Cost-effective scat-detection dogs: unleashing a powerful new tool for international mammalian conservation biology

Conservation detection dogs: A critical review of efficacy and methodology

Conservation detection dogs (CDD) use their exceptional olfactory abilities to assist a wide range of conservation projects through the detection of target specimens or species. CDD are generally quicker, can cover wider areas and find more samples than humans and other analytical tools. However, their efficacy varies between studies; methodological and procedural standardisation in the field is lacking. Considering the cost of deploying a CDD team and the limited financial resources within conservation, it is vital that their performance is quantified and reliable. This review aims to summarise what is currently known about the use of scent detection dogs in conservation and elucidate which factors affect efficacy. We describe the efficacy of CDD across species and situational contexts like training and fieldwork. Reported sensitivities (i.e. the proportion of target samples found out of total available) ranged from 23.8% to 100% and precision rates (i.e. proportion of alerts that are true positives) from 27% to 100%. CDD are consistently shown to be better than other techniques, but performance varies substantially across the literature. There is no consistent difference in efficacy between training, testing and fieldwork, hence we need to understand the factors affecting this. We highlight the key variables that can alter CDD performance. External effects include target odour, training methods, sample management, search methodology, environment and the CDD handler. Internal effects include dog breed, personality, diet, age and health. Unfortunately, much of the research fails to provide adequate information on the dogs, handlers, training, experience and samples. This results in an inability to determine precisely why an individual study has high or low efficacy. It is clear that CDDs can be effective and applied to possibly limitless conservation scenarios, but moving forward researchers must provide more consistent and detailed methodologies so that comparisons can be conducted, results are more easily replicated and progress can be made in standardising CDD work.

The health of working dogs in conservation in Africa

Introduction

Dogs are increasingly being employed for conservation purposes worldwide. In Africa, they work in challenging environments with unique health risks which have not been investigated until now.

Methods

To understand the health challenges faced by the dogs, semi-structured interviews were conducted with participants from 14 organisations that used working dogs in their conservation programmes. The data was qualitatively analysed by thematic analysis.

Results

Five themes were generated. Three affective themes influenced how participants responded to the challenges associated with having a successful conservation dog programme. A strong handler-dog attachment, proficient handler training, and the acknowledgement of the challenging environment were pivotal to maintaining dog health. Two themes related to the difficulties in managing these programmes and how veterinary support interacts with the management choices being made.

Discussion

To have healthy conservation dogs, current and future programmes should focus on fostering the handler-dog relationship and provide continuous handler training. The management of conservation dogs' health should adopt an evidence-based approach. Future research should focus on areas where the evidence base is lacking, particularly in the areas of prevention and treatment of African canine trypanosomiasis. Programmes should develop a good working relationship with a veterinarian that has access to evidence-based veterinary medical information.

Collection of triatomines from sylvatic habitats by a Trypanosoma cruzi-infected scent detection dog in Texas, USA

BACKGROUND

Triatomine insects, vectors of the etiologic agent of Chagas disease (Trypanosoma cruzi), are challenging to locate in sylvatic habitats. Collection techniques used in the United States often rely on methods to intercept seasonally dispersing adults or on community scientists' encounters. Neither method is suited for detecting nest habitats likely to harbor triatomines, which is important for vector surveillance and control. Furthermore, manual inspection of suspected harborages is difficult and unlikely to reveal novel locations and host associations. Similar to a team that used a trained dog to detect sylvatic triatomines in Paraguay, we worked with a trained scent detection dog to detect triatomines in sylvatic locations across Texas.

PRINCIPLE METHODOLOGY/FINDINGS

Ziza, a 3-year-old German Shorthaired Pointer previously naturally infected with T. cruzi, was trained to detect triatomines. Over the course of 6 weeks in the fall of 2017, the dog and her handler searched at 17 sites across Texas. The dog detected 60 triatomines at 6 sites; an additional 50 triatomines were contemporaneously collected at 1 of these sites and 2 additional sites without the assistance of the dog. Approximately 0.98 triatomines per hour were found when only humans were conducting searches; when working with the dog, approximately 1.71 triatomines per hour were found. In total, 3 adults and 107 nymphs of four species (Triatoma gerstaeckeri, Triatoma protracta, Triatoma sanguisuga, and Triatoma indictiva) were collected. PCR testing of a subset revealed T. cruzi infection, including DTUs TcI and TcIV, in 27% of nymphs (n = 103) and 66% of adults (n = 3). Bloodmeal analysis of a subset of triatomines (n = 5) revealed feeding on Virginia opossum (Didelphis virginiana), Southern plains woodrat (Neotoma micropus), and eastern cottontail (Sylvilagus floridanus).

CONCLUSION/SIGNIFICANCE

A trained scent detection dog enhanced triatomine detections in sylvatic habitats. This approach is effective at detecting nidicolous triatomines. Control of sylvatic sources of triatomines is challenging, but this new knowledge of specific sylvatic habitats and key hosts may reveal opportunities for novel vector control methods to block the transmission of T. cruzi to humans and domestic animals.

Field quantifications of probability of detection and search patterns to form protocols for the use of detector dogs for eradication assessments

The use of detector dogs within environmental programs has increased greatly over the past few decades, yet their search methods are not standardized, and variation in dog performance remains not well quantified or understood. There is much science to be done to improve the general utility of detector dogs, especially for invertebrate surveys.

We report research for detector dog work conducted as part of yellow crazy ant eradication. One dog was first used to quantify the probability of detection (POD) within a strictly controlled trial. We then investigated the search patterns of two dogs when worked through sites using different transect spacings. Specifically, we quantified their presence within set distances of all locations in each assessment area, as well as the time they took to assess each area. In a GIS, we then calculated the relative percentage of the entire search area within six distance categories, and combined this information with the POD values to obtain a site‐level POD.

The calculated relationship between distance and POD was extremely strong (R² = 0.998), with POD being 86% at 2 m and 28% at 25 m. For site‐level assessments conducted by the two dogs, both dogs achieved the highest site‐level POD when operated on the lowest transect spacing (15 m), with POD decreasing significantly as transect spacing increased. Both dogs had strong linear relationships between area assessed and time, with the area assessed being greater when the transects had greater spacing. The working style of the two dogs also resulted in significantly different assessment outcomes. In 1 h one dog could assess approximately 9.2 ha with transects spaced 20 m apart, and 6.8 ha with transects spaced 15 m apart, whereas the second dog could only assess approximately 6.9 ha with transects spaced 20 m apart, and 4.9 ha with transects spaced 15 m apart.

Our study provides insight into the ability of dogs to detect yellow crazy ants, and sets the basis for further science and protocol development for ant detection. With the lessons learned from this work, we then detail protocols for using detector dogs for ant eradication assessments.

205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates

Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high‐quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long‐standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade‐specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.

Mink ( Neovison vison ) fecal microbiomes are influenced by sex, temperature, and time postdefecation

Gut microbiomes encode myriad metabolic functions critical to mammalian ecology and evolution. While fresh fecal samples provide an efficient, noninvasive method of sampling gut microbiomes, collecting fresh feces from elusive species is logistically challenging. Nonfresh feces, however, may not accurately represent the gut microbiome of the host due to succession of gut microbial consortia postdefecation as well as colonization by microbes from the surrounding environment. Using American mink (Neovison vison) as a model species, we examined postdefecation microbial community succession to learn how ambient temperature and temporal sampling constraints influence the reliability of nonfresh feces to represent host gut microbiomes. To achieve our goal, we analyzed fresh mink feces (n = 5 females; n = 5 males) collected at the time of defecation from captive mink at a farm in the Upper Peninsula of Michigan and we subsequently subsampled each fecal specimen to investigate microbial community succession over five days, under both warm (21°C) and cold (–17°C to –1°C) temperature treatments. We found that both temperature and time influenced fecal microbiome composition; and we also detected significant sexual dimorphism in microbial community structures, with female mink microbiomes exhibiting significantly greater variation than males’ when exposed to the warm temperature treatment. Our results demonstrate that feces from unknown individuals can be a powerful tool for examining carnivore gut microbiomes, though rigorous study design is required because sex, ambient temperature, and time since defecation drive significant microbial variation and the sample size requirements necessary for detecting statistically significant differences between target populations is an important consideration for future ecologically meaningful research.

Pest detection dogs for wood boring longhorn beetles

Invasive alien species are increasing due to globalization. Their spread has resulted in global economic losses. Asian [Anoplophora glabripennis (Motschulsky)] (ALB) and citrus [A. chinensis (Forster)] (CLB) longhorn beetles are two introduced wood borers which contribute to these economic losses e.g. the destruction of tree plantations. Early detection is key to reduce the ecological influence alongside the detrimental and expensive eradication. Dogs (Canis lupus familiaris) can detect these insects, potentially at an early stage. We trained two privately owned dogs to investigate their use as detection tools. We tested the dog's ability to discriminate ALB and CLB from native wood borers by carrying out double-blind and randomized experiments in three search conditions; (1) laboratory, (2) semi-field and (3) standardized field. For condition one, a mean sensitivity of 80%, specificity of 95% and accuracy of 92% were achieved. For condition two and three, a mean sensitivity of 88% and 95%, specificity of 94% and 92% and accuracy of 92% and 93% were achieved. We conclude that dogs can detect all types of traces and remains of ALB and CLB and discriminate them from native wood borers and uninfested wood, but further tests on live insects should be initiated.

Impact of weather conditions on cheetah monitoring with scat detection dogs

Knowledge on cheetah population densities across their current range is limited. Therefore, new and efficient assessment tools are needed to gain more knowledge on species distribution, ecology and behaviour. Scat detection dogs have emerged as an efficient and non-invasive method to monitor elusive and vulnerable animal species, like cheetahs, due to the dog’s superior olfactory system. However, the success of locating scat using detection dogs can be significantly improved under suitable weather conditions. We examined the impact of temperature, humidity and wind speed on detection rates of scat from cheetahs during a scat detection dog survey in Northern Kenya. We found that average wind speed positively influences the scat detection rate of detection dogs working on leash. Humidity showed no significant influence. Temperature showed a strong negative correlation with humidity and thus was excluded from our model analyses. While it is likely that wind speed is especially invalid for dogs working off leash, this study did not demonstrate this. Wind speed could thus influence the success of monitoring cheetahs or other target species. Our findings help to improve the survey and thus maximise the coverage of study area and the collection of target samples of elusive and rare species.

The Promise of Genetics and Genomics for Improving Invasive Mammal Management on Islands

Invasive species are major contributors to global biodiversity decline. Invasive mammalian species (IMS), in particular, have profound negative effects in island systems that contain disproportionally high levels of species richness and endemism. The eradication and control of IMS have become important conservation tools for managing species invasions on islands, yet these management operations are often subject to failure due to knowledge gaps surrounding species- and system-specific characteristics, including invasion pathways and contemporary migration patterns. Here, we synthesize the literature on ways in which genetic and genomic tools have effectively informed IMS management on islands, specifically associated with the development and modification of biosecurity protocols, and the design and implementation of eradication and control programs. In spite of their demonstrated utility, we then explore the challenges that are preventing genetics and genomics from being implemented more frequently in IMS management operations from both academic and non-academic perspectives, and suggest possible solutions for breaking down these barriers. Finally, we discuss the potential application of genome editing to the future management of invasive species on islands, including the current state of the field and why islands may be effective targets for this emerging technology.

Egg masses as training aids for spotted lanternfly Lycorma delicatula detection dogs

The spotted lanternfly (Lycorma delicatula) is an invasive species first detected in 2014. The insect feeds on plants causing severe damage in vineyards such as the occurrence of sooty mold fungus that impairs leaf photosynthesis. Currently, there is extensive research on how to track and ultimately prevent the spread of this species. It lays eggs that persist through the winter, while the adults die out, which presents a unique opportunity to enter infested or suspected infested areas to begin quarantine and management of the spread while the species is dormant. Detection dogs may be a tool that can be used to search out the spotted lanternfly egg masses during this overwintering period, however it is not known whether dogs can detect any specific odor from the spotted lanternfly eggs. Moreover, as the eggs are only available during certain times of the year, and hatch based on temperature, finding training aids for the dogs could prove difficult. In this study, we investigated whether three detection dogs could learn the odor from dead spotted lanternfly egg masses and if so, whether that would allow them to recognize live spotted lanternfly egg masses. We found that dogs could be trained to find dead spotted lanternfly egg masses, and could learn to ignore relevant controls, with high levels of sensitivity and specificity (up to 94.6% and 92.8%, respectively). Further, we found that after the training, dogs could find live spotted lanternfly egg masses without additional training and returned to previous levels of sensitivity and specificity within a few sessions. Coded videos of training and testing sessions showed that dogs spent more time at the egg masses than at controls, as expected from training. These results suggest that dead spotted lanternfly egg masses could be a useful training aid for spotted lanternfly detection dogs.

How quoll-ified are northern and spotted-tailed quoll detection dogs?

Abstract ContextWildlife detection dogs have been used globally in environmental monitoring. However, their effectiveness in the Australian context has been only minimally researched. Increased understanding of detection dog accuracy and efficacy is required for their inclusion in survey guidelines used by proponents of referred actions potentially impacting Australia’s threatened mammals. Evaluation of new methods is also important for advancing population monitoring, particularly for threatened species. AimsTo determine the efficacy of wildlife detection dogs as a survey tool for low-density, cryptic species, using northern (Dasyurus hallucatus) and spotted-tailed (D. maculatus) quolls as subjects. We compared detection dogs, human search effort and camera trapping results, in simulated accuracy and efficacy trials, and field surveys. MethodsTwo wildlife detection dogs’ scores for sensitivity (ability to identify a target species scat) and specificity (ability to distinguish target from non-target species scats) were calculated during accuracy trials. The dogs were tested using 288 samples, of which 32 were targets, where northern and spotted-tailed quoll scat were the targets in separate trials. Survey efficacy was determined following completing 12 simulated surveys (6 per target species) involving a single, randomly placed scat sample in a 1–1.5ha search area. During the northern quoll simulated surveys the dogs’ survey efficacy was compared with that of a human surveyor. The dogs also undertook field surveys for both northern and spotted-tailed quolls, in conjunction with camera trapping for comparison. Key resultsDuring accuracy trials the dogs had an average sensitivity and specificity respectively of 100% and 98.4% for northern quoll, and 100% and 98% for spotted-tailed quoll. Their average search time in efficacy trials for northern quoll was 11.07min (significantly faster than the human surveyor), and 2.98min for spotted-tailed quoll in the 1–1.5ha search areas. During field surveys, northern quoll scats were detected at sites where camera trapping failed to determine their presence. No spotted-tailed quoll scat was detected by the dogs during field surveys. ConclusionsTrained and experienced detection dogs can work very accurately and efficiently, which is vital to their field success. Detection dogs are therefore capable of detecting evidence of species presence where alternative methods may be unsuccessful. ImplicationsOur study supports the future use of highly trained detection dogs for wildlife surveys and monitoring in Australia. Our results demonstrate that detection dogs can be highly accurate and are a beneficial stand-alone or complimentary method.

Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments

Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal samples with an endogenous DNA content below 1% is a common problem when prior selection of samples from a large collection is not possible. However, samples classified as unfavourable for target capture sequencing might be the only representatives of unique specific geographical locations, or to answer the question of interest. To explore how library complexity may be increased without repeating DNA extractions and generating new libraries, in this study we captured the exome of 60 chimpanzees (Pan troglodytes) using faecal samples with very low proportions of endogenous content (<1%). Our results indicate that by performing additional hybridizations of the same libraries, the molecular complexity can be maintained to achieve higher coverage. Also, whenever possible, the starting DNA material for capture should be increased. Finally, we specifically calculated the sequencing effort needed to avoid exhausting the library complexity of enriched faecal samples with low endogenous DNA content. This study provides guidelines, schemes and tools for laboratories facing the challenges of working with noninvasive samples containing extremely low amounts of endogenous DNA.

The Diversity of Primates: From Biomedicine to Conservation Genomics

Until now, the field of primate genomics has focused on two major themes: understanding human evolution and advancing biomedical research. We propose that it is now time for a third theme to receive attention: conservation genomics. As a result of anthropogenic effects, the majority of primate species have become threatened with extinction. A more robust primate conservation genomics will allow for genetically informed population management. Thanks to a steady decline in the cost of sequencing, it has now become feasible to sequence whole primate genomes at the population level. Furthermore, technological advances in noninvasive genomic methods have made it possible to acquire genome-scale data from noninvasive biomaterials. Here, we review recent advances in the analysis of primate diversity, with a focus on genomic data sets across the radiation.

Jackal in hide: detection dogs show first success in the quest for golden jackal (Canis aureus) scats

Golden jackal (Canis aureus) monitoring in central Europe generates more interest and becomes increasingly important with the species’ appearance in areas where it was previously unestablished. For genetic monitoring of golden jackals via scat collection, the distinction of jackal scats from those of related species such as the red fox (Vulpes vulpes) is crucial: if done incorrectly, it can falsify diet studies or inflate costs of DNA analyses. In this study, we tested the potential benefits of using domestic dogs to specifically find jackal scats. We used trained scat detection dogs to locate and identify golden jackal scats in an area of dense shrubland, with the species’ presence previously confirmed via bioacoustic monitoring. On a total of 133 km of transects covering at least two golden jackal groups, two human-dog teams found 34 putative golden jackal scats. A total of 26 of these were successfully genetically analysed, of which 19 were attributed to 13 individual golden jackals, an accuracy rate of 73%. Our results show that detection dogs can successfully differentiate golden jackal scats from other species. This tool can be applied to detect golden jackal presence and establish more reliable estimates of group number and size than previously determined through bioacoustic stimulation. By combining both methods, questions about family structures and kinship, seasonal differences in habitat use and territory sizes can be answered. The regular use of detection dogs can present an efficient method to monitor golden jackals on a long-term basis and to learn more about their behaviour and population dynamics.

Evaluating conservation dogs in the search for rare species

Detecting rare species is important for both threatened species management and invasive species eradication programs. Conservation scent dogs provide an olfactory survey tool that has advantages over traditional visual and auditory survey techniques for some cryptic species. From the literature, we identified 5 measures important in evaluating the use of scent dogs: precision, sensitivity, effort, cost, and comparison with other techniques. We explored the scale at which performance is evaluated and examined when field testing under real working conditions is achievable. We also identified cost differences among studies. We examined 61 studies published in 1976-2018 that reported conservation dog performance, and considered the inconsistencies in the reporting of scent dog performance among these studies. The majority of studies reported some measure of performance; however, only 8 studies reported all 3 aspects necessary for performance evaluation: precision, sensitivity, and effort. Although effort was considered in 43 studies, inconsistent methods and incomplete reporting prevented meaningful evaluation of performance and comparison among studies. Differences in cost between similar studies were influenced by geographical location and how the dog and handler were sourced for the study. To develop consistent reporting for evaluation, we recommend adoption of sensitivity, precision, and effort as standard performance measures. We recommend reporting effort as the total area and total time spent searching and reporting sensitivity and precision as proportions of the sample size. Additionally, reporting of costs, survey objectives, dog training and experience, type of detection task, and human influences will provide better opportunities for comparison within and among studies.

Canines (Canis lupus familiaris) as biodetectors for conservation work: Can they discriminate the rock ptarmigan (Lagopus muta) from the willow grouse (L. lagopus) in a yes/no task?

Alpine and arctic bird populations have shown an unmistakable decrease over the last three decades, and the need for conservation is highly necessary. We investigated the use of five privately-owned dogs (Canis lupus familiaris) as a non-invasive tool to determine the presence of rock ptarmigan (Lagopus muta), through sniffing out faecal pellets, using a yes/no training regime. We carried out 36 double-blind experimental trials per dog and hypothesised that dogs could discriminate the rock ptarmigan from similar species, such as black grouse (Tetrao tetrix), western capercaillie (T. urogallus) and willow grouse (L. lagopus). Our dogs detected differences between the avian species with an average accuracy of 65.9%, sensitivity of 66.7% and specificity of 65.3%. We showed that privately-owned dogs have the potential to be used as biodetectors for conservational work within controlled laboratory conditions for declining species, but overall, only one dog was considered proficient enough. We concluded that dogs could be used as a non-invasive tool to detect the rock ptarmigan, and with further field training and testing, operate in the field for detection surveys.

A multiyear survey of helminths from wild saddleback (Leontocebus weddelli) and emperor (Saguinus imperator) tamarins

The establishment of baseline data on parasites from wild primates is essential to understand how changes in habitat or climatic disturbances will impact parasite-host relationships. In nature, multiparasitic infections of primates usually fluctuate temporally and seasonally, implying that the acquisition of reliable data must occur over time. Individual parasite infection data from two wild populations of New World primates, the saddleback (Leontocebus weddelli) and emperor (Saguinus imperator) tamarin, were collected over 3 years to establish baseline levels of helminth prevalence and parasite species richness (PSR). Secondarily, we explored variation in parasite prevalence across age and sex classes, test nonrandom associations of parasite co-occurrence, and assess the relationship between group size and PSR. From 288 fecal samples across 105 individuals (71 saddleback and 34 emperor tamarins), 10 parasite taxa were identified by light microscopy following centrifugation and ethyl-acetate sedimentation. Of these taxa, none were host-specific, Dicrocoeliidae and Cestoda prevalences differed between host species, Prosthenorchis and Strongylida were the most prevalent. Host age was positively associated with Prosthenorchis ova and filariform larva, but negatively with cestode and the Rhabditoidea ova. We detected no differences between expected and observed levels of co-infection, nor between group size and parasite species richness over 30 group-years. Logistic models of individual infection status did not identify a sex bias; however, age and species predicted the presence of four and three parasite taxa, respectively, with saddleback tamarins exhibiting higher PSR. Now that we have reliable baseline data for future monitoring of these populations, next steps involve the molecular characterization of these parasites, and exploration of linkages with health parameters.

Scent-sniffing dogs can discriminate between native Eurasian and invasive North American beavers

The invasion of a species can cause population reduction or extinction of a similar native species due to replacement competition. There is a potential risk that the native Eurasian beaver (Castor fiber) may eventually be competitively excluded by the invasive North American beaver (C. canadensis) from areas where they overlap in Eurasia. Yet currently available methods of census and population estimates are costly and time-consuming. In a laboratory environment, we investigated the potential of using dogs (Canis lupus familiaris) as a conservation tool to determine whether the Eurasian or the North American beaver is present in a specific beaver colony. We hypothesized that dogs can discriminate between the two beaver species, via the odorant signal of castoreum from males and females, in two floor platform experiments. We show that dogs detect scent differences between the two species, both from dead beaver samples and from scent marks collected in the field. Our results suggest that dogs can be used as an “animal biosensor” to discriminate olfactory signals of beaver species, however more tests are needed. Next step should be to test if dogs discern between beaver species in the field under a range of weather conditions and habitat types and use beaver samples collected from areas where the two species share the same habitat. So far, our results show that dogs can be used as a promising tool in the future to promote conservation of the native beaver species and eradication of the invasive one. We therefore conclude that dogs may be an efficient non-invasive tool to help conservationist to manage invasive species in Europe, and advocate for European wildlife agencies to invest in this new tool.

Developing noninvasive methodologies to assess koala population health through detecting Chlamydia from scats

Wildlife diseases are a recognized driver of global biodiversity loss, have substantial economic impacts, and are increasingly becoming a threat to human health. Disease surveillance is critical but remains difficult in the wild due to the substantial costs and potential biases associated with most disease detection methods. Noninvasive scat surveys have been proposed as a health monitoring methodology to overcome some of these limitations. Here, we use the known threat of Chlamydia disease to the iconic, yet vulnerable, koala Phascolarctos cinereus to compare three methods for Chlamydia detection in scats: multiplex quantitative PCR, next generation sequencing, and a detection dog specifically trained on scats from Chlamydia-infected koalas. All three methods demonstrated 100% specificity, while sensitivity was variable. Of particular interest is the variable sensitivity of these diagnostic tests to detect sick individuals (i.e., not only infection as confirmed by Chlamydia-positive swabs, but with observable clinical signs of the disease); for koalas with urogenital tract disease signs, sensitivity was 78% with quantitative PCR, 50% with next generation genotyping and 100% with the detection dog method. This may be due to molecular methods having to rely on high-quality DNA whereas the dog most likely detects volatile organic compounds. The most appropriate diagnostic test will vary with disease prevalence and the specific aims of disease surveillance. Acknowledging that detection dogs might not be easily accessible to all, the future development of affordable and portable "artificial noses" to detect diseases from scats in the field might enable cost-effective, rapid and large-scale disease surveillance.

Who's a Good Handler? Important Skills and Personality Profiles of Wildlife Detection Dog Handlers

Simple Summary

Professional working dog teams perform a range of functions faster and more accurately than other methods. Therefore, these teams are highly valuable to our society. Whilst some information is available on the skills that are important for dog handlers to possess, this isn’t always sourced from the handlers themselves. As a result, information may be missing, or the provided information may not be relevant. Through questionnaires, we collected information on the skills that wildlife detection dog handlers believe to be important for working success. Handler personality evaluations were also completed to determine whether specific personalities are better suited to this unique working field. Knowledge and understanding of dog body language and behaviour were rated highly. The handlers’ personality profiles had large ranges, indicating that no personality is attracted to, or perhaps best suited for, working with wildlife detection dogs. Dog handler dedication, training, and the dog–handler relationship are likely more influential factors.

Abstract

Wildlife detection dog teams are employed internationally for environmental surveys, and their success often depends on the dog handler. Minimal research is available on the skills that dog handlers believe are important, and no research has been published on the personality profiles of wildlife detection dog handlers. This may reveal the skills that people should acquire to be successful at, or suitable for, this work. An online questionnaire was distributed to Australian and New Zealand wildlife detection dog handlers. This questionnaire provided a list of skills to be rated based on importance, and a personality assessment measured their five main personality domains (Neuroticism, Extraversion, Openness, Agreeableness, and Conscientiousness). A total of 35 questionnaires were collected, which represented over half of the estimated Australian wildlife detection dog handler population. The handlers had on average 7.2 years of dog handling experience, and 54% were female. More than half (57%) of the handlers stated that they were very emotionally attached to their dogs; however, 9% stated they were either not attached or mildly attached to their working dogs. The skill that was rated highest for importance was ‘ability to read dog body language’, and the lowest was ‘skilled in report writing’. On average, the handlers scored high in the Agreeableness domain, low in the Neuroticism domain, and average in the Extraversion, Conscientiousness, and Openness domains. However, all of the personality scores had large ranges. Therefore, a dog handler’s personality may not be as influential on their success as their training or their dog–handler bond. Further research would be beneficial regarding the direct impact that the dog–handler bond and the handler’s knowledge have on working team outcomes.

How Behavior of Nontarget Species Affects Perceived Accuracy of Scat Detection Dog Surveys

Detection dogs, specially trained domestic dogs (Canis familiaris), have become a valuable, noninvasive, conservation tool because they remove the dependence of attracting species to a particular location. Further, detection dogs locate samples independent of appearance, composition, or visibility allowing researchers to collect large sets of unbiased samples that can be used in complex ecological queries. One question not fully addressed is why samples from nontarget species are inadvertently collected during detection dog surveys. While a common explanation has been incomplete handler or dog training, our study aimed to explore alternative explanations. Our trials demonstrate that a scat’s genetic profile can be altered by interactions of nontarget species with target scat via urine-marking, coprophagy, and moving scats with their mouths, all pathways to contamination by nontarget species’ DNA. Because detection dogs are trained to locate odor independent of masking, the collection of samples with a mixed olfactory profile (target and nontarget) is possible. These scats will likely have characteristics of target species’ scats and are therefore only discovered faulty once genetic results indicate a nontarget species. While the collection of nontarget scats will not impact research conclusions so long as samples are DNA tested, we suggest ways to minimize their collection and associated costs.

An environmental DNA sampling method for aye-ayes from their feeding traces

Noninvasive sampling is an important development in population genetic monitoring of wild animals. Particularly, the collection of environmental DNA (eDNA) which can be collected without needing to encounter the target animal facilitates the genetic analysis of endangered species. One method that has been applied to these sample types is target capture and enrichment which overcomes the issue of high proportions of exogenous (nonhost) DNA from these lower quality samples. We tested whether target capture of mitochondrial DNA from sampled feeding traces of the aye-aye, an endangered lemur species would yield mitochondrial DNA sequences for population genetic monitoring. We sampled gnawed wood where aye-ayes excavate wood-boring insect larvae from trees. We designed RNA probes complementary to the aye-aye's mitochondrial genome and used these to isolate aye-aye DNA from other nontarget DNA in these samples. We successfully retrieved six near-complete mitochondrial genomes from two sites within the aye-aye's geographic range that had not been sampled previously. Our method demonstrates the application of next-generation molecular techniques to species of conservation concern. This method can likely be applied to alternative foraged remains to sample endangered species other than aye-ayes.

Seasonality of the gut microbiota of free-ranging white-faced capuchins in a tropical dry forest

Research on the gut microbiota of free-ranging mammals is offering new insights into dietary ecology. However, for free-ranging primates, little information is available for how microbiomes are influenced by ecological variation through time. Primates inhabiting seasonal tropical dry forests undergo seasonally specific decreases in food abundance and water availability, which have been linked to adverse health effects. Throughout the course of a seasonal transition in 2014, we collected fecal samples from three social groups of free-ranging white-faced capuchin monkeys (Cebus capucinus imitator) in Sector Santa Rosa, Área de Conservación Guanacaste, Costa Rica. 16S rRNA sequencing data reveal that unlike other primates, the white-faced capuchin monkey gut is dominated by Bifidobacterium and Streptococcus. Linear mixed effects models indicate that abundances of these genera are associated with fluctuating availability and consumption of fruit and arthropods, whereas beta diversity clusters by rainfall season. Whole shotgun metagenomics revealed that the capuchin gut is dominated by carbohydrate-binding modules associated with digestion of plant polysaccharides and chitin, matching seasonal dietary patterns. We conclude that rainfall and diet are associated with the diversity, composition, and function of the capuchin gut microbiome. Additionally, microbial fluctuations are likely contributing to nutrient uptake and the health of wild primate populations.

Extraction of DNA from captive-sourced feces and molted feathers provides a novel method for conservation management of New Zealand kiwi (Apteryx spp.)

Although some taxa are increasing in number due to active management and predator control, the overall number of kiwi (Apteryx spp.) is declining. Kiwi are cryptic and rare, meaning current monitoring tools, such as call counts, radio telemetry, and surveys using detection dogs are labor-intensive, yield small datasets, and require substantial resources or provide inaccurate estimates of population sizes. A noninvasive genetic approach could help the conservation effort. We optimized a panel of 23 genetic markers (22 autosomal microsatellite loci and an allosomal marker) to discriminate between all species of kiwi and major lineages within species, while simultaneously determining sex. Markers successfully amplified from both fecal and shed feather DNA samples collected in captivity. We found that DNA extraction was more efficient from shed feathers, but DNA quality was greater with feces, although this was sampling dependent. Our microsatellite panel was able to distinguish between contemporary kiwi populations and lineages and provided PI values in the range of 4.3 × 10-5 to 2.0 × 10-19, which in some cases were sufficient for individualization and mark-recapture studies. As such, we have tested a wide-reaching, noninvasive molecular approach that will improve conservation management by providing better parameter estimates associated with population ecology and demographics such as abundance, growth rates, and genetic diversity.

Non-invasive genetic censusing and monitoring of primate populations

Knowing the density or abundance of primate populations is essential for their conservation management and contextualizing socio-demographic and behavioral observations. When direct counts of animals are not possible, genetic analysis of non-invasive samples collected from wildlife populations allows estimates of population size with higher accuracy and precision than is possible using indirect signs. Furthermore, in contrast to traditional indirect survey methods, prolonged or periodic genetic sampling across months or years enables inference of group membership, movement, dynamics, and some kin relationships. Data may also be used to estimate sex ratios, sex differences in dispersal distances, and detect gene flow among locations. Recent advances in capture-recapture models have further improved the precision of population estimates derived from non-invasive samples. Simulations using these methods have shown that the confidence interval of point estimates includes the true population size when assumptions of the models are met, and therefore this range of population size minima and maxima should be emphasized in population monitoring studies. Innovations such as the use of sniffer dogs or anti-poaching patrols for sample collection are important to ensure adequate sampling, and the expected development of efficient and cost-effective genotyping by sequencing methods for DNAs derived from non-invasive samples will automate and speed analyses.

Non-dietary analytical features of chimpanzee scats

Non-dietary aspects of ape scats such as scat weight and diameter are correlated with age and sex of defaecator for gorillas and orangutans. Defaecation rates of primates, including apes, illuminate their role as primary seed dispersers. We assess if non-dietary features of scats for East African chimpanzees (Pan troglodytes schweinfurthii) reveal such insights for members of the Kanyawara community in Kibale National Park, Uganda. Our objective is to see if such data yield useful perspectives for future census work on unhabituated chimpanzees, that is, what can scats tell us about a wild study population, beyond diet? We followed ten adults from this community, as well as travelling parties, comparing observed vs. unobserved defaecations, and collected data on scat weight and dimensions, defaecation rate, scat encounter rate, and interval between defaecations. Few non-dietary features of chimpanzee scats significantly differentiated sex or age of the defaecator, but total scat length and height distinguished adults from juveniles/infants. Defaecation rates and distance travelled were similar for adult males and females, indicating the importance of both sexes as potential primary seed dispersers. Observed travelling parties vs. non-observed travelling parties yielded similar data, indicating the potential to assess party size from scat encounter rates over a set distance. We provide detailed measurements of scat dimensions for this ape taxon which previously have been lacking. This research builds upon prior work by recording more in-depth data for focal subjects and travelling parties on defaecation and scat encounter rates. The findings presented should assist in the interpretation of scat data when censusing unhabituated chimpanzees.