SEARCH · Geology Reports
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.
We conducted standardized visual searches at night for brown treesnakes (Boiga irregularis) and geckos, where we alternated between spotlight and floodlight lamps. Floodlights rendered us 25% more snakes and 71% more geckos than did spotlights. We show data on searcher variability and discuss what might affect the relative benefit of different lamp types. ?? 2009 Brill Academic Publishers.
A review of morphological characters for the western Nearctic genus Kincaidiana indicated that the two described species should be assigned to separate genera. Kincaidiana freidris Cook was transferred to a new genus, Altmanella. New material resembling A. freidris was obtained from many sites throughout western North America. Morphology of the male reproductive structures varied among populations, and the most distinctive morphological differences were accounted for by splitting the taxon into two species, which roughly corresponded to large scale regional patterns. Typical A. freidris occurred in several Pacific Coast drainages. Altmanella idahoensis n. sp., mostly associated with the Snake River drainage, was distinguished from A. freidris by shorter and less muscular atria and penial structures. A second new lumbriculid species with the same basic arrangement of reproductive organs was collected in southeastern North America, and was provisionally assigned to Altmanella. However, in contrast to the petiolate atria and large penial structures of A. freidris and A. idahoensis, Altmanella lenati n. sp. has tubular atria and simple male porophores.
Viral erythrocytic necrosis (VEN) is a disease of marine and anadromous fish that is caused by the erythrocytic necrosis virus (ENV), which was recently identified as a novel member of family Iridoviridae by next-generation sequencing. Phylogenetic analysis of the ENV DNA polymerase grouped ENV with other erythrocytic iridoviruses from snakes and lizards. In the present study, we identified the gene encoding the ENV major capsid protein (MCP) and developed a quantitative real-time PCR (qPCR) assay targeting this gene. Phylogenetic analysis of the MCP gene sequence supported the conclusion that ENV does not group with any of the currently described iridovirus genera. Because there is no information regarding genetic variation of the MCP gene across the reported host and geographic range for ENV, we also developed a second qPCR assay for a more conserved ATPase-like gene region. The MCP and ATPase qPCR assays demonstrated good analytical and diagnostic sensitivity and specificity based on samples from laboratory challenges of Pacific herring Clupea pallasii . The qPCR assays had similar diagnostic sensitivity and specificity as light microscopy of stained blood smears for the presence of intraerythrocytic inclusion bodies. However, the qPCR assays may detect viral DNA early in infection prior to the formation of inclusion bodies. Both qPCR assays appear suitable for viral surveillance or as a confirmatory test for ENV in Pacific herring from the Salish Sea.
Background Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon ( Falco peregrinus ) have been conducted, no similar studies have been done of the closely-related prairie falcon ( F. mexicanus ) and it is unclear how much genetic variation and population structure exists across the species’ range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge. Results We sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated > 16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring > 140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~ 100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population. Conclusions Our study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating population of prairie falcons across our sampling locations. Prairie falcons are highly mobile and relatively rare long-distance dispersal events may promote gene flow throughout the range. As such, California’s prairie falcons might be managed as a single population, indicating that management actions undertaken to benefit the species at the local level have the potential to influence the species as a whole.
Background Studies on the spatial ecology of invasive species provide critical information for conservation managers such as habitat preferences and identification of native species at risk of predation. To understand the spatial ecology of non-native Burmese pythons ( Python molurus bivittatus ), now well-established in Everglades National Park and much of South Florida USA, we radio-tracked 19 wild-caught adult pythons, 16 with VHF tags during 2006 through 2009 and 3 by GPS tags between 2010 and 2011. Our goal was to identify individual core-use areas and quantify home ranges, as well as to explore correlations of python movements with environmental parameters such as the presence of surface water. Results Radio-tracking periods ranged from 87 to 697 days for snakes with VHF tags, with a total of 5,119 tracking days (mean ± 1 SD = 319.9 ± 184.3 days); GPS tracking periods ranged from 12 to 93 days, with a total of 146 tracking days (mean ± 1 SD = 48.7 ± 40.7 days). We observed mean individual radio-tracked python home ranges of 22.5 km 2 (2250 ha) with overall low site fidelity; all home ranges were within the park boundary. Python core-use areas included slough and coastal habitat types, and we delineated 18 common-use areas (that is, areas where individual core-use areas spatially overlapped). Tree islands were a principal feature of common-use areas, even if they were not the predominant habitat type. Multiple common-use areas were in proximity to roads. The longest movements of individual pythons correlated well with presence of surface water, and occurred during both wet and dry seasons. Conclusions High-use areas determined from python habitat-use and movement data may be optimal locations for targeted control efforts and further studies on impacts to native fauna.
Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python ( Python molurus bivittatus ), Northern African python ( P . sebae ), boa constrictor ( Boa constrictor ), and the green ( Eunectes murinus ) and yellow anaconda ( E . notaeus ). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors. Generic sampling design and terminology are proposed to standardize and clarify interpretations of eDNA-based occupancy models.
Successful eutrophication control strategies need to address the limiting nutrient. We conducted a battery of laboratory and in situ nutrient-limitation tests with waters collected from 9 streams in an agricultural region of the upper Snake River basin, Idaho, USA. Laboratory tests used the green alga Raphidocelis subcapitata , the macrophyte Lemna minor (duckweed) with native epiphytes, and in situ nutrient-limitation tests of periphyton were conducted with nutrient-diffusing substrates (NDS). In the duckweed/epiphyte test, P saturation occurred when concentrations reached about 100 μg/L. Chlorophyll a in epiphytic periphyton was stimulated at low P additions and by about 100 μg/L P, epiphytic periphyton chlorophyll a appeared to be P saturated. Both duckweed and epiphyte response patterns with total N were weaker but suggested a growth stimulation threshold for duckweed when total N concentrations exceeded about 300 μg/L and approached saturation at the highest N concentration tested, 1300 μg/L. Nutrient uptake by epiphytes and macrophytes removed up to 70 and 90% of the N and P, respectively. The green algae and the NDS nutrient-limitation test results were mostly congruent; N and P co-limitation was the most frequent result for both test series. Across all tests, when N:P molar ratios >30 (mass ratios >14), algae or macrophyte growth was P limited; N limitation was observed at N:P molar ratios up to 23 (mass ratios up to 10). A comparison of ambient periphyton chlorophyll a concentrations with chlorophyll a accrued on control artificial substrates in N-limited streams, suggests that total N concentrations associated with a periphyton chlorophyll a benchmark for desirable or undesirable conditions for recreation would be about 600 to 1000 μg/L total N, respectively. For P-limited streams, the corresponding benchmark concentrations were about 50 to 90 μg/L total P, respectively. Our approach of integrating controlled experiments and matched biomonitoring field surveys was cost effective and more informative than either approach alone.
We provide an initial checklist of the herpetofauna of Baramita, a lowland rainforest site in the Northwest Region of Guyana. Twenty-five amphibian and 28 reptile species were collected during two separate dry-season visits. New country records for two species of snakes are documented, contributing to the knowledge on the incompletely known herpetofauna of Guyana.
The South Fork basin of the Coeur d'Alene River, Idaho has been an area of heavy mining activity since the 1880s. The mining operations have resulted in elevated concentrations of metals in surface water, most notably cadmium, lead, zinc, and, to a lesser extent, copper. The metals affected surface water quality downstream in the Coeur d'Alene basin and are suspected to be one of the primary reasons for the reduction in populations of native westslope cutthroat trout Oncorhynchus clarki lewisi. The avoidance response of a surrogate species, Snake River cutthroat trout O. clarki (unnamed subspecies), was evaluated against conditions simulating those in the Coeur d'Alene River basin. Cutthroat trout avoided a metals mixture of these concentrations: Cd (0.30 ??g/L), Cu (6.0 ??g/L), Pb (0.6 ??g/L), and Zn (28 ??g/L). The avoidance response to either Cu or Zn alone was similar to the avoidance response to the mixture, suggesting that avoidance to the mixture was due to these metals. After acclimation to Zn at 55 ??g/L for 90 d, cutthroat trout detected and preferred a lower Zn concentration of 28 ??g/L. The lowest Zn concentrations avoided (28 ??g/L) were 1/6 to 1/78 the Zn concentrations measured in the South Fork and lower Coeur d'Alene River basins. Avoidance of metals-contaminated habitats by cutthroat trout may be, in part, responsible for reduced fish populations.
Spill at dams has caused supersaturation of atmospheric gas in waters of the Columbia and Snake rivers and raised concerns about the effects of dissolved gas supersaturation (DGS) on white sturgeons Acipenser transmontanus. The timing and location of white sturgeon spawning and the dispersal of white sturgeon larvae from incubation areas makes the larval stage potentially vulnerable to the effects of DGS. To assess the effects of DGS on white sturgeon larvae, we exposed larvae to mean total dissolved gas (TDG) levels of 118% and 131% saturation in laboratory bioassay tests. Gas bubble trauma (GBT) was manifested as a gas bubble in the buccal cavity, nares, or both and it first occurred at developmental stages characterized by the formation of the mouth and gills. Exposure times of 15 min were sufficient to elicit these signs in larvae in various stages of development. No mortality was observed in larvae exposed to 118% TDG for 10 d, but 50% mortality occurred after a 13-d exposure to 131% TDG. The signs of GBT we observed resulted in positive buoyancy and alterations in behavior that may affect the dispersal and predation vulnerability of white sturgeon larvae. The exact depth distribution of dispersing white sturgeon larvae in the Columbia River currently is unknown. Thus, our results may represent a worst-case scenario if white sturgeon larvae are dispersed at depths with insufficient hydrostatic pressure to compensate for high TDG levels.
A marker based on randomly amplified polymorphic DNA (RAPD), OT-38, was discovered that nonlethally discriminates between stream-type and ocean-type populations of chinook salmon Oncorhynchus tshawytscha in the Columbia River basin, including the threatened fall-run (ocean-type) and spring-run (stream-type) Snake River populations. This marker was developed by amplifying chinook salmon genomic DNA with a single RAPD primer, sequencing the termini of the polymorphic products, and designing primer pairs for allele-specific amplification. It was used to assay 18-80 individuals from several wild and hatchery populations differing in year-class, freshwater life history, and location along the Columbia River OT-38 unambiguously distinguished ocean-type from stream-type populations in 93.1% of the chinook salmon sampled.
Infectious hematopoietic necrosis virus (IHNV) is a pathogen that infects many Pacific salmonid stocks from the watersheds of North America. Previous studies have thoroughly characterized the genetic diversity of IHNV isolates from Alaska and the Hagerman Valley in Idaho. To enhance understanding of the evolution and viral transmission patterns of IHNV within the Pacific Northwest geographic range, we analyzed the G gene of IHNV isolates from the coastal watersheds of Washington State by ribonuclease protection assay (RPA) and nucleotide sequencing. The RPA analysis of 23 isolates indicated that the Skagit basin IHNV isolates were relatively homogeneous as a result of the dominance of one G gene haplotype (S). Sequence analysis of 303 bases in the middle of the G gene (midG region) of 61 isolates confirmed the high frequency of a Skagit River basin sequence and identified another sequence commonly found in isolates from the Lake Washington basin. Overall, both the RPA and sequence analysis showed that the Washington coastal IHNV isolates are genetically homogeneous and have little genetic diversity. This is similar to the genetic diversity pattern of IHNV from Alaska and contrasts sharply with the high genetic diversity demonstrated for IHNV isolates from fish farms along the Snake River in Idaho. The high degree of sequence and haplotype similarity between the Washington coastal IHNV isolates and those from Alaska and British Columbia suggests that they have a common viral ancestor. Phylogenetic analyses of the isolates we studied and those from different regions throughout the virus's geographic range confirms a conserved pattern of evolution of the virus in salmonid stocks north of the Columbia River, which forms Washington's southern border.
We developed methods to forecast survival and cumulative percent passage for subyearling chinook salmon Oncorhynchus tshawytscha at a dam to help managers effectively time the release of reservoir water to mitigate for passage delays and reduced survival. We tagged Snake River subyearling chinook salmon upstream of a dam from 1993 to 1998 and determined when a subsample of the tagged fish passed the dam. We randomly selected data (1993, 1994, 1996, and 1998) to develop a quadratic discriminant function for predicting which fish would survive to the dam and to develop a multiple-regression equation to predict the date survivors would pass the dam. We used the predicted passage dates within a year to calculate a daily cumulative percent passage forecast and then calculated a 90% forecast interval that varied by year, depending on the number of predicted survivors. We validated the forecast method using data for 1995 and 1997. The 1995 forecasted passage curve differed from the observed passage curve for 25 d of the 168-d emigration season. The 1997 forecasted and observed passage curves were similar for the entire 168-d emigration season. The 90% forecast interval was ±18.8% in 1995 and ±22.4% in 1997. We conclude that our method is a valid tool for in-season water management but acknowledge the potential for interannual variability in forecast performance.
The amount of time radio-tagged juvenile spring chinook salmon Oncorhynchus tshawytscha and juvenile steelhead O. mykiss spent within a gatewell and the juvenile collection channel at McNary Dam, Columbia River, USA, was measured to determine the diel passage behavior and residence times within these portions of the juvenile bypass system. The median gatewell residence times were 8.9 h for juvenile chinook salmon and 3.2 h for steelhead. Juvenile spring chinook salmon spent 83% of their time in the 18-m-deep gatewell at depths of 9 m or less, and juvenile steelhead spent 96% of their time in the upper 11 m. Fish released during midday and those released in the evening generally exited the gatewell in the evening, indicating that fish entering the gatewell during daylight will have prolonged residence times. Median collection-channel residence times of juvenile chinook salmon were much shorter (2.3 min) than those of steelhead (28.0 min), most likely because of the greater size of the steelhead and the high water velocities within the channel (2.1 m/s). This and other studies indicate most juvenile salmonids enter gatewells of several Columbia and Snake river dams in the evening and pass into the collection channels quickly. However, this is not consistent with the natural in-river migration patterns of these species and represents a delay in dam passage.
Between 1993 and 2000, precocious yearling males of hatchery-produced fall and spring chinook salmon Oncorhynchus tshawytscha composed 3.6-82.1% of chinook salmon runs to the Umatilla River, Oregon. These yearling males are smaller than typical jack salmon, which spend a full winter in the ocean, and are commonly referred to as "mini jacks." Minijack fall chinook salmon are characterized by enlarged testes and an increased gonadosomatic index. Our goal was to determine if minijacks migrated to saltwater between the time they are released from the hatchery and the time they return to the Umatilla River, a period of 4-6 months. During 1999-2000, we collected otoliths from an adult male fall chinook salmon, 12 spring chinook salmon minijacks, and 10 fall chinook salmon minijacks. We measured strontium:calcium (Sr:Ca) ratios from the age-1 annulus to the edge of the otolith to determine whether these fish had migrated to the ocean. The Sr:Ca ratios increased from low values near the age-1 annulus, similar to ratios expected from freshwaters, to higher values near the edge of the otolith. The Sr:Ca ratios increased to levels similar to ratios expected in saltwater, indicating that these fish had migrated to saltwater before returning to the Umatilla River. Analysis of published water chemistry data from the Columbia and Snake rivers and rearing experiments in the main-stem Columbia River confirmed that high Sr:Ca ratios measured in otoliths were not the result of high strontium levels encountered in the freshwater environment. Previously assumed to remain within freshwater and near the point of release, our results suggest these minijack salmon migrated at least 800 km and past three hydroelectric dams to reach saltwater and return to the Umatilla River.
We compared three methods to determine nest predators of the Least Bell's Vireo ( Vireo bellii pusillus ) in San Diego County, California, during spring and summer 2000. Point counts and tracking stations were used to identify potential predators and video photography to document actual nest predators. Parental behavior at depredated nests was compared to that at successful nests to determine whether activity (frequency of trips to and from the nest) and singing vs. non-singing on the nest affected nest predation. Yellow-breasted Chats ( Icteria virens ) were the most abundant potential avian predator, followed by Western Scrub-Jays ( Aphelocoma californica ). Coyotes ( Canis latrans ) were abundant, with smaller mammalian predators occurring in low abundance. Cameras documented a 48% predation rate with scrub-jays as the major nest predators (67%), but Virginia opossums ( Didelphis virginiana , 17%), gopher snakes ( Pituophis melanoleucus , 8%) and Argentine ants ( Linepithema humile , 8%) were also confirmed predators. Identification of potential predators from tracking stations and point counts demonstrated only moderate correspondence with actual nest predators. Parental behavior at the nest prior to depredation was not related to nest outcome.
The twin-spotted rattlesnake ( Crotalus pricei ) is a small-bodied pitviper that has received little attention in the literature to date. The species reaches the northern limit of its range in southeastern Arizona, where it inhabits higher elevations than any of the state's 10 other rattlesnake species. During 1997–2000, we captured, measured, and marked 127 C. pricei in Arizona's Chiricahua Mountains between 2530 and 2900 m elevation. We also used radiotelemetry to track the movements of 16 C. pricei in the study area during 1997–1998. Mean (± SE) snout–vent length of C. pricei was 387.8 ± 8.3 mm (range = 168–572), and mean mass was 53.5 ± 3.3 g (range = 3.6–188.5). Based on fecal analyses, lizards constituted the bulk of prey (74%), but the diet of C. pricei also included mammals, birds, and a conspecific. Mating was concentrated in August and early September and parturition took place during late July and August. Mean number of embryos was 3.94 ± 0.34 (range = 1–6) and female reproduction appeared biennial or less frequent. Based on shed and growth rates, female C. pricei develop embryos at 4–5 years of age. Gravid females maintained warmer body temperatures relative to substrate temperature than nongravid females or males, presumably by spending more time basking than other snakes. Radiotelemetry revealed that movement patterns varied from year to year, as males moved over six times farther per week during the 1998 monsoon season (July to September) than during the 1997 monsoon season. Additionally, use of talus slopes by males decreased during 1998. During dry years, such as 1998, males may be forced off talus into cooler microclimates where resources are less concentrated than on talus.
We conducted a three-year study to describe the ecology and behavior of the Midget Faded Rattlesnake, Crotalus organus concolor. We encountered 426 and telemetered 50 C. o. concolor between 2000 and 2002. We found that their primary diet was lizards (associated with rock outcrops), though they will consume small mammals and birds. They den in aggregations, although in low numbers when compared to other subspecies. Movements and activity ranges were among the largest reported for rattlesnakes. Minimum convex polygon area was 117.8 ha for males, 63.9 ha for nongravid females, and 4.8 ha for gravid females. Mean distances traveled per year were 2122.0 m for males, 1956.0 m for nongravid females, and 296.7 m for gravid and postpartum females. Following emergence from hibernation, they spent several weeks shedding, often in aggregations before migration, and migrations occurred in early summer. Most snakes made straight-line movements to and from discrete summer activity ranges where short, multidirectional movements ensued, although others made multidirectional movements throughout the active season. We observed mating behavior between 21 July and 12 August. Gravid females gave birth during the third week of August. Mean clutch size was 4.17 (range 2-7). We found that the sex ratio was skewed favoring females 1:1.24, and they were sexually dimorphic in size (males SVL = 44.1 cm; females SVL = 40.8 cm). Our data further illustrate the diversity within the large group of Western Rattlesnakes (Crotalus viridis). Copyright 2007 Society for the Study of Amphibians and Reptiles.