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At least 379 records · Page 21Linked to original sources
USGS2017

An evaluation of the efficacy of using environmental DNA (eDNA) to detect giant gartersnakes (Thamnophis gigas)

Detecting populations of rare or cryptic species is essential for their conservation. For species like giant gartersnakes ( Thamnophis gigas ), conventional survey methods can be expensive and inefficient. These sampling difficulties might be overcome by modern techniques that detect deoxyribonucleic acid (DNA) shed by organisms into the environment (eDNA). We evaluated the efficacy of detecting giant gartersnake eDNA in water samples from the laboratory and at locations with known giant gartersnake populations in the Sacramento Valley of California, and failed to detect giant gartersnake DNA in most laboratory and all field samples. Aspects of giant gartersnake biology—such as highly keratinized skin and spending extensive time in the terrestrial environment, as well as hot, sunny, and turbid conditions in wetlands and canals of the Sacramento Valley—likely contributed to low detection probabilities. Although detection of eDNA shows promise under many conditions, further development is needed before sampling for eDNA is a viable option for detecting giant gartersnake populations.

California↗
USGS2022

Assessing population genomic structure and polyploidy: A crucial step for native plant restoration

Establishing an effective restoration program requires baseline genetic information to make sound decisions for seed increase and transfer. For many plants this information is lacking, especially among native forbs that are critical for pollinator health. Erigeron speciosus is a widespread, perennial forb occupying montane environments in the western United States and Canada. This species is important in fostering pollinator diversity. Our study examines the population genetic patterns across the species range using reduced-representation sequencing and surveys for genome duplication using flow cytometry and cytology. These genomic tools provide critical information for seed increase and seed transfer, necessary for restoration programs. Population genetic differentiation ( F ST ) average was 0.13 and ranged from 0.05 to 0.24 among 23 collection sites. Model-based Bayesian clustering supported a model with collection sites grouped into two populations, occupying distinct geographic regions of this species range. A genetic distance-based neighbor-joining tree also supported this division. Flow cytometry of 53 samples from 17 populations had 2C values that ranged from 1.7 to 3.6 pg with a mean 2C value of 2.3 pg. Putative triploids were found in two individuals from one collection site. The spatial distribution of genetic structure supports regionally based taxonomic descriptions of two varieties: speciosus in the North and macranthus in the South. This assessment of genetic structure and genome duplication describes an effective approach in developing baseline genetic information for restoration species, especially those species that may harbor complex taxonomy and polyploidy.

Colorado, Idaho, Montana, Oregon, South Dakota, Ut↗
USGS2008

Techniques for Monitoring Razorback Sucker in the Lower Colorado River, Hoover to Parker Dams, 2006-2007, Final Report

Trammel netting is generally the accepted method of monitoring razorback sucker in reservoirs, but this method is ineffective for monitoring this fish in rivers. Trammel nets set in the current become fouled with debris, and nets set in backwaters capture high numbers of nontarget species. Nontargeted fish composed 97 percent of fish captured in previous studies (1999-2005). In 2005, discovery of a large spawning aggregation of razorback sucker in midchannel near Needles, Calif., prompted the development of more effective methods to monitor this and possibly other riverine fish populations. This study examined the effectiveness of four methods of monitoring razorback sucker in a riverine environment. Hoop netting, electrofishing, boat surveys, and aerial photography were evaluated in terms of data accuracy, costs, stress on targeted fish, and effect on nontargeted fish as compared with trammel netting. Trammel netting in the riverine portion of the Colorado River downstream of Davis Dam, Arizona-Nevada yielded an average of 43 razorback suckers a year (1999 to 2005). Capture rates averaged 0.5 razorback suckers per staff day effort, at a cost exceeding $1,100 per fish. Population estimates calculated for 2003-2005 were 3,570 (95 percent confidence limits [CL] = 1,306i??i??i??-8,925), 1,768 (CL = 878-3,867) and 1,652 (CL = 706-5,164); wide confidence ranges reflect the small sample size. By-catch associated with trammel netting included common carp, game fish and, occasionally, shorebirds, waterfowl, and muskrats. Hoop nets were prone to downstream drift owing to design and anchoring problems aggravated by hydropower ramping. Tests were dropped after the 2006 field season and replaced with electrofishing. Electrofishing at night during low flow and when spawning razorback suckers moved to the shoreline proved extremely effective. In 2006 and 2007, 263 and 299 (respectively) razorback suckers were taken. Capture rates averaged 8.3 razorback suckers per staff day at a cost of $62 per fish. The adult population was estimated at 1,196 (925-1,546) fish. Compared with trammel netting, confidence limits narrowed substantially, from +or- 500 percent to +or- 30 percent, reflecting more precise estimates. By-catch was limited to two common carp. No recreational game fish, waterfowl, or mammals were captured or handled during use of electrofishing. Aerial photography (2006 and 2007) suggested an annual average of 580 fish detected on imagery. Identification of species was not possible; carp commonly have been mistaken for razorback sucker. Field verification determined that the proportion of razorback suckers to other fish was 3:1. On that basis, we estimated 435 razorback suckers were photographed, which equals 8.4 razorback suckers per staff day at a cost of $78 per fish. The data did not lend itself to population estimates. Fish were more easily identified from boats, where their lateral rather than their dorsal aspect is visible. On average, 888 razorback suckers were positively identified each year. Observation rates averaged 29.6 razorback suckers per staff day at a cost less than $18 per fish observed. Sucker densities averaged 20.5 and 9.6 fish/hectare which equated to an average spawning population at Needles, Calif., of 2,520 in 2006 and 1152 in 2007. The lower 2007 estimate reflected a refinement in sampling approach which removed a sampling bias. Electrofishing and boat surveys were more cost effective than other methods tested, and they provided more accurate information without the by-catch associated with trammel netting. However, they provided different types of data. Handling fish may be necessary for research purposes but unnecessary for general trend analysis. Electrofishing was extremely effective but can harm fish if not used with caution. Unnecessary electrofishing increases the likelihood of spinal damage and possible damage to eggs and potential young, and it may alter spawning behavior or duration. B

Open-File Report↗
USGS2011

Habitat suitability of patch types: a case study of the Yosemite toad

Understanding patch variability is crucial in understanding the spatial population structure of wildlife species, especially for rare or threatened species. We used a well-tested maximum entropy species distribution model (Maxent) to map the Yosemite toad (Anaxyrus (= Bufo) canorus) in the Sierra Nevada mountains of California. Twenty-six environmental variables were included in the model representing climate, topography, land cover type, and disturbance factors (e.g., distances to agricultural lands, fire perimeters, and timber harvest areas) throughout the historic range of the toad. We then took a novel approach to the study of spatially structured populations by applying the species-environmental matching model separately for 49 consistently occupied sites of the Yosemite toad compared to 27 intermittently occupied sites. We found that the distribution of the entire population was highly predictable (AUC = 0.95±0.03 SD), and associated with low slopes, specific vegetation types (wet meadow, alpine-dwarf shrub, montane chaparral, red fir, and subalpine conifer), and warm temperatures. The consistently occupied sites were also associated with these same factors, and they were also highly predictable (AUC = 0.95±0.05 SD). However, the intermittently occupied sites were associated with distance to fire perimeter, a slightly different response to vegetation types, distance to timber harvests, and a much broader set of aspect classes (AUC = 0.90±0.11 SD). We conclude that many studies of species distributions may benefit by modeling spatially structured populations separately. Modeling and monitoring consistently-occupied sites may provide a realistic snapshot of current species-environment relationships, important climatic and topographic patterns associated with species persistence patterns, and an understanding of the plasticity of the species to respond to varying climate regimes across its range. Meanwhile, modeling and monitoring of widely dispersing individuals and intermittently occupied sites may uncover environmental thresholds and human-related threats to population persistence.

Frontiers of Earth Science↗
USGS1999

Inclusion body disease of cranes

In March 1978, a previously unidentified herpesvirus was isolated at the National Wildlife Health Center (NWHC) from a die-off of captive cranes housed at the International Crane Foundation (ICF) in Baraboo, Wisconsin. Serological testing of this virus against other previously isolated avian herpesviruses does not result in cross-reactions, thereby supporting this agent’s status as a distinctly new virus. The NWHC assigned the descriptive name, “inclusion body disease of cranes” (IBDC) to this disease when reporting the outbreak in the scientific literature, because the disease is characterized by microscopic inclusions in cell nuclei throughout the liver and spleen. Very little is known about how this disease is transmitted. As with duck plague and avian cholera, outbreaks are thought to be initiated by disease carriers within a population of birds. The disease likely spreads by direct contact between infected birds and other susceptible birds and by contact with a virus-contaminated environment. Findings of antibody in sera of cranes bled nearly 3 years before the deaths at ICF indicates that the IBDC virus can be maintained in a captive crane population for at least 2 years and 8 months without causing mortality. The IBDC virus has been isolated from the cloaca of antibody-positive cranes, which indicates the potential for fecal shedding of the virus.

Information and Technology Report↗
USGS1963

Disease and infection in the Tetraonidae

Disease is one of many factors advanced to explain the fluctuations of grouse populations, but no profound study of natural disease losses in Tetraonidae exists. The literature contains frequent references to THE grouse disease, although many potential pathogens are listed in numerous surveys and limited investigations, and the relevant data indicate that no single etiologic agent is universally responsible for disease in grouse. Few experimental infections or related studies on parasite biology have been attempted. Well-trained personnel and specialized facilities are required for research and analysis (1) to develop new methods of interpretation to be used with existing census techniques, (2) to conduct intensive studies of ecological factors of host and habitat, and (3) to establish base lines for recognition of deviations from the norm. Disease in wildlife can be controlled only through management procedures based on information concerning the biology of pathogens, hosts, and environments. It cannot be studied as a separate entity if its impact on survival or population fluctuations of grouse is to be correctly assessed.

Journal of Wildlife Management↗
USGS2021

Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms

Advances in environmental DNA (eDNA) methodologies have led to improvements in the ability to detect species and communities in aquatic environments, yet the majority of studies emphasize biological diversity at the species level by targeting variable sites within the mitochondrial genome. Here, we demonstrate that eDNA approaches also have the capacity to detect intraspecific diversity in the nuclear genome, allowing for assessments of population-level genetic diversity and estimates of the number of genetic contributors in a sample. Using a panel of microsatellite loci, we evaluated intraspecific genetic diversity in the round goby (Neogobius melanostomus) using eDNA samples from experimental mesocosms. First, we tested the similarity between eDNA and individual tissue-based estimates of allele frequencies. Subsequently, we used a likelihood-based DNA mixture framework to estimate the number of unique genetic contributors in mesocosm eDNA samples and in simulated mixtures of alleles. Allele frequencies from eDNA accurately reflected allele frequencies from genotyped round goby tissue samples, indicating nuclear markers can be reliably amplified from water samples under controlled conditions. DNA mixture analyses were able to estimate the number of genetic contributors from eDNA samples and simulated mixtures of DNA from up to 58 individuals, with the degree of positive or negative bias dependent on the filtering scheme of low-frequency alleles. This study is the first to document the application of eDNA and multiple amplicon-based methods to obtain intraspecific nuclear genetic information and estimate the absolute abundance of a species in mesocosms. With proper validation, this approach has the potential to advance non-invasive survey methods to characterize populations and broadens the application of eDNA methodologies to inform population-level management objectives.

New York↗
USGS1992

Public water-supply systems and water use in Tennessee, 1988

This report summarizes the results of a study conducted by the U.S. Geological Survey, in cooperation with the Tennessee Department of Environment and Conservation (TDEC), Division of Water Supply in 1988. Data gathered during an inventory by the TDEC were collated to determine water use, supply sources, population served, and design and storage capacities of the systems. The inventory was limited to systems that were active on June 30, 1988. Results of a survey of the systems conducted by the Tennessee Department of Health and Environment during 1988 were a primary source of data for this report. Data from computer and manual files maintained by the Tennessee Department of Health and Environment and the U.S. Geological Survey also were used. The Division of Water Supply, TDEC, surveyed 541 public water-supply systems. These systems served 81 percent of the population of the State, or 3.95 million people. The gross per capita use statewide for public-supplied water was 179 gallons per day. Total water withdrawals for public supply increased about 39 percent from 510 million gallons per day (Mgal/d) in 1980, to 708 Mgalld in 1988. During the same period, the population increased about 7 percent. Surface-water withdrawals accounted for 63 percent (446 Mgal/d) of the total water withdrawn in the State. All of these withdrawals occurred in the Tennessee (56 percent or 249 Mgal/d) and the Ohio (44 percent or 197 Mgalld) hydrologic regions. Ground water supplied 262 Mgal/d or 37 percent of the total water withdrawn by public-supply systems statewide. Of that amount, 79 percent, or 208 Mgalld, was used in western Tennessee.

Tennessee↗
USGS2016

A shift in bloater consumption in Lake Michigan between 1993 and 2011 and its effects on Diporeia and Mysis prey

Bioenergetics modeling was used to determine individual and population consumption by Bloater Coregonus hoyi in Lake Michigan during three time periods with variable Bloater density: 1993–1996 (high), 1998–2002 (intermediate), and 2009–2011 (low). Despite declines in Bloater abundance between 1993 and 2011, our results did not show any density-dependent compensatory response in annual individual consumption, specific consumption, or proportion of maximum consumption consumed. Diporeia spp. accounted for a steadily decreasing fraction of annual consumption, and Bloater were apparently unable to eat enough Mysis diluviana or other prey to account for the loss of Diporeia in the environment. The fraction of production of both Diporeia and Mysis that was consumed by the Bloater population decreased over time so that the consumption-to-production ratio for Diporeia + Mysis was 0.74, 0.26, and 0.14 in 1993–1996, 1998–2002, and 2009–2011, respectively. Although high Bloater numbers in the 1980s to 1990s may have had an influence on populations of Diporeia, Bloater were not the main factor driving Diporeia to a nearly complete disappearance because Diporeia continued to decline when Bloater predation demands were lessening. Thus, there appears to be a decoupling in the inverse relationship between predator and prey abundance in Lake Michigan. Compared with Alewife Alosa pseudoharengus, the other dominant planktivore in the lake, Bloater have a lower specific consumption and higher gross conversion efficiency (GCE), indicating that the lake can support a higher biomass of Bloater than Alewife. However, declines in Bloater GCE since the 1970s and the absence of positive responses in consumption variables following declines in abundance suggest that productivity in Lake Michigan might not be able to support the same biomass of Bloater as in the past.

Lake Michigan↗
USGS2025

Bait trapping of waterfowl increases the environmental contamination of avian influenza virus (AIV)

Highly pathogenic avian influenza virus (HPAIV) H5Nx clade 2.3.4.4b has circulated in North America since late 2021, resulting in higher rates of morbidity and mortality in wild birds than observed in this region before. The objective of this study was to determine whether baiting, which is widely conducted in Canada and the United States as part of waterfowl management practices (e.g., duck banding), influences the occurrence of avian influenza virus (AIV) in wetlands. We used a quasi-experimental design, collecting superficial sediment samples ( n = 336) and fecal samples ( n = 242) from paired baited (treatment) and non-baited (control) sites at 2 wetlands in Saskatchewan, Canada, between August and September 2022. We visited sampling sites 3 times during the sampling period: prior to the commencement of baiting activities ( t0 ), approximately 14 days after t0 ( t1 ), and 24 days after t0 ( t2 ). We screened samples for AIV using real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) targeting the matrix gene and subjected the PCR-positive samples to next-generation sequencing. We used a mixed-effects logistic regression model to estimate the effect of baiting on the odds of AIV positivity in sediment samples, while controlling for clustering by wetland. At control sites, we did not detect evidence for a difference in the odds of AIV detection in sediment at t1 or t2 versus t0 ; however, at baited sites, the odds of AIV detection at t1 were 5.43 (95% CI = 1.99, 14.79) times the odds at t0 and at t2 the odds of AIV detection were 8.73 (95% CI = 3.29, 23.18) times the odds at t0 . We detected HPAIV clade 2.3.4.4b H5N1 in sediment at 1 treatment site following baiting. There was also a trend towards increased fecal AIV positivity and increased fecal and sediment AIV diversity in baited versus non-baited sites; however, there was insufficient power to determine if these findings were statistically significant. Overall, our results indicate that baiting is associated with localized increases in AIV environmental contamination, with baiting potentially creating concentrated areas of AIV accumulation. As such, wetland baiting activities may pose a risk to wildlife population health through the propagation of AIV in wetlands and the waterfowl using those environments and efforts to replace, refine, or reduce this activity may be warranted depending on local ecosystem contexts and cost-benefit analyses.

Saskatchewan↗
USGS2014

Learning rate and temperament in a high predation risk environment

Living in challenging environments can influence the behavior of animals in a number of ways. For instance, populations of prey fish that experience frequent, nonlethal interactions with predators have a high proportion of individuals that express greater reaction to risk and increased activity and exploration—collectively known as temperament traits. Temperament traits are often correlated, such that individuals that are risk-prone also tend to be active and explore more. Spatial learning, which requires the integration of many sensory cues, has also been shown to vary in fish exposed to different levels of predation threat. Fish from areas of low predation risk learn to solve spatial tasks faster than fish from high predation areas. However, it is not yet known whether simpler forms of learning, such as learning associations between two events, are similarly influenced. Simple forms of associative learning are likely to be affected by temperament because a willingness to approach and explore novel situations could provide animals with a learning advantage. However, it is possible that routine-forming and inflexible traits associated with risk-prone and increased exploratory behavior may act in the opposite way and make risk-prone individuals poorer at learning associations. To investigate this, we measured temperament in Panamanian bishop fish ( Brachyrhaphis episcopi ) sampled from a site known to contain many predators. The B. episcopi were then tested with an associative learning task. Within this population, fish that explored more were faster at learning a cue that predicted access to food, indicating a link between temperament and basic learning abilities.

Oecologia↗
USGS2004

Dust storms and their impact on ocean and human health: dust in Earth's atmosphere

Satellite imagery has greatly influenced our understanding of dust activity on a global scale. A number of different satellites such as NASA's Earth-Probe Total Ozone Mapping Spectrometer (TOMS) and Se-viewing Field-of-view Sensor (SeaWiFS) acquire daily global-scale data used to produce imagery for monitoring dust storm formation and movement. This global-scale imagery has documented the frequent transmission of dust storm-derived soils through Earth's atmosphere and the magnitude of many of these events. While various research projects have been undertaken to understand this normal planetary process, little has been done to address its impact on ocean and human health. This review will address the ability of dust storms to influence marine microbial population densities and transport of soil-associated toxins and pathogenic microorganisms to marine environments. The implications of dust on ocean and human health in this emerging scientific field will be discussed.

EcoHealth↗
USGS2021

Evidence for continental-scale dispersal of antimicrobial resistant bacteria by landfill-foraging gulls

Anthropogenic inputs into the environment may serve as sources of antimicrobial resistant bacteria and alter the ecology and population dynamics of synanthropic wild animals by providing supplemental forage. In this study, we used a combination of phenotypic and genomic approaches to characterize antimicrobial resistant indicator bacteria, animal telemetry to describe host movement patterns, and a novel modeling approach to combine information from these diverse data streams to investigate the acquisition and long-distance dispersal of antimicrobial resistant bacteria by landfill-foraging gulls. Our results provide evidence that gulls acquire antimicrobial resistant bacteria from anthropogenic sources, which they may subsequently disperse across and between continents via migratory movements. Furthermore, we introduce a flexible modeling framework to estimate the relative dispersal risk of antimicrobial resistant bacteria in western North America and adjacent areas within East Asia, which may be adapted to provide information on the risk of dissemination of other organisms and pathogens maintained by wildlife through space and time.

Article↗
USGS2015

Trade-offs in osmoregulation and parallel shifts in molecular function follow ecological transitions to freshwater in the Alewife

Adaptation to freshwater may be expected to reduce performance in seawater because these environments represent opposing selective regimes. We tested for such a trade-off in populations of the Alewife ( Alosa pseudoharengus ). Alewives are ancestrally anadromous, and multiple populations have been independently restricted to freshwater (landlocked). We conducted salinity challenge experiments, whereby juvenile Alewives from one anadromous and multiple landlocked populations were exposed to freshwater and seawater on acute and acclimation timescales. In response to acute salinity challenge trials, independently derived landlocked populations varied in the degree to which seawater tolerance has been lost. In laboratory-acclimation experiments, landlocked Alewives exhibited improved freshwater tolerance, which was correlated with reductions in seawater tolerance and hypo-osmotic balance, suggesting that trade-offs in osmoregulation may be associated with local adaptation to freshwater. We detected differentiation between life-history forms in the expression of an ion-uptake gene ( NHE3 ), and in gill Na + /K + -ATPase activity. Trade-offs in osmoregulation, therefore, may be mediated by differentiation in ion-uptake and salt-secreting pathways.

Evolution↗
USGS2003

Using semipermeable membrane devices (SPMDs) to assess the toxicity and teratogenicity of aquatic amphibian habitats

Environmental contamination has been suspected of being partially responsible for recent declines in amphibian populations. It is often not feasible to identify all of the compounds in an environment, nor the concentrations in which they are present. SPMDs are passive sampling devices that uptake lipophilic compounds from the environment in a manner similar to aquatic organisms. The extracts from the SPMDs, therefore, contain a composite sample of the compounds that are present in the environment. In this paper, we outline the methods from studies in which we have used extracts from SPMDs in toxicity tests on amphibian larvae. Using SPMD extracts makes it possible to establish potential links between amphibian deformities and declines and environmental contamination by lipophilic compounds.

ASTM Special Technical Publication↗
USGS2016

Peatlands and green frogs: A relationship regulated by acidity?

The effects of site acidification on amphibian populations have been thoroughly addressed in the last decades. However, amphibians in naturally acidic environments, such as peatlands facing pressure from the peat mining industry, have received little attention. Through two field studies and an experiment, I assessed the use of bog habitats by the green frog (Rana clamitans melanota), a species sensitive to various forestry and peat mining disturbances. First, I compared the occurrence and breeding patterns of frogs in bog and upland ponds. I then evaluated frog movements between forest and bog habitats to determine whether they corresponded to breeding or postbreeding movements. Finally, I investigated, through a field experiment, the value of bogs as rehydrating areas for amphibians by offering living Sphagnum moss and two media associated with uplands (i.e., water with pH ca 6.5 and water-saturated soil) to acutely dehydrated frogs. Green frog reproduction at bog ponds was a rare event, and no net movements occurred between forest and bog habitats. However, acutely dehydrated frogs did not avoid Sphagnum. Results show that although green frogs rarely breed in bogs and do not move en masse between forest and bog habitats, they do not avoid bog substrates for rehydrating, despite their acidity. Thus, bogs offer viable summering habitat to amphibians, which highlights the value of these threatened environments in terrestrial amphibian ecology.

Écoscience↗
USGS2023

The 3D Elevation Program—Supporting Oregon's economy

Introduction Oregon’s physical environments and vegetation are diverse. The varied geologic and climatic conditions combined with increasing population have created the need for high-quality elevation data that can be used for infrastructure management, forestry and wildfire management, agriculture, natural resources conservation, and other business uses. Critical applications that meet the State’s management needs depend on light detection and ranging (lidar) data that provide a highly detailed three-dimensional (3D) model of the Earth’s surface and aboveground features.

Oregon↗
USGS2024

Freshwater mussel viromes increase rapidly in diversity and abundance when hosts are released from captivity into the wild

Freshwater mussels create habitat, filter water, and enhance food webs, but they are also among the world’s most imperiled taxa. Conservation efforts largely rely on captive propagation in which mussels are grown in protected aquaculture environments (hatcheries) for later release. Recent evidence has highlighted the importance of pathogens in population losses of freshwater mussels. In response to ongoing mass mortality events of freshwater mussels in the Upper Tennessee River Basin in Virginia and Tennessee, USA, we conducted a multi-year study to document viruses across multiple restoration sites and compare them to viruses in mussels from the hatchery. Viral communities changed greatly after mussels were released. Of the 681 viruses of the 27 families we documented, only 20 viruses were found exclusively in hatchery mussels, compared to 451 viruses found only in mussels stocked to the wild. After release, mussels rapidly acquired new viruses, and the number of viruses increased steadily over time. These findings have implications for how mussel introduction programs might be managed for greater success, for example, by incorporating acclimatization periods prior to full release.

Tennessee, Virgnia↗