineta bicolor), associated with this extremely high exposure to PFASs. The lack of exposure above background to other contaminants at this site allowed for an assessment of PFAS effects without the complication that responses may be caused by other contaminants. A...
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Invasive species may vary in their seasonal distribution and abundance due to environmental conditions such as precipitation and temperature. Bigheaded carps, which include silver and bighead carp, are one such taxon of invasive species that appear to change habitats seasonally. Seasonal changes in bigheaded carp distribution may occur because of hydrological changes, water temperature changes, and spawning activities. Monitoring this seasonal dispersal and migration is important for management to control the population size and spread of the species. We examined if environmental DNA (eDNA) approaches could detect seasonal changes in the occurrence of DNA in water samples and used these approaches to calculate the...
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To determine if invasive annual grasses increased around energy developments after the construction phase, we calculated an invasives index using Landsat TM and ETM+ imagery for a 34-year time period (1985-2018) and assessed trends for 1,755 wind turbines (from the U.S. Wind Turbine Database) installed between 1988 and 2013 in the southern California desert. The index uses the maximum normalized difference vegetation index (NDVI) for early season greenness (January-June), and mean NDVI (July-October) for the later dry season. We estimated the relative cover of invasive annuals each year at turbine locations and control sites and tested for changes before and after each turbine was installed. These data were used...
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These data sets are is a compilation of bird and environmental samples obtained from 6 sites in Maricopa County, Arizona on the dates shown. Sites were only visited and sampled if they had Rosy-cheeked lovebirds coming to bird feeders at the location and with the permission of the property owner. Two swab samples were obtained from each captured bird and 3 swab samples were collected from the environment at each site. Each sample was tested by PCR for Chlamydia psittaci, Psittacine Circovirus genotype 1 [PCV-1]), and Psittacine Circovirus genotype 2 (PCV-2) and, for appropriate samples (love birds and environmental samples) and where enough sample material remained for PBFD virus Pathotype 2.
Fibropapillomatosis (FP) is a tumor disease of marine turtles associated with Chelonid herpesvirus 5 (ChHV5) that has historically been refractory to growth in tissue culture. Here, we show for the first time de novo formation of ChHV5-positive intranuclear inclusions in cultured green turtle cells, which is indicative for active lytic replication of the virus. The minimal requirements to achieve lytic replication in cultured cells included 1) either in-vitro culturing of ChHV5-positive tumor biopsies or organotypic cultures consisting of ChHV5-positive turtle fibroblasts in collagen rafts seeded with ChHV5-negative or -positive turtle keratinocytes and 2) keratinocyte maturation, which occurred naturally in explanted...
The data set contains results for nine serum biochemistries in molting Pacific black brant (Branta bernicla nigricans). These data were used to calculate reference intervals (sometimes referred to as normal values) for the nine serum biochemistries. All brant were after-hatch year. All samples were collected in 2006 and 2007 in the Teshekpuk Lake Special Area, Alaska.
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To understand the genetic structure of six rare plant species (Acanthomintha ilicifolia, Baccharis vanessae, Chloropyron maritimum ssp. maritimus, Deinandra conjugens, Dicranostegia orcuttiana, Monardella viminea), we obtained samples from known occurrences in San Diego County, prepared and sequenced ddRAD genomic libraries, and developed and analyzed a panel of genetic markers to assess population diversity and divergence. We provide this SNP genotype dataset in Structure format, produced in Stacks v2.0b8, for future monitoring efforts and population genetic analysis. These data support the following publication: Milano, E.R., and Vandergast, A.G., 2018, Population genomic surveys for six rare plant species in...
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To describe calling activity of Pseudacris crucifer in relation to temperature, precipitation, and wetland water levels, we programmed an acoustic recorder (Wildlife Acoustics) to sample seasonal amphibian calls remotely at study site SC4DAI2 in the St. Croix National Scenic Riverway from 2008 to 2012. We programmed the recorder to sample for five minutes at the top of every hour of every day from late winter/early spring through late summer. We used the Songscape option in Songscope software to generate annual summaries of all of our acoustic samples from SC4DAI2. These summaries included a median dB level for each prescribed frequency within each recording. Pseudacris crucifer, the spring peeper, inhabited SC4DAI2...
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From 1994-1997 I surveyed breeding birds and sampled vegetation at 391 random points on UMR floodplain forest along a latitudinal gradient to characterize bird assemblages and associations with gradients in forest structure at the local survey point and land cover composition within 200m radius of survey points (landscape scale). We conducted 10 minute 50m fixed radius point counts (Ralph et al. 1993) to survey birds during the breeding period between 30 May and 10 July in all years. We sampled the southernmost pool (13) first and then progressed to each pool in succession northward, finishing in Pool 4, sampling each point once a season. Surveys were conducted from 30 minutes before to five hours after local sunrise....
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Data set includes water Sr:Ca, Ba:Ca, and δ18O for the Upper Mississippi River and tributaries and otolith Sr:Ca, Ba:Ca, and δ18O data from bigheaded carp collected in pools 19-21 of the Upper Mississippi River. Abstract from manuscript: Knowledge of environments used during early life history and movement patterns of Bighead Carp (Hypophthalmichthys nobilis) and Silver Carp (H. molitrix), collectively termed bigheaded carps, in the Upper Mississippi River (UMR) would be valuable for informing control measures to limit further population expansion and impacts of these species. Lock and Dam 19 (LD19) is a high-head dam on the UMR that delineates downriver areas where bigheaded carps are well-established from upriver...
These datasets were developed to represent the genetic diversity, population structure, and geographic distribution of Plantago ovata in the Mojave Desert. This data release consists of two tab-delimited text files representing the genetic diversity and structure of Plantago ovata (.genepop and .vcf), and two raster spatial datasets (GeoTIFF) reflecting predicted habitat for the species within the Mojave Desert. The genetic datasets record genetic variation at an individual level, with the file structures varying based on the programs within which the files are intended to be edited. Each file contains 13,111 SNPs genotyped in 748 individuals. The genepop file can be viewed in GENEPOP software (Rousset 2008) or...
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Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail ( Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11...
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This data release contains three 10-meter resolution GeoTIFFs representing 10-meter (35-foot), 30-meter (100-foot) and 90-meter (300-foot) riparian buffer zones along shorelines, rivers, streams, and other lotic (flowing) water features. The layers are binary, where the value of each cell represents the presence or absence of the buffer zone. In addition, the data release contains shapefile layers that document the extent of corrections that were made to the data to address errors in the stream network (see processing steps section for more details). The methodology combines various fine-scale input layers, including a 1:24k stream network and Chesapeake Bay 1-meter resolution Land Use/Land Cover to approximate...
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Atmospheric deposition of reactive nitrogen (Nr) due to human activities can have measurable effects on ecosystem processing and export of nutrients, groundwater and surface-water quality. Rates of Nr deposition to lower-elevation forests immediately adjacent to the Denver/Boulder urban area, however, have only recently been measured. The focus of this study was to determine the extent of urban and agricultural N pollution transport to the Colorado Front Range. In conjunction with the Network for Urban Atmospheric Nitrogen Chemistry (NUANC) and the National Atmospheric Deposition Program (NADP), we measured wet-plus-dry Nr deposition and evaluated spatial and seasonal variations in N deposition along an elevational...
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In 2007, a phase shift from corals to corallimorpharians (CM) was documented at Palmyra Atoll, Line Islands, centered around a shipwreck. Subsequent surveys revealed CM to be overgrowing the reef benthos, including corals and coralline algae, potentially placing coral ecosystems in the atoll at risk. This prompted the U.S. Fish and Wildlife Service, the lead management agency of the atoll, to remove the shipwreck. Subsequent surveys showed reversal of spread of CM around the ship impact site. We explain patterns of spread of the CM in terms of life history and local currents and show with a pilot study that pulverized bleach may be an effective tool to eradicate CM on a local scale. If applied strategically, particularly...
map background search result map search result map Mortality factors for dead trees from a subset of plots from the Sierra Nevada Forest Dynamics Plot Network from 1998 to 2010 A Century of Landscape Disturbance and Urbanization of the San Francisco Bay Region affects the Present-day Genetic Diversity of the California Ridgway’s Rail (Rallus obsoletus obsoletus) Seasonal trends in eDNA detection and occupancy of bigheaded carps, Wabash River, IN: Raw Data Data for calculating population, collision and displacement vulnerability among marine birds of the California Current System associated with offshore wind energy infrastructure (ver. 2.0, June 2017) Serum biochemistries of Pacific black brant Effects of Flood Inundation and Invasion by Phalaris arundinacea on Nitrogen Cycling in an Upper Mississippi River Floodplain Forest data SPV field trials bait uptake data Chelonid herpesvirus 5 virus isolation data Corallimorph Invasion Palmyra: Data Occurrence of Chlamydia sp in apparently healthy birds associated with a mortality event caused by chlamydiosis: Data Daily calling activity for Pseudacris crucifer at site SC4DAI2 in the St. Croix National Scenic Riverway from 2008 to 2012, as indicated by the results of integrating daily median dB values across 2900 to 3200 Hz and 2100 to 2300 h Genotypes for six rare plant species found in San Diego County in 2016-2017 Upper Mississippi River water and bigheaded carp otolith chemistry data Pathology and bacteriology of 178 tadpoles with histologically confirmed Severe Perkinsea Infections: Data 1990s bird and vegetation data from UMR floodplain forest Perfluoroalkyl contaminant exposure in tree swallows nesting at Clarks Marsh, Oscoda, MI Dataset Data supporting Landsat time series assessment of invasive annual grasses following energy development Genetic and Habitat Data for Plantago ovata in the Mojave Desert Seasonal Atmospheric Nitrate and Ammonium Deposition along an Elevation Gradient in the Colorado Front Range using Ion Exchange Resin Columns (2018-2019) Chesapeake Bay Watershed 1:24k 10, 30 and 90-meter Riparian Buffer Zones Effects of Flood Inundation and Invasion by Phalaris arundinacea on Nitrogen Cycling in an Upper Mississippi River Floodplain Forest data Perfluoroalkyl contaminant exposure in tree swallows nesting at Clarks Marsh, Oscoda, MI Dataset Corallimorph Invasion Palmyra: Data Seasonal Atmospheric Nitrate and Ammonium Deposition along an Elevation Gradient in the Colorado Front Range using Ion Exchange Resin Columns (2018-2019) Upper Mississippi River water and bigheaded carp otolith chemistry data Genotypes for six rare plant species found in San Diego County in 2016-2017 Mortality factors for dead trees from a subset of plots from the Sierra Nevada Forest Dynamics Plot Network from 1998 to 2010 Occurrence of Chlamydia sp in apparently healthy birds associated with a mortality event caused by chlamydiosis: Data Daily calling activity for Pseudacris crucifer at site SC4DAI2 in the St. Croix National Scenic Riverway from 2008 to 2012, as indicated by the results of integrating daily median dB values across 2900 to 3200 Hz and 2100 to 2300 h Data supporting Landsat time series assessment of invasive annual grasses following energy development Seasonal trends in eDNA detection and occupancy of bigheaded carps, Wabash River, IN: Raw Data Genetic and Habitat Data for Plantago ovata in the Mojave Desert Chelonid herpesvirus 5 virus isolation data Chesapeake Bay Watershed 1:24k 10, 30 and 90-meter Riparian Buffer Zones Serum biochemistries of Pacific black brant 1990s bird and vegetation data from UMR floodplain forest SPV field trials bait uptake data Data for calculating population, collision and displacement vulnerability among marine birds of the California Current System associated with offshore wind energy infrastructure (ver. 2.0, June 2017) Pathology and bacteriology of 178 tadpoles with histologically confirmed Severe Perkinsea Infections: Data