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Developing transmissible vaccines for animal infections

Many emerging and reemerging pathogens originate from wildlife, but nearly all wild species are unreachable using conventional vaccination, which requires capture of and vaccine administration to individual animals. By enabling immunization at scales sufficient to interrupt pathogen transmission, transmissible vaccines (TVs) that spread themselves through wildlife populations by infectious processes could potentially transform the management of otherwise intractable challenges to public health, wildlife conservation, and animal welfare. However, generating TVs likely requires modifying viruses that would be intended to spread in nature, which raises concerns ranging from technical feasibility, to safety and security risks, to regulatory uncertainties ( 1 , 2 ). We propose a series of commitments and strategies for vaccine development—beginning with a priori decisions on vaccine design and continuing through to stakeholder codevelopment [see supplementary materials (SM)]—that we believe increase the likelihood that the potential risks of vaccine transmission are outweighed by benefits to conservation, animal welfare, and zoonosis prevention.

Science

The environmental-data automated track annotation (Env-DATA) system: linking animal tracks with environmental data

The movement of animals is strongly influenced by external factors in their surrounding environment such as weather, habitat types, and human land use. With advances in positioning and sensor technologies, it is now possible to capture animal locations at high spatial and temporal granularities. Likewise, scientists have an increasing access to large volumes of environmental data. Environmental data are heterogeneous in source and format, and are usually obtained at different spatiotemporal scales than movement data. Indeed, there remain scientific and technical challenges in developing linkages between the growing collections of animal movement data and the large repositories of heterogeneous remote sensing observations, as well as in the developments of new statistical and computational methods for the analysis of movement in its environmental context. These challenges include retrieval, indexing, efficient storage, data integration, and analytical techniques.

Movement Ecology

Toxicological significance of soil ingestion by wild and domestic animals

Most wild and domestic animals ingest some soil or sediment, and some species may routinely, or under special circumstances, ingest considerable amounts. Ingested soil supplies nutrients, exposes animals to parasites and pathogens, and may play a role in developing immune systems. 1 Soil ingestion is also sometimes the principal route of exposure to various environmental contaminants. 2-7 Ingestion of soil and earthy material is defined as geophagy and may be either intentional or unintentional, occurring as an animal eats or grooms.

Book chapter

Improving size estimates of open animal populations by incorporating information on age

Around the world, a great deal of effort is expended each year to estimate the sizes of wild animal populations. Unfortunately, population size has proven to be one of the most intractable parameters to estimate. The capture-recapture estimation models most commonly used (of the Jolly-Seber type) are complicated and require numerous, sometimes questionable, assumptions. The derived estimates usually have large variances and lack consistency over time. In capture–recapture studies of long-lived animals, the ages of captured animals can often be determined with great accuracy and relative ease. We show how to incorporate age information into size estimates for open populations, where the size changes through births, deaths, immigration, and emigration. The proposed method allows more precise estimates of population size than the usual models, and it can provide these estimates from two sample occasions rather than the three usually required. Moreover, this method does not require specialized programs for capture-recapture data; researchers can derive their estimates using the logistic regression module in any standard statistical package.

BioScience

Can orchards help connect Mediterranean ecosystems? Animal movement data alter conservation priorities

As natural habitats become fragmented by human activities, animals must increasingly move through human-dominated systems, particularly agricultural landscapes. Mapping areas important for animal movement has therefore become a key part of conservation planning. Models of landscape connectivity are often parameterized using expert opinion and seldom distinguish between the risks and barriers presented by different crop types. Recent research, however, suggests different crop types, such as row crops and orchards, differ in the degree to which they facilitate or impede species movements. Like many mammalian carnivores, bobcats ( Lynx rufus ) are sensitive to fragmentation and loss of connectivity between habitat patches. We investigated how distinguishing between different agricultural land covers might change conclusions about the relative conservation importance of different land uses in a Mediterranean ecosystem. Bobcats moved relatively quickly in row crops but relatively slowly in orchards, at rates similar to those in natural habitats of woodlands and scrub. We found that parameterizing a connectivity model using empirical data on bobcat movements in agricultural lands and other land covers, instead of parameterizing the model using habitat suitability indices based on expert opinion, altered locations of predicted animal movement routes. These results emphasize that differentiating between types of agriculture can alter conservation planning outcomes.

California

On the choice of statistical models for estimating occurrence and extinction from animal surveys

In surveys of natural animal populations the number of animals that are present and available to be detected at a sample location is often low, resulting in few or no detections. Low detection frequencies are especially common in surveys of imperiled species; however, the choice of sampling method and protocol also may influence the size of the population that is vulnerable to detection. In these circumstances, probabilities of animal occurrence and extinction will generally be estimated more accurately if the models used in data analysis account for differences in abundance among sample locations and for the dependence between site-specific abundance and detection. Simulation experiments are used to illustrate conditions wherein these types of models can be expected to outperform alternative estimators of population site occupancy and extinction. ?? 2007 by the Ecological Society of America.

Ecology

Uncertainty in spatially explicit animal dispersal models

Uncertainty in estimates of survival of dispersing animals is a vexing difficulty in conservation biology. The current notion is that this uncertainty decreases the usefulness of spatially explicit population models in particular. We examined this problem by comparing dispersal models of three levels of complexity: (1) an event-based binomial model that considers only the occurrence of mortality or arrival, (2) a temporally explicit exponential model that employs mortality and arrival rates, and (3) a spatially explicit grid-walk model that simulates the movement of animals through an artificial landscape. Each model was fitted to the same set of field data. A first objective of the paper is to illustrate how the maximum-likelihood method can be used in all three cases to estimate the means and confidence limits for the relevant model parameters, given a particular set of data on dispersal survival. Using this framework we show that the structure of the uncertainty for all three models is strikingly similar. In fact, the results of our unified approach imply that spatially explicit dispersal models, which take advantage of information on landscape details, suffer less from uncertainly than do simpler models. Moreover, we show that the proposed strategy of model development safeguards one from error propagation in these more complex models. Finally, our approach shows that all models related to animal dispersal, ranging from simple to complex, can be related in a hierarchical fashion, so that the various approaches to modeling such dispersal can be viewed from a unified perspective.

Ecological Applications

Mapping behavioral landscapes for animal movement: a finite mixture modeling approach

Because of its role in many ecological processes, movement of animals in response to landscape features is an important subject in ecology and conservation biology. In this paper, we develop models of animal movement in relation to objects or fields in a landscape. We take a finite mixture modeling approach in which the component densities are conceptually related to different choices for movement in response to a landscape feature, and the mixing proportions are related to the probability of selecting each response as a function of one or more covariates. We combine particle swarm optimization and an Expectation-Maximization (EM) algorithm to obtain maximum likelihood estimates of the model parameters. We use this approach to analyze data for movement of three bobcats in relation to urban areas in southern California, USA. A behavioral interpretation of the models revealed similarities and differences in bobcat movement response to urbanization. All three bobcats avoided urbanization by moving either parallel to urban boundaries or toward less urban areas as the proportion of urban land cover in the surrounding area increased. However, one bobcat, a male with a dispersal-like large-scale movement pattern, avoided urbanization at lower densities and responded strictly by moving parallel to the urban edge. The other two bobcats, which were both residents and occupied similar geographic areas, avoided urban areas using a combination of movements parallel to the urban edge and movement toward areas of less urbanization. However, the resident female appeared to exhibit greater repulsion at lower levels of urbanization than the resident male, consistent with empirical observations of bobcats in southern California. Using the parameterized finite mixture models, we mapped behavioral states to geographic space, creating a representation of a behavioral landscape. This approach can provide guidance for conservation planning based on analysis of animal movement data using statistical models, thereby linking connectivity evaluations to empirical data.

Ecological Applications

Successful aquatic animal disease emergency programmes

The authors provide examples of emergency programmes which have been successful in eradicating or controlling certain diseases of aquatic animals. The paper is divided into four parts. The first part describes the initial isolation of viral haemorrhagic septicaemia (VHS) virus in North America in the autumn of 1988 from feral adult chinook ( Oncorhynchus tshawytscha ) and coho salmon ( O.kisutch ) returning for spawning. The fish disease control policies at both State and Federal levels in the United States of America required quarantine and emergency eradication measures upon the finding of certain exotic fish pathogens, including VHS virus. The procedures for emergency plans, destruction of stocks and disinfection of facilities are described, as well as challenge experiments with the North American strains of VHS virus and the detection of the virus in marine fish species (cod [ Gadus macrocephalus ] and herring [ Clupea harengus pallasi ]) in the Pacific Ocean. The second part of the paper outlines the aquatic animal legislation in Great Britain and within the European Union, in regard to contingency plans, initial investigations, action on the suspicion of notifiable disease and action on confirmation of infection. The legal description is followed by an account of an outbreak of viral haemorrhagic septicaemia in turbot (Scophthalmus maximus) in Great Britain, including the stamping-out process at the affected farm and investigations conducted to screen other farms in the vicinity for possible infection. The third part provides a historical review of the build-up of infectious salmon anaemia (ISA) in Norway and the attempts to control the disease using legal measures in the absence of detailed knowledge of the aetiology, epizootiology, pathogenesis, etc. of the disease. The measures taken show that the spread of ISA can be controlled using restrictions on the movement of fish, disinfection procedures, etc. However, acceptance and understanding of the chosen strategy by the fish farmers is a pre-requisite to reach that goal. Finally, the paper summarises future needs for national and international legislation, including the development of standard approaches for control, the creation of appropriate infrastructures and a better understanding of the epidemiology of aquatic animal diseases.

Revue Scientifique et Technique

The foods of fur animals of the Patuxent Research Refuge, Maryland

Approximately 300 digestive tracts of fur animals obtained mostly during the winter trapping season and 560 scats from animals live-trapped on the Patuxent Research Refuge near Laurel, Maryland, were analyzed. The resulting data are summarized and a brief description of the area and important habitat types is given. The animals studied include the raccoon, red fox, gray fox, mink, New York weasel, skunk, opossum, and house cat.

Maryland

County-level estimates of nitrogen and phosphorus from animal manure for the conterminous United States, 2002

County-level nitrogen and phosphorus inputs from animal manure for the conterminous United States for 2002 were estimated from animal populations from the 2002 Census of Agriculture by using methods described in U.S. Geological Survey Scientific Investigations Report 2006–5012. These estimates of nitrogen and phosphorus from animal manure were compiled in support of the U.S. Geological Survey’s National Water-Quality Assessment Program.

Open-File Report

County-level estimates of nitrogen and phosphorus from animal manure for the conterminous United States, 2007 and 2012

County-level estimates of nitrogen and phosphorus inputs from animal manure for the conterminous United States were calculated from animal population inventories in the 2007 and 2012 Census of Agriculture, using previously published methods. These estimates of non-point nitrogen and phosphorus inputs from animal manure were compiled in support of the U.S. Geological Survey’s National Water-Quality Assessment Project of the National Water Quality Program and are needed to support national-scale investigations of stream and groundwater water quality. The estimates published in this report are comparable with older estimates which can be compared to show changes in nitrogen and phosphorus inputs from manure over time.

Open-File Report

Arctic delta processes: A computer animation and paper models

This report shows, by means of a computer animation and paper models, how deltas are affected by fresh and salt water currents, topography and location. The report is intended to help students and others visualize how ice shapes and forms a delta. By studying the animations and the paper models, students will come to understand why deltas have different shapes and different interior structures. The diskette version has an animation of arctic delta processes. While both the diskette and paper versions have teacher guide and paper models.

Open-File Report

Antarctic ice sheet; computer animations and paper model

This report illustrates, through computer animation and a paper model, why there are changes on the ice sheet that covers the Antarctica continent. By studying the animations and the paper model, students will better understand the evolution of the Antarctic ice sheet. Included in the paper and diskette versions of this report are templates for making a paper-model, instructions for its assembly, and a discussion of development of the Antarctic ice sheet. In addition, the diskette version includes a animation of how Antarctica and its ice cover changes through time. Many people provided help and encouragement in the development of this HyperCard stack, particularly Page Mosier, Sue Priest and Art Ford. This report was enhanced by reviews from Bonnie Murchey, Peter Stauffer and Stephen Eittreim.

Open-File Report

Assessing monkeypox virus prevalence in small mammals at the human-animal interface in the Democratic Republic of the Congo

During 2012, 2013 and 2015, we collected small mammals within 25 km of the town of Boende in Tshuapa Province, the Democratic Republic of the Congo. The prevalence of monkeypox virus (MPXV) in this area is unknown; however, cases of human infection were previously confirmed near these collection sites. Samples were collected from 353 mammals (rodents, shrews, pangolins, elephant shrews, a potamogale, and a hyrax). Some rodents and shrews were captured from houses where human monkeypox cases have recently been identified, but most were trapped in forests and agricultural areas near villages. Real-time PCR and ELISA were used to assess evidence of MPXV infection and other Orthopoxvirus (OPXV) infections in these small mammals. Seven (2.0%) of these animal samples were found to be anti-orthopoxvirus immunoglobulin G (IgG) antibody positive (six rodents: two Funisciurus spp.; one Graphiurus lorraineus ; one Cricetomys emini ; one Heliosciurus sp.; one Oenomys hypoxanthus , and one elephant shrew Petrodromus tetradactylus ); no individuals were found positive in PCR-based assays. These results suggest that a variety of animals can be infected with OPXVs, and that epidemiology studies and educational campaigns should focus on animals that people are regularly contacting, including larger rodents used as protein sources.

Viruses

Estimating the number of animals in wildlife populations

INTRODUCTION In 1938, Howard M. Wight devoted 9 pages, which was an entire chapter in the first wildlife management techniques manual, to what he termed 'census' methods. As books and chapters such as this attest, the volume of literature on this subject has grown tremendously. Abundance estimation remains an active area of biometrical research, as reflected in the many differences between this chapter and the similar contribution in the previous manual. Our intent in this chapter is to present an overview of the basic and most widely used population estimation techniques and to provide an entree to the relevant literature. Several possible approaches could be taken in writing a chapter dealing with population estimation. For example, we could provide a detailed treatment focusing on statistical models and on derivation of estimators based on these models. Although a chapter using this approach might provide a valuable reference for quantitative biologists and biometricians, it would be of limited use to many field biologists and wildlife managers. Another approach would be to focus on details of actually applying different population estimation techniques. This approach would include both field application (e.g., how to set out a trapping grid or conduct an aerial survey) and detailed instructions on how to use the resulting data with appropriate estimation equations. We are reluctant to attempt such an approach, however, because of the tremendous diversity of real-world field situations defined by factors such as the animal being studied, habitat, available resources, and because of our resultant inability to provide detailed instructions for all possible cases. We believe it is more useful to provide the reader with the conceptual basis underlying estimation methods. Thus, we have tried to provide intuitive explanations for how basic methods work. In doing so, we present relevant estimation equations for many methods and provide citations of more detailed treatments covering both statistical considerations and field applications. We have chosen to present methods that are representative of classes of estimators, rather than address every available method. Our hope is that this chapter will provide the reader with enough background to make an informed decision about what general method(s) will likely perform well in any particular field situation. Readers with a more quantitative background may then be able to consult detailed references and tailor the selected method to suit their particular needs. Less quantitative readers should consult a biometrician, preferably one with experience in wildlife studies, for this 'tailoring,' with the hope they will be able to do so with a basic understanding of the general method, thereby permitting useful interaction and discussion with the biometrician. SUMMARY Estimating the abundance or density of animals in wild populations is not a trivial matter. Virtually all techniques involve the basic problem of estimating the probability of seeing, capturing, or otherwise detecting animals during some type of survey and, in many cases, sampling concerns as well. In the case of indices, the detection probability is assumed to be constant (but unknown). We caution against use of indices unless this assumption can be verified for the comparison(s) of interest. In the case of population estimation, many methods have been developed over the years to estimate the probability of detection associated with various kinds of count statistics. Techniques range from complete counts, where sampling concerns often dominate, to incomplete counts where detection probabilities are also important. Some examples of the latter are multiple observers, removal methods, and capture-recapture. Before embarking on a survey to estimate the size of a population, one must understand clearly what information is needed and for what purpose the information will be used. The key to derivin

Book chapter

The Animal Welfare Act and the zoo: A positive approach

Interpretations of the Animal Welfare Act and other regulations governing use of research animals in the United States are changing. Recent amendments to the Act have resulted in the inclusion of more species under the umbrella of regulation. The role of the zoo and wildlife veterinarian should be that of leading his or her institution into a positive endorsement of these regulations and their application. Recent additions to the Code of Federal Regulations spell out the roles of the veterinarian and the Animal Care and Use Committee at an institution.

Journal of Zoo and Wildlife Medicine

Animal movement: Statistical models for telemetry data

The study of animal movement has always been a key element in ecological science, because it is inherently linked to critical processes that scale from individuals to populations and communities to ecosystems. Rapid improvements in biotelemetry data collection and processing technology have given rise to a variety of statistical methods for characterizing animal movement. The book serves as a comprehensive reference for the types of statistical models used to study individual-based animal movement.

Book