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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,099 records · Page 61Linked to original sources

USGS1992

Evaluating enhancement of striped bass in the context of potential predation on anadromous salmonids in Coos Bay, Oregon

We describe an approach for evaluating the predation on anadromous salmonids that could result from enhancement of striped bass Morone saxatilis in Coos Bay, Oregon. Predation by striped bass on juvenile salmonids has been documented there since 1930. To provide a basis for the decision about enhancement of striped bass in Coos Bay, we estimated the losses of anadromous salmonids in 1950 and 1960–1964. In this evaluation, we used information on striped bass in Coos Bay and collateral information about striped bass in other waters. Estimated numbers of juvenile salmonids consumed by striped bass in Coos Bay (April–June) ranged from more than 41,000 in 1950 to about 383,000 in 1963. Estimated losses of adult salmonids ranged from about 1,000 in 1950 to about 46,000 in 1963. This approach was useful in conveying the potential consequences of large‐scale striped bass enhancement to decision makers and to the public. The evaluation also helped identify information needs that are now considered in managing the fishery and in evaluating impacts on salmonids.

Oregon↗

USGS1994

Evaluation of tire reefs for enhancing aquatic communities in concrete-lined canals

Large earthen canals in the arid southwest are being lined with concrete to reduce seepage and conserve limited water supplies. Lining reduces habitat and increases operational velocities (relative to unaltered streams), which are detrimental to aquatic communities. Fish communities that become reestablished in these waterways exhibit lower species diversity, densities, and biomass than they did in the former earthen canals. Placement of low-profile tire reefs in the Coachella Canal, California, and the Hayden-Rhodes Aqueduct, Arizona, reversed these trends. Comparative sampling revealed that invertebrate and fish densities were 3 and 20 times higher, respectively, in reef areas than in typical canal sections without reefs. Tire reefs are recommended as an effective means of enhancing aquatic communities in concrete canals.

North American Journal of Fisheries Management↗

USGS1995

Management briefs: Phototaxis of larval and juvenile northern pike

Age-0 northern pike Esox lucius prefer vegetated habitats that are difficult to sample with standard towed gears. Light traps can be effective for sampling larval fishes in dense vegetation, given positive phototaxis offish. We evaluated the phototactic response of young northern pike by comparing the catches of larvae and juveniles obtained with plexiglass traps deployed with a chemical light stick versus traps deployed without a light source (controls) in a laboratory raceway and in a vegetated pond. In the laboratory tests, catches of protolarvae and mesolarvae in lighted traps were 11–35 times greater than catches in control traps. The catches of juvenile northern pike in field and laboratory experiments were 3–15 times greater in lighted traps than in control traps, even though the maximum body width of the larger juveniles was similar to the width of the entrance slots of the traps (5 mm). Larval and juvenile northern pike were photopositive; thus, light traps should effectively sample age-0 northern pike for at least 6 weeks after hatching.

Wisconsin↗

USGS2000

Seasonal changes in ruffe abundance in two Lake Superior tributaries: Implications for control

Since the discovery of ruffe Gymnocephalus cernuus in the St. Louis River in 1987, state, federal, and tribal management agencies have sought to slow its spread to areas outside the western end of Lake Superior. A debate over control strategies highlighted uncertainties about seasonal movements of this species between Lake Superior and its western tributaries. One strategy called for eliminating reproducing populations in tributaries on the periphery of the range using chemical piscicides. That strategy rested on the assumption that ruffe congregate in tributaries during a predictable time of year. This study was designed to explore that assumption. Ruffe collections from the Iron and Sand rivers during 1995 indicated that ruffe were present in those tributaries throughout the summer but that abundance was not highest at the predicted time: June 19–22. Maximum abundance in the Iron River did not coincide with that in the Sand River and did not occur during June 19–22 in either river. The timing of peak abundance was not clearly related to changes in water temperature. Ruffe were present in substantial numbers in Lake Superior during June 19–22 when aggregations in the tributaries had been predicted. These findings do not support the assumption of the chemical control strategy.

North American Journal of Fisheries Management↗

USGS2004

High doses of corticosteroid suppress resistance to Ichthyophonus in starry flounder

Application of pharmacological doses of the corticosteroid dexamethasone phosphate to starry flounder Platichthys stellatus resulted in a predisposition to clinical ichthyophoniasis and a progression from latent Ichthyophonus infections to patent, histologically identifiable infections. Among Ichthyophonus -challenged starry flounder, the prevalences of clinical infections and histologically identifiable infections were significantly greater in two groups that received dexamethasone (100% and 31%, respectively) than in the respective control groups (8% and 0%). Proliferation of Ichthyophonus infections in corticosteroid-treated groups may have resulted from suppression of the cellular immune response that typically follows corticosteroid application; however, further studies are needed to determine whether these effects occur at lower, physiological concentrations of corticosteroids.

Journal of Aquatic Animal Health↗

USGS2004

Distribution of Tubifex tubifex lineages and Myxobolus cerebralis infection in the tailwater of the San Juan River, New Mexico

We chose a hypolimnetic-release tailwater of the San Juan River, New Mexico, to characterize the etiology of whirling disease, a parasitic infection of salmonids. We sampled a 2-km reach of the tailwater in August and December 2001 and June 2002 to characterize environmental factors influencing the distribution and density of Tubifex tubifex lineages and Myxobolus cerebralis infection rates. Shortly after the scouring flow, organic matter in sediments and T. tubifex densities increased within deep habitats. In contrast, no differences were observed in T. tubifex densities and organic matter collected from shallow habitats throughout the three sampling dates. Within this study area, we found three sympatric lineages of T. tubifex (lineages I, III, and VI). Lineage VI dominated riffle reaches, whereas lineages I, III, and VI were observed in pool habitats. Myxobolus cerebralis infection rates were higher in T. tubifex collected in pool habitats (3.01%) than in those collected in riffle habitats (0.51%). Only lineage III exhibited infection with M. cerebralis. We suggest that the habitat and genotype of T. tubifex are important in characterizing prevalence of disease within the San Juan River tailwater. Scouring flow may have a beneficial effect on disease severity in salmonid hosts by reducing organic loading and hence T. tubifex abundance in deep habitats.

Journal of Aquatic Animal Health↗

USGS2004

Reintroduction of the flannelmouth sucker in the lower Colorado River

A single stocking of 611 wild flannelmouth suckers Catostomus latipinnis in 1976 represented the first successful reintroduction of a native fish in the lower Colorado River. Flannelmouth suckers ranging in age from young of the year to 24 years were captured during 1999–2001; their population was estimated as at least 2,286 (95% confidence interval, 1,847–2,998). Recruitment appeared sporadic, consisting of consecutive years of low recruitment (<10%) supplemented by a stronger (31%) year-class. Historically, this native fish was rare and was believed extirpated from the lower river by 1975, but it now reproduces naturally in a reach dramatically altered by water development. This successful reintroduction indicates that one native fish can successfully tolerate environmental alterations whereas another, the razorback sucker Xyrauchen texanus , apparently cannot. Other opportunities may exist in altered rivers to benefit native fishes where they were absent or historically rare.

North American Journal of Fisheries Management↗

USGS2005

Multilevel assessment of fish species traits to evaluate habitat degradation in streams of the upper midwest

We used species traits to examine the variation in fish assemblages for 21 streams in the Northern Lakes and Forests Ecoregion along a gradient of habitat disturbance. Fish species were classified based on five species trait-classes (trophic ecology, substrate preference, geomorphic preference, locomotion morphology, and reproductive strategy) and 29 categories within those classes. We used a habitat quality index to define a reference stream and then calculated Euclidean distances between the reference and each of the other sites for the five traits. Three levels of species trait analyses were conducted: (1) a composite measure (the sum of Euclidean distances across all five species traits), (2) Euclidean distances for the five individual species trait-classes, and (3) frequencies of occurrence of individual trait categories. The composite Euclidean distance was significantly correlated to the habitat index (r = -0.81; P = 0.001), as were the Euclidean distances for four of the five individual species traits (substrate preference: r = -0.70, P = 0.001; geomorphic preference: r = -0.69, P = 0.001; trophic ecology: r = -0.73, P = 0.001; and reproductive strategy: r = -0.64, P = 0.002). Although Euclidean distances for locomotion morphology were not significantly correlated to habitat index scores (r = -0.21; P = 0.368), analysis of variance and principal components analysis indicated that Euclidean distances for locomotion morphology contributed to significant variation in the fish assemblages among sites. Examination of trait categories indicated that low habitat index scores (degraded streams) were associated with changes in frequency of occurrence within the categories of all five of the species traits. Though the objectives and spatial scale of a study will dictate the level of species trait information required, our results suggest that species traits can provide critical information at multiple levels of data analysis. ?? Copyright by the American Fisheries Society 2005.

North American Journal of Fisheries Management↗

USGS2010

Evidence of panmixia between sympatric life history forms of coastal cutthroat trout in two lower Columbia River tributaries

Coastal cutthroat trout Oncorhynchus clarkii clarkii exhibit resident and migratory life history strategies that often occur sympatrically, but the relationship between these forms within a population is poorly characterized. Through use of passive integrated transponder technology, migratory and resident coastal cutthroat trout were identified in two lower Columbia River tributaries (Abernathy Creek and the Chinook River) separated by more than 80 km. Genetic data from 17 highly variable microsatellite loci were used to ascertain the genetic population structure of these life history forms within and between streams. No distinct genetic separation was observed between the life history forms within a stream, as assessed by four different statistical approaches: permutation tests based on the genetic differentiation index F ST , principal components analysis of individuals, analysis of molecular variance, and contingency tests of allele frequency heterogeneity. Genetic differences were an order of magnitude higher between stream samples ( F ST > 0.03) than between life history forms within a stream ( F ST < 0.003). The contingency test detected allele frequency differences between migratory and resident life history forms in Abernathy Creek ( P = 0.001), but this result was influenced more by age-class structure than by reproductive isolation between life history forms. Results are consistent with a single, randomly mating population in each stream producing both migratory and resident life history forms. These data suggest that individual life history strategy in coastal cutthroat trout is predominantly determined by phenotypic plasticity rather than genotype.

Washington↗

USGS2010

Influence of drought conditions on brown trout biomass and size structure in the Black Hills, South Dakota

We evaluated the influence of drought conditions on the biomass of brown trout Salmo trutta in Spearfish Creek, upper Rapid Creek, and lower Rapid Creek in the Black Hills of western South Dakota. Stream discharge, mean summer water temperature, the biomass of juvenile and adult brown trout, and brown trout size structure were compared between two time periods: early (2000–2002) and late drought (2005–2007). Mean summer water temperatures were similar between the early- and late-drought periods in Spearfish Creek (12.4°C versus 11.5°C), lower Rapid Creek (19.2°C versus 19.3°C), and upper Rapid Creek (9.8°C in both periods). In contrast, mean annual discharge differed significantly between the two time periods in Spearfish Creek (1.95 versus 1.50 m 3 /s), lower Rapid Creek (2.01 versus 0.94 m 3 /s), and upper Rapid Creek (1.41 versus 0.84 m 3 /s). The mean biomass of adult brown trout in all three stream sections was significantly higher in the early-drought than in the late-drought period (238 versus 69 kg/ha in Spearfish Creek, 272 versus 91 kg/ha in lower Rapid Creek, and 159 versus 32 kg/ha in upper Rapid Creek). The biomass of juvenile brown trout was similar (43 versus 23 kg/ha) in Spearfish Creek in the two periods, declined from 136 to 45 kg/ha in lower Rapid Creek, and increased from 14 to 73 kg/ha in upper Rapid Creek. Size structure did not differ between the early- and late-drought periods in lower Rapid and Spearfish creeks, but it did in upper Rapid Creek. In addition to drought conditions, factors such as angler harvest, fish movements, and the nuisance algal species Didymosphenia geminata are discussed as possible contributors to the observed changes in brown trout biomass and size structure in Black Hills streams.

South Dakota↗

USGS2010

A digital underwater video camera system for aquatic research in regulated rivers

We designed a digital underwater video camera system to monitor nesting centrarchid behavior in the Tallapoosa River, Alabama, 20 km below a peaking hydropower dam with a highly variable flow regime. Major components of the system included a digital video recorder, multiple underwater cameras, and specially fabricated substrate stakes. The innovative design of the substrate stakes allowed us to effectively observe nesting redbreast sunfish Lepomis auritus in a highly regulated river. Substrate stakes, which were constructed for the specific substratum complex (i.e., sand, gravel, and cobble) identified at our study site, were able to withstand a discharge level of approximately 300 m 3 /s and allowed us to simultaneously record 10 active nests before and during water releases from the dam. We believe our technique will be valuable for other researchers that work in regulated rivers to quantify behavior of aquatic fauna in response to a discharge disturbance.

Alabama↗

USGS2006

Comparison of methods used to diagnose generalized inflammatory disease in manatees (Trichechus manatus latirostris)

Manatees ( Trichechus manatus latirostris ) are afflicted with inflammatory and infectious disease secondary to human interaction, such as boat strike and entanglement, as well as “cold stress syndrome” and pneumonia. White-blood-cell count and fever, primary indicators of systemic inflammation in most species, are insensitive in diagnosing inflammatory disease in manatees. Acute phase-response proteins, such as haptoglobin and serum amyloid A, have proven to be sensitive measures of inflammation/infection in domestic large animal species. This study assessed diagnosis of generalized inflammatory disease by different methods including total white-blood-cell count, albumin: globulin ratio, gel electrophoresis analysis, C-reactive protein, alpha 1 acid glycoprotein, haptoglobin, fibrinogen, and serum amyloid A. Samples were collected from 71 apparently healthy and 27 diseased animals during diagnostic medical examination. Serum amyloid A, measured by ELISA, followed by albumin:globulin ratio, measured by plasma gel electrophoresis, were most sensitive in diagnosing inflammatory disease, with diagnostic sensitivity and specificity of approximately 90%. The reference interval for serum amyloid A is <10–50 μg/ml with an equivocal interval of 51–70 μg/ml. The reference interval for albumin:globulin ratio by plasma gel electrophoresis is 0.7–1.1. Albumin: globulin ratio, calculated using biochemical techniques, was not accurate due to overestimation of albumin by bromcresol green dye-binding methodology. Albumin:globulin ratio, measured by serum gel electrophoresis, has a low sensitivity of 15% due to the lack of fibrinogen in the sample. Haptoglobin, measured by hemoglobin titration, had a reference interval of 0.4–2.4 mg/ml, a diagnostic sensitivity of 60%, and a diagnostic specificity of 93%. The haptoglobin assay is significantly affected by hemolysis. Fibrinogen, measured by heat precipitation, has a reference interval of 100–400 mg/dl, a diagnostic sensitivity of 40%, and a diagnostic specificity of 95%.

Journal of Zoo and Wildlife Medicine↗

USGS2008

Variability in triactinomyxon production from Tubifex tubifex populations from the same mitochondrial DNA lineage infected with Myxobolus cerebralis, the causative agent of whirling disease in salmonids

Myxobolus cerebralis, the causative agent of whirling disease, infects both salmonid fish and an aquatic oligochaete, Tubifex tubifex. Although M. cerebralis has been detected in river drainages throughout the United States, disease severity among wild fish populations has been highly variable. Tubifex tubifex populations have been genetically characterized using sequences from the 16S mitochondrial DNA (mtDNA) gene, the 18S ribosomal RNA gene, the internal transcribed spacer region 1 (ITS1), and randomly amplified polymorphic DNA (RAPD). Our earlier work indicated that large differences in compatibility between the parasite and populations of T. tubifex may play a substantial role in the distribution of whirling disease and resulting mortality in different watersheds. In the present study, we examined 4 laboratory populations of T. tubifex belonging to 16S mtDNA lineage III and 1 population belonging to 16S mtDNA lineage I for triactinomyxon (TAM) production after infection with M. cerebralis myxospores. All 4 16S mtDNA lineage III populations produced TAMs, but statistically significant differences in TAM production were observed. Most individuals in the 16S mtDNA lineage III-infected populations produced TAMs. The 16S mtDNA lineage I population produced few TAMs. Further genetic characterization of the 16S mtDNA lineage III populations with RAPD markers indicated that populations producing similar levels of TAMs had more genetic similarity. ?? American Society of Parasitologists 2008.

Journal of Parasitology↗

USGS2005

A new Sunwaptan (Late Cambrian) trilobite fauna from the Upper Mississippi Valley

A single bed at the base of the Jordan Sandstone in a road cut at Arcadia, Wisconsin, yielded an undescribed Late Sunwaptan (Saukia Zone) trilobite fauna that includes at least four species from the families Dikelocephalidae Miller, 1889 and Eurekiidae Hupe??, 1953. Arcadiaspis bispinata n. gen. and sp. is a distinctive eurekiid that is characterized by paired occipital and thoracic axial spines, long genal spines, and a nonspinose pygidial margin. Other genera present are the dikelocephalids, Dikelocephalus Owen, 1852 and Calvinella Walcott, 1914, and the eurekiid, Eurekia Walcott, 1916. Type material of Calvinella spiniger (Hall, 1863) is illustrated photographically for the first time. A new eurekiid species, Corbinia burkhalteri from the Fort Sill Formation, Oklahoma, is also described.

Journal of Paleontology↗

USGS2002

An evaluation of population index and estimation techniques for tadpoles in desert pools

Using visual (VI) and dip net indices (DI) and double-observer (DOE), removal (RE), and neutral red dye capture-recapture (CRE) estimates, we counted, estimated, and censused Couch's spadefoot ( Scaphiopus couchii ) and canyon treefrog ( Hyla arenicolor ) tadpole populations in Big Bend National Park, Texas. Initial dye experiments helped us determine appropriate dye concentrations and exposure times to use in mesocosm and field trials. The mesocosm study revealed higher tadpole detection rates, more accurate population estimates, and lower coefficients of variation among pools compared to those from the field study. In both mesocosm and field studies, CRE was the best method for estimating tadpole populations, followed by DOE and RE. In the field, RE, DI, and VI often underestimated populations in pools with higher tadpole numbers. DI improved with increased sampling. Larger pools supported larger tadpole populations, and tadpole detection rates in general decreased with increasing pool volume and surface area. Hence, pool size influenced bias in tadpole sampling. Across all techniques, tadpole detection rates differed among pools, indicating that sampling bias was inherent and techniques did not consistently sample the same proportion of tadpoles in each pool. Estimating bias (i.e., calculating detection rates) therefore was essential in assessing tadpole abundance. Unlike VI and DOE, DI, RE, and CRE could be used in turbid waters in which tadpoles are not visible. The tadpole population estimates we used accommodated differences in detection probabilities in simple desert pool environments but may not work in more complex habitats.

Journal of Herpetology↗

USGS2012

Body condition of Morelet’s Crocodiles ( Crocodylus moreletii ) from northern Belize

Body condition factors have been used as an indicator of health and well-being of crocodilians. We evaluated body condition of Morelet's Crocodiles ( Crocodylus moreletii ) in northern Belize in relation to biotic (size, sex, and habitat) and abiotic (location, water level, and air temperature) factors. We also tested the hypothesis that high water levels and warm temperatures combine or interact to result in a decrease in body condition. Size class, temperature, and water level explained 20% of the variability in condition of Morelet's Crocodiles in this study. We found that adult crocodiles had higher condition scores than juveniles/subadults but that sex, habitat, and site had no effect. We confirmed our hypothesis that warm temperatures and high water levels interact to decrease body condition. We related body condition of Morelet's Crocodiles to natural fluctuations in air temperatures and water levels in northern Belize, providing baseline conditions for population and ecosystem monitoring.

Journal of Herpetology↗

USGS2013

Potential effects of sea-level rise on coastal wetlands in southeastern Louisiana

Coastal Louisiana wetlands contain about 37% of the estuarine herbaceous marshes in the conterminous United States. The long-term stability of coastal wetlands is often a function of a wetland's ability to maintain elevation equilibrium with mean sea level through processes such as primary production and sediment accretion. However, Louisiana has sustained more coastal wetland loss than all other states in the continental United States combined due to a combination of natural and anthropogenic factors, including sea-level rise. This study investigates the potential impact of current and accelerating sea-level rise rates on key coastal wetland habitats in southeastern Louisiana using the Sea Level Affecting Marshes Model (SLAMM). Model calibration was conducted using a 1956–2007 observation period and hindcasting results predicted 35% versus observed 39% total marsh loss. Multiple sea-level-rise scenarios were then simulated for the period of 2007–2100. Results indicate a range of potential wetland losses by 2100, from an additional 2,188.97 km 2 (218,897 ha, 9% of the 2007 wetland area) under the lowest sea-level-rise scenario (0.34 m), to a potential loss of 5,875.27 km 2 (587,527 ha, 24% of the 2007 wetland area) in the highest sea-level-rise scenario (1.9 m). Model results suggest that one area of particular concern is the potential vulnerability of the region's baldcypress-water tupelo ( Taxodium distichum-Nyssa aquatica ) swamp habitat, much of which is projected to become permanently flooded (affecting regeneration) under all modeled scenarios for sea-level rise. These findings will aid in the development of ecosystem management plans that support the processes and conditions that result in sustainable coastal ecosystems.

Louisiana↗

USGS2013

Marsh collapse thresholds for coastal Louisiana estimated using elevation and vegetation index data

Forecasting marsh collapse in coastal Louisiana as a result of changes in sea-level rise, subsidence, and accretion deficits necessitates an understanding of thresholds beyond which inundation stress impedes marsh survival. The variability in thresholds at which different marsh types cease to occur (i.e., marsh collapse) is not well understood. We utilized remotely sensed imagery, field data, and elevation data to help gain insight into the relationships between vegetation health and inundation. A Normalized Difference Vegetation Index (NDVI) dataset was calculated using remotely sensed data at peak biomass (August) and used as a proxy for vegetation health and productivity. Statistics were calculated for NDVI values by marsh type for intermediate, brackish, and saline marsh in coastal Louisiana. Marsh-type specific NDVI values of 1.5 and 2 standard deviations below the mean were used as upper and lower limits to identify conditions indicative of collapse. As marshes seldom occur beyond these values, they are believed to represent a range within which marsh collapse is likely to occur. Inundation depth was selected as the primary candidate for evaluation of marsh collapse thresholds. Elevation relative to mean water level (MWL) was calculated by subtracting MWL from an elevation dataset compiled from multiple data types including light detection and ranging (lidar) and bathymetry. A polynomial cubic regression was used to examine a random subset of pixels to determine the relationship between elevation (relative to MWL) and NDVI. The marsh collapse uncertainty range values were found by locating the intercept of the regression line with the 1.5 and 2 standard deviations below the mean NDVI value for each marsh type. Results indicate marsh collapse uncertainty ranges of 30.7–35.8 cm below MWL for intermediate marsh, 20–25.6 cm below MWL for brackish marsh, and 16.9–23.5 cm below MWL for saline marsh. These values are thought to represent the ranges of inundation depths within which marsh collapse is probable.

Louisiana↗