Developing loop-mediated isothermal amplification (LAMP) assays for detecting pathogens in wild animal populations

Grantee: Cameron Semper

Institution: University of Calgary, University of Lethbridge, Canada

Grant amount: $30,000

Grant type: Small grants

Focal species: Deer mice (Peromyscus sp.)

Conservation status: Least concern

Disciplines: Infectious disease, physiology, animal welfare science

Research location: Canada

---

Project summary

Loop-mediated isothermal amplification (LAMP) is a low-cost technique that amplifies specific DNA to levels that can enable visual detection. LAMP has been extensively applied as a point-of-care diagnostic tool for human health, but its application in wild animal populations remains underexplored. This project aims to develop LAMP assays for rapid, in situ detection of representative viral and bacterial pathogens as well as parasitic worm infections in wild animals. This project will develop two methods for detecting viral and bacterial infections, respectively. The viral test will focus on viruses that have caused epidemics in wild frigatebird and sooty tern populations, while the bacterial test will focus on tick-borne illnesses and parasitic worms which infect deer mice. After developing the LAMP assays, the researchers will validate their potential contribution to monitoring wild animal welfare in a non-invasive manner by using them to test for pathogenic load in fecal samples from deer mice. 

Why we funded this project

This research will serve as a proof-of-concept for the applicability of LAMP for monitoring infectious disease, a key determinant of wild animal welfare. Additionally, the project is specifically targeting diseases that affect a large number of animals. LAMP is simple to perform, and results can be interpreted visually without the need for sophisticated equipment, reducing the cost in time and materials for assessing disease in wild animals. Because it can be carried out in the field, follow-up treatment or further study can be immediately given to the same animal.

---

Photos

---

Raman spectroscopy as a novel non-invasive technique to assess wildlife welfare

Grantee: Teresa Romero

Institution: University of Lincoln, University of Portsmouth, United Kingdom

Grant amount: $19,100

Grant type: Small grants

Focal species: Tufted capuchin monkey (Cebus apella)

Conservation status: Critically endangered

Disciplines: Physiology, animal welfare science

Research location: United Kingdom

---

Project summary

Steroid hormones are routinely used as biomarkers of stress and can be measured in different biological matrices, such as serum, saliva, feces, and urine. However, commonly used collection methods in wildlife are challenging; the stress they induce in the animals may affect hormone levels and also presents ethical issues. More recently, analysis of hormones accumulated in the hair has emerged as a non-invasive tool for measuring chronic stress in wildlife, but current limitations of hair analyses include variation in cortisol concentrations depending on sample preparation and the amount of hair required for cortisol extraction. This project will test whether Raman spectroscopy, which is suitable for the field and does not require sample pre-treatment, is a better way to use hair samples to assess steroid hormones. The planned methodology will make use of samples of mammalian hair with a known cortisol content using a control technique — liquid chromatography mass spectrometry — for comparison. The samples will be subjected to analysis by Raman to validate the technique and establish a robust analytical methodology for the non-invasive analysis of welfare biomarkers in wildlife.

Why we funded this project

Although this project is focused on development of chemical methods, we expect that the method, if validated, could make glucocorticoid assessment in the hair of wild animals much easier, increasing the future quantity and quality of that type of data. Hair is an especially interesting medium for glucocorticoid analysis because it integrates glucocorticoid levels in the body over time, causing the measurements to be more stable over time and potentially more indicative of baseline welfare, since the values are less sensitive to an animal’s most recent activities.

---

Photos

---

Paying to play? Social time allocation, emotional contagion, and social attention as assays of welfare in wild animals

Grantee: Patrick Tkaczynski

Institution: Liverpool John Moores University, United Kingdom

Grant amount: $29,323

Grant type: Small grants

Focal species: Barbary macaque (Macaca sylvanus)

Conservation status: Endangered

Disciplines: Animal welfare science, animal behavior

Research location: Morocco, United Kingdom

---

Project summary

For group-living vertebrates, play and grooming have a number of facets that could be potential indicators of positive welfare, but analysis of such behaviors are yet to be put into a formal framework for monitoring wild animal populations. The Middle Atlas region of Morocco hosts one of the largest populations of wild Barbary macaques, an endangered primate species. These animals face a number of environmental challenges that may disrupt positive social experiences, including anthropogenic disturbance, threats from natural and introduced predators, and an extreme climate. Focusing on six different macaque groups with variable group sizes and facing varying degrees of human exposure, this pilot project will use play and grooming behavior to quantify social time allocation, emotional contagion/synchronization, and social attention as potential assays of positive welfare. As human exposure is typically associated with poor health outcomes in wild animals, this pilot project will focus on this specific environmental challenge to help validate our assays, which can later be applied to examine how positive welfare varies across different gradients, such as climate change or variation in predator pressure. 

Why we funded this project

Most animal welfare research is focused on minimizing suffering, but it’s also vital to maximize positive experiences. The links between positive welfare and evolutionary fitness are also less obvious than for negative welfare, where factors like poor health seem to be associated with both poor welfare and low evolutionary fitness. Because more research focuses on fitness than welfare, the unclear relationship between fitness and positive welfare has contributed to the neglectedness of indicators of positive welfare. This project was one of the few we received that addressed the theme of positive welfare, and we hope that this pilot in primates will provide information to support similar studies in other social species.

---

Photos

---

A bird’s eye view to the five domains of welfare: a quantitative framework and proof-of-concept evaluation in a cetacean, Orcinus orca

Grantees: Saana Isojunno and Eve Jourdain

Institutions: University of St. Andrews, Scotland, and Norwegian Orca Survey, Norway

Grant amount: $28,707

Grant type: Small grants

Focal species: Orca (Orcinus orca)

Conservation status: Data deficient

Disciplines: Animal welfare science, bio/eco-informatics, physiology, animal behavior, marine biology

Research location: Scotland, Norway

---

Project summary

This project will carry out body condition and welfare assessment for inshore-foraging killer whales (Orcinus orca) in the northeast Atlantic as an extension to ongoing research in Scotland and Norway. The researchers will use the Five Domains model to categorize likely factors influencing killer whale welfare, and then quantify some of those factors using aerial photography from drones. Specifically, the researchers intend to gather data on foraging time and feeding rates (nutrition), group composition and surface behavior (behavior), and body shape as a proxy for body condition and blubber reserves (health). Data will also be collected on reproductive success (e.g., calf loss). The researchers will then develop a proof-of-concept statistical model to infer latent motivational states (i.e., “true” welfare as a psychological state) beneath the observable data. The project will also utilize data from known cases of poor welfare (where individual social and nutritional needs are not met) to help define their welfare scale.

Why we funded this project

We funded this project because we see hidden state models as promising statistical tools for representing the relationship between disparate data types and welfare, and would like to see this project provide a proof of the concept. This project will also implement a cost-effective and non-invasive approach method based on photogrammetry to assess cetacean health and behavior. Finally, we wanted to fund this project because it spans multiple universities and a citizen science community, creating significant networking opportunities to promote welfare biology.

---

Photos

---

Mapping welfare for conservation management

Grantee: Lisa Olivier

Institutions: Game Rangers International, Zambia

Grant amount: $29,791

Grant type: Small grants

Focal species: African elephant (Loxodonta)

Conservation status: Endangered

Disciplines: Animal behavior, animal welfare science, wildlife management

Research location: Zambia

---

Project summary

To effectively steward wild animal welfare, leading indicators are needed that predict the future rather than summarizing the past.  These must be easy to measure, respond quickly to ecosystem changes and highlight potential detrimental impacts that need addressing, including anthropogenic activities. This project aims to test the approach of mapping wild animals’ perception of their environment by monitoring an array of behavioral and physiological parameters in African elephants over a year as they navigate the landscape. These measures will be aggregated to define a scale representing the animals’ perceptions of threat that can be estimated for a given time and place. The researchers will then project these data onto maps to identify areas of high and low welfare, where animals may be feeling alternatively secure or fearful. The researchers intend for the project to help conservation practitioners create better management plans to protect wild animal populations by providing a head start in assessing changes in their surroundings.

Why we funded this project

We are excited by this project’s analysis of a long-term longitudinal dataset because of the importance of understanding how wild animals’ welfare varies with demographic factors such as age and sex, as these groups often face different challenges and have different ecological and behavioral requirements, and negative welfare impacts that fall on young individuals may also have ripple effects throughout their lives. We also appreciate this project’s holistic approach. The long-term monitoring means it is possible to consider not only the usual downstream welfare indicators based on health and behavior, but also upstream factors that might influence them, such as social interactions and exposure to predators.

---

Photos

---

City living – assessing the welfare costs of urban living in spotted hyaena (Crocuta crocuta)

Grantee: Emma Stone

Institutions: Carnivore Research Malawi and University of the West of England, United Kingdom

Grant amount: $30,000

Grant type: Small grants

Focal species: Spotted hyaena (Crocuta crocuta)

Conservation status: Least concern

Disciplines: Human-wildlife conflict, physiology, animal welfare science, animal behavior, infections disease

Research location: Malawi

---

Project summary

Lilongwe City (the capital of Malawi, central Africa) has a good network of green spaces and river corridors, supporting a population of urban spotted hyena (Crocuta crocuta). However, human-wildlife conflict (HWC) is frequent, often resulting in persecution of these animals. Using non-invasive techniques, this project will measure and compare the fecal and hair cortisol levels (as a proxy of stress), mean body condition, tooth ware, hematological parameters, and disease (toxoplasmosis and rabies) in spotted hyena between urban (Lilongwe district) and rural (Kasungu National Park) populations. Behavioral experiments (exposure to novel objects and threatening scents) will also be used to assess individual boldness in urban and rural populations as a risk factor, which may increase propensity for HWC and therefore mortality and stress. Results will be used to inform policies to reduce HWC and implement welfare considerations as part of the population’s conservation management plan.

Why we funded this project

Interactions between people and wildlife are increasing as urban areas expand. This is of particular concern with carnivores, as even small species can be perceived as threatening. Despite the fact that the developing world has the highest rate of urbanization, urban carnivore studies have generally focused on European and Asian cities, with research on African cities being relatively neglected. Although HWC is a traditional issue in conservation, we have encountered few projects that effectively address the more neglected question of how HWC interacts with non-anthropogenic welfare impacts. By considering a variety of welfare indicators/factors, including disease transmission and social dynamics, this project will help us understand that interaction, producing results that can be translated into more abundant urban species. Additionally, by funding at least some projects on endangered species, we increase the likelihood of our welfare-focused message reaching conservation practitioners, potentially leading to a greater emphasis on and interest in welfare within that community.

---

Photos

---

From rehabilitation centers to the wild: Evaluating brown bear stress using blood and scat parameters

Grantee: Morteza Naderi

Institution: Koç University, Turkey

Grant amount: $29,955

Grant type: Small grants

Focal species: Brown bear (Ursus arctos)

Conservation status: Least concern

Disciplines: Population ecology, animal welfare science, human-wildlife conflict

Research location: Turkey

---

Project summary

Brown bears play a prominent role in the ecosystems of northern and eastern Turkey. However, there are serious long-term threats to their welfare and viability that are common to other large omnivores, such as habitat fragmentation and increasing contact with humans. For example, open garbage dumps are located across the bear’s distribution and affect behavioral patterns in bears, including seasonal migration habits, whereby the bears would normally move into different areas to exploit seasonal resources. This project will involve a collaboration with KuzeyDoga, one of the only nature conservation NGOs in Turkey, to monitor the behavior and stress physiology of individual free-living bears using GPS collars, camera traps, and blood and fecal glucocorticoids (GCs). The location and behavior data will allow them to document what stimuli individual bears have been exposed to (e.g. use of garbage dumps, proximity to roads), and when. This information can then be paired with the GC results to better understand the welfare implications of those exposures. The study of wild bears will also be complemented by the same physiological measurements on bears residing at a rehabilitation center in the region, which come from a similar genetic and early-life background to the free-living bears.

Why we funded this project

This project addresses our objective of validating non-invasive physiological welfare indicators (e.g. fecal GCs) against behavior and known environmental stressors. The pairing of wild and captive (rescued/rehabilitated) individuals is also notable because the captive individuals can serve as a sort of control group due to their controlled environment at the rehabilitation center. Although brown bears in Turkey are not as numerous as some other species we tend to prioritize research on, they and the threats they face are ecologically similar to those faced by most bears worldwide, especially North American black bears, who number many hundreds of thousands. Therefore, we expect the findings of this project to be at least partially generalizable to more than one million potentially long-lived individuals.

---

Photos

---

Investigating ways to assess and improve the welfare of leopards captured in response to conflict, in Nepal

Grantee: Jessica Bodgener

Institution: University of Kent and Wildlife Vets International, United Kingdom

Grant amount: $16,850

Grant type: Small grants

Focal species: Leopard (Panthera pardus)

Conservation status: Vulnerable

Disciplines: Wildlife rehabilitation, animal welfare science

Research location: Nepal, United Kingdom

---

Project summary

Leopards are the most widespread and adaptable of the world’s big cats, occupying a wide variety of habitats ranging from remote rainforests to busy urban centers. In Nepal, the successful recovery of tiger populations is displacing leopards from protected parks and forcing them into more populated areas. Low densities of natural prey in these areas, coupled with an abundance of easily hunted feral dogs around settlements, have resulted in leopards colonizing urban and suburban environments. This has caused an increase in conflict with people, including the predation of farmed animals and occasional human attacks. Organizations responding to conflict events have limited resources and must attempt to balance animal welfare and conservation aims with public safety and sociopolitical demands. This has resulted in an ad hoc approach, with frequent interventions, but little to no opportunity to reflect and evaluate the impact or success of these actions. This project will focus on validating entirely non-invasive post-release monitoring techniques, including photogrammetric assessment of body condition and measurement of hair cortisol from fecal samples, to monitor the impact of translocation of leopards away from conflict areas on their health and welfare. 

Why we funded this project

We funded this project because it addresses two of our research priorities by seeking to validate non-invasive monitoring techniques, including hair cortisol as a measurement of chronic stress (which may be more informative of welfare than short-term measures of stress physiology). Although it focuses on leopards, the validation of these methods should be transferable to other species. The researcher, Jess Bodgener, also seems to have a long-term interest in wild animal welfare, and has genuine partnerships in place to build capacity and regard for wild animal welfare in Nepal.

---

WellSeal: Non-invasive quantification of welfare in lactating harbour seals

Grantee: Jess Harvey-Carroll

Institution: University of Gothenburg, Sweden

Grant amount: $30,000

Grant type: Small grants

Focal species: Harbour seal (Phoca vitulina)

Conservation status: Least concern

Disciplines: Population ecology, animal behavior, animal welfare science

Research location: Sweden

---

Project summary

Harbor seals require locations protected from adverse weather and other disturbances during the birthing season, when vulnerable pups are left on land while mothers forage. The limited availability of such sites leads to high intraspecific competition, in which larger seals are likely to dominate more desirable locations due both to their physical strength and their lower need to forage. Mothers must choose when and for how long to forage, leading to trade-offs between maternal and offspring welfare which may lay the foundation for the welfare of younger generations. Currently, little information is available on time spent foraging during the lactation period. As harbor seals are facing unprecedented stress from overfishing, seals are swimming increasingly large distances to obtain food. It is not known how this change affects the trade-off between maternal foraging and offspring care, and the resulting welfare of the pups. This project will use camera trap footage and state-of-the-art 3D modeling to non-invasively assess the influence of maternal welfare on the time spent away from the pups. Pup welfare during periods of maternal absence will also be assessed. Welfare will be assessed in terms of the Five Domains framework, based on individual body condition (health), an index of the optimality of their haul-out position (environment), and a record of positive and negative interactions (behavior). Such welfare assessment will be aggregated at a colony level to compare welfare between colonies with more and less access to food.

Why we funded this project

We funded this project because it seeks to evaluate welfare impacts of population density — likely a common cause of welfare issues — in a relatively abundant species, using a robust approach that is only possible thanks to the species-specific knowledge of the PI and her collaborators. For example, we value their use of image analyses to identify haul-out site suitability and welfare impacts on a fine spatial scale that takes into account both environmental and social factors. We also valued the focus on juvenile welfare and the conflict of interest that may arise between parent and offspring. Improving our understanding of the fundamental relationships between population density, parental care, and juvenile welfare will allow the results of this project to extend to other contexts.

---

Introducing a novel tool to compare stress levels in captive and wild Macaca fascicularis

Grantee: Vets4welfare

Institution: Vets4welfare Foundation, Netherlands

Grant amount: $20,000

Grant type: Small grants

Focal species: Crab-eating macaque (Macaca fascicularis)

Conservation status: Endangered

Disciplines: Physiology, wildlife rehabilitation, human-wildlife conflict

Research location: Indonesia, Netherlands

---

Project summary

This project will compare cortisol concentrations in the hair of Indonesian monkeys (Macaca fascicularis) from three groups: a group whose members have spent their whole lives in the wild, a group that has been kept in captivity for the entertainment industry, and a group that are in the process of rehabilitation following rescue from the entertainment industry. Hair measurements can reflect welfare over a long period, as they integrate cortisol as they slowly grow. The concentration of cortisol in a segment of a hair is thought to reflect the activity of the animal’s physiological stress response at the time that segment was produced. On that premise, the project aims to compare the stress response of M. fascicularis under wild, poor-welfare captive (entertainment), and high-welfare captive (rehabilitation) environments. The hair cortisol data will be compared with veterinary and forensic records and other welfare-relevant observations (e.g., of infections or injuries) where possible. The researchers also intend to determine whether mistreatment in captivity leaves a signal in hair cortisol that could be detected after the fact and used to identify monkeys that have been illegally trafficked. 

Why we funded this project

Although this project focuses narrowly on anthropogenic harms in a particular threatened species, we funded it because their approach is interesting and very similar to one we have been interested in applying to study the welfare of stocked fish (i.e., fish raised in a hatchery and then released into the wild) using biological aging methods, another category of putative welfare indicators that integrate stress over time. Between these two funded studies, we are interested to see 1) how welfare indicators for wild and captive environments of varying quality compare and 2) whether hair cortisol from individuals whose environment changed is consistent (at the corresponding points in time) with that of individuals who were only exposed to one environment or the other. We anticipate that the relationship for the latter question is more complex than described, but investigating it will help us learn more about the validity of hair cortisol measurements and the importance of prior experiences in shaping animals’ stress responses.

---

Photos

---