Search USGS⌕ Search

SEARCH · Search USGS

Results for “Snake”

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 379 records · Page 21Linked to original sources
USGS2021

Monitoring native, resident nonsalmonids for the incidence of gas bubble trauma downstream of Snake and Columbia River Dams, 2021

In 2020, a new spill program was implemented to aid the downstream passage of juvenile salmonids at mainstem dams on the Snake and Columbia rivers. Under this program, the total dissolved gas (TDG) cap was increased to 125% and monitoring of native, resident nonsalmonid (NRN) fishes for gas bubble trauma (GBT) became a requirement. The primary objective of this work was to measure the incidence and severity of GBT in NRN fishes resulting from increased juvenile fish passage spill and associated levels of TDG during the spring spill period. A secondary objective was to measure the incidence of GBT in incidentally collected juvenile salmonids when NRN sample size targets were met. NRN fishes were collected downstream from Bonneville, McNary, and Ice Harbor dams and examined for the incidence and severity of GBT in 2021. Fish were collected at each location weekly (6 April to 17 June) during the spring spill period by backpack electrofishing and beach seining. Washington and Oregon state water quality agencies established minimum and target sample sizes for monitoring, and in all weeks the minimum sample size of 50 fish was met and in most weeks the target sample size of 100 fish was met. Collected fish were examined for GBT according to the criteria and protocol established for the regional smolt monitoring program (SMP). Overall, GBT incidence and severity rankings were low and did not exceed the thresholds that would have triggered changes to the spill program. Using SMP criteria, weekly GBT incidences ranged from 0 to 1.0% downstream from Bonneville Dam, 0 to 6.2% downstream from McNary Dam, and 0 to 1.9% downstream from Ice Harbor Dam. Except for one three-spined stickleback (Gasterosteus aculeatus) collected downstream of Bonneville Dam, the only NRN species that showed signs of GBT was sculpin spp. GBT was observed in sculpin in body locations other than the unpaired fins and eyes (i.e., SMP criteria). If GBT incidence in all areas on the fish (i.e., paired fins, unpaired fins, eyes, body) are combined, then weekly GBT incidence rates increase and range from 0 to 4.3% downstream from Bonneville Dam, 0 to 15.4% downstream from McNary Dam, and 0 to 4.7% downstream from Ice Harbor Dam. This illustrates the effect of using different criteria to determine the incidence of GBT in NRN fishes. It also shows how the proportion of a species in a sample that is more prone to show GBT can influence GBT incidence rate. On a number of occasions, incidental catch of subyearling fall Chinook salmon were examined for GBT downstream of Bonneville Dam but none showed any signs. The DG was generally below 120% and never reached the 125% gas cap during the spring spill season, which may be why GBT incidence rates were so low as past research has shown that GBT signs in NRN fishes are relatively low below this TDG level.

Oregon, Washington↗
USGS2023

Monitoring native nonsalmonids for the incidence of gas bubble trauma downstream of Snake and Columbia River dams during the spring spill season, 2022

In 2020, a new spill program was implemented to aid the downstream passage of juvenile salmonids at mainstem dams on the Snake and Columbia rivers. Under this program, the total dissolved gas (TDG) cap was increased to 125% and monitoring of native nonsalmonids for gas bubble trauma (GBT) became a requirement. The primary objective of this work was to measure the incidence and severity of GBT in native nonsalmonids resulting from increased juvenile fish passage spill and associated levels of TDG during the spring spill period. Native nonsalmonids were collected downstream from Bonneville, McNary, Ice Harbor, and Lower Granite dams and examined for the incidence and severity of GBT in 2022. Fish were collected at each location weekly (4 April to 13 June) during the spring spill period by backpack electrofishing and beach seining. Washington and Oregon state water quality agencies established minimum and target sample sizes for monitoring, but the minimum sample size of 50 fish and target sample size of 100 fish were not met in all weeks at individual projects due to high water flows and resulting low fish collections. Collected fish were examined for GBT according to the criteria and protocol established for the regional smolt monitoring program (SMP). Overall, GBT incidence and severity rankings were low and did not exceed the thresholds that would have triggered changes to the spill program. Using SMP criteria, maximum weekly GBT incidences were 1.9% downstream from Bonneville Dam, 8.6% downstream from McNary Dam, 7.7% downstream from Ice Harbor Dam, and 3.4% downstream from Lower Granite Dam. In contrast to 2021, several species showed signs of GBT in 2022, and GBT was commonly observed in fins and body locations other than the unpaired fins and eyes (i.e., SMP criteria). In general, the observed signs of GBT according to SMP criteria were not severe (i.e., ranks 1 and 2). Although TDG reached the gas cap, particularly late in the spring spill season, GBT incidence rates were not high probably due to factors such as habitat-related variability in TDG, species composition and varying tolerance to high TDG, low power to detect GBT incidence at small sample sizes, and unknown exposure history.

Oregon, Washington↗
USGS2023

Eastern Indigo snake (Drymarchon couperi) shelter site use In peninsular Florida, USA, and implicatIons for habItat conservatIon

Shelters are critical for many species as protection from predators and extreme temperatures. Successful conservation of reptiles requires understanding both shelter site requirements and availability. The Eastern Indigo Snake (EIS; Drymarchon couperi ) is endemic to the southeastern U.S. and is federally listed. Recovery has focused on maximizing unfragmented landscapes, with less attention on fine-scale features such as shelter sites. In the northern EIS range, Gopher Tortoise ( Gopherus polyphemus ) burrows are used extensively for shelter. Although EIS in peninsular Florida often shelter in tortoise burrows, they also use other shelters where tortoise burrows are scarce or absent. Solely focusing EIS survey and management efforts where Gopher Tortoises are present may overlook occupied habitats and misallocate resources. We investigated the importance of different shelter sites in central Florida using data from radio-tracked EIS. We modeled the use of shelter categories as a function of sex, season, and habitat using Bayesian multinomial Generalized Linear Models. Results showed that EIS in peninsular Florida used Gopher Tortoise burrows across all seasons and habitats. Tortoise burrow use was highest in xeric habitats and lowest in mesic habitats where burrows are most and least abundant, respectively. There was less variability in shelter site use in disturbed habitats and flatwoods. Tortoise burrow use by EIS in the cool season across sexes and habitats in our study was much lower than in southern Georgia. Our results indicate that EIS are less dependent on Gopher Tortoise burrows in peninsular Florida and that suitable habitats with few or no tortoise burrows could still provide conservation value for EIS.

Florida, Georgia↗
USGS2024

Encounter rates and catch-and-release mortality of steelhead in the Snake River basin

Objective The potential influence (i.e., impact rate) of catch-and-release fisheries on wild steelhead Oncorhynchus mykiss is poorly understood and is a function of the abundance of wild fish, how many fish are encountered by anglers (i.e., encounter rate), and the mortality of fish that are caught and released. In Idaho, estimates of wild steelhead encounter rates have been derived using the number of wild and hatchery steelhead passing Lower Granite Dam, the number of hatchery steelhead harvested, and the number of hatchery steelhead caught and released. The method includes assumptions that hatchery and wild steelhead have equal encounter rates and catch-and-release mortality is 5% for wild steelhead. Here, we investigated wild and hatchery steelhead encounter rates by anglers, estimated catch-and-release mortality, and concatenated both aspects to examine how existing recreational steelhead fisheries influence wild steelhead mortality. Methods We sampled, tagged, and released 1,251 spawn-year 2020 (SY2020) and 1,956 spawn-year 2021 (SY2021) adult steelhead at Lower Granite Dam with T-bar anchor tags and passive integrated transponder (PIT) tags to estimate steelhead encounter rates and catch-and-release mortality. Differences in survival of caught steelhead and those not reported as caught were evaluated using detections at various locations (e.g., PIT arrays, weirs). Result Estimated encounter rates were 43.7% (95% credible interval; 28.2%, 100.0%) for wild fish and 46.7% (29.6%, 100.0%) for adipose-clipped fish in SY2020. In SY2021, encounter rates were 47.2% (32.4%, 100.0%) for wild fish and 52.3% (37.1%, 100.0%) for adipose-clipped fish. Based on detections of caught fish and those not reported as caught, catch-and-release mortality of wild steelhead was estimated to be 1.6% (0.0%, 5.2%). Wild steelhead impact rates were 0.7% (0.0%, 2.7%) in SY2020 and 0.7% (0.0%, 2.8%) in SY2021. Conclusion Estimated rates of impact on wild steelhead were consistent and low across years despite major differences in the structure of the fisheries. Our results suggest assuming that encounter rates are equal between hatchery and wild steelhead, and that steelhead catch-and-release mortality is 5%, will likely lead to a conservative estimate of the wild steelhead impact occurring from catch-and-release fisheries.

Idaho, Oregon, Washington↗
USGS2008

Effect of soil disturbance on recharging fluxes: Case study on the Snake River Plain, Idaho National Laboratory, USA

Soil structural disturbance influences the downward flow of water that percolates deep enough to become aquifer recharge. Data from identical experiments in an undisturbed silt-loam soil and in an adjacent simulated waste trench composed of the same soil material, but disturbed, included (1) laboratory- and field-measured unsaturated hydraulic properties and (2) field-measured transient water content profiles through 24 h of ponded infiltration and 75 d of redistribution. In undisturbed soil, wetting fronts were highly diffuse above 2 m depth, and did not go much deeper than 2 m. Darcian analysis suggests an average recharge rate less than 2 mm/year. In disturbed soil, wetting fronts were sharp and initial infiltration slower; water moved slowly below 2 m without obvious impediment. Richards' equation simulations with realistic conditions predicted sharp wetting fronts, as observed for disturbed soil. Such simulations were adequate for undisturbed soil only if started from a post-initial moisture distribution that included about 3 h of infiltration. These late-started simulations remained good, however, through the 76 d of data. Overall results suggest the net effect of soil disturbance, although it reduces preferential flow, may be to increase recharge by disrupting layer contrasts. ?? Springer-Verlag 2007.

Hydrogeology Journal↗
USGS2015

Defining population structure and genetic signatures of decline in the giant garter snake ( Thamnophis gigas ): implications for conserving threatened species within highly altered landscapes

Anthropogenic habitat fragmentation can disrupt the ability of species to disperse across landscapes, which can alter the levels and distribution of genetic diversity within populations and negatively impact long-term viability. The giant gartersnake ( Thamnophis gigas ) is a state and federally threatened species that historically occurred in the wetland habitats of California’s Great Central Valley. Despite the loss of 93 % of historic wetlands throughout the Central Valley, giant gartersnakes continue to persist in relatively small, isolated patches of highly modified agricultural wetlands. Gathering information regarding genetic diversity and effective population size represents an essential component for conservation management programs aimed at this species. Previous mitochondrial sequence studies have revealed historical patterns of differentiation, yet little is known about contemporary population structure and diversity. On the basis of 15 microsatellite loci, we estimate population structure and compare indices of genetic diversity among populations spanning seven drainage basins within the Central Valley. We sought to understand how habitat loss may have affected genetic differentiation, genetic diversity and effective population size, and what these patterns suggest in terms of management and restoration actions. We recovered five genetic clusters that were consistent with regional drainage basins, although three northern basins within the Sacramento Valley formed a single genetic cluster. Our results show that northern drainage basin populations have higher connectivity than among central and southern basins populations, and that greater differentiation exists among the more geographically isolated populations in the central and southern portion of the species’ range. Genetic diversity measures among basins were significantly different, and were generally lower in southern basin populations. Levels of inbreeding and evidence of population bottlenecks were detected in about half the populations we sampled, and effective population size estimates were well below recommended minimum thresholds to avoid inbreeding. Efforts focused on maintaining and enhancing existing wetlands to facilitate dispersal between basins and increase local effective population sizes may be critical for these otherwise isolated populations.

Conservation Genetics↗
USGS2018

Effects of urbanization, and habitat composition on site occupancy of two snake species using regional monitoring data from southern California

Detection data from a regional, reptile-monitoring program conducted by the U.S. Geological Survey were analyzed to understand the effects of urbanization and habitat composition on site occupancy of the coachwhip ( Masticophis flagellum ) and striped racer ( M. lateralis ) in coastal southern California. Likelihood-based occupancy models indicated striped racers responded to habitat composition, favoring scrub-dominated sites. Coachwhips also responded to habitat composition, favoring open habitats. However, unlike racers, coachwhip spatial population dynamics were strongly associated with the fragmentation and isolation of natural areas caused by urbanization. The odds of coachwhips occupying a site were 64 times greater in large connected areas than the most urbanized and fragmented sites. For coachwhips within urbanized and fragmented sites, the odds of extinction were 10 times greater and odds of colonization were five times lower than in large connected sites. Observed differences between both species in habitat use and specificity are supported by telemetry studies and corroborate existing knowledge of historical patterns of occurrence within the region. Movement data on the coachwhip and striped racer indicate the coachwhip is a wider-ranging species with a greater propensity to encounter roads and other edge environments. Collectively, the results suggest there is widespread loss of the coachwhip from the region, and that long-term persistence of remaining populations is dependent on metapopulation dynamics. The substantially different response of the two species to land-use change serves as a caution against the casual use of closely related species as surrogates in the development of species-specific conservation plans.

California↗
USGS2020

Conservation reliance of a threatened snake on rice agriculture

Conservation-reliant species require perpetual management by humans to persist. But do species that persist largely in human-dominated landscapes actually require conditions maintained by humans? Because most extant populations of giant gartersnakes (Thamnophis gigas) inhabit the highly modified rice agricultural regions of the Sacramento Valley, we sought to evaluate whether giant gartersnakes are indeed a conservation-reliant species dependent on maintenance of rice agriculture and its infrastructure for their continued existence. Specifically, we examined the extent to which giant gartersnakes use rice fields themselves, and whether survival of adult giant gartersnakes was influenced by the amount of rice grown near their home ranges and daily movements. We found that although giant gartersnakes only use rice fields minimally and then only between mid-June and early September, their survival was lower when less rice agriculture was available near the areas they inhabited. Survival was particularly low in early spring, when giant gartersnakes emerge from brumation but rice fields are not yet flooded. The incongruity between the phenology of rice growing and giant gartersnake foraging requirements suggests that although giant gartersnakes are reliant on the rice agroecosystem, rice agriculture is likely suboptimal habitat for giant gartersnakes. Giant gartersnakes’ reliance on the rice agroecosystem challenges the notion of preservation-based conservation, but provides opportunities for win-win scenarios benefitting both rice farmers and giant gartersnakes. Our study highlights that in addition to land use, the timing of land management might be crucial for conservation-reliant species.

Global Ecology and Conservation↗
USGS2000

Use of chlorine-36 to determine regional-scale aquifer dispersivity, eastern Snake River Plain aquifer, Idaho/USA

Chlorine-36 (36Cl) derived from processed nuclear waste that was disposed at the US Department of Energy's Idaho National Engineering and Environmental Laboratory (INEEL) through a deep injection well in 1958, was detected 24-28 yr later in groundwater monitoring wells approximately 26 km downgradient from the source. Groundwater samples covering the period 1966-1995 were selected from the US Geological Survey's archived-sample library at the INEEL and analyzed for 36Cl by accelerator mass spectrometry (AMS). The smaller 36Cl peak concentrations in water from the far-field monitoring wells relative to the input suggest that aquifer dispersivity may be large. However, the sharpness of the 1958 disposal peak of 36Cl is matched by the measured 36Cl concentrations in water from these wells. This implies that a small aquifer dispersivity may be attributed to preferential groundwater flowpaths. Assuming that tracer arrival times at monitoring wells are controlled by preferential flow, a 1-D system-response model was used to estimate dispersivity by comparing the shape of predicted 36Cl-concentration curves to the shape of 36Cl-concentration curves measured in water from these observation wells. The comparisons suggest that a 1-D dispersivity of 5 m provides the best fit to the tracer data. Previous work using a 2-D equivalent porous-media model concluded that longitudinal dispersivity (equivalent to 1-D dispersivity in our model) was 90 m (Ackerman, 1991). A 90 m dispersivity value eliminates the 1958 disposal peak in our model output curves. The implications of the arrival of 36Cl at downgradient monitoring wells are important for three reasons: (1) the arrival times and associated 36Cl concentrations provide quantitative constraints on residence times, velocities, and dispersivities in the aquifer; (2) they help to refine our working hypotheses of groundwater flow in this aquifer and (3) they may suggest a means of estimating the distribution of preferential flowpaths in the aquifer. ?? 2000 Elsevier Science B.V. All rights reserved.

Nuclear Instruments and Methods in Physics Researc↗
USGS2026

Biological, environmental, and geomorphological factors influencing reach-specific survival of spring Chinook Salmon smolts upstream of the Columbia–Snake River hydrosystem

Objective Pacific salmon Oncorhynchus spp. are exhibiting catastrophic declines throughout much of the Pacific Northwest, and juvenile mortality contributions are disproportionately high. Many Pacific salmon smolt populations are exhibiting high natal stream mortality; however, detailed natal stream reach-specific survival knowledge is lacking. Our objectives were to estimate natal stream reach-specific survival and identify influential covariates for spring Chinook Salmon O. tshawytscha smolts. An additional objective was to evaluate (i.e., estimate postrestoration cumulative survival) a novel and strategic large-scale river restoration approach (i.e., stream confluence restoration) in two Pacific Northwest spring Chinook Salmon natal streams. Methods Using radiotelemetry techniques during March–June (2011–2017), we estimated natal stream reach-specific survival for spring Chinook Salmon smolts in Catherine Creek and the Grande Ronde River, northeast Oregon. We examined the interrelated influences of temporal, biological, environmental, and geomorphological covariates on the behavior, travel time, and reach-specific survival of spring Chinook Salmon smolts that were emigrating through two hydrologically altered natal streams in the interior Columbia River basin. For each natal stream smolt tag-group, Cormack–Jolly–Seber reach-specific survival estimates that were adjusted for premature tag failure (i.e., bias-corrected) were generated. Subsequently, smolt effects were estimated using reach-specific travel times and survival estimates coupled with individual time-varying covariates from radio-tagged smolts and occupied reaches using an existing predator–prey model (i.e., mean free-path length [ XT ] model). Complementary population-specific principal coordinate analyses (PCoAs) were conducted to facilitate visualization of multicovariate resemblances in ordination space. Last, we employed our best-fitting XT model to model cumulative changes in smolt survival that were associated with a large-scale stream channel restoration scenario (i.e., restoration of the historical Catherine Creek and Grande Ronde River confluence). Results In aggregate, Catherine Creek smolts exhibited high mortality throughout Catherine Creek but near-100% survival upon entering the Grande Ronde River. In contrast, Grande Ronde River smolts generally exhibited low mortality upstream from the Grande Ronde Valley and high mortality throughout the Grande Ronde Valley. Our best-fitting XT model indicated that smolt survival was positively correlated with discharge, body size, and current velocity but negatively correlated with avian predation. Natural-origin smolts from Catherine Creek displayed higher λ-values (i.e., distance between predator–prey encounters) than their significantly larger and faster emigrating hatchery conspecifics, indicating that hatchery smolts may be more susceptible to predation. Our population-specific PCoAs further revealed that novel water (i.e., unique water chemistry) and emigration rate were the strongest predictors of reach occupancy in multivariate ordination space. Under a stream restoration scenario of restoring the historical hydrological template (i.e., restored channel configuration), our best-fitting XT model predicted changes in population-specific cumulative survivals to the lower Grande Ronde Valley (Imbler, Oregon) ranging from −38.4% to 69.0% for Grande Ronde River and Catherine Creek spring Chinook Salmon smolts, respectively. Conclusions Our best-fitting XT model and PCoAs identified the relative importance of biological, environmental, and geomorphological factors to both natural- and hatchery-origin Chinook Salmon smolt survival in two neighboring interior natal streams in the Columbia River basin. Our research indicates that concurrent habitat restoration and fish management strategies, including focused attention on smolt-rearing nursery habitat restoration, piscivorous avian control plans, adaptive management strategies for hatchery smolt releases, and discharge and novel water regime restoration projects, may yield survival benefits to “in-basin” Chinook Salmon smolts. Our research can inform origin-type-specific Chinook Salmon smolt management, habitat restoration, and future research decisions throughout the upper Grande Ronde River subbasin and potentially the Pacific Northwest.

Oregon, Washington↗