USGS Science⌕ Search

SEARCH · USGS Science

Results for “The R Journal”

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 325 records · Page 18Linked to original sources
USGS2022

Understanding the water resources of a mountain-block aquifer: Tucson Mountains, Arizona

Water resources are limited in arid locations such as Tucson Basin. Residential development in the Tucson Mountains to the west of Tucson, Arizona, is limited by groundwater resources. Groundwater samples were collected from fractured bedrock and alluvial aquifers surrounding the Tucson Mountains to assess water quality and recharge history through measurement of stable O, H, and S isotopes; tritium; and 14 C. Most groundwater is a mixture of different ages but is commonly several thousand years old. A few sampling locations indicated a component of water recharged after the above-ground nuclear testing of the mid 1950s, and these sites may represent locations near where the aquifer receives present-day recharge. The Tucson Mountains also host sulfide deposits associated with fractures and replacement zones; these locally contribute to poor-quality groundwater. Projections of future climate predict intensifying drought in southwestern North America. In the study area, a combination of strategies such as rainwater harvesting, exploitation of renewable water, and low groundwater use could be used for sustainable use of the groundwater supply.

Arizona↗
USGS2010

The use of early summer mosquito surveillance to predict late summer West Nile virus activity

Utility of early-season mosquito surveillance to predict West Nile virus activity in late summer was assessed in Suffolk County, NY. Dry ice-baited CDC miniature light traps paired with gravid traps were set weekly. Maximum-likelihood estimates of WNV positivity, minimum infection rates, and % positive pools were generally well correlated. However, positivity in gravid traps was not correlated with positivity in CDC light traps. The best early-season predictors of WNV activity in late summer (estimated using maximum-likelihood estimates of Culex positivity in August and September) were early date of first positive pool, low numbers of mosquitoes in July, and low numbers of mosquito species in July. These results suggest that early-season entomological samples can be used to predict WNV activity later in the summer, when most human cases are acquired. Additional research is needed to establish which surveillance variables are most predictive and to characterize the reliability of the predictions.

New York↗
USGS2015

Age estimations of wild pallid sturgeon ( Scaphirhynchus albus , Forbes & Richardson 1905) based on pectoral fin spines, otoliths and bomb radiocarbon: inferences on recruitment in the dam-fragmented Missouri River

An extant stock of wild pallid sturgeon Scaphirhynchus albus persists in the fragmented upper Missouri River basin of Montana and North Dakota. Although successful spawning and hatch of embryos has been verified, long-term catch records suggest that recruitment has not occurred for several decades as the extant stock lacks juvenile size classes and is comprised exclusively of large, presumably old individuals. Ages of 11 deceased (death years 1997–2007) wild S. albus (136–166 cm fork length) were estimated based on pectoral fin spines, sagittal otoliths and bomb radiocarbon ( 14 C) assays of otoliths to test the hypothesis that members of this stock are old and to provide inferences on recruitment years that produced the extant stock. Age estimations based on counts of presumed annuli were about 2 years greater for otoliths (mean = 51 years, range = 43–57 years) than spines (mean = 49 years, range = 37–59 years). Based on 14 C assays, confirmed birth years for all individuals occurred prior to 1957, thus establishing known longevity of at least 50 years. Estimated age based on presumed otolith annuli for one S. albus was validated to at least age 49. Although 14 C assays confirmed pre-1957 birth years for all S. albus , only 56% of estimated ages from spines and 91% of estimated ages from otoliths depicted pre-1957 birth years. Both ageing structures were subject to under-ageing error (up to 15 years). Lack of or severe curtailment of S. albus recruitment in the upper Missouri River basin since the mid-1950s closely parallels the 1953–1957 timeframe when a mainstem reservoir was constructed and started to fill. This reservoir may function as a system-wide stressor to diminish recruitment success of S. albus in the upper Missouri River basin.

Montana, North Dakota↗
USGS2017

Diet, feeding patterns, and prey selection of subyearling Atlantic salmon (Salmo salar) and subyearling chinook salmon (Oncorhynchus tshawytscha) in a tributary of Lake Ontario

Since juvenile Atlantic salmon ( Salmo salar ) and Chinook salmon ( Oncorhynchus tshawytscha ) occupy a similar habitat in Lake Ontario tributaries, we sought to determine the degree of diet similarity between these species in order to assess the potential for interspecific competition. Atlantic salmon, an historically important but currently extirpated component of the Lake Ontario fish community, are the focus of a bi-national restoration effort. Presently this effort includes the release of hatchery produced juvenile Atlantic salmon in Lake Ontario tributaries. These same tributaries support substantial numbers of naturally reproduced juvenile Pacific salmonids including Chinook salmon. Subyearling Atlantic salmon and subyearling Chinook salmon had significantly different diets during each of the three time periods examined. Atlantic salmon fed slightly more from the benthos than from the drift and consumed mainly chirononmids (47.0%) and ephemeropterans (21.1%). The diet of subyearling Chinook salmon was more closely associated with the drift and consisted mainly of chironomids (60.2%) and terrestrial invertebrates (16.0%). Low diet similarity between subyearling Atlantic salmon and subyearling Chinook salmon likely minimizes competitive interactions for food between these species in Lake Ontario tributaries. However, the availability of small prey such as chironomids which comprise over 50% of the diet of each species, soon after emergence, could constitute a short term resource limitation. To our knowledge this is the first study of interspecific diet associations between these two important salmonid species.

Journal of Applied Ichthyology↗
USGS2020

Fort Peck paddlefish population survival and abundance in the Missouri River

Excessive fishing pressure can induce population declines or complete collapse of fisheries. Unless commercial and recreational fisheries for K-selected fishes, or those with slow growth and late maturation, are carefully managed, declines in abundance or fishery collapse is probable. Paddlefish Polyodon spathula, are a K-selected species that experienced historical declines in abundance as a result of habitat degradation and overfishing. Mark-recapture studies are well-suited for long-lived fishes by providing information on population density and vital rates. For sustainable commercial or recreational fisheries targeting species such as the paddlefish, managers require accurate estimates of population vital rates including survival, abundance, and exploitation. We used a Montana Fish, Wildlife & Parks (MFWP) mark-recapture dataset and modified Jolly-Seber (POPAN) models to estimate survival, recapture, probability of entry, and abundance of 8,518 tagged paddlefish over a 25-year period. With many supporting estimates including stable survival (0.92 for females, mean of 0.82 for males), low exploitation rates (means of 2.6% for females and 2.9% for males), and stable abundance estimates (25-year mean of 12,309 individuals for both sexes), the Fort Peck paddlefish population appears to be stable and well-managed over the past 25 years. Presently, this is the only study focused on paddlefish in North America that has estimated survival and abundance for both male and female paddlefish using contemporary analyses. This research provided a unique opportunity to highlight that the effort exerted by management agencies to collect long-term field data is extremely useful to our understanding of fish populations and management.

Montana↗
USGS2012

Nutrient enrichment and fish nutrient tolerance: Assessing biologically relevant nutrient criteria

Relationships between nutrient concentrations and fish nutrient tolerance were assessed relative to established nutrient criteria. Fish community, nitrate plus nitrite (nitrate), and total phosphorus (TP) data were collected during summer low-flow periods in 2003 and 2004 at stream sites along a nutrient-enrichment gradient in an agricultural basin in Indiana and Ohio and an urban basin in the Atlanta, Georgia, area. Tolerance indicator values for nitrate and TP were assigned for each species and averaged separately for fish communities at each site (TIV o ). Models were used to predict fish species expected to occur at a site under minimally disturbed conditions and average tolerance indicator values were determined for nitrate and TP separately for expected communities (TIV e ). In both areas, tolerance scores (TIV o /TIV e ) for nitrate increased significantly with increased nitrate concentrations whereas no significant relationships were detected between TP tolerance scores and TP concentrations. A 0% increase in the tolerance score (TIV o /TIV e = 1) for nitrate corresponded to a nitrate concentration of 0.19 mg/l (compared with a USEPA summer nitrate criterion of 0.17 mg/l) in the urban area and 0.31 mg/l (compared with a USEPA summer nitrate criterion of 0.86 mg/l) in the agricultural area. Fish nutrient tolerance values offer the ability to evaluate nutrient enrichment based on a quantitative approach that can provide insights into biologically relevant nutrient criteria.

Georgia, Indiana, Ohio↗
USGS2013

Development and application of an agricultural intensity index to invertebrate and algal metrics from streams at two scales

Research was conducted at 28-30 sites within eight study areas across the United States along a gradient of nutrient enrichment/agricultural land use between 2003 and 2007. Objectives were to test the application of an agricultural intensity index (AG-Index) and compare among various invertebrate and algal metrics to determine indicators of nutrient enrichment nationally and within three regions. The agricultural index was based on total nitrogen and phosphorus input to the watershed, percent watershed agriculture, and percent riparian agriculture. Among data sources, agriculture within riparian zone showed significant differences among values generated from remote sensing or from higher resolution orthophotography; median values dropped significantly when estimated by orthophotography. Percent agriculture in the watershed consistently had lower correlations to invertebrate and algal metrics than the developed AG-Index across all regions. Percent agriculture showed fewer pairwise comparisons that were significant than the same comparisons using the AG-Index. Highest correlations to the AG-Index regionally were −0.75 for Ephemeroptera, Plecoptera, and Trichoptera richness (EPTR) and −0.70 for algae Observed/Expected (O/E), nationally the highest was −0.43 for EPTR vs. total nitrogen and −0.62 for algae O/E vs. AG-Index. Results suggest that analysis of metrics at national scale can often detect large differences in disturbance, but more detail and specificity is obtained by analyzing data at regional scales.

Journal of the American Water Resources Associatio↗
USGS2013

Dissipation of contaminants of emerging concern in biosolids applied to non-irrigated farmland in eastern Colorado

In 2007, a 1.5-year field-scale study was initiated by the U.S. Geological Survey to evaluate the dissipation of contaminants of emerging concern (CECs) following a first agronomic biosolids application to nonirrigated farmland. CECs with the greatest decrease in concentration in the surface biosolids at 180 days post-application included indole, d-limonene, p-cresol, phenol, and skatol. CECs that were present in the largest concentration in 180-day-weathered biosolids included stanols, nonylphenols, bisphenol A, bis(2-ethylhexyl) phthalate, hexahydrohexamethyl cyclopenta-benzopyran (HHCB), and triclosan. CECs that were detected in pre-application soil were 3-beta coprostanol, skatol, acetophenone, beta-sitosterol, beta-stigmastanol, cholesterol, indole, p-cresol, and phenol, most of which are biogenic sterols or fragrances that have natural plant sources in addition to anthropogenic sources, yet their concentrations increased (in some cases, substantially) following biosolids application. Preliminary data indicate the nonylphenols (including NPEO1, NPEO2), OPEO1, benzo[a]pyrene, diethyl phthalate, d-limonene, HHCB, triclosan, and possibly 3-beta coprostanol, skatol, beta-sitosterol, cholesterol, indole, and p-cresol, migrated downward through the soil by 468 days post-application, but indicated little uptake by mature wheat plants. This study indicates that some CECs are sufficiently persistent and mobile to be vertically transported into the soil column following biosolids applications to the land surface, even in semiarid regions.

Journal of the American Water Resources Associatio↗
USGS2016

Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient

Evolutionary theory predicts that divergent selection pressures across elevational gradients could cause adaptive divergence and reproductive isolation in the process of ecological speciation. Although there is substantial evidence for adaptive divergence across elevation, there is less evidence that this restricts gene flow. Previous work in the boreal chorus frog (Pseudacris maculata) has demonstrated adaptive divergence in morphological, life history and physiological traits across an elevational gradient from approximately 1500–3000 m in the Colorado Front Range, USA. We tested whether this adaptive divergence is associated with restricted gene flow across elevation – as would be expected if incipient speciation were occurring – and, if so, whether behavioural isolation contributes to reproductive isolation. Our analysis of 12 microsatellite loci in 797 frogs from 53 populations revealed restricted gene flow across elevation, even after controlling for geographic distance and topography. Calls also varied significantly across elevation in dominant frequency, pulse number and pulse duration, which was partly, but not entirely, due to variation in body size and temperature across elevation. However, call variation did not result in strong behavioural isolation: in phonotaxis experiments, low-elevation females tended to prefer an average low-elevation call over a high-elevation call, and vice versa for high-elevation females, but this trend was not statistically significant. In summary, our results show that adaptive divergence across elevation restricts gene flow in P. maculata, but the mechanisms for this potential incipient speciation remain open.

Colorado↗
USGS2020

Effect of water velocity and temperature on energy use, behaviour and mortality of pallid sturgeon Scaphirhynchus albus larvae

Natural reproduction of pallid sturgeon Scaphirhynchus albus has been limited for decades and a recruitment bottleneck is hypothesized to occur during the larval stage of development. In this study, we evaluated the effects of water velocity and temperature on the swimming activity, energy use, settling behaviour and mortality of endogenously feeding larvae. The swimming activity of drifting sturgeon larvae ( i.e. , fish exhibiting negative rheotaxis) increased at low water velocity. In subsequent experiments, we observed greater energy depletion and resultant mortality of larvae in no-flow environments (0 cm s −1 ) compared to tanks with water velocity ranging from 3.5 to 8.3 cm s −1 . The growth rate of drifting larvae was positively related to water temperature (18.7–23.3°C), but reduced growth rate at low water temperature (18.7°C) resulted in protracted development that extended average drift duration by ~4 days compared to larvae reared at 23.3°C. This study provides evidence that cooler summer water temperatures, characteristic of present-day conditions in the upper Missouri River, can reduce larval development and extend both the drift duration and distance requirements of S. albus . Moreover, if dispersed into low velocity environments, such as in reservoir headwaters, larvae may experience increased mortality owing to a mismatch between early life stage drift requirements and habitat conditions in the river. Manipulation of water releases to increase seasonal water temperature below dams may aid survival of S. albus larvae by shortening the time and distance spent drifting.

Journal of Fish Biology↗
USGS2015

Effects of temperature on Renibacterium salmoninarum infection and transmission potential in Chinook salmon, Oncorhynchus tshawytscha (Walbaum)

Renibacterium salmoninarum is a significant pathogen of salmonids and the causative agent of bacterial kidney disease (BKD). Water temperature affects the replication rate of pathogens and the function of the fish immune system to influence the progression of disease. In addition, rapid shifts in temperature may serve as stressors that reduce host resistance. This study evaluated the effect of shifts in water temperature on established R. salmoninarum infections. We challenged Chinook salmon with R. salmoninarum at 12°C for 2 weeks and then divided the fish into three temperature groups (8, 12 and 15°C). Fish in the 8°C group had significantly higher R. salmoninarum -specific mortality, kidney R. salmoninarum loads and bacterial shedding rates relative to the fish held at 12 or 15°C. There was a trend towards suppressed bacterial load and shedding in the 15°C group, but the results were not significant. Bacterial load was a significant predictor of shedding for the 8 and 12°C groups but not for the 15°C group. Overall, our results showed little effect of temperature stress on the progress of infection, but do support the conclusion that cooler water temperatures contribute to infection progression and increased transmission potential in Chinook salmon infected with R. salmoninarum .

Journal of Fish Diseases↗
USGS2017

A systematic surveillance programme for infectious salmon anaemia virus supports its absence in the Pacific Northwest of the United States

In response to reported findings of infectious salmon anaemia virus (ISAV) in British Columbia (BC), Canada, in 2011, U.S. national, state and tribal fisheries managers and fish health specialists developed and implemented a collaborative ISAV surveillance plan for the Pacific Northwest region of the United States. Accordingly, over a 3-1/2-year period, 4,962 salmonids were sampled and successfully tested by real-time reverse-transcription PCR. The sample set included multiple tissues from free-ranging Pacific salmonids from coastal regions of Alaska and Washington and farmed Atlantic salmon ( Salmo salar L.) from Washington, all representing fish exposed to marine environments. The survey design targeted physiologically compromised or moribund animals more vulnerable to infection as well as species considered susceptible to ISAV. Samples were handled with a documented chain of custody and testing protocols, and criteria for interpretation of test results were defined in advance. All 4,962 completed tests were negative for ISAV RNA. Results of this surveillance effort provide sound evidence to support the absence of ISAV in represented populations of free-ranging and marine-farmed salmonids on the northwest coast of the United States.

Pacific Northwest↗
USGS2019

Malignant melanoma of Brown Bullhead (Ameiurus nebulosus) in Lake Memphremagog, Vermont/Quebec

In 2012, brown bullhead ( Ameiurus nebulosus ) with large, raised, black growths were first reported from multiple areas within the Vermont portion of Lake Memphremagog. Subsequent surveys conducted from 2014 to 2017 at two sites within the lake indicated a prevalence of 30% in adult brown bullhead 200 mm and above total length. These lesions ranged from slightly raised smooth black areas to large nodular areas on the body surface and fins and within the oral cavity. Microscopically, these lesions were determined to be malignant melanoma with invasion into surrounding hypodermis, skeletal muscle and bone as well as metastases to gill, ovary and intestine. Liver neoplasms were also observed in 8% of the bullhead collected from Lake Memphremagog in 2015. Neither skin nor liver neoplasms were noted in Ticklenaked Pond, a site used for comparison.

Quebec, Vermont↗
USGS2022

Dual resistance to Flavobacterium psychrophilum and Myxobolus cerebralis in rainbow trout (Oncorhynchus mykiss, Walbaum)

Aquatic pathogens are a major concern for fish hatchery production, fisheries management, and conservation, and disease control needs to be addressed. Two important salmonid pathogens are Myxobolus cerebralis and Flavobacterium psychrophilum that cause whirling disease and bacterial coldwater disease (BCWD), respectively. Innate disease resistance is a potential option for reducing disease-related mortality in hatchery-reared rainbow trout ( Oncorhynchus mykiss , Walbaum). Two experiments were conducted to assess pathogen resistance of first-generation (F1) rainbow trout created by crossing M. cerebralis - and F. psychrophilum -resistant strains. In the first experiment, we exposed two rainbow trout strains and one F1 cross to six treatments: control (no exposure), mock injection, F. psychrophilum only, M. cerebralis only, F. psychrophilum then M. cerebralis , and M. cerebralis then F. psychrophilum . Results indicated that the F1 cross was not resistant to either pathogen. In the second experiment, we exposed five rainbow trout strains and four rainbow trout crosses to F. psychrophilum . The second experiment indicated that at least one rainbow trout cross was F . psychrophilum -resistant. Achieving dual resistance may be possible using selective breeding but only some multigenerational strains are suitable candidates for further evaluation.

Journal of Fish Diseases↗
USGS2015

Efficacy of an extract from garlic, Allium sativum, against infection with the furunculosis bacterium, Aeromonas salmonicida, in rainbow trout, Oncorhynchus mykiss

Juvenile rainbow trout, Oncorhynchus mykiss , were fed diets containing 0, 0.5, 1.0, and 2.0% of a garlic extract, challenged with a modified 50% lethal dose of Aeromonas salmonicida and monitored for 28 d. There were significant increases in survival of trout fed 0.5 and 1.0% garlic extract as compared to the control and 2.0% garlic extract groups. A target animal safety study was performed at varying increments using the target dose of 0.5% garlic extract at 0× (0% garlic extract), 1× (0.5% garlic extract), 3× (1.5% garlic extract), and 5× (2.5% garlic extract) for 3× (6 wk) the duration of the original study. There was a significant increase in the level of circulating lymphocytes and a significant decrease in the level of circulating monocytes. The latter correlated to an increased level of pigment-containing macrophage centers within the renal tissue as garlic extract dosing increased, denoting a potential deleterious inflammatory effect as macrophage infiltration became severe at the highest dose. These studies suggest that feeding low-dose (0.5% or 1.0%) garlic extract improves survivability in rainbow trout when challenged with A. salmonicida and appears safe; however, higher levels do not appear to be effective and may cause deleterious effects on health.

Journal of the World Aquaculture Society↗
USGS2016

Reevaluating geographic variation in life-history traits of a widespread Nearctic amphibian

Animals from cold environments are usually larger than animals from warm environments, which often produce clines in body size. Because variation in body size can lead to trade-offs between growth and reproduction, life-history traits should also vary across climatic gradients. To determine if life-history traits of wood frogs Rana sylvatica vary with climate, we examined female and male body length, clutch size, and ovum size from 37 locations across an unprecedented 32° of latitude. In conflict with recent research, body size, and ovum size decreased in cold climates and at higher latitudes. Clutch size did not vary with climate or latitude, but reproductive effort (clutch size:female size) did, suggesting selection for a life-history traits that favors maximizing propagule number over propagule size in cold climates. With accelerating climate change that will expose populations to novel environmental conditions, it is important to identify the limits of adaptation, which can be informed by greater understanding of variation in life-history traits.

Journal of Zoology↗
USGS2018

Risky behavior and its effect on survival: snowshoe hare behavior under varying moonlight conditions

Predation and predation risk can exert strong influences on the behavior of prey species. However, risk avoidance behaviors may vary among populations of the same species. We studied a population of snowshoe hares ( Lepus americanus ) near the southern edge of their range, in Pennsylvania. This population occupies different habitat types, experiences different environmental conditions, and are exposed to different predator species and densities than northern hare populations; therefore, they might exhibit differences in risk avoidance behaviors. We analyzed hare survival, movement rates, and habitat use under different levels of predation risk, as indexed by moonlight. Similar to previous work, we found snowshoe hare survival decreased with increased moon illumination during the winter, but we found differences in behavioral responses to increased predation risk. We found that snowshoe hares did not reduce movement rates during high‐risk nights, but instead found that hares selected areas with denser canopy cover, compared to low‐risk nights. We suggest that behavioral plasticity in response to predation risk allows populations of the same species to respond to localized conditions.

Journal of Zoology↗
USGS2020

Resolving species boundaries in the critically imperiled freshwater mussel species, Fusconaia mitchelli (Bivalvia: Unionidae)

Species are a fundamental unit of biology, and defining accurate species boundaries is integral to effective conservation and management of imperiled taxa. Freshwater mussels (Bivalvia: Unionidae) are among the most imperiled groups of organisms in North America, yet species boundaries remain uncertain for many taxa. The False Spike, Fusconaia mitchelli (Simpson in Dall, 1895), is a freshwater mussel considered to be endemic to central Texas (Brazos, Colorado, and Guadalupe drainages). Recent research revealed significant intraspecific genetic variation between geographically separated populations of F . mitchelli , which could be indicative of speciation; however, small sample sizes for several of the populations precluded formal taxonomic revision. Here, we increase taxon sampling and use multilocus DNA sequence data and traditional morphometrics to re‐evaluate species boundaries in F . mitchelli . We sequenced three loci: the protein‐coding mitochondrial DNA genes cytochrome c oxidase subunit 1 and NADH dehydrogenase 1 , and the nuclear internal transcribed spacer 1 . Phylogenetic analyses depicted deep genetic divergence between F . mitchelli in the Guadalupe and those in the Brazos and Colorado drainages, which was further supported by available biogeographic information. Morphometric analyses and coalescent‐based species delimitation models integrating both DNA sequence and morphological data provided strong support for the divergence observed between the two geographically isolated clades of F . mitchelli . Based on these results, we revise taxonomy accordingly by elevating the junior synonym Fusconaia iheringi (Wright, 1898) to represent the Brazos and Colorado populations and restrict the distribution of F . mitchelli to the Guadalupe River drainage. Our findings may impact pending management decisions to protect F . mitchelli under the U.S. Endangered Species Act.

Journal of Zoological Systematics and Evolutionary↗