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At least 1,567 records · Page 87Linked to original sources
USGS1989

Suppression of antibody-producing cells in rainbow trout spleen sections exposed to copper in vitro

Immunosuppression was demonstrated in sections of rainbow trout Oncorhynchus mykiss (formerly Salmo gairdneri ) spleens immunized in vitro and exposed in culture to different concentrations of copper chloride. The sections were immunized with dinitrophenyl-Ficoll and cultured in Eagle's minimum essential medium with 2% fetal calf serum; half of the medium was withdrawn and replaced every other day. The passive hemolytic plaque assay was used to determine the number of antibody-producing cells 10 d after injection. In the sections cultured with the high copper concentration (100 μg/mL), all cells died; at copper concentrations of 0.1–10 μg/mL, leukocytes remained viable, but fewer antibody-producing cells were present than in organ sections cultured in medium without copper. This in vitro method reduces the number of animals needed and the length of time required to determine toxicity and immunosuppression, and it provides information on the effects of certain environmental pollutants on fish.

Journal of Aquatic Animal Health↗
USGS1990

Growth and equilibrium in sea otter populations

(1) Counts through time were compiled for five sea otter ( Enhydra lutris ) populations in the north-east Pacific Ocean that were below equilibrium density: Attu Island, south-east Alaska, British Columbia, Washington State, and central California. Similar data were obtained from the equilibrium density population at Amchitka Island in 1971 and 1986. (2) Shorelines of Attu and Amchitka islands each were divided into forty-five segments, within which lineal (length of shore at mean higher high water) and areal (mean higher high water to the 10-fathom (18.3-m) depth contour) measures were made of the amount of habitat. (3) Rate of increase for the four northern populations was 17-20% year-1. Density- or size-dependent changes in rate of increase could not be demonstrated for any of these populations. The California population, in contrast, has undergone three apparent growth phases: the early 1900s to the mid-1970s when it increased about 5% year-1; the mid-1970s to the mid-1980s when it declined about 5% year-1; and the mid-1980s to 1988 when it increased about 7% year-1. An exponential growth model accounted for 92-98% of the variation in counts through time in all cases. (4) Population increase at Attu Island was achieved largely by range expansion as opposed to increased density. Range expansion in lineal and areal habitat occurred at 11% and 13% year-1, respectively; neither rate was lower (P > 0.25) than the observed rate of increase in numbers of animals counted. (5) Despite similarities in island size and physical environment, the most conservative estimates of population density at Amchitka Island were > 3 X greater than maximum density estimates for Attu Island. (6) Surveys of Amchitka Island from the mid-1930s through the mid-1980s indicate that the population increased to a peak in the 1940s; declined abruptly thereafter; and subsequently increased to a new and higher equilibrium in the 1960s, where it has since remained. (7) These population data, together with information on sea otter foraging and benthic community structure at Attu and Amchitka islands, suggest that multiple population equilibria exist in this system, emanating from complex trophic interactions low in the food web. I hypothesize that the lower population equilibrium is achieved largely or exclusively on an invertebrate diet consisting principally of herbivorous sea urchins. When unregulated by sea otter predation, the rocky benthos is deforested by sea urchin grazing. As growing otter populations compete increasingly for food, grazing intensity declines and the system shifts to one dominated by kelp beds, in turn leading to increased production, a shift in habitat structure, and population increases of kelp bed fishes. Apparently this new food resource elevates the sea otter population to a higher and more stable equilibrium.

Journal of Animal Ecology↗
USGS2021

Wolf use of humanmade objects during pup-rearing

Some animals use humanmade objects for building and constructing nests or shelter and even for play. Gray wolves ( Canis lupus ) gather and use humanmade objects discovered in their natural environment. Gathering humanmade objects is a peculiar behavior particularly when there is no immediately apparent benefit to survival or reproduction. I opportunistically documented 46 different types of humanmade objects with plastic bottles and aluminum cans being the most common items found at wolf pup-rearing sites. Many objects were made of materials that appeared suitable to alleviate pain in teething pups. For some objects, however, it was not immediately obvious that they would alleviate teething pain due to their unpliable material. Additionally, such objects were quite rare in wolves’ natural environment although it was not uncommon to find them at pup-rearing sites. Rare humanmade objects may provide a novelty that stimulates pups more than common objects. I hypothesize that objects used by wolf pups 1) alleviate pain from teething, and 2) provide adults respite from energetic pups. The latter is an important distinction because it implies the benefit of object play is to the adults and not the pups per se. Gathering novel objects that occupy energetic and hungry pups may influence the overall ability of social carnivores to leave young unattended while they hunt, to rest upon their return, and ultimately rear young successfully.

Animal Behavior and Cognition↗
USGS2018

Raptor nest-site use in relation to the proximity of coalbed methane development

Raptor nest–site use in relation to the proximity of coalbed–methane development. Energy development such as coalbed–methane (CBM) extraction is a major land use with largely unknown consequences for many animal species. Some raptor species may be especially vulnerable to habitat changes due to energy development given their ecological requirements and population trajectories. Using 12,977 observations of 3,074 nests of 12 raptor species across nine years (2003–2011) in the Powder River Basin, Wyoming, USA, we evaluated relationships between raptor nest–site use and CBM development. Our objectives were to determine temporal trends in nest–use rates, and whether nest–site use was related to the proximity of CBM development. Across the study area, nest–use rates varied across species and years in a non–linear fashion. We developed a novel randomization test to assess differences in use between nests at developed and undeveloped sites, while controlling for annual variation in nest–site use. Red–tailed hawks (Buteo jamaicensis), burrowing owls (Athene cunicularia), and long–eared owls (Asio otus) used nests in undeveloped areas more than nests in developed areas (i.e. nests near CBM development). Differences between development groups were equivocal for the remaining nine species; however, we caution that we likely had lower statistical power to detect differences for rarer species. Our findings suggest potential avoidance of nesting in areas near CBM development by some species and reveal that CBM effects may be fairly consistent across distances between 400–2,415 m from wells. Future work should consider habitat preferences and fitness outcomes, and control for other key factors such as local prey availability, raptor densities, and weather.

Wyoming↗
USGS2026

Multiscale resource selection for a reintroduced elk population

Patterns of resource selection are driven by the decision-making processes of animals occurring at multiple scales from where to establish a home range (i.e., second order selection) to which resource patches to use within the home range (i.e., third order selection). Elk ( Cervus canadensis ) were reintroduced to southwestern Virginia, USA, from 2012 to 2014 following successful translocations onto reclaimed surface coal mines in the region. We sought to understand how elk have acclimated following their translocation using location data from GPS-collared adult female elk ( n = 33) collected from 2019 to 2022 along with remotely sensed terrain and land cover data. We utilized continuous-time movement models paired with generalized linear mixed-effects modeling to describe seasonal resource selection at second and third orders. At both scales of selection and throughout the year, female elk selected reclaimed surface mines, conifer forests, ridgetops, and areas with lower terrain roughness, while avoiding mixed hardwood and oak ( Quercus spp.) forests. Unmined open land was only selected at the third order during periods of forage scarcity (i.e., winter) and increased metabolic requirements (i.e., late gestation). Although surface coal mining leaves legacy environmental impacts on the landscape, management of these sites provides benefits to elk and maintains open habitat that is otherwise limited.

Virginia↗
USGS2004

Computing and software

The reality is that the statistical methods used for analysis of data depend upon the availability of software. Analysis of marked animal data is no different than the rest of the statistical field. The methods used for analysis are those that are available in reliable software packages. Thus, the critical importance of having reliable, up–to–date software available to biologists is obvious. Statisticians have continued to develop more robust models, ever expanding the suite of potential analysis methods available. But without software to implement these newer methods, they will languish in the abstract, and not be applied to the problems deserving them. In the Computers and Software Session, two new software packages are described, a comparison of implementation of methods for the estimation of nest survival is provided, and a more speculative paper about how the next generation of software might be structured is presented. Rotella et al. (2004) compare nest survival estimation with different software packages: SAS logistic regression, SAS non–linear mixed models, and Program MARK. Nests are assumed to be visited at various, possibly infrequent, intervals. All of the approaches described compute nest survival with the same likelihood, and require that the age of the nest is known to account for nests that eventually hatch. However, each approach offers advantages and disadvantages, explored by Rotella et al. (2004). Efford et al. (2004) present a new software package called DENSITY. The package computes population abundance and density from trapping arrays and other detection methods with a new and unique approach. DENSITY represents the first major addition to the analysis of trapping arrays in 20 years. Barker & White (2004) discuss how existing software such as Program MARK require that each new model’s likelihood must be programmed specifically for that model. They wishfully think that future software might allow the user to combine pieces of likelihood functions together to generate estimates. The idea is interesting, and maybe some bright young statistician can work out the specifics to implement the procedure. Choquet et al. (2004) describe MSURGE, a software package that implements the multistate capture–recapture models. The unique feature of MSURGE is that the design matrix is constructed with an interpreted language called GEMACO. Because MSURGE is limited to just multistate models, the special requirements of these likelihoods can be provided. The software and methods presented in these papers gives biologists and wildlife managers an expanding range of possibilities for data analysis. Although ease–of–use is generally getting better, it does not replace the need for understanding of the requirements and structure of the models being computed. The internet provides access to many free software packages as well as user–discussion groups to share knowledge and ideas. (A starting point for wildlife–related applications is (http://www.phidot.org).

Animal Biodiversity and Conservation↗
USGS2004

Evolution of quantitative methods for the study and management of avian populations: on the importance of individual contributions

The EURING meetings and the scientists who have attended them have contributed substantially to the growth of knowledge in the field of estimating parameters of animal populations. The contributions of David R. Anderson to process modeling, parameter estimation and decision analysis are briefly reviewed. Metrics are considered for assessing individual contributions to a field of inquiry, and it is concluded that Anderson’s contributions have been substantial. Important characteristics of Anderson and his career are the ability to identify and focus on important topics, the premium placed on dissemination of new methods to prospective users, the ability to assemble teams of complementary researchers, and the innovation and vision that characterized so much of his work. The paper concludes with a list of interesting current research topics for consideration by EURING participants.

Animal Biodiversity and Conservation↗
USGS1998

Modelling of instream flow needs: The link between sediment and aquatic habitat

Instream flows are needed to remove undesirable accumulations of sediment. Fines and sand accumulate on and in gravels during periods of low flow and must be removed (flushed) periodically in order for the gravel to continue as suitable habitat for aquatic animals. Sediment of all sizes can also fill pools in the river and must be removed in order to maintain pool habitat. A new technique relates the sizes of sediment important in the biological process to the size transported as wash, suspended and bed loads. The technique has a biological component, a hydraulic component and a selection component that links the two. The technique was used to determine the instream flows needed to maintain habitat for Colorado squawfish in the Gunnison River in western Colorado. Flows included a flushing flow to remove course sand form the riffles where Colorado squawfish spawn, to remove fines and sand from the river in general, to remove gravel from pools, and to scour side channels. The Gunnison River has a mean discharge of 73 m 3 /s and the flows of both sediment and water in the river have been modified by the construction of reservoirs and by major diversions for irrigation. The flows needed to maintain the spawning habitat for the Colorado squawfish by removing fines and sand from the riffles is 355 m 3 /s, to remove sand and fines from the river is 354 m 3 /s, to remove gravel from pools is 484 m 3 /s and to scour side channels is 210 m 3 /s. The flow required to maintain the riffles during spawning is 210 m 3 /s. These flushing flows are not required each year but they are required periodically (usually not less than once in every 3 years); and the maintenance flow is needed every year.

Regulated Rivers: Research & Management↗
USGS2000

Rehabilitation of lands mined for limestone in the Indian desert

In the Indian desert, the economics of mining is second only to agriculture in importance. However, research on the rehabilitation of land disturbed by mining has only recently received serious attention. An attempt has been made to determine both the qualitative and quantitative success of rehabilitation plans used to revegetate limestone mine spoils in an area near Barna, northwest arid India. Rehabilitation success was achieved using a combination of rainwater harvesting techniques, soil amendment application approaches, plant establishment methods and the selection of appropriate germplasm material (trees, shrubs and grasses). It is expected that the resulting vegetative cover will be capable of self-perpetuation under natural conditions while at the same time meeting the land-use needs of the local people. The minespoils have adequate levels of the major nutrients (except P, Mo and Se) for proper plant and grazing animal health. Levels of organic matter are low whereas total B concentrations are exceptionally high. Also, the population of soil fungi, Azotobactor, and nitrifying bacteria is negligible. Enhanced plant growth was achieved in treated plots, compared to control plots, where spoil moisture storage was improved by 5-45 per cent. Due to the decomposition of farmyard manure and nitrogen fixation by planted leguminous plant species, the electrical conductance of treated mine spoils increased threefold, CaCO3 content decreased from 20??0 to 5??2 per cent, and organic carbon, P, K, and biological activity increased significantly. The rehabilitation protocol used at the site appears to have been successful because plant self-regeneration is occurring. The increased diversity of woody perennials resulted in 'dominance' being better shared among species and 'evenness' being increased within the plant community elements. The early to mid-successional trends are continuing for six years following initial rehabilitation. This study developed methods for the rehabilitation of lands mined for limestone and has also resulted in an understanding of rehabilitation processes in arid regions with an emphasis on the long-term monitoring of rehabilitation success. Copyright ?? 2000 John Wiley & Sons, Ltd.

Land Degradation and Development↗
USGS2019

Variation of annual apparent survival and detection rates with age, year, and individual identity in male Weddell seals (Leptonychotes weddellii) from long-term mark-recapture data

Exploring age- and sex-specific survival rates provides insight regarding population behavior and life-history trait evolution, but many population studies exclude males. Accordingly, our understanding of how age-specific patterns of survival, including actuarial senescence, compare between the sexes remains inadequate. Using 35 years of mark-recapture data for 7,516 male Weddell seals (Leptonychotes weddellii) born in Erebus Bay, Antarctica, we estimated age- specific annual survival rates using a hierarchical model for mark-recapture data in a Bayesian framework. Our male survival estimates were moderate for pups and yearlings, highest for 2- year-olds, and gradually declined with age thereafter such that the oldest animals observed had the lowest rates of any age. Reports of senescence in other wildlife populations of species with similar longevity occurred at older ages than those presented here. When compared to recently published estimates for reproductive Weddell seal females, we found that peak survival rates were similar (males: 0.94, 95% CI = 0.92-0.96; females: 0.92, 95% CI = 0.93-0.95), but rates declined more rapidly in males. Costs of reproduction for males seem to exceed costs incurred by females, but age-specific reproductive data for males are necessary to fully evaluate survival- reproduction tradeoffs in males. Similar studies on a broad range of species are needed to contextualize these results for a better understanding of the variation in senescence patterns between the sexes of the same species, but our study adds information for a marine mammal species to a research topic dominated by avian and ungulate species.

Population Ecology↗
USGS2020

Highly variable rates of survival to metamorphosis in wild boreal toads (Anaxyrus boreas boreas)

Life history theory suggests that long‐lived, pond‐breeding amphibians should have low and highly variable early life‐stage survival rates, but this theoretical expectation is often untested and the causes of variation are usually unknown. We evaluated the impact of hydroperiod, presence of a pathogen ( Batrachochytrium dendrobatidis [Bd]), presence of a potential predator (cutthroat trout Oncorhychus clarki stomias) , and whether animals had been reintroduced into a site on survival of early life stages of boreal toads ( Anaxyrus boreas boreas ). We used a multistate mark‐recapture framework to estimate survival of boreal toad embryos from egg to metamorphosis at four sites over 5 years. We found substantial spatial and temporal variation in survival to metamorphosis and documented some evidence that monthly tadpole survival was lower in sites with Bd, without trout, and at permanent sites. Our results support theories of amphibian life history, aid in the management of this species of conservation concern, and contribute to our knowledge of the ecology of the species. Additionally, we present methodology that allows practitioners to account for different lengths of time between sampling periods when estimating survival probabilities which is especially applicable to organisms with distinct biological stages.

Population Ecology↗
USGS2001

Effect of 2,4-Dichlorophenoxyacetic acid herbicide Escherichia coli growth, chemical, composition, and cellular envelope

2,4-Dichlorophenoxyacetic acid (2,4-D) is a herbicide widely used in the world and mainly excreted by the renal route in exposed humans and animals. Herbicides can affect other nontarget organisms, such as Escherichia coli. We observed that a single exposure to 1 mM 2,4-D diminished growth and total protein content in all E. coli strains tested in vitro. In addition, successive exposures to 0.01 mM 2,4-D had a toxic effect decreasing growth up to early stationary phase. Uropathogenic E. coli adhere to epithelial cells mediated by fimbriae, adhesins, and hydrophobic properties. 2,4-D exposure of uropathogenic E. coli demonstrated altered hydrophobicity and fimbriation. Hydrophobicity index values obtained by partition in p-xylene/water were 300-420% higher in exposed cells than in control ones. Furthermore, values of hemagglutination titer, protein contents in fimbrial crude extract, and electron microscopy demonstrated a significant diminution of fimbriation in treated cells. Other envelope alterations could be detected, such as lipoperoxidation, evidenced by decreased polyunsaturated fatty acids and increased lipid degradation products (malonaldehyde), and motility diminution. These alterations decreased cell adherence to erythrocytes, indicating a diminished pathogenic capacity of the 2,4-D-exposed E. coli. ?? 2001 by John Wiley & Sons, Inc.

Environmental Toxicology↗
USGS2013

The false spring of 2012, earliest in North American record

Phenology - the study of recurring plant and animal life cycle stages, especially their timing and relationships with weather and climate - is becoming an essential tool for documenting, communicating, and anticipating the consequences of climate variability and change. For example, March 2012 broke numerous records for warm temperatures and early flowering in the United States [Karl et al., 2012; Elwood et al., 2013]. Many regions experienced a “false spring,” a period of weather in late winter or early spring sufficiently mild and long to bring vegetation out of dormancy prematurely, rendering it vulnerable to late frost and drought. As global climate warms, increasingly warmer springs may combine with the random climatological occurrence of advective freezes, which result from cold air moving from one region to another, to dramatically increase the future risk of false springs, with profound ecological and economic consequences [e.g., Gu et al., 2008; Marino et al., 2011; Augspurger, 2013]. For example, in the false spring of 2012, an event embedded in long-term trends toward earlier spring [e.g., Schwartz et al., 2006], the frost damage to fruit trees totaled half a billion dollars in Michigan alone, prompting the federal government to declare the state a disaster area [Knudson, 2012].

Eos, Transactions, American Geophysical Union↗
USGS2016

Dendritic network models: Improving isoscapes and quantifying influence of landscape and in-stream processes on strontium isotopes in rivers

A critical challenge for the Earth sciences is to trace the transport and flux of matter within and among aquatic, terrestrial, and atmospheric systems. Robust descriptions of isotopic patterns across space and time, called “isoscapes,” form the basis of a rapidly growing and wide-ranging body of research aimed at quantifying connectivity within and among Earth's systems. However, isoscapes of rivers have been limited by conventional Euclidean approaches in geostatistics and the lack of a quantitative framework to apportion the influence of processes driven by landscape features versus in-stream phenomena. Here we demonstrate how dendritic network models substantially improve the accuracy of isoscapes of strontium isotopes and partition the influence of hydrologic transport versus local geologic features on strontium isotope ratios in a large Alaska river. This work illustrates the analytical power of dendritic network models for the field of isotope biogeochemistry, particularly for provenance studies of modern and ancient animals.

Geophysical Research Letters↗
USGS2025

Using community-reported data to understand how boat speed affects marine wildlife: An example with the Florida manatee

Boat collisions are a known and increasing threat to many marine wildlife populations. The Florida manatee Trichechus manatus latirostris is a key example of a species with high boat-related mortality, whose long-term viability and population are limited by human activities in shared habitats. The goal of this work was to quantify the probability of lethal injury to Florida manatees using community-reported data on collisions with boats. We test the hypothesis that higher boat speeds increase the probability of lethal injury to manatees. Empirical data to test this hypothesis are collected opportunistically, with low sample sizes and uncertainty in reported boat speed. We fit a logistic regression model using Bayesian inference with Markov Chain Monte Carlo to community-reported collision data. We also present results for two errors-in-variables modelling approaches that account for uncertainty in boat speeds reported as qualitative values. The first uses a multiple imputation approach, whereas the second uses Bayesian estimation with informed priors. We evaluated issues related to quasi-separation, sample size, and measurement errors using simulated data. The models predicted that the probability of lethal injury increased at greater strike speed. However, the small number of records with low boat speed or where the injury was considered non-lethal contributed to uncertainty around this functional relationship. Although the relationships were consistent among models, the uncertainty was greater for the errors-in-variables models. Practical implication . When combined with information on manatee and boat abundance and behaviour, the results of this analysis can be used to predict the number of deadly collisions, test alternative management scenarios and inform speed zone regulations. We also identify ways to improve data reporting to reduce uncertainty in the effect of boat speed on lethal injury to marine wildlife. This type of analysis can be applied to any marine animal where records of collisions with boats are kept.

Florida↗
USGS2026

Survey protocols drive heterogeneity in occupancy estimates that cannot be standardized using post hoc analyses

Site occupancy models are widely used to estimate species distributions from presence–nondetection data, yet for mobile animals, the true proportion of sites occupied varies in time. Thus, true occupancy and estimates generated from different protocols are affected by temporal characteristics of survey design. Here we tested whether we could standardize occupancy estimates across different sampling protocols with a post hoc statistical test. Using an individual-based movement model of Wood Thrush ( Hylocichla mustelina ), we simulated point count surveys across 3000 populations under 90 spatially and temporally variable sampling protocols. For each simulation, we fit a standard occupancy model, then used minute-level detections to truncate surveys and generate occupancy estimates across increasing survey lengths. We fit asymptotic models to these series to estimate intercepts (instantaneous occupancy) and asymptotes (longer-term occupancy) and evaluated how well they approximated true instantaneous, daily and seasonal occupancy. We were unable to recover instantaneous or seasonal occupancy from any approach. Both standard occupancy models and asymptotic regression (the top-performing asymptotic model) most closely approximated daily occupancy; although asymptotic regression produced slightly less biased estimates, it showed substantially greater variability, resulting in greater overall error. Our results show that post hoc analytical approaches cannot, at present, reliably standardize occupancy estimates across heterogeneous survey designs. Instead, ensuring biologically informative and comparable estimates will depend on standardized survey protocols. Practical implication : Monitoring programs using presence–nondetection data should prioritize consistent survey protocols when estimating occupancy for mobile species, with a focus on daily occupancy as the most attainable and useful metric. Although the highest accuracy and precision were achieved under the most intensive survey protocols, for point counts of Wood Thrush and similar species, four consecutive 15–20 min surveys provide near-optimal precision and can be completed in a single visit, making them well suited for estimating relative occupancy under logistical constraints. Three 20-min surveys spaced ~24 h apart closely approximate daily occupancy while maintaining reasonable precision. Developing similar protocols for other species and survey methods will be critical to ensuring comparable occupancy estimates across space and time.

Ecological Solutions and Evidence↗
USGS2006

Abundance: Population size and density estimation

Estimates of population size (total number of individuals) or density (number of individuals per unit area) are some of the most basic requirements for wildlife research and management. This article provides a brief overview of approaches for wildlife population estimation. These include habitat-based approaches such as quadrat, line intercept, distance, and repeated count methods, as well as animal-based approaches such as capture–recapture and harvest methods. In contrast to methods that only index changes in these parameters, estimates of size or density must account for the probability that an individual will be included in the sample used for estimation. The essential differences in the approaches are in how the samples are obtained and how the sampling probabilities are estimated.

Book chapter↗