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At least 613 records · Page 34Linked to original sources

Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis

Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive independent estimates of eDNA production rates and downstream persistence from brook trout ( Salvelinus fontinalis ) in streams. We use these estimates to parameterize models comparing the false negative detection rates of eDNA sampling and traditional backpack electrofishing. We find that using the protocols in this study eDNA had reasonable detection probabilities at extremely low animal densities (e.g., probability of detection 0.18 at densities of one fish per stream kilometer) and very high detection probabilities at population-level densities (e.g., probability of detection > 0.99 at densities of ≥ 3 fish per 100 m). This is substantially more sensitive than traditional electrofishing for determining the presence of brook trout and may translate into important cost savings when animals are rare. Our findings are consistent with a growing body of literature showing that eDNA sampling is a powerful tool for the detection of aquatic species, particularly those that are rare and difficult to sample using traditional methods.

Montana

Summary of reported agriculture and irrigation water use in Phillips County, Arkansas, 1991

This report summarizes the 1991 water-use reporting through the Conservation District Office in Phillips County, Arkansas. The number of withdrawal registrations for Phillips County was 1,109 (1,103 groundwater and 6 surface water). Water withdrawals reported during the registration process total 0.15 Mgal/d (0.15 Mgal/d groundwater and none from surface water) for agriculture and 123.75 Mgal/d (122.66 Mgal/d groundwater and 1.09 Mgal/d surface water) for irrigation. The registration reports for 1991 indicate that this water was applied to 96,502 acres of land to irrigate wheat, rice, corn, soybeans, milo, cotton, hay, vegetables, grapes, nuts, fruit trees, and sod, as well as for the agricultural use of animal aquaculture.

Open-File Report

Summary of reported agriculture and irrigation water use in Prairie County, Arkansas, 1991

This report summarizes the 1991 water-use reporting through the Conservation District Office in Prairie County, Arkansas. The number of withdrawal registrations for Prairie County was 2,187 (1,786 groundwater and 401 surface water). Water with- drawals reported during the registration process total 26.93 Mgal/d (26.84 Mgal/d groundwater and 0.09 Mgal/d surface water) for agriculture and 191.08 Mgal/d (138.79 Mgal/d groundwater and 52.29 Mgal/d surface water) for irrigation. The registration reports for 1991 indicate that this water was applied to 144,956 acres of land to irrigate rice, corn, soybeans, milo, cash grains, unknown crop, cotton hay, berries, and fruit trees as well as for the agricultural uses of animal aquaculture, minnows, timber, and ducks.

Open-File Report

Characterizing Golden Eagle risk to lead and anticoagulant rodenticide exposure: A review

Contaminant exposure is among the many threats to Golden Eagle ( Aquila chrysaetos ) populations throughout North America, particularly lead poisoning and anticoagulant rodenticides (AR). These threats may act in concert with others (e.g., lead poisoning and trauma associated with striking objects) to exacerbate risk. Golden Eagles are skilled hunters but also exploit scavenging opportunities, making them particularly susceptible to contaminant exposure from ingesting tissues of poisoned or shot animals. Lead poisoning has long been recognized as an important source of mortality for Golden Eagles throughout North America. More recently, ARs have been associated with both sublethal and lethal effects in raptor species worldwide. In this review, we examine the current state of knowledge for lead and AR exposure in Golden Eagles, drawing from the broader raptor contaminant ecology literature. We examine lead and AR sources within Golden Eagle habitats, exposure routes and toxicity, effects on individuals and populations, synergistic effects, and data and information needs. Continued research addressing data needs and information gaps will help with Golden Eagle conservation planning.

Journal of Raptor Research

Pheromone pollution from invasive sea lamprey misguides a native confamilial

Animals living in the Anthropocene search for mates facing a barrage of pollutants. Few studies consider pheromones from invasive species as pollution, but their central role in the lives of many animals indicates cross-reaction among historically allopatric relatives has potentially damaging impacts. We hypothesized the sex pheromone of sea lamprey (Petromyzon marinus), an invasive fish in the Laurentian Great Lakes, misguides mate search in native chestnut lamprey (Ichthyomyzon castaneus). In a field test, 100 % of female I. castaneus chose male odourants from P. marinus over conspecifics. Chemical analysis of water in which males were held confirmed both species signal with 3-keto petromyzonol sulfate but revealed higher release rates in P. marinus. Our results indicate sex pheromones from invasive species can be an influential type of pollution and underscore the conservation implications of studies on pheromone evolution.

Current Zoology

Management of wetlands for wildlife

Wetlands are highly productive ecosystems that provide habitat for a diversity of wildlife species and afford various ecosystem services. Managing wetlands effectively requires an understanding of basic ecosystem processes, animal and plant life history strategies, and principles of wildlife management. Management techniques that are used differ depending on target species, coastal versus interior wetlands, and available infrastructure, resources, and management objectives. Ideally, wetlands are managed as a complex, with many successional stages and hydroperiods represented in close proximity. Managing wetland wildlife typically involves manipulating water levels and vegetation in the wetland, and providing an upland buffer. Commonly, levees and water control structures are used to manipulate wetland hydrology in combination with other management techniques (e.g., disking, burning, herbicide application) to create desired plant and wildlife responses. In the United States, several conservation programs are available to assist landowners in developing wetland management infrastructure on their property. Managing wetlands to increase habitat quality for wildlife is critical, considering this ecosystem is one of the most imperiled in the world.

Book chapter

California condors

The California condor ( Gymnogyps californianus ) is a member of the vulture family. With a wingspan of about 3 m (9 ft) and weighing about 9 kg (20 lb), it spends much of its time in soaring flight visually seeking dead animals as food. The California condor has always been rare (Wilbur 1978; Pattee and Wilbur 1989). Although probably numbering in the thousands during the Pleistocene epoch in North America, its numbers likely declined dramatically with the extinction of most of North America's large mammals 10,000 years ago. Condors probably numbered in the hundreds and were nesting residents in British Columbia, Washington, Oregon, California, and Baja California around 1800. In 1939 the condor population was estimated at 60-100 birds, and its home range was reduced to the mountains and foothills of California, south of San Francisco and north of Los Angeles. Conservation to halt the condor's decline included establishing the Sisquoc (1937) and Sespe (1947) condor sanctuaries within the Los Padres National Forest, obtaining fully protected status under California Fish and Game Code (1953), placement on California's first state endangered species list (1971), and, finally, being listed by the federal government under the Endangered Species Act of 1973 (Wilbur 1978). The success of these efforts could not be judged, however, because verifiable status and trends data did not become available until 1982. By using these data, we confirmed the decline in condor numbers over the past 50 years was even greater than thought.

Book chapter

Chronic wasting disease—Research by the U.S. Geological Survey and partners

Introduction Chronic wasting disease (CWD) is the only transmissible spongiform encephalopathy, a class of invariably fatal neurodegenerative mammalian diseases associated with a misfolded cellular prion protein found in wild free-ranging animals. Because it has a long incubation period, affected animals in Cervidae (the deer family; referred to as “cervids”) may not show signs of disease for several years. While signs are not specific to CWD, affected cervids (deer, elk, moose, and reindeer) show changes in appearance (such as progressive weight loss) and changes in behavior such as stumbling, tremors, and teeth grinding. CWD can be transmitted by direct contact or through a contaminated environment. The causative prion agent is highly resistant to degradation. In recent decades, CWD has transitioned from a novel, obscure prion disease of cervids with limited geographical distribution, to a disease that poses substantial ecological, agricultural, and economic risks across large regions of North America. Since its discovery in free-ranging elk and deer populations in the western United States in the 1980s, CWD has been reported in captive or free-ranging cervid populations in 26 States, 3 Canadian Provinces, the Republic of South Korea, Finland, Sweden, and Norway. In addition, the proportion of CWD-infected animals is increasing in many areas where the disease is already established. In some heavily affected areas, total cervid numbers have decreased over time due to CWD, which suggests that these cervid populations may not be sustainable in the long-term. The U.S. Geological Survey (USGS) conducts wildlife disease surveillance and research to support management of CWD-affected species and their habitats. The scientific information is relevant to governmental agencies that manage wildlife and their habitats including the U.S. Fish and Wildlife Service, the National Park Service, the U.S. Department of Agriculture, and other Federal, State, and Tribal agencies as well as conservation partners (non-governmental organizations, businesses, and private landowners). Each project description in this report (1–30) includes the non-USGS collaborators (Federal, State, Tribal agencies, universities) and a USGS point of contact (principal investigator). If there are USGS publications associated with the project, a publication list is provided at the end of each project description.

Alberta, California, Colorado, Idaho, Iowa, Kansas

Restoration of bighorn sheep metapopulations in and near 15 national parks: Conservation of a severely fragmented species; Volume I, Planning, problem definition, findings, and restoration

Bighorn sheep ( Ovis canadensis ) were historically a ubiquitous species. Prior to the arrival of Europeans, they were seemingly widespread in nearly all steep habitats in the mountains, foothills, river breaks, and prairie badlands of the western United States. However, since catastrophic declines in the late 1800s and early 1900s, most extant populations have existed as small, isolated groups in a highly fragmented distribution. Stochastic events such as seasonal weather change or population fluctuations render these small populations more prone to extirpation than larger populations. Three different subspecies of bighorn sheep were eliminated from 14 of 18 National Park System (NPS) units in the 6-state Intermountain Region of the western United States (Singer 1994). In 1990, when this restoration was initiated, only 4 (18%) of 22 discrete park populations or metapopulations were considered large enough (300-500 animals) to be secure for long-term management. Five (23%) other populations numbered 100-299 animals and 3 (14%) populations numbered 75-99 animals. But, the remaining 10 populations (45%) were either extirpated (n = 2), remnant populations (n = 5, populations of 7-10 animals), or vulnerable to extirpation (n = 3, populations of less than 50 animals). Restoration prior to 1991-96 was largely completed in one NPS unit, but was incomplete in the remaining units. Most bighorn sheep are not federally listed as endangered or threatened species, although the California peninsular population of desert bighorn sheep was recently listed as endangered. The bighorn sheep is a rare or uncommon species that is declining in many parts of its range but is abundant in other areas and still relatively easy to study and manage. The Secretary of the Department of the Interior, Bruce Babbitt, directed the Biological Resources Division of the U.S. Geological Survey in 1993 (when this agency was still the National Biological Service) to research and recover species that were declining to avoid expensive and controversial federal listing. Because the capture and moving of the species are still relatively uncomplicated and because some source stocks are available, aggressive restoration in 15 National Park System units in the former Rocky Mountain Region was recommended in 1990. This report details the 7-year restoration of bighorn sheep to all currently suitable historic habitats in the national parks of the former Rocky Mountain Region (now the Intermountain and Midwest regions of the National Park Service). The purpose of the first phase of the restoration during 1991-93 was to conduct research and population surveys and to formulate the restoration plans. The purpose of the second phase of the initiative during 1994-97 was to conduct GIS-based habitat and biological assessments of prospective restoration sites, write restoration plans, and restore and monitor the released bighorn sheep.

Colorado, Montana, North Dakota, South Dakota, Uta

Extinction rates in North American freshwater fishes, 1900-2010

Widespread evidence shows that the modern rates of extinction in many plants and animals exceed background rates in the fossil record. In the present article, I investigate this issue with regard to North American freshwater fishes. From 1898 to 2006, 57 taxa became extinct, and three distinct populations were extirpated from the continent. Since 1989, the numbers of extinct North American fishes have increased by 25%. From the end of the nineteenth century to the present, modern extinctions varied by decade but significantly increased after 1950 (post-1950s mean = 7.5 extinct taxa per decade). In the twentieth century, freshwater fishes had the highest extinction rate worldwide among vertebrates. The modern extinction rate for North American freshwater fishes is conservatively estimated to be 877 times greater than the background extinction rate for freshwater fishes (one extinction every 3 million years). Reasonable estimates project that future increases in extinctions will range from 53 to 86 species by 2050.

BioScience

Development of a genotyping protocol for Mojave desert tortoise scat

Noninvasive fecal genotyping can be a useful tool for population monitoring of elusive species. We tested extraction protocols on scat samples from the threatened Mojave Desert tortoise, Gopherus agassizii, to evaluate whether scat-based mark–recapture and population genetic monitoring studies are feasible.We extracted DNA from G. agassizii scat samples collected in California and Nevada using several extraction protocols and evaluated the reliability of resulting genotypes using quality scores, maximum likelihood reliability estimates, and paired scat and blood genotypes from the same individuals. Finally, we assessed probabilities of identity and sibship, and locus amplification quality, and calculated genotyping error rates for 19 microsatellite loci to determine the best set of loci to use with G. agassizii scat extractions. We found that genotype quality depended more on the sample quality than on the extraction method, and that the Qiagen DNeasy Plant Mini extraction kit is an efficient method for extracting tortoise DNA from tortoise scat. We identified 6 G. agassizii microsatellite loci that can be used to generate a unique molecular tag for individual tortoises. We characterized the reliability of an additional 13 microsatellite loci for use in population genetic analyses where additional power at the expense of some increase in error may be advantageous. As proof of concept, with very low error rates, we matched 3 opportunistically collected scat samples to blood genotypes from animals captured during population surveys within the study area and discovered at least 3 new individuals, even after 2 yrs of extensive survey work. These results suggest that genotyping of field-collected scat can complement existing methods used in long-term demographic and movement studies of G. agassizii and other, closely related, tortoise species.

California

The effect of size on postrelease survival of head-started Mojave desert tortoises

Captive-rearing conservation programs focus primarily on maximizing postrelease survival. Survival increases with size in a variety of taxa, often leading to the use of enhanced size as a means to minimize postrelease losses. Head-starting is a specific captive-rearing approach used to accelerate growth in captivity prior to release in the wild. We explored the effect of size at release, among other potential factors, on postrelease survival in head-started Mojave desert tortoises Gopherus agassizii . Juvenile tortoises were reared for different durations of captivity (2–7 y) and under varying husbandry protocols, resulting in a wide range of juvenile sizes (68–145 mm midline carapace length) at release. We released all animals ( n = 78) in the Mojave National Preserve, California, United States, on 25 September 2018. Release size and surface activity were the only significant predictors of fate during the first year postrelease. Larger sized head-starts had higher predicted survival rates when compared with smaller individuals. This trend was also observed in animals of the same age but reared under different protocols, suggesting that accelerating the growth of head-started tortoises may increase efficiency of head-starting programs without decreasing postrelease success. Excluding five missing animals, released head-starts had 82.2% survival in their first year postrelease (September 2018–September 2019), with all mortalities resulting from predation. No animals with >90-mm midline carapace length were predated by ravens. Our findings suggest the utility of head-starting may be substantially improved by incorporating indoor rearing to accelerate growth. Target release size for head-started chelonians will vary among head-start programs based on release site conditions and project-specific constraints.

California

Effects of landcover on mesocarnivore density and detection rate along an urban to rural gradient

Human development has major implications for wildlife populations. Urban-exploiter species can benefit from human subsidized resources, whereas urban-avoider species can vanish from wildlife communities in highly developed areas. Therefore, understanding how the density of different species varies in response to landcover changes associated with human development can provide important insight into how wildlife communities are likely to change and provide a starting point for predicting the consequences of those changes. Here, we estimated the population density of five common mesocarnivore species (coyote ( Canis latrans ), bobcat ( Lynx rufus ), red fox ( Vulpes vulpes ), raccoon ( Procyon lotor ), and Virginia opossum ( Didelphis virginiana) ) at 12 study sites along an urban to rural gradient in the greater Fayetteville Area, Northwest Arkansas, USA between November 2021, and March 2022. At each study site, we applied the Random Encounter Model (REM) to data from camera traps to calculate the density of five focal species. Coyote density ranged from 0.5 to 0.93 individuals/km 2 . Raccoon density ranged from 0.19 to 20.25 individuals/km 2 . Bobcat density ranged from 0 to 1.06 individuals/km 2 . Opossum density ranged from 0 to 3.43 individuals/km 2 . Red fox density ranged from 0 to 0.10 individuals/km 2 . Coyote and raccoon density showed a positive relationship with anthropogenic noise. Opossum density increased with HUD. Red Fox and bobcat density showed a negative relationship with forest area and a positive relationship with distance to water respectively, however confidence intervals for both species overlapped zero. The density estimates we report based on camera trap data of unmarked animals were consistent with reports from the literature for these same species derived from traditional methods, providing additional support to the REM as a viable, non-invasive method to calculate density of unmarked species. Our second analysis consisted of taking camera level density estimates and treating them as detection rates corrected for camera viewshed and animal movement. Coyote and raccoon detection rate showed a positive relationship with anthropogenic noise. Red Fox detection rate was positively related to developed open space, and negatively related to distance to water. Similarly to red fox, opossums detection rate was higher in areas with more developed open space. We found no evidence that bobcat density or detection rate varied with any of the landcover or anthropogenic variables we measured.

Arkansas

The tortoise and the antilocaprid: Adapting GPS tracking and terrain data to model wildlife walking functions

Context The relationship between slope and terrestrial animal locomotion is key to landscape ecology but underexplored across species. This is partly due to a lack of scalable methodology that applies to a diversity of wildlife. Objectives This study investigates the slope-speed relationship for two species, Texas tortoise ( Gopherus berlandieri ) and pronghorn ( Antilocapra americana ), through the combined application of remote sensing, GPS tracking, behavior models, and parametric distribution. While using readily available Digital Elevation Models (DEM) for pronghorn, we explore the use of very high-resolution lidar Digital Terrain Models (DTM) from Unoccupied Aerial Systems (UAS) to characterize tortoise movements at micro-scales. Methods After classifying animal behavior with GPS tracking data and Hidden Markov Models (HMMs), we analyzed the relationship between the speed of the animals and the slope of the terrain using a 30-m DEM for pronghorn, and a fine-scale UAS DTM for Texas tortoise, and three nonlinear models: Laplace, Gauss, and Lorentz. Results High-resolution DTM, coupled with GPS tracking, accurately models the relationship of speed and slope at a micro-scale, while a DEM is suitable for a larger scale. Laplace models best predicted the speed of both the Texas tortoise and pronghorn. Models showed tortoises, which are not known for rapid and agile movement like the pronghorn, have a broader tolerance for varying slopes at a fine scale. Conclusions These findings enhance understanding of species-specific movement offering valuable insights for habitat management and conservation tailored to species’ behaviors and capabilities.

Colorado, Texas, Wyoming

Optimal population prediction of sandhill crane recruitment based on climate-mediated habitat limitations

Prediction is fundamental to scientific enquiry and application; however, ecologists tend to favour explanatory modelling. We discuss a predictive modelling framework to evaluate ecological hypotheses and to explore novel/unobserved environmental scenarios to assist conservation and management decision-makers. We apply this framework to develop an optimal predictive model for juvenile (<1 year old) sandhill crane Grus canadensis recruitment of the Rocky Mountain Population (RMP). We consider spatial climate predictors motivated by hypotheses of how drought across multiple time-scales and spring/summer weather affects recruitment. Our predictive modelling framework focuses on developing a single model that includes all relevant predictor variables, regardless of collinearity. This model is then optimized for prediction by controlling model complexity using a data-driven approach that marginalizes or removes irrelevant predictors from the model. Specifically, we highlight two approaches of statistical regularization, Bayesian least absolute shrinkage and selection operator (LASSO) and ridge regression. Our optimal predictive Bayesian LASSO and ridge regression models were similar and on average 37% superior in predictive accuracy to an explanatory modelling approach. Our predictive models confirmed a priori hypotheses that drought and cold summers negatively affect juvenile recruitment in the RMP. The effects of long-term drought can be alleviated by short-term wet spring–summer months; however, the alleviation of long-term drought has a much greater positive effect on juvenile recruitment. The number of freezing days and snowpack during the summer months can also negatively affect recruitment, while spring snowpack has a positive effect. Breeding habitat, mediated through climate, is a limiting factor on population growth of sandhill cranes in the RMP, which could become more limiting with a changing climate (i.e. increased drought). These effects are likely not unique to cranes. The alteration of hydrological patterns and water levels by drought may impact many migratory, wetland nesting birds in the Rocky Mountains and beyond. Generalizable predictive models (trained by out-of-sample fit and based on ecological hypotheses) are needed by conservation and management decision-makers. Statistical regularization improves predictions and provides a general framework for fitting models with a large number of predictors, even those with collinearity, to simultaneously identify an optimal predictive model while conducting rigorous Bayesian model selection. Our framework is important for understanding population dynamics under a changing climate and has direct applications for making harvest and habitat management decisions.

Journal of Animal Ecology

Pedological and geological relationships with soil lichen and moss distribution in the eastern Mojave Desert, CA, USA

Biological soil crusts (biocrusts) are ubiquitous in drylands globally. Lichens and mosses are essential biocrust components and provide a variety of ecosystem services, making their conservation and management of interest. Accordingly, understanding what factors are correlated with their distribution is important to land managers. We hypothesized that cover would be related to geologic and pedologic factors. We sampled 32 sites throughout the eastern Mojave Desert, stratifying by parent material and the age of the geomorphic surfaces. The cover of lichens and mosses on ‘available ground’ (L + M av ; available ground excludes ground covered by rocks or plant stems) was higher on limestone and quartzite-derived soils than granite-derived soils. Cover was also higher on moderately younger-aged geomorphic surfaces (Qya2, Qya3, Qya4) and cutbanks than on very young (Qya1), older-aged surfaces (Qia1, Qia2), or soils associated with coppice mounds or animal burrowing under Larrea tridentata. When all sites and parent materials were combined, soil texture was the most important factor predicting the occurrence of L + M av , with cover positively associated with higher silt, very fine sand, and fine sand fractions and negatively associated with the very coarse sand fraction. When parent materials were examined separately, nutrients such as available potassium, iron, and calcium became the most important predictors of L + M av cover.

California

Evaluating mixed samples as a source of error in non-invasive genetic studies using microsatellites

The use of noninvasive genetic sampling (NGS) for surveying wild populations is increasing rapidly. Currently, only a limited number of studies have evaluated potential biases associated with NGS. This paper evaluates the potential errors associated with analysing mixed samples drawn from multiple animals. Most NGS studies assume that mixed samples will be identified and removed during the genotyping process. We evaluated this assumption by creating 128 mixed samples of extracted DNA from brown bear (Ursus arctos) hair samples. These mixed samples were genotyped and screened for errors at six microsatellite loci according to protocols consistent with those used in other NGS studies. Five mixed samples produced acceptable genotypes after the first screening. However, all mixed samples produced multiple alleles at one or more loci, amplified as only one of the source samples, or yielded inconsistent electropherograms by the final stage of the error-checking process. These processes could potentially reduce the number of individuals observed in NGS studies, but errors should be conservative within demographic estimates. Researchers should be aware of the potential for mixed samples and carefully design gel analysis criteria and error checking protocols to detect mixed samples.

Molecular Ecology

The δ2H and δ18O of tap water from 349 sites in the United States and selected territories

Because the stable isotopic compositions of hydrogen (δ 2 H) and oxygen (δ 18 O) of animal (including human) tissues, such as hair, nail, and urine, reflect the δ 2 H and δ 18 O of water and food ingested by an animal or a human and because the δ 2 H and δ 18 O of environmental waters vary geographically, δ 2 H and δ 18 O values of tap water samples collected in 2007-2008 from 349 sites in the United States and three selected U.S. territories have been measured in support of forensic science applications, creating one of the largest databases of tap water δ 2 H and δ 18 O values to date. The results of replicate isotopic measurements for these tap water samples confirm that the expanded uncertainties (U = 2μ c ) obtained over a period of years by the Reston Stable Isotope Laboratory from δ 2 H and δ 18 O dual-inlet mass spectrometric measurements are conservative, at ±2‰ and ±0.2 ‰, respectively. These uncertainties are important because U.S. Geological Survey data may be needed for forensic science applications, including providing evidence in court cases. Half way through the investigation, an isotope-laser spectrometer was acquired, enabling comparison of dual-inlet isotope-ratio mass spectrometric results with isotope-laser spectrometric results. The uncertainty of the laser-based δ 2 H measurement results for these tap water samples is comparable to the uncertainty of the mass spectrometric method, with the laser-based method having a slightly lower uncertainty. However, the δ 18 O uncertainty of the laser-based method is more than a factor of ten higher than that of the dual-inlet isotoperatio mass spectrometric method.

Guam, Puerto Rico, St. John, U.S. Virgin Islands