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USGS2018

Rapid discovery of SNPs differentiating hatchery steelhead trout from ESA-listed natural-origin steelhead trout using a 57K SNP array

Natural-origin steelhead trout ( Oncorhynchus mykiss (Walbaum, 1792)) in the Pacific Northwest, USA, are threatened by a number of factors including habitat destruction, disease, decline in marine survival, and a potential erosion of genetic viability due to introgression from hatchery strains. Our major goal was to use a recently developed SNP array containing ∼57 000 SNPs to identify a subset of SNPs that differentiate hatchery and natural-origin populations. We analyzed 35 765 polymorphic SNPs in nine populations of steelhead trout sampled from Puget Sound, Washington, USA. We then conducted two outlier tests and found 360 loci that were candidates for divergent selection between hatchery and natural-origin populations (mean F CT = 0.29, maximum = 0.65) and 595 SNPs that were candidates for selection among natural-origin populations (mean F ST = 0.25, maximum = 0.51). Comparisons with a linkage map revealed that two chromosomes (Omy05 and Omy25) contained significantly more outliers than other chromosomes, suggesting that regions on Omy05 and Omy25 may be of adaptive significance. Our results highlight several advantages of the 57 000 SNP array as a tool for population and conservation genomics studies.

British Columbia, Washington↗

USGS2014

A mapping and monitoring assessment of the Philippines' mangrove forests from 1990 to 2010

Information on the present condition and spatiotemporal dynamics of mangrove forests is needed for land-change studies and integrated natural resources planning and management. Although several national mangrove estimates for the Philippines exist, information is unavailable at sufficient spatial and thematic detail for change analysis. Historical and contemporary mangrove distribution maps of the Philippines for 1990 and 2010 were prepared at nominal 30-m spatial resolution using Landsat satellite data. Image classification was performed using a supervised decision tree classification approach. Additionally, decadal land-cover change maps from 1990 to 2010 were prepared to depict changes in mangrove area. Total mangrove area decreased 10.5% from 1990 to 2010. Comparison of estimates produced from this study with selected historical mangrove area estimates revealed that total mangrove area decreased by approximately half (51.8%) from 1918 to 2010. This study provides the most current and reliable data regarding the Philippines mangrove area and spatial distribution and delineates where and when mangrove change has occurred in recent decades. The results from this study are useful for developing conservation strategies, biodiversity loss mitigation efforts, and future monitoring and analysis.

Journal of Coastal Research↗

USGS2008

General and specialized media routinely employed for primary isolation of bacterial pathogens of fishes

There are a number of significant diseases among cultured and free-ranging freshwater fishes that have a bacterial etiology; these represent a variety of gram-negative and gram-positive genera. Confirmatory diagnosis of these diseases involves primary isolation of the causative bacterium on bacteriologic media. Frequently used "general" bacteriologic media simply provide the essential nutrients for growth. For most of the major pathogens, however, there are differential and/or selective media that facilitate primary recovery. Some specialized media are available as "ready-to-use" from suppliers, while others must be prepared. Differential media employ various types of indicator systems, such as pH indicators, that allow diagnosticians to observe assimilation of selected substrates. An advantage to the use of differential media for primary isolation is that they hasten bacterial characterization by yielding the appropriate positive or negative result for a particular substrate, often leading to a presumptive identification. Selective media also incorporate agent(s) that inhibit the growth of contaminants typically encountered with samples from aquatic environments. Media that incorporate differential and/or selective components are ideally based on characters that are unique to the targeted bacterium, and their use can reduce the time associated with diagnosis and facilitate early intervention in affected fish populations. In this review, the concepts of general and differential/selective bacteriologic media and their use and development for fish pathogens are discussed. The media routinely employed for primary isolation of the significant bacterial pathogens of fishes are presented. ?? Wildlife Disease Association 2008.

Journal of Wildlife Diseases↗

USGS2001

Geoarchaeology at Gilman Falls: An Archaic Quarry and Manufacturing Site in Central Maine, U.S.A

Interdisciplinary investigations at the Milford Reservoir, central Maine, resulted in excavation and analysis of a Middle Archaic quarry and manufacturing site at Gilman Falls, dated to between 7300 and 6300 yr B.P. Lithological analysis indicates that the majority of the artifacts came from very local outcrops, providing low-grade metamorphic rocks. Native Americans used a specialized technique to reduce the granofels and other rocks to long rods, artifacts commonly placed in local cemeteries. The Gilman Falls site was largely abandoned once these artifacts were no longer in vogue. Therefore, access to particular bedrock outcrops seems to have played an important role in site selection. Gilman Falls and other early to middle Holocene sites are preserved where bedrock sill dams ponded water that deposited fine sand. Early site sedimentation history is paralleled by a drainage change in the headwaters of the Penobscot River. Evidence for lower mid-Holocene lake levels and a period of higher temperatures and lower precipitation may correlate with the sedimentation history. ?? 2001 John Wiley & Sons, Inc.

Geoarchaeology - An International Journal↗

USGS2025

Population estimates and land cover use of wintering Mountain Plovers in Texas

Conservation of migratory birds throughout the full annual cycle requires a comprehensive understanding of abundance and distribution in interconnected breeding, migration, and wintering habitats. The Mountain Plover ( Anarhynchus montanus ) is a rare endemic breeder of the Rocky Mountain and Great Plains regions that migrates to wintering grounds in the southwestern USA and northern Mexico. Information regarding its wintering abundance and distribution, particularly in Texas, is limited. This study provides the first population estimate for Mountain Plovers wintering in Texas and examines factors influencing their land cover use. Through distance sampling surveys in six ecoregions of Texas, we estimated an annual wintering population of 3096 (95% CI 1464–6547) Mountain Plovers during 2019–2020, with the greatest abundances in the Southern Texas Plains and Western Gulf Coastal Plain ecoregions. The highest plover densities were in the Southern Texas Plains and Central Great Plains ecoregions. Most plovers were found in cultivated crops, particularly tilled fields and sod farms, and plovers preferentially selected crop fields without residual vegetation or stubble. Grass/hay fields were used less, perhaps because of tall vegetation. Our findings highlight the significance of Texas as a wintering area for Mountain Plovers and emphasize the importance of specific cropland habitats for this species. These results provide crucial insights for conservation and management efforts aimed at protecting Mountain Plovers throughout their annual cycle.

Texas↗

USGS1987

Pure shear and simple shear calcite textures. Comparison of experimental, theoretical and natural data

The pattern of lattice preferred orientation (texture) in deformed rocks is an expression of the strain path and the acting deformation mechanisms. A first indication about the strain path is given by the symmetry of pole figures: coaxial deformation produces orthorhombic pole figures, while non-coaxial deformation yields monoclinic or triclinic pole figures. More quantitative information about the strain history can be obtained by comparing natural textures with experimental ones and with theoretical models. For this comparison, a representation in the sensitive three-dimensional orientation distribution space is extremely important and efforts are made to explain this concept. We have been investigating differences between pure shear and simple shear deformation incarbonate rocks and have found considerable agreement between textures produced in plane strain experiments and predictions based on the Taylor model. We were able to simulate the observed changes with strain history (coaxial vs non-coaxial) and the profound texture transition which occurs with increasing temperature. Two natural calcite textures were then selected which we interpreted by comparing them with the experimental and theoretical results. A marble from the Santa Rosa mylonite zone in southern California displays orthorhombic pole figures with patterns consistent with low temperature deformation in pure shear. A limestone from the Tanque Verde detachment fault in Arizona has a monoclinic fabric from which we can interpret that 60% of the deformation occurred by simple shear.

Journal of Structural Geology↗

USGS2024

Temporal habitat use of mule deer in the Pueblo of Santa Ana, New Mexico

Mule deer ( Odocoileus hemionus ) are important economically, culturally, and recreationally to the Pueblo of Santa Ana in central New Mexico, USA. Studies of habitat selection improve our understanding of mule deer ecology in central New Mexico and provide the Tribe with valuable information for management of mule deer. We used global positioning system telemetry-collar data collected on mule deer around the Pueblo of Santa Ana to create resource selection functions from proximity-based habitat predictors using a generalized linear mixed model. We created separate resource selection functions for females and males during summer and winter at different times of the day. Season generally had a greater effect on mule deer habitat use than the time of day. Female and male mule deer selected for similar habitats but were sexually segregated in their summer distributions. These findings are consistent with results from other locations where mule deer partitioned habitat similarly between seasons and sexes. Supported models reaffirm accepted patterns of habitat selection for mule deer to the Pueblo of Santa Ana where local results were lacking. Our results can help managers identify locations in and around the Pueblo of Santa Ana where future development such as highway expansion are likely to conflict with mule deer activity and locations where habitat enhancement projects such as adding water sources can have the greatest effect for the deer population.

New Mexico↗

USGS2011

Effects of spatial disturbance on common loon nest site selection and territory success

The common loon ( Gavia immer ) breeds during the summer on northern lakes and water bodies that are also often desirable areas for aquatic recreation and human habitation. In northern New England, we assessed how the spatial nature of disturbance affects common loon nest site selection and territory success. We found through classification and regression analysis that distance to and density of disturbance factors can be used to classify observed nest site locations versus random points, suggesting that these factors affect loon nest site selection (model 1: Correct classification = 75%, null = 50%, K = 0.507, P < 0.001; model 2: Correct classification = 78%, null = 50%, K = 0.551, P < 0.001). However, in an exploratory analysis, we were unable to show a relation between spatial disturbance variables and breeding success ( P = 0.595, R 2 = 0.436), possibly because breeding success was so low during the breeding seasons of 2007–2008. We suggest that by selecting nest site locations that avoid disturbance factors, loons thereby limit the effect that disturbance will have on their breeding success. Still, disturbance may force loons to use sub-optimal nesting habitat, limiting the available number of territories, and overall productivity. We advise that management efforts focus on limiting disturbance factors to allow breeding pairs access to the best nesting territories, relieving disturbance pressures that may force sub-optimal nest placement.

Maine, New Hampshire↗

USGS2011

Feeding rate of young-of-the-year ruffe on eggs of lake whitefish

We measured the feeding rate of individual (0.6-12.2 g) young-of-the-year ruffe (Gymnocephalus cernuus) on the live eggs of lake whitefish (Coregonus clupeaformis) at 3, 5, and 9 degrees C in the laboratory. These temperatures were selected because they covered the range of lake temperatures over which eggs of most Great Lakes coregonines would be most vulnerable to predation by ruffe. Ruffe readily consumed lake whitefish eggs, and regression analysis showed consumption increased with ruffe size and water temperature. Mean daily egg consumption as a percent of mean ruffe body weight was 0.25% at 3 degrees C, 0.59% at 5 degrees C, and 1.00% at 9 degrees C.

Journal of Freshwater Ecology↗

USGS2020

Latitudinal variation in snowshoe hare (Lepus americanus) body mass: A test of Bergmann’s Rule

The relationship between body size and latitude have been the focus of dozens of studies across many species. However, results of testing Bergmann’s Rule – that organisms in colder climates or at higher latitudes possess larger body sizes – have been inconsistent across studies. We investigated whether snowshoe hares (Lepus americanus) follow the Rule by investigating differences in body mass using data from six published studies and from data of 755 individual hares captured from ten populations across North America covering 26° of latitude. We also explored alternative hypotheses related to variation in hare body mass, including winter severity, length of growing season, elevation, and snow depth. We found body mass of hares varied throughout their range, but the drivers of body mass differed based on geographic location. Females in northern populations followed Bergmann’s rule, whereas males did not. In northern populations male mass was related to average snow depth. In contrast, in southern populations body mass of both sexes was related to length of the growing season. These differences likely represent variation in the drivers of selection. Specifically, in the north, a large body size is beneficial to conserve heat because of low winter temperatures, whereas in the south, it is likely due to increased food supply associated with longer growing seasons.

Canadian Journal of Zoology↗

USGS1999

Effect of seasonal differences in dietary meat intake on changes in body mass and composition in wild and captive brown bears

The influence of seasonal dietary meat intake on changes in body mass and composition in wild and captive brown bears ( Ursus arctos ) was investigated because the importance and availability of meat to brown bear populations is currently an important management consideration in several North American ecosystems. Adult female brown bears on the Kenai Peninsula, Alaska, utilized meat heavily in both spring and fall. Meat accounted for 76.2 ± 26.0% (mean ± 1 SD; primarily moose carrion and calves) of assimilated carbon and nitrogen in the spring and 80.4 ± 22.2% (primarily salmon) in the fall. Mass increases in the spring (71.8 ± 28.2%) were mostly lean body mass, but increases in the fall (81.0 ± 19.5%) were primarily fat. Daily intake by captive brown bears fed meat ad libitum during 12-day trials was positively related to body mass. Mass change was positively related to intake in both seasons, but the composition of the gain varied by season, with spring gains primarily lean body mass (64.2 ± 9.4%), while fall gains were 78.8 ± 19.6% lipid. Absolute rates of gain by wild bears occasionally equaled, but were usually much less than, those of captive bears. This was likely due to a combination of factors, which included the time required to locate and handle meat resources, the limited availability of or access to meat resources, and (or) the duration of meat resource availability. Estimated intake by bears not feeding selectively on high-energy components of moose and salmon were 8.5 ± 1.5 kg/day and 541 ± 156 kg/year and 10.8 ± 4.6 kg/day and 1003 ± 489 kg/year, respectively. Intake would drop by as much as 58% for bears feeding exclusively on salmon roe. Management strategies for areas with brown bears that consume significant amounts of meat should address the perpetuation and availability of these meat resources.

Alaska↗

USGS1990

Use of social indices to predict reproductive success in canvasbacks

We correlated temporal changes in social groupings of canvasbacks ( Aythya valisineria ) breeding near Minnedosa, Manitoba, with an independent estimate of hen success during 1974-80. Roadside counts of pairs, lone males, and flocked males were made along transects at 5-day intervals, normalized to percentages to allow comparisons among years, and plotted to obtain measurements of selected areas between and under the curves. An estimate of hen success was regressed on these selected graph areas each year to derive a predictive equation. Graph areas (social indices) determined from temporal changes in the proportion of pairs, lone males, and flocked males correlated (r 2 = 0.69-0.93) with hen success. This technique avoids the need for pair counts, nest searches, and brood counts and provides managers with a useful index to evaluate local management practices and to predict yearly production in time for setting hunting regulations.

Minnedosa↗

USGS1989

Nesting phenology and success of ring-necked ducks in east-central Maine

Selected aspects of the nesting biology of Ring-necked Ducks in east-central Maine were studied during 1983-1985 and compared to previous studies. Nesting chronology, clutch size, and hatching success were similar to results reported from previous studies, but nest success was 32-42% lower. Thirty-eight percent of the nests were successful; % of the eggs in successful nests hatched. Among unsuccessful nests, predation and flooding caused most failures.

Journal of Field Ornithology↗

USGS1984

Use of dissolved oxygen modeling results in the management of river quality

In 1973, the U.S. Geological Survey initiated a study of the Willamette River, Oregon, to determine the major causes of dissolved oxygen (DO) depletion, and whether advanced treatment of municipal wastewaters was needed to achieve the DO standards. The study showed that rates of carbonaceous decay were low (kr = 0.03-0.06/day) and that point-source loadings of carbonaceous biochemical oxygen demand (BOD) accounted for less than one-third of the satisfied oxygen demand. Nitrification of industrially discharged ammonia was the dominant cause of DO depletion. The study led to the calibration and verification of a steady-state DO model which was used to examine selected scenarios of BOD loading, ammonia loading, and flow augmentation. In 1976, the modeling projections for the Willamette River were presented to resource managers. A review in 1981 indicated that the State of Oregon had instituted an effluent standard on the major discharger of ammonia, rescinded an order for all municipal wastewaters to receive advanced secondary treatment by 1980, and more fully acknowledged the need for flow augmentation during summer to attain the DO standards.

Journal of the Water Pollution Control Federation↗

USGS2012

Studying biodiversity: is a new paradigm really needed?

Authors in this journal have recommended a new approach to the conduct of biodiversity science. This data-driven approach requires the organization of large amounts of ecological data, analysis of these data to discover complex patterns, and subsequent development of hypotheses corresponding to detected patterns. This proposed new approach has been contrasted with more-traditional knowledge-based approaches in which investigators deduce consequences of competing hypotheses to be confronted with actual data, providing a basis for discriminating among the hypotheses. We note that one approach is directed at hypothesis generation, whereas the other is also focused on discriminating among competing hypotheses. Here, we argue for the importance of using existing knowledge to the separate issues of (a) hypothesis selection and generation and (b) hypothesis discrimination and testing. In times of limited conservation funding, the relative efficiency of different approaches to learning should be an important consideration in decisions about how to study biodiversity.

BioScience↗

USGS1991

Emulsification of hydrocarbons by subsurface bacteria

Biosurfactants have potential for use in enhancement of in situ biorestoration by increasing the bioavailability of contaminants. Microorganisms isolated from biostimulated, contaminated and uncontaminated zones at the site of an aviation fuel spill and hydrocarbon-degrading microorganisms isolated from sites contaminated with unleaded gasoline were examined for their abilities to emulsify petroleum hydrocarbons. Emulsifying ability was quantified by a method involving agitation and visual inspection. Biostimulated-zone microbes and hydrocarbon-degrading microorganisms were the best emulsifiers as compared to contaminated and uncontaminated zone microbes. Biostimulation (nutrient and oxygen addition) may have been the dominant factor which selected for and encouraged growth of emulsifiers; exposure to hydrocarbon was also important. Biostimulated microorganisms were better emulsifiers of aviation fuel (the contaminant hydrocarbon) than of heavier hydrocarbon to which they were not previously exposed. By measuring surface tension changes of culture broths, 11 out of 41 emulsifiers tested were identified as possible biosurfactant producers and two isolates produced large surface tension reductions indicating the high probability of biosurfactant production.

Journal of Industrial Microbiology↗

USGS2004

Impacts of land use and climate change on carbon dynamics in south-central Senegal

Total carbon stock in vegetation and soils was reduced 37% in south-central Senegal from 1900 to 2000. The decreasing trend will continue during the 21st century unless forest clearing is stopped, selective logging dramatically reduced, and climate change, if any, relatively small. Developing a sustainable fuelwood and charcoal production system could be the most feasible and significant carbon sequestration project in the region. If future climate changes dramatically as some models have predicted, cropland productivity will drop more than 65% around 2100, posing a serious threat to food security and the efficiency of carbon sequestration projects.

Journal of Arid Environments↗

USGS2014

Common raven occurrence in relation to energy transmission line corridors transiting human-altered sagebrush steppe

Energy-related infrastructure and other human enterprises within sagebrush steppe of the American West often results in changes that promote common raven ( Corvus corax ; hereafter, raven) populations. Ravens, a generalist predator capable of behavioral innovation, present a threat to many species of conservation concern. We evaluate the effects of detailed features of an altered landscape on the probability of raven occurrence using extensive raven survey ( n = 1045) and mapping data from southern Idaho, USA. We found nonlinear relationships between raven occurrence and distances to transmission lines, roads, and facilities. Most importantly, raven occurrence was greater with presence of transmission lines up to 2.2 km from the corridor.We further explain variation in raven occurrence along anthropogenic features based on the amount of non-native vegetation and cover type edge, such that ravens select fragmented sagebrush stands with patchy, exotic vegetative introgression. Raven occurrence also increased with greater length of edge formed by the contact of big sagebrush ( Artemisia tridentate spp.) with non-native vegetation cover types. In consideration of increasing alteration of sagebrush steppe, these findings will be useful for planning energy transmission corridor placement and other management activities where conservation of sagebrush obligate species is a priority.

Idaho↗