John B. Hopkins

Estimating the Diets of Animals Using Stable Isotopes and a Comprehensive Bayesian Mixing Model

Using stable isotope mixing models (SIMMs) as a tool to investigate the foraging ecology of animals is gaining popularity among researchers. As a result, statistical methods are rapidly evolving and numerous models have been produced to estimate the diets of animals—each with their benefits and their limitations. Deciding which SIMM to use is contingent on factors such as the consumer of interest, its food sources, sample size, the familiarity a user has with a particular framework for statistical analysis, or the level of inference the researcher desires to make (e.g., population- or individual-level). In this paper, we provide a review of commonly used SIMM models and describe a comprehensive SIMM that includes all features commonly used in SIMM analysis and two new features. We used data collected in Yosemite National Park to demonstrate IsotopeRs ability to estimate dietary parameters. We then examined the importance of each feature in the model and compared our results to inferences from commonly used SIMMs. IsotopeRs user interface (in R) will provide researchers a user-friendly tool for SIMM analysis. The model is also applicable for use in paleontology, archaeology, and forensic studies as well as estimating pollution inputs.

A proposed lexicon of terms and concepts for human-bear management in North America

Abstract We believe that communication within and among agency personnel in the United States and Canada about the successes and failures of their human–bear (Ursidae) management programs will increase the effectiveness of these programs and of bear research. To communicate more effectively, we suggest agencies clearly define terms and concepts used in human–bear management and use them in a consistent manner. We constructed a human–bear management lexicon of terms and concepts using a modified Delphi method to provide a resource that facilitates more effective communication among human–bear management agencies. Specifically, we defined 40 terms and concepts in human–bear management and suggest definitions based on discussions with 13 other professionals from the United States and Canada. Although new terms and concepts will emerge in the future and definitions will evolve as we learn more about bear behavior and ecology, our purpose is to suggest working definitions for terms and concepts to help guide human–bear management and research activities in North America. Applications or revisions of these definitions may be useful outside of North America.

The changing anthropogenic diets of American black bears over the past century in Yosemite National Park

We used carbon (δ13C) and nitrogen (δ15N) stable isotopes derived from the tissues of American black bears (Ursus americanus) to estimate the proportion of human-derived foodstuffs and food waste (“human foods”) in the diets of human food-conditioned bears over the past century in Yosemite National Park, located in central–eastern California. Our goal was to understand how the foraging ecology of bears responded to changing management strategies. We found that the proportion of human foods increased in bear diets when park personnel and visitors fed bears intentionally in 1923–1971, remained relatively high and constant after artificial feeding areas were closed, and declined drastically in 1999–2007, following a

Use of genetics to investigate socially learned foraging behavior in free-ranging black bears

500 000 annual government appropriation used to mitigate human–bear conflicts in the park. This reduction in the amount of human foods in bear diets suggests that Yosemite managers have been successful in reducing the availability of human foods to bears. Yosemite bears currently consume human f...

Measuring the realized niches of animals using stable isotopes: from rats to bears

Abstract Investigating social learning in free-ranging mammals is gaining popularity among researchers. Natural experiments are ideal for studying social learning, but are rare compared to captive studies because of practical limitations and ethical concerns. Such experiments are often restricted or forbidden because they require manipulation of the environment, ecology, or behavior of free-ranging species. As a result, developing new methods to investigate social learning in the field is essential. The main goal of this study was to use genetic data and a new testing framework to determine if social learning from mothers to their offspring is at least partly responsible for free-ranging black bears foraging on human foods in Yosemite National Park. I estimated a relatedness coefficient and the most probable relationship for all combinations of 2 bears (n = 150) sampled in 2004–2007. I then grouped these pairs by their foraging behavior to test predictions deduced from asocial learning, transmission, gene...Abstract Investigating social learning in free-ranging mammals is gaining popularity among researchers. Natural experiments are ideal for studying social learning, but are rare compared to captive studies because of practical limitations and ethical concerns. Such experiments are often restricted or forbidden because they require manipulation of the environment, ecology, or behavior of free-ranging species. As a result, developing new methods to investigate social learning in the field is essential. The main goal of this study was to use genetic data and a new testing framework to determine if social learning from mothers to their offspring is at least partly responsible for free-ranging black bears foraging on human foods in Yosemite National Park. I estimated a relatedness coefficient and the most probable relationship for all combinations of 2 bears (n = 150) sampled in 2004–2007. I then grouped these pairs by their foraging behavior to test predictions deduced from asocial learning, transmission, genetic inheritance, and social learning hypotheses. Results from both analyses suggest that mother–offspring social learning is the primary mechanism responsible for black bears foraging on human food in Yosemite. In addition, results also suggest that some bears are innovators, learning to forage on human food as independents. I found no support for the genetic inheritance hypothesis.

Stable Isotopes Confirm a Coastal Diet for Critically Endangered Mediterranean Monk Seals

© 2015 The Authors. Stable isotope analysis is a powerful method for estimating the impacts animals have on their environment (resource use), revealing their ecological niches. We demonstrated the use of a stable isotope mixing model for measuring the ecological niches of consumers. In particular, we used the model IsotopeR to estimate the resource use of two species with complex, omnivorous diets: invasive Norway rats from the Aleutian Islands, AK, and American black bears from Yosemite National Park, CA. Marginal posterior distributions for major food sources (for populations, groups and individuals) described the resource axes that partly define the realized niches of these omnivores. We used measures of these resource axes to inform resource management in the Aleutians and Yosemite. Results from our analyses confirm that coastal rats did not rely on marine birds on rat-infested islands in the Aleutians. Instead, rats foraged primarily on terrestrial plants and preferred amphipods when they were available. We also use stable isotopes to confirm that plants and acorns are the largest contributors to black bear nutrition in Yosemite and learned that female bears foraged for acorns and pine nuts more heavily than males. Although it is unclear if Norway rats can maintain viable populations in the Aleutians without access to marine-derived animal protein, results from our analyses suggest their dependence on such nutrients. In addition, sex-specific differences in foraging for high-fat acorns and pine nuts in Yosemite suggest black bear populations in the Sierra Nevada may be limited by the productivity and health of hard mast species. As demonstrated here, stable isotope analysis has wide applicability for investigating the resource use and ecological niches of animals. We anticipate and encourage its rapid development in this fundamental field of ecology.

The fate of transported American black bears in Yosemite National Park

Understanding the ecology and behaviour of endangered species is essential for developing effective management and conservation strategies. We used stable isotope analysis to investigate the foraging behaviour of critically endangered Mediterranean monk seals (Monachus monachus) in Greece. We measured carbon and nitrogen isotope ratios (expressed as δ13C and δ15N values, respectively) derived from the hair of deceased adult and juvenile seals and the muscle of their known prey to quantify their diets. We tested the hypothesis that monk seals primarily foraged for prey that occupy coastal habitats in Greece. We compared isotope values from seal hair to their coastal and pelagic prey (after correcting all prey for isotopic discrimination) and used these isotopic data and a stable isotope mixing model to estimate the proportion of coastal and pelagic resources consumed by seals. As predicted, we found that seals had similar δ13C values as many coastal prey species and higher δ13C values than pelagic species; these results, in conjunction with mean dietary estimates (coastal=61 % vs. pelagic=39 %), suggest that seals have a diverse diet comprising prey from multiple trophic levels that primarily occupy the coast. Marine resource managers should consider using the results from this study to inform the future management of coastal habitats in Greece to protect Mediterranean monk seals.

Use of Stable Isotopes to Investigate Keratin Deposition in the Claw Tips of Ducks

Abstract Wildlife management personnel often transport human food-conditioned (FC) bears (Ursidae) from developed areas (areas with high human-use) to undeveloped areas to reduce the number of bear incidents and property damage in developed areas. Our goal was to determine if American black bears (Ursus americanus) return to developed areas after being transported to undeveloped areas in Yosemite National Park. Using capture records (1992–2011) for 29 bears transported in 2006–08, we determined if FC (n  =  20) and not human food-conditioned (NFC; n  =  9) bears were equally likely to return to developed areas following transport. We also reported the fate of these transported bears through 2011. We found that FC bears were more likely to return to developed areas than NFC bears. Of the 16 returning bears, 15 were FC (9 juveniles, 6 adults) and one was NFC. The other 8 NFC bears were never reported as entering developed areas, and no NFC bears were reported as killed. By 2011, 65% of FC bears (13 of 20) were euthanized by wildlife management personnel (n  =  10) or harvested near developed areas (n  =  3). We recommend that Yosemite National Park discontinue the transport of FC bears and consider removing problem bears from the population.

Applications of stable isotope analysis in mammalian ecology.

Stable isotopes derived from the claws of birds could be used to determine the migratory origins of birds if the time periods represented in excised sections of claws were known. We investigated new keratin growth in the claws of adult female Lesser Scaup (Aythya affinis) by estimating the equilibration rates of stable isotopes (δ 13C, δ 15N, and δ 2H) from the breeding grounds into 1 mm claw tips. We sampled birds on their breeding ground through time and found that it took approximately 3–3.5 months for isotope values in most claw tips to equilibrate to isotope values that reflected those present in the environment on their breeding grounds. Results from this study suggest that isotopes equilibrate slowly into claw tips of Lesser Scaup, suggesting isotopes could potentially be used to determine the wintering grounds of birds. We suggest using controlled feeding experiments or longitudinal field investigations to understand claw growth and isotopic equilibration in claw tips. Such information would be valuable in ascertaining whether claw tips can be used in future studies to identify the migratory origins of birds.

Selecting the best stable isotope mixing model to estimate grizzly bear diets in the Greater Yellowstone Ecosystem

In this editorial, we provide a brief introduction and summarize the 10 research articles included in this Special Issue on Applications of stable isotope analysis in mammalian ecology. The first three articles report correction and discrimination factors that can be used to more accurately estimate the diets of extinct and extant mammals using stable isotope analysis. The remaining seven applied research articles use stable isotope analysis to address a variety of wildlife conservation and management questions from the oceans to the mountains.