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USGS1995

Water-quality assessment of the upper Snake River Basin, Idaho and western Wyoming — Environmental setting, 1980-92

The 35,800-square-mile upper Snake River Basin is one of 20 areas studied as part of the National Water-Quality Assessment (NAWQA) Program of the U.S. Geological Survey. Objectives of NAWQA are to study ground- and surface-water quality, biology, and their relations to land-use activities. Major land and water uses that affect water quality in the basin are irrigated agriculture, grazing, aquaculture, food processing, and wastewater treatment. Data summarized in this report are used in companion reports to help define the relations among land use, water use, water quality, and biological conditions. The upper Snake River Basin is located in southeastern Idaho and northwestern Wyoming and includes small parts of Nevada and Utah. Total population in the basin was about 425,000 in 1990. Major urban areas are Idaho Falls, Pocatello, Rexburg, and Twin Falls, Idaho, which make up 10, 11,3, and 6 percent of the total population, respectively. Climate in the basin is mostly semiarid and mean annual precipitation ranges from 8 to more than 60 inches. The eastern Snake River Plain is the major geologic feature in the basin and is delineated mostly by Quaternary and Tertiary basalt flows. It is about 55 to 62 miles wide and 320 miles long and bisects the basin in a northeast-southwest direction. The Snake River is the dominant surface-water feature and flows about 453 miles from the southern border of Yellowstone National Park in Wyoming to King Hill, Idaho, where it leaves the basin. The Snake River flows through five reservoirs that provide a total storage capacity of more than 4 million acre-feet. Gravity-flow diversions are predominant in the upper part of the basin and totaled 8.8 million.acre-feet in 1980. Pumped diversions occur mainly in the lower part of the basin and totaled 408,500 acre-feet in 1980. The Snake River Plain aquifer is the predominant ground-water feature in the upper Snake River Basin and underlies the eastern Snake River Plain. The upper 500 feet of the aquifer may store 200 to 300 million acre-feet of water. Ground-water resources that supply agricultural lands are sustained by recharge from surface-water irrigation, precipitation, and tributary inflow. Major ground-water discharges are at springs and seeps or from ground-water pumpage for irrigation. Water use in the basin is dominated by irrigated agriculture, which is the largest consumptive water use in the basin. Major crops in the basin include potatoes, wheat, sugar beets, hay, and barley. Most irrigation needs are supplied from surface-water sources through a series of canals and laterals. In 1990, about 2.5 million acres were irrigated with more than 14.2 million acre-feet of surface and ground water. About 21 percent of the basin is agricultural land and 50 percent is rangeland. Idaho leads the Nation in trout production for commercial sale. Combined mean annual discharges from 12 aquacultural facilities in the basin (1985-90) were about 787,000 acre-feet. These facilities are clustered in a reach of the Snake River between Milner Dam and King Hill where ground-water discharge is from many seeps and springs that provide sufficient quantities of good-quality water. Other facilities that release effluent to the Snake River include 13 municipal wastewater treatment plants and 3 industrial facilities.

Idaho, Wyoming↗

USGS2018

Behavioral differences following ingestion of large meals and consequences for management of a harmful invasive snake: A field experiment

Many snakes are uniquely adapted to ingest large prey at infrequent intervals. Digestion of large prey is metabolically and aerobically costly, and large prey boluses can impair snake locomotion, increasing vulnerability to predation. Cessation of foraging and use of refugia with microclimates facilitating digestion are expected to be strategies employed by free‐ranging snakes to cope with the demands of digestion while minimizing risk of predation. However, empirical observations of such submergent behavior from field experiments are limited. The brown treesnake (Serpentes: Colubridae: Boiga irregularis ) is a nocturnal, arboreal, colubrid snake that was accidentally introduced to the island of Guam, with ecologically and economically costly consequences. Because tools for brown treesnake damage prevention generally rely on snakes being visible or responding to lures or baits while foraging, cessation of foraging activities after feeding would complicate management. We sought to characterize differences in brown treesnake activity, movement, habitat use, and detectability following feeding of large meals (rodents 33% of the snake's unfed body mass) via radio telemetry, trapping, and visual surveys. Compared to unfed snakes, snakes in the feeding treatment group showed drastic decreases in hourly and nightly activity rates, differences in refuge height and microhabitat type, and a marked decrease in detectability by trapping and visual surveys. Depression of activity lasted approximately 5–7 days, a period that corresponds to previous studies of brown treesnake digestion and cycles of detectability. Our results indicate that management strategies for invasive brown treesnakes need to account for cycles of unavailability and underscore the importance of preventing spread of brown treesnakes to new environments where large prey are abundant and periods of cryptic behavior are likely to be frequent. Characterization of postfeeding behavior changes provides a richer understanding of snake ecology and foraging models for species that consume large prey.

Ecology and Evolution↗

USGS2020

Highly competent native snake hosts extend the range of an introduced parasite beyond its invasive Burmese python host

Invasive Burmese pythons ( Python bivittatus ) have introduced a nonnative pentastomid parasite ( Raillietiella orientalis ) to southern Florida that has spilled over to infect native snakes. However, the extent of spillover, regarding prevalence and intensity, is unknown. We examined native snakes ( n = 523) and invasive pythons ( n = 1003) collected from Florida to determine the degree to which parasite spillover is occurring. We found R. orientalis has infected 13 species of native snakes collected from areas of sympatry with pythons. Prevalence and infection intensity of R. orientalis were significantly higher among native snakes compared with pythons. Moreover, adult female pentastomes achieved larger sizes and represented a greater proportion of the overall parasite population in native snakes vs. pythons, indicating native snakes are more competent hosts of R. orientalis than pythons. We also examined native snakes from regions of allopatry with pythons to determine how far R. orientalis has spread. We found an infected native snake 348 km north of the northernmost infected python. Our data show that native snakes are highly competent hosts of R. orientalis and have facilitated the rapid spread of this nonnative pentastome beyond the range of its invasive host.

Alabama, Florida, Georgia↗

USGS1984

A review of crust and upper mantle structure studies of the Snake River Plain-Yellowstone volcanic system: A major lithospheric anomaly in the western U.S.A.

The Snake River Plain-Yellowstone volcanic system is one of the largest, basaltic, volcanic field in the world. Here, there is clear evidence for northeasterly progression of rhyolitic volcanism with its present position in Yellowstone. Many theories have been advanced for the origin of the Snake River Plain-Yellowstone system. Yellowstone and Eastern Snake River Plain have been studied intensively using various geophysical techniques. Some sparse geophysical data are available for the Western Snake River Plain as well. Teleseismic data show the presence of a large anomalous body with low P- and S-wave velocities in the crust and upper mantle under the Yellowstone caldera. A similar body in which compressional wave velocity is lower than in the surrounding rock is present under the Eastern Snake River Plain. No data on upper mantle anomalies are available for the Western Snake River Plain. Detailed seismic refraction data for the Eastern Snake River Plain show strong lateral heterogeneities and suggest thinning of the granitic crust from below by mafic intrusion. Available data for the Western Snake River Plain also show similar thinning of the upper crust and its replacement by mafic material. The seismic refraction results in Yellowstone show no evidence of the low-velocity anomalies in the lower crust suggested by teleseismic P-delay data and interpreted as due to extensive partial melting. However, the seismic refraction models indicate lower-than-normal velocities and strong lateral inhomogeneities in the upper crust. Particularly obvious in the refraction data are two regions of very low seismic velocities near the Mallard Eake and Sour Creek resurgent domes in the Yellowstone caldera. The low-velocity body near the Sour Creek resurgent dome is interpreted as partially molten rock. Together with other geophysical and thermal data, the seismic results indicate that a sub-lithospheric thermal anomaly is responsible for the time-progressive volcanism along the Eastern Snake River Plain. However, the exact mechanism responsible for the volcanism and details of magma storage and migration are not yet fully understood.

California, Idaho, Montana, Nevada, Oregon, Washin↗

USGS2023

A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus

Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus , has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed “ring species” around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis , as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.

Journal of Heredity↗

USGS2026

Long-term intermittent connection between the western Snake River Plain and Columbia basin: A two-phased incision history of Hells Canyon

For more than a century, researchers have debated the route of the Snake River across the northern Cordillera and U.S. Pacific Northwest, including the associated incision history of Hells Canyon. Here, we use detrital zircon U-Pb provenance analysis of Miocene strata upstream and downstream of Hells Canyon to constrain the evolution in fluvial pathways over time. Downstream of Hells Canyon, we show that the ca. 10−6 Ma Clarkston Heights gravel was dominantly sourced from the nearby Salmon and Clearwater rivers but also with substantial input from drainages that now flow into the western Snake River Plain. These same western Snake River Plain drainages were contributing to time-equivalent Lake Idaho strata, upstream of Hells Canyon, indicating a Hells Canyon fluvial connection between the western Snake River Plain and Columbia basin before 6 Ma. Results from Lake Idaho strata suggest a two-phased lacustrine history in the western Snake River Plain: Before ca. 6.0 Ma, lake strata were derived from local tributaries, suggesting that the western Snake River Plain was isolated from the modern upper Snake River system. Between ca. 4.3 Ma and 2.2 Ma, the source area expanded to include eastern tributaries in conjunction with migration of high-standing topography of the Yellowstone hotspot. Our results challenge the long-held hypothesis of “capture” of the Snake River through Hells Canyon. Instead, we infer that Hells Canyon was a long-established route for outflow of lakes occupying the western Snake River Plain, possibly intermittently, during a ca. 10−2 Ma phase of slow regional incision, followed by rapid incision in Hells Canyon starting ca. 2 Ma in conjunction with erosion of the topographic barrier impounding Lake Idaho.

Idaho, Oregon↗

USGS2008

Brown treesnake (Boiga irregularis) trappability: Attributes of the snake, environment and trap

We examined three classes of factors that may influence brown treesnake (Boiga irregularis) trappability on Guam: (1) attributes of the snake, (2) attributes of the environment and (3) attributes of the trap. The attributes of the snake we considered included body condition, length and sex. Heavier snakes for a given size (better body condition) moved less and were less easily trapped. Longer snakes were easier to trap. Males were also slightly more easily trapped than females. We compared brown treesnake trappability between two study sites that differed greatly in the abundance of diurnal skinks, an important prey item for smaller snakes. We predicted that snakes, especially small individuals (<800 mm snout-vent length), would be more easily trapped in the low prey environment, a result that received only weak support from our data. However, small snakes were rarely trapped under any circumstance. We also predicted that diurnal foraging would be observed in the site with a higher density of diurnal prey, but daytime snake captures were negligible at both sites. Two attributes of traps that we varied were attractant (mouse vs. skink) and entrance flaps (present vs. absent). Traps with mice as attractant registered 6-16 fold more snake captures. We found little influence of entrances on captures. These modulators of brown treesnake trappability may have analogues in a variety of species, especially species that undergo an ontogenetic shift in diet. ?? 2008 Brill Academic Publishers.

Applied Herpetology↗

USGS2023

Evaluating growth rates of captive, wild, and reintroduced populations of the imperiled Eastern Indigo Snake (Drymarchon couperi)

Reintroduction of species at sites where populations have been extirpated has become a common technique in wildlife conservation. To track progress towards reintroduction success, effective postrelease monitoring is needed to document vital rates of individuals and the corresponding impact on population trajectories. We assessed growth and body size in Eastern Indigo Snakes (Drymarchon couperi) using a data set from multiple projects across the species' distribution, including free-ranging wild snakes, snakes reared in captive-breeding programs, and snakes released at two reintroduction sites. We used these data to fit a von Bertalanffy growth model in a Bayesian framework to quantify differences in growth among three broad categories of snakes (wild, captive, and reintroduced), while accounting for measurement error across various projects. We also compared changes in body mass of captive-born individuals from four captive rearing facilities. Asymptotic snout–vent length across all groups was 185 cm (95% credible interval = 177–194 cm) for males and 157 cm (95% credible interval = 153–161 cm) for females. Reintroduced snakes had a higher growth coefficient than either captive or wild snakes (e.g., captive females = 1.20 [1.06–1.35] d –1 ; wild females = 1.22 [0.95–1.49] d –1 ; reintroduced females = 1.62 [1.21–2.05] d –1 ), indicating that current captive-breeding and rearing efforts for indigo snakes produce similar or faster growth trends compared to wild populations. Furthermore, daily changes in juvenile body weight relative to body size were similar in three of the four captive rearing facilities (mean for females at Orianne Center for Indigo Conservation = 0.57 [0.48–0.65]; Zoo Atlanta = 0.55 [0.37–0.72]; Welaka National Fish Hatchery = 0.55, [0.36–0.73]; Auburn University = 0.39 [0.21–0.58]). Long-term project success for indigo snake reintroductions will depend on continuing to implement best practices in an adaptive management framework.

Herpetologica↗

USGS2018

Snake fungal disease in North America: U.S. Geological Survey updates

Snake fungal disease (SFD) results from a skin infection that has been documented only in snakes. Historically, reports of snakes with skin infections of unknown origin have been sporadic. Recently, the number of reported cases of skin infections in snakes has increased substantially. This emerging infectious disease, confirmed in numerous species of snakes, is caused by the fungus Ophidiomyces ophiodiicola . As of August 2017, O. ophiodiicola has been detected in at least 23 States and one Canadian Province. However, researchers suspect that SFD may be more widely distributed than these documented cases suggest, because efforts to monitor the health of many snake populations are limited. Snake fungal disease may also be underreported in populations where it affects snakes infrequently or in species that develop less severe illness. Signs of SFD include crusted or ulcerated scales, nodules (that is, abnormal bumps) under the skin, and facial disfiguration that can be quite severe, leading to emaciation and death. Many snake populations are already in decline due to habitat loss and dwindling prey populations, and the recent emergence of SFD may accelerate this decline, causing certain species to disappear entirely from some locations.

Fact Sheet↗

USGS1996

Summary of the Snake River plain Regional Aquifer-System Analysis in Idaho and eastern Oregon

Regional aquifers underlying the 15,600-square-mile Snake River Plain in southern Idaho and eastern Oregon was studied as part of the U.S. Geological Survey's Regional Aquifer-System Analysis program. The largest and most productive aquifers in the Snake River Plain are composed of Quaternary basalt of the Snake River Group, which underlies most of the 10,8000-square-mile eastern plain. Aquifer tests and simulation indicate that transmissivity of the upper 200 feet of the basalt aquifer in the eastern plain commonly ranges from about 100,000 to 1,000,000 feet squared per day. However, transmissivity of the total aquifer thickness may be as much as 10 million feet squared per day. Specific yield of the upper 200 feet of the aquifer ranges from about 0.01 to 0.20. Average horizontal hydraulic conductivity of the upper 200 feet of the basalt aquifer ranges from less than 100 to 9,000 feet per day. Values may be one to several orders of magnitude higher in parts in individual flows, such as flow tops. Vertical hydraulic conductivity is probably several orders of magnitude lower than horizontal hydraulic conductivity and is generally related to the number of joints. Pillow lava in ancestral Snake River channels has the highest hydraulic conductivity of all rock types. Hydraulic conductivity of the basalt decreases with depth because of secondary filling of voids with calcite and silica. An estimated 80 to 120 million acre-feet of water is believed to be stored in the upper 200 feet of the basalt aquifer in the eastern plain. The most productive aquifers in the 4,800-square-mile western plain are alluvial sand and gravel in the Boise River valley. Although aquifer tests indicate that transmissivity of alluvium in the Boise River valley ranges from 5,000 to 160,000 feet squared per day, simulation suggests that average transmissivity of the upper 500 feet is generally less than 20,000 feet squared per day. Vertically averaged horizontal hydraulic conductivity of the upper 500 feet of alluvium ranges from about 4 to 40 feet per day; higher values can be expected in individual sand and gravel zones. Vertical hydraulic conductivity is considerably lower because of the presence of clay layers. Hydraulic heads measured in piezometers, interpreted from diagrams showing ground-water flow and equipotential lines and estimated by computer simulation, demonstrate that water movement is three dimensional through the rock framework. Natural recharge takes place along the margins of the plain where head decreases with depth; discharge takes place near some reaches of the Snake River and the Boise River where head increases with depth. Geothermal water in rhyolitic rocks in the western plain and western part of the eastern plain has higher hydraulic head than the overlying cold water. Geothermal water, therefore, moves upward and merges into the cold-water system. Basin water-budget analyses indicate that the volume of cold water. Carbon-14 age determinations, which indicate that residence time of geothermal water is 17,700 to 20,300 years, plus or minus 4,000 years, imply slow movement of water through the geothermal system. Along much of its length, the Snake River gains large quantities of ground water. On the eastern plain, the river gained about 1.9 million acre-feet of water between Blackfoot and Neeley, Idaho, in 1980. Between Milner and King Hill, Idaho, the river gained 4.7 million acre-feet, mostly as spring flow from the north side. Upstream from Blackfoot and in the vicinity of Lake Walcott, the rover loses flow to ground water during parts or all of the year. On the western plain, river gains from ground water are small relative to those on the eastern plain; most are from seepage. Streams in tributary drainage basins supply calcium/bicarbonate type and calcium/magnesium/bicarbonate type water to the plain. Water type is a reflection of the chemical composition of rocks in the drainage basin, Concentrations of dissolved solids are smallest, about 50 milligrams per liter, in streams such as the Boise River that drain areas of granitic rocks; concentrations are greatest, about 400 milligrams per liter, in streams such as the Owyhee and Raft Rivers that drain area of sedimentary rocks. Water chemistry reflects the interaction of surface water and ground water. The chemical composition of ground water in the plain is essentially the same as that in streamflow and groundwater discharge from tributary drainage basins. Tributary drainage basins supplied 85 percent of the ground-water recharge in the eastern plain during 1980 and a nearly equivalent percentage of the solute load in ground water; human activities and dissolution of minerals supplied the other solutes. Dissolved-solids concentrations in ground water were generally less than 400 milligrams per liter. Water from the lower geothermal system is chemically different from water from the upper cold-water system. Geothermal water typically has greater concentrations of sodium, bicarbonate, sulfate, chloride, fluoride, silica, arsenic, boron, and lithium and smaller concentrations of calcium, magnesium, and hydrogen. Difference are attributed to ion exchange as geothermal moves through the rock framework. Irrigation, mostly on the Snake River Plain, accounted for about 96 percent of consumptive water use in Idaho during 1980. The use of surface water for irrigation for more than 100 years has caused major changes in the hydrologic system on the plain. Construction of dams, reservoirs, and diversifications effected planned changes in the surface-water system but resulted in largely unplanned changes in the ground-water system. During those years of irrigation, annual recharge in the main part of the eastern plain increased to about 6.7 million acre-feet in 1980, or by about 70 percent. Most of the increase was from percolation of surface water diverted for irrigation. From preirrigation to 1952, groundwater storage increased about 24 million acre-feet, and storage decreased from 1952 to 1964 and from 1976 to 1980 because of below-normal precipitation and increased withdrawals of ground water for irrigation. Annual ground-water discharge increased to about 7.1 million acre-feet in 1980, or about 80 percent since the start of irrigation. About 10 percent of the 1980 total discharge was ground-water pumpage. About 3.1 million acres, or almost one-third of the plain, was irrigated during 1980: 2.0 million acres with surface water, 1.0 million acres with ground water, and 0.1 million acres with combined surface and ground water. About 8.9 million acre-feet of Snake River water was diverted for irrigation during 1980 and 2.3 million acre-feet of ground water was pumped from 5,300 wells. Most irrigation wells on the eastern plain are open to basalt. About two-thirds of them yield more than 1,500 gallons per minute with a reported maximum of 7,240 gallons per minute; drawdown is less than 20 feet in two-thirds of the wells. Most irrigation wells on the western plain are open to sedimentary rocks. About one-third of them yield more than 1,00 gallons per minute with a reported maximum of 3,850 gallons per minute; drawndown is less than 20 feet in about one-fifth of the wells. The major instream use of water on the Snake River Plain is hydroelectric power generation. Fifty-two million acre-feet of water generated 2.6 million megawatthours of electricity during 1980. Digital computer ground-water flows models of the eastern and western plain reasonably simulated regional changes in water levels and ground-water discharges from 1880 (preirrigation) to 1980. Model results support the concept of three-dimensional flow and the hypotheses of no underflow between the eastern and western plain. Simulation of the regional aquifer system in the eastern plain indicates that is 1980 hydrologic conditions, including pumpage, were to remain the same for another 30 years, moderate declines in ground-water levels and decreases in spring discharges would continue. Increased ground-water pumpage to irrigate an additional 1 million acres could cause ground-water levels to decline a few tens of feet in the central part of the plain and could cause corresponding decreases in ground-water discharge. A combination of actions such as increased ground-water pumpage and decreased use of surface water for irrigation (resulting in reduced recharge) would accentuate the changes.

Idaho;Oregon↗

USGS2014

Evaluation of seepage and discharge uncertainty in the middle Snake River, southwestern Idaho

The U.S. Geological Survey, in cooperation with the State of Idaho, Idaho Power Company, and the Idaho Department of Water Resources, evaluated seasonal seepage gains and losses in selected reaches of the middle Snake River, Idaho, during November 2012 and July 2013, and uncertainty in measured and computed discharge at four Idaho Power Company streamgages. Results from this investigation will be used by resource managers in developing a protocol to calculate and report Adjusted Average Daily Flow at the Idaho Power Company streamgage on the Snake River below Swan Falls Dam, near Murphy, Idaho, which is the measurement point for distributing water to owners of hydropower and minimum flow water rights in the middle Snake River. The evaluated reaches of the Snake River were from King Hill to Murphy, Idaho, for the seepage studies and downstream of Lower Salmon Falls Dam to Murphy, Idaho, for evaluations of discharge uncertainty. Computed seepage was greater than cumulative measurement uncertainty for subreaches along the middle Snake River during November 2012, the non-irrigation season, but not during July 2013, the irrigation season. During the November 2012 seepage study, the subreach between King Hill and C J Strike Dam had a meaningful (greater than cumulative measurement uncertainty) seepage gain of 415 cubic feet per second (ft 3 /s), and the subreach between Loveridge Bridge and C J Strike Dam had a meaningful seepage gain of 217 ft 3 /s. The meaningful seepage gain measured in the November 2012 seepage study was expected on the basis of several small seeps and springs present along the subreach, regional groundwater table contour maps, and results of regional groundwater flow model simulations. Computed seepage along the subreach from C J Strike Dam to Murphy was less than cumulative measurement uncertainty during November 2012 and July 2013; therefore, seepage cannot be quantified with certainty along this subreach. For the uncertainty evaluation, average uncertainty in discharge measurements at the four Idaho Power Company streamgages in the study reach ranged from 4.3 percent (Snake River below Lower Salmon Falls Dam) to 7.8 percent (Snake River below C J Strike Dam) for discharges less than 7,000 ft3/s in water years 2007–11. This range in uncertainty constituted most of the total quantifiable uncertainty in computed discharge, represented by prediction intervals calculated from the discharge rating of each streamgage. Uncertainty in computed discharge in the Snake River below Swan Falls Dam near Murphy was 10.1 and 6.0 percent at the Adjusted Average Daily Flow thresholds of 3,900 and 5,600 ft3/s, respectively. All discharge measurements and records computed at streamgages have some level of uncertainty that cannot be entirely eliminated. Knowledge of uncertainty at the Adjusted Average Daily Flow thresholds is useful for developing a measurement and reporting protocol for purposes of distributing water to hydropower and minimum flow water rights in the middle Snake River.

Idaho↗

USGS2023

Paranannizziopsis spp. infections in wild snakes and a qPCR assay for detection of the fungus

The emergence of ophidiomycosis (or snake fungal disease) in snakes has prompted increased awareness of the potential effects of fungal infections on wild reptile populations. Yet, aside from Ophidiomyces ophidiicola , little is known about other mycoses affecting wild reptiles. The closely related genus Paranannizziopsis has been associated with dermatomycosis in snakes and tuataras in captive collections, and P. australasiensis was recently identified as the cause of skin infections in non-native wild panther chameleons ( Furcifer pardalis ) in Florida, USA. Here we describe five cases of Paranannizziopsis spp. associated with skin lesions in wild snakes in North America and one additional case from a captive snake from Connecticut, USA. In addition to demonstrating that wild Nearctic snakes can serve as a host for these fungi, we also provide evidence that the genus Paranannizziopsis is widespread in wild snakes, with cases being identified in Louisiana (USA), Minnesota (USA), Virginia (USA), and British Columbia (Canada). Phylogenetic analyses conducted on multiple loci of the fungal strains we isolated identified P. australasiensis in Louisiana and Virginia; the remaining strains from Minnesota and British Columbia did not cluster with any of the described species of Paranannizziopsis , although the strains from British Columbia appear to represent a single lineage. Finally, we designed a pan- Paranannizziopsis real-time PCR assay targeting the internal transcribed spacer region 2. This assay successfully detected DNA of all described species of Paranannizziopsis and the two potentially novel taxa isolated in this study and did not cross-react with closely related fungi or other fungi commonly found on the skin of snakes. The assay was 100% sensitive and specific when screening clinical (skin tissue or skin swab) samples, although full determination of the assay’s performance will require additional follow up due to the small number of clinical samples ( n = 14 from 11 snakes) available for testing in our study. Nonetheless, the PCR assay can provide an important tool in further investigating the prevalence, distribution, and host range of Paranannizziopsis spp. and facilitate more rapid diagnosis of Paranannizziopsis spp. infections that are otherwise difficult to differentiate from other dermatomycoses.

Frontiers in Microbiology↗

USGS1999

Snake species of the world: A taxonomic and geographic reference. v. 1

Given the absence of a current source on snake diversity and nomenclature and the expressed global need to understand better the diversity of our biota, we think that a catalogue of the world snake fauna complete with synonymies at the familial, generic, and specific levels is essential. We provide that here beginning with publication of the first volume. This compendium will facilitate comparative studies on the ecology, genetics, and behavior of snakes and, we hope, contribute to their conservation. At the very least, this work, when completed, will provide a readily available reference to the current taxonomic statuses and geographic distributions of snakes on a global scale. No comprehensive, up-to-date catalogue of snake species exists, and it is obvious that a detailed and inclusive treatment is long overdue. Snake Species of the World provides a comprehensive treatment of 31 families, 450 genera, and more than 2500 species of living snakes. The magnitude of the compilation requires publication in several volumes. This volume, the first of three, covers 682 species. A primary goal of this synthesis is to provide interested readers with a means for tracking scientific names that have been applied to a snake and determining the currently accepted name of that species. A secondary goal is to alert those interested in snakes as research subjects that in general many species are poorly known, that some have limited distributions, and that several are characterized by taxonomic problems.

Book↗

USGS2013

Snake River fall Chinook salmon life history investigations: Annual report 2011 (April 2011 - March 2012)

Executive Summary Chapter One – This chapter was published in the Transactions of the American Fisheries Society in 2012. We conducted a three-year radiotelemetry study in the lower Snake River to answer the questions: do fall Chinook salmon juveniles pass dams during winter when bypass systems and structures designed to prevent mortality are not operated; does downstream movement rate vary annually, seasonally, and from reservoir to reservoir; and, what are some of the factors that contribute to annual, seasonal, and spatial variation in downstream movement rate? Fall Chinook salmon juveniles moved downstream up to 169 km and fast enough (7.5 km/d) such that large percentages (up to 93%) of the fish passed one or more dams during winter. Mean downstream movement rate varied annually (9.2-11.3 km/d), increased from winter (7.5 km/d) to spring (16.4 km/d), and increased (6.9-16.8 km/d) as fish moved downstream from reservoir to reservoir. Fish condition factor at tagging explained some of the annual variation ( P ≤ 0.01) in downstream movement rate, whereas water particle velocity ( P ≤0.0001) and temperature ( P ≤0.0001) explained portions of the seasonal variation. An increase in migrational disposition as fish moved downstream helped explain the spatial variation ( P =0.05-0.07). The potential cost of winter movement might be reduced survival due to turbine passage when the bypass systems and spillway passage structures are not operated. Efforts to understand and increase passage survival of winter migrants in large impoundments might help to rehabilitate some imperiled anadromous salmonid populations. Chapter Two – Natural juvenile fall Chinook salmon in the Snake and Clearwater rivers exhibit two life history strategies. “Ocean-type” fish migrate out to the ocean in their first summer of life as subyearlings, but “reservoir-type” fish delay seaward migration during the summer, and some overwinter in reservoirs before continuing their migration the following spring as yearlings. Earlier emerging fish produced in the Snake River tend to adopt the ocean-type life history whereas many of the later emerging fish from the Clearwater River tend to adopt the reservoirtype life history. The underlying cause of the reservoir-type life history is poorly understood, but we believe there may be link to physiological development. We used traditional markers of the parr-smolt transformation (smoltification), including gill Na + /K + -ATPase activity and thyroid hormone levels, along with gene expression microarrays to assess the development of ocean-type juvenile fall Chinook salmon and then compared it to that of juvenile fall Chinook salmon from the Clearwater River. We showed that parr in the Snake River are physiologically distinct from actively-migrating smolts but smolts migrating early and late in the summer and fall are physiologically similar. Juvenile fall Chinook salmon collected from the Clearwater River were similar in size to early-migrating smolts in the Snake River but were most physiologically similar to Snake River parr. Genes differentially expressed between Snake River parr and smolts and between fish from the Clearwater River and smolts from the Snake River were involved in the cell cycle, steroid metabolism and other metabolic pathways, and DNA repair and packaging. Many of the genes differentially expressed in these comparisons had expression patterns that correlated with gill Na + /K + -ATPase activity, suggesting that they were related to smoltification and migration status. Chapter Three – Natural subyearlings produced in the Clearwater River are exposed to cool (~10-12°C) temperatures when water is released from Dworshak Reservoir for summer flow augmentation. Total dissolved gas (TDG) levels range from 100-110% in the lower Clearwater iv River. When fish move into the Snake River, they encounter temperatures up to 24°C at the surface which have the potential to incur gas bubble disease (GBD) in fish as dissolved gases in their bodies expand under warmer temperatures. This may result in both direct and indirect mortality, but this situation has been little studied. We conducted laboratory experiments to examine subyearling mortality rates and incidence and severity of GBD in fish that were moved between waters that varied in TDG and temperature. Fish experienced significant mortality only at temperatures of 25°C, which increased with exposure time. However there was no significance difference in mortality between fish acclimated to 100% TDG and 110% TDG. Fish that died did show signs of GBD. Generally, signs of GBD such as bubbles in the lateral line and unpaired fins were higher in fish acclimated at 110% TDG than in fish acclimated at 100% TDG, but there were few trends related to exposure temperature. Field measurements of TDG showed that TDG ranged from about 100% to 122.5% at some locations. Generally, TDG fluctuated daily, up to 8% during August and early September, and was highest late in the afternoon and lowest in the early morning. Laboratory results and field monitoring demonstrated that emigrating juvenile salmon can potentially be at risk from elevated temperatures, TDG, and GBD albeit to an unknown extent, which may increase their vulnerability to predation. Chapter Four – We conducted monthly beam trawling in Lower Granite and Little Goose reservoirs to describe the seasonal abundance of benthic epifauna that are potentially important as prey to juvenile fall Chinook salmon. The predominant taxa collected were Siberian prawns, the opossum shrimp Neomysis mercedis , and the amphipod Corophium sp. Prawns were relatively abundant at shallow sites in both reservoirs in June, but were more abundant at deep sites in lower and middle reservoir reaches in autumn. Prawn densities were commonly <0.2/m2. Prawn length-frequency data indicated that there were at least two size classes. Juvenile prawns present in shallow water more often than adult prawns, which were generally only found in deep water by autumn. Ovigerous prawns had an average of 171 eggs, which represented about 11.5% of their body weight. Limited diet analyses suggested that prawns consumed Corophium , Neomysis , and aquatic insects. Neomysis dominated all catches both in terms of abundance and biomass, and they were more abundant in Lower Granite compared to Little Goose reservoir. Neomysis were more abundant at shallow sites than at deep sites. Corophium were present in our collections but were never abundant, probably because our trawl was not effective at capturing them. The caloric content of prawns (4,782 Kcal), Neomysis (4,962 Kcal), and Corophium (4,926 Kcal) indicates that these prey would be energetically profitable for juvenile salmon. Subyearling fall Chinook salmon prey heavily on Neomysis and Corophium at times, but the importance of prawns as prey is uncertain.

Oregon, Washington↗

USGS2017

Snake River Fall Chinook Salmon life history investigations

Predation by nonnative fishes is one factor that has been implicated in the decline of juvenile salmonids in the Pacific Northwest. Impoundment of much of the Snake and Columbia rivers has altered food webs and created habitat favorable for species such as Smallmouth Bass Micropterus dolomieu . Smallmouth Bass are common throughout the Columbia River basin and have become the most abundant predator in lower Snake River reservoirs (Zimmerman and Parker 1995). This is a concern for Snake River Fall Chinook Salmon Oncorhynchus tshawytscha (hereafter, subyearlings) that may be particularly vulnerable due to their relatively small size and because their main-stem rearing habitats often overlap or are in close proximity to habitats used by Smallmouth Bass (Curet 1993; Tabor et al. 1993). Concern over juvenile salmon predation spawned a number of large-scale studies to quantify its effect in the late 1980s, 1990s, and early 2000s (Poe et al. 1991; Rieman et al. 1991; Vigg et al. 1991; Fritts and Pearsons 2004; Naughton et al. 2004). Smallmouth Bass predation represented 9% of total salmon consumption by predatory fishes in John Day Reservoir, Columbia River, from 1983 through 1986 (Rieman et al. 1991). In transitional habitat between the Hanford Reach of the Columbia River and McNary Reservoir, juvenile salmon (presumably subyearlings) were found in 65% of Smallmouth Bass (>200 mm) stomachs and comprised 59% of the diet by weight (Tabor et al. 1993). Within Lower Granite Reservoir on the Snake River, Naughton et al. (2004) showed that monthly consumption (based on weight) ranged from 5% in the upper reaches of the reservoir to 11% in the forebay. However, studies in the Snake River were conducted soon after Endangered Species Act (ESA) listing of Snake River Fall Chinook Salmon (NMFS 1992). During this time, Fall Chinook Salmon abundance was at an historic low, which may explain why consumption rates were relatively low compared to those from studies conducted in the Columbia and Yakima rivers where abundance was higher (e.g., Tabor et al. 1993; Fritts and Pearsons 2004). We speculate that predation on subyearlings by Smallmouth Bass in the Snake River may have increased in recent years for several reasons. Since their ESA listing, recovery measures implemented for Snake River Fall Chinook salmon have resulted in a large increase in the juvenile population (Connor et al. 2013). Considering that subyearlings probably now make up a larger portion of the forage fish population, it is plausible they should make up a large portion of Smallmouth Bass diets. Second, migrating subyearlings delay downstream movement in the transition zones of the Clearwater River and Snake River for varying lengths of time (Tiffan et al. 2010), which increases their exposure and vulnerability to predators. Spatial overlap in locations of Smallmouth Bass and subyearlings that died during migration provides support for this (Tiffan et al. 2010). Finally, the later outmigration of subyearlings from the Clearwater River results in their presence in Lower Granite Reservoir during the warmest summer months when predation rates of Smallmouth Bass should be highest. In 2016, we focused our efforts on Smallmouth Bass predation in Lower Granite Reservoir downstream of the transition zones and the confluence area where we worked during 2012–2015. Similar to past years, our first objective was to quantify Smallmouth Bass consumption rates of subyearlings, determine relative bass abundance, and describe bass diets. In addition, Tiffan et al. (2016a) posited that predation risk to subyearlings may be higher in shoreline habitats that are more suitable for Smallmouth Bass and lower in shoreline habitats that are more suitable for subyearlings. To test this hypothesis, our second objective examines the relationship between Smallmouth Bass predation of subyearlings and habitat suitability.

Idaho, Washington↗

USGS2020

Effects of flow diversion on Snake Creek and its riparian cottonwood forest, Great Basin National Park

Snake Creek flows east from the southern Snake Range in Nevada over complex lithology before leaving Great Basin National Park. The river travels over a section of karst limestone where some surface water naturally recharges the groundwater flow system. In 1961 a water diversion pipeline was constructed by downstream water users to transport surface water through the groundwater recharge zone to reduce potential water losses. The diversion pipeline dewaters a 5-km reach for most of the year by transporting water past the recharge zone then returning it to the channel downstream. Snake Creek was incorporated into the newly established Great Basin National Park in 1986, and today park managers and visitors are concerned that the diversion has destabilized Snake Creek’s riparian ecosystem in this arid region where it has high ecological value. The objectives of this study were to 1) document riparian cottonwood forest conditions in the pipeline-dewatered (DW) reach, 2) evaluate Snake Creek water availability and whether it can support a healthy riparian ecosystem, and 3) determine if dewatering has shifted the fluvial system into an unnatural and poorly functioning state. We pursued these ecohydrological study objectives in 11 research investigations of Snake Creek’s DW reach and nearby reference reaches. The research investigations analyzed: 1) riparian forest condition, tree age, growth, and death; 2) tree ring chronologies through time and space; 3) hydroclimatic drivers of tree growth; 4) stable carbon isotopes extracted from tree rings; 5) cottonwood ecophysiology related to water transport and water stress; 6) historical aerial photography; 7) stand-level riparian forest production; 8) groundwater availability as related to surface water and plant rooting zones; 9) near-surface geophysics using electrical resistivity imaging; 10) channel and valley geomorphology; and 11) in-channel wood jams caused by fallen trees. Integrating these diverse research topics provided a full perspective of historical and modern conditions along Snake Creek. We found that modern hydrological conditions in Snake Creek’s DW reach could not maintain the drought-sensitive ecosystem. The riparian cottonwoods ( Populus angustifolia and P. angustifolia x P. trichocarpa ) have experienced significant dieback. Tree mortality was 2.4 times higher in the DW reach than in reference reaches, and surviving trees supported only 60% of the live canopy compared to trees in reference reaches. Changes in the DW reach forest began in the 1960s and became more severe during the last two decades. Stable carbon isotope ratios and branch dieback analyses both demonstrated initial forest adjustments related to water stress beginning in the early 1960s. Tree ring width chronologies indicated two periods of growth decline in the DW relative to control reaches. The first decline in the 1960s represented an immediate adjustment to the modified flow regime, and the second decline in the 2000s demonstrated reduced resilience to atmospheric drought. Aerial photos and stand-level forest production calculations indicated that substantial riparian forest decline occurred in the 1990s–2010s in the DW reach compared to reference reaches. Stable carbon isotope ratios and leaf water potentials revealed that trees in the DW reach experienced greater drought stress than those in reference reaches. Monitoring wells and electrical resistivity surveys both showed riparian water tables to be largely supported by in-channel surface water flow, indicating that the flow diversion removed water that recharges alluvial groundwater and sustains riparian plants. Areas of widespread tree mortality in the DW reach also corresponded to a larger and more unstable channel with a high instream wood load from fallen trees. Modern conditions of Snake Creek in the DW reach robustly suggest that dewatering the river and its associated riparian corridor adversely affected the riparian ecosystem. The degraded condition is likely to persist and intensify unless water is returned to the channel. As we documented during the wet 1980s and the scientific literature suggest, a partial recovery of the riparian ecosystem is likely possible with restored flows.

Nevada↗

USGS2020

Use of visual surveys and radiotelemetry reveals sources of detection bias for a cryptic snake at low densities

Transect surveys are frequently used to estimate distribution and abundance of species across a landscape, yet a proportion of individuals present will be missed because either they were out of view and unavailable for detection or they were available but not detected because the surveyors missed them. These situations lead to availability and perception bias, respectively, and can result in misleading estimates of abundance and habitat use. In this study, we examined potential biases of visual surveys used for the brown tree snake ( Boiga irregularis ), a cryptic invasive snake responsible for the extirpation of at least 15 vertebrates on Guam. We simultaneously executed visual surveys and radiotelemetry in a low‐density population of brown tree snakes with two goals in mind: to assess the efficacy of visual surveys in detecting subjects at low densities and to identify sources of perception and availability bias in such surveys. Results indicated that with considerable effort, visual surveys can predict the presence of this cryptic reptile even at low densities (0.4 animals/ha) but perform poorly at predicting areas of high use resulting in inaccurate estimates of relative habitat importance. Telemetered snakes used densely foliated plants including Pandanus tectorius and ferns (epiphytic and terrestrial species) for nearly half of their time, yet <9% of visual survey observations occurred in these microhabitats. Visibility of snakes decreased as they perched higher in the canopy mirroring the disparity between visual survey and telemetry detections but was also surprisingly low near the forest floor (0–1 m). Microhabitats identified in this study are likely to disproportionately affect visual surveys and would be appropriate resources to target for management purposes. When there is critical need to prevent false negatives, such as during an incipient invasion elsewhere, targeted searches of high‐use resources could augment other detection tools to improve detection probabilities of this and other cryptic species. ble for detection or they were available but not detected because the surveyors missed them. These situations lead to availability and perception bias, respectively, and can result in misleading estimates of abundance and habitat use. In this study, we examined potential biases of visual surveys used for the brown treesnake (Boiga irregularis), a cryptic invasive snake responsible for the extirpation of at least 15 vertebrates on Guam. We simultaneously executed visual surveys and radiotelemetry in a low-density population of brown treesnakes with two goals in mind: to assess the efficacy of visual surveys in detecting subjects at low densities and to identify sources of perception and availability bias in such surveys. Results indicated that with considerable effort, visual surveys can predict the presence of this cryptic reptile even at low densities (0.4 animals/ha) but perform poorly at predicting areas of high use resulting in inaccurate estimates of relative habitat importance. Telemetered snakes used densely foliated plants including Pandanus tectorius and ferns (epiphytic and terrestrial species) for nearly half of their time yet less than 9% of visual survey observations occurred in these microhabitats. Visibility of snakes decreased as they perched higher in the canopy mirroring the disparity between visual survey and telemetry detections but was also surprisingly low near the forest floor (0-1 meter). Microhabitats identified in this study are likely to disproportionately affect visual surveys and would be appropriate resources to target for management purposes. When there is critical need to prevent false negatives, such as during an incipient invasion elsewhere, targeted searches of high-use resources could augment other detection tools to improve detection probabilities of this and other cryptic species.

Ecosphere↗

USGS2016

Geothermal solute flux monitoring and the source and fate of solutes in the Snake River, Yellowstone National Park, WY

The combined geothermal discharge from over 10,000 features in Yellowstone National Park (YNP) can be can be estimated from the Cl flux in the Madison, Yellowstone, Falls, and Snake Rivers. Over the last 30 years, the Cl flux in YNP Rivers has been calculated using discharge measurements and Cl concentrations determined in discrete water samples and it has been determined that approximately 12% of the Cl flux exiting YNP is from the Snake River. The relationship between electrical conductivity and concentrations of Cl and other geothermal solutes was quantified at a monitoring site located downstream from the thermal inputs in the Snake River. Beginning in 2012, continuous (15 min) electrical conductivity measurements have been made at the monitoring site. Combining continuous electrical conductivity and discharge data, the Cl and other geothermal solute fluxes were determined. The 2013–2015 Cl fluxes (5.3–5.8 kt/yr) determined using electrical conductivity are comparable to historical data. In addition, synoptic water samples and discharge data were obtained from sites along the Snake River under low-flow conditions of September 2014. The synoptic water study extended 17 km upstream from the monitoring site. Surface inflows were sampled to identify sources and to quantify solute loading. The Lewis River was the primary source of Cl, Na, K, Cl, SiO 2 , Rb, and As loads (50–80%) in the Snake River. The largest source of SO 4 was from the upper Snake River (50%). Most of the Ca and Mg (50–55%) originate from the Snake Hot Springs. Chloride, Ca, Mg, Na, K, SiO 2 , F, HCO 3 , SO 4 , B, Li, Rb, and As behave conservatively in the Snake River, and therefore correlate well with conductivity (R 2 ≥ 0.97).

Wyoming↗