Impacts of sampling location within a faeces on DNA quality in two carnivore species

Resource pulses shape seasonal and individual variation in the diet of an omnivorous carnivore

Resource pulses are ecologically important phenomenon that occur in most ecosystems globally. Following optimal foraging theory, many consumers switch to pulsatile foods when available, examples of which include fruit mast and vulnerable young prey. Yet how the availability of resource pulses shapes the ecology of predators is still an emerging area of research; and how much individual variation there is in response to pulses is not well understood. We hypothesized that resource pulses would lead to dietary convergence in our population, which we tested by tracking both population-level and individual coyote diets for 3 years in South Carolina, USA. We (1) described seasonal dietary shifts in relation to resource pulses; (2) compared male and female diets across seasons; and (3) tested this dietary convergence hypothesis by quantifying individual dietary variation both across and within periods when resource pulses were available. We found that pulses of white-tailed deer fawns and blackberries composed over half of coyote diet in summer, and persimmon fruits were an important component in fall. Male and female coyotes generally had similar diets, but males consumed more deer in fall, perhaps driven by scavenging more. We found support for our dietary convergence hypothesis, where individuals had more similar diets during resource pulses compared to a non-pulse period. We also found that this convergence happened before peak availability, suggesting a non-symmetric response to pulse availability. We show that nearly all coyotes eat fawns, suggesting that targeted efforts to remove "fawn killers" would be in vain. Instead, given how quickly coyotes collectively converge on resource pulses, our findings show that resource pulses could potentially be used by managers to alter the behavior of apex predators. More broadly, we open a new line of inquiry into how variation in individual foraging decisions scales up to shape the effects of resource pulses on ecological communities.

A new DNA extraction method (HV-CTAB-PCI) for amplification of nuclear markers from open ocean-retrieved faeces of an herbivorous marine mammal, the dugong

Non-invasively collected faecal samples are an alternative source of DNA to tissue samples, that may be used in genetic studies of wildlife when direct sampling of animals is difficult. Although several faecal DNA extraction methods exist, their efficacy varies between species. Previous attempts to amplify mitochondrial DNA (mtDNA) markers from faeces of wild dugongs (Dugong dugon) have met with limited success and nuclear markers (microsatellites) have been unsuccessful. This study aimed to establish a tool for sampling both mtDNA and nuclear DNA (nDNA) from dugong faeces by modifying approaches used in studies of other large herbivores. First, a streamlined, cost-effective DNA extraction method that enabled the amplification of both mitochondrial and nuclear markers from large quantities of dugong faeces was developed. Faecal DNA extracted using a new 'High Volume- Cetyltrimethyl Ammonium Bromide- Phenol-Chloroform-Isoamyl Alcohol' (HV-CTAB-PCI) method was found to achieve comparable amplification results to extraction of DNA from dugong skin. As most prevailing practices advocate sampling from the outer surface of a stool to maximise capture of sloughed intestinal cells, this study compared amplification success of mtDNA between the outer and inner layers of faeces, but no difference in amplification was found. Assessment of the impacts of faecal age or degradation on extraction, however, demonstrated that fresher faeces with shorter duration of environmental (seawater) exposure amplified both markers better than eroded scats. Using the HV-CTAB-PCI method, nuclear markers were successfully amplified for the first time from dugong faeces. The successful amplification of single nucleotide polymorphism (SNP) markers represents a proof-of-concept showing that DNA from dugong faeces can potentially be utilised in population genetic studies. This novel DNA extraction protocol offers a new tool that will facilitate genetic studies of dugongs and other large and cryptic marine herbivores in remote locations.

Scat as a source of DNA for population monitoring

Sampling fecal droppings (scat) to genetically identify individual animals is an established method for monitoring mammal populations and could be highly useful for monitoring reptile populations. Whereas existing protocols for obtaining DNA from reptile scat focus on analyses of whole, fresh scat deposited during animal handling, the collection of scat naturally deposited by reptiles in situ, as required for non-invasive population monitoring, requires protocols to extract highly degraded DNA. Using surface swabs from such scats can reduce PCR inhibition and increase genotyping success. We report on three related but independently designed studies of DNA analyses from scat swabs of herbivorous reptiles under natural desert conditions: two free-ranging desert tortoise species (Agassiz's desert tortoise, Gopherus agassizii, California, US, and Morafka's desert tortoise, G. morafkai, Arizona, US) and the common chuckwalla (Sauromalus atar) (Arizona, US, and Sonora, MX). We analyzed samples from both tortoise species with the same set of 16 microsatellites and chuckwalla samples with four mtDNA markers; studies also varied in swab preservation medium and DNA extraction method. Microsatellite amplification success per sample, defined as ≥9 loci with amplification, was 15% for the study of Agassiz's desert tortoise and for the study of 42% Morafka's desert tortoise. For chuckwallas, we successfully amplified and sequenced 50% of samples. We recovered fragments up to 400 bp for tortoises and 980 bp for chuckwallas from scat swab samples. This study indicates that genotypes can successfully be obtained from swabs of scat from herbivorous reptiles collected in the field under natural environmental conditions and emphasizes that repeat amplifications are necessary for the genetic identification of individuals from non-invasive samples.

Genetic diversity and mate selection in a reintroduced population of gray wolves

The genetic composition of an individual can markedly affect its survival, reproduction, and ultimately fitness. As some wildlife populations become smaller, conserving genetic diversity will be a conservation challenge. Many imperiled species are already supported through population augmentation efforts and we often do not know if or how genetic diversity is maintained in translocated species. As a case study for understanding the maintenance of genetic diversity in augmented populations, I wanted to know if genetic diversity (i.e., observed heterozygosity) remained high in a population of gray wolves in the Rocky Mountains of the U.S. > 20 years after reintroduction. Additionally, I wanted to know if a potential mechanism for such diversity was individuals with below average genetic diversity choosing mates with above average diversity. I also asked whether there was a preference for mating with unrelated individuals. Finally, I hypothesized that mated pairs with above average heterozygosity would have increased survival of young. Ultimately, I found that females with below average heterozygosity did not choose mates with above average heterozygosity and wolves chose mates randomly with respect to genetic relatedness. Pup survival was not higher for mated pairs with above average heterozygosity in my models. The dominant variables predicting pup survival were harvest rate during their first year of life and years pairs were mated. Ultimately, genetic diversity was relatively unchanged > 20 years after reintroduction. The mechanism for maintaining such diversity does not appear related to individuals preferentially choosing more genetically diverse mates. Inbreeding avoidance, however, appears to be at least one mechanism maintaining genetic diversity in this population.

Testing the effectiveness of genetic monitoring using genetic non-invasive sampling

Effective conservation requires accurate data on population genetic diversity, inbreeding, and genetic structure. Increasingly, scientists are adopting genetic non-invasive sampling (gNIS) as a cost-effective population-wide genetic monitoring approach. gNIS has, however, known limitations which may impact the accuracy of downstream genetic analyses. Here, using high-quality single nucleotide polymorphism (SNP) data from blood/tissue sampling of a free-ranging koala population (n = 430), we investigated how the reduced SNP panel size and call rate typical of genetic non-invasive samples (derived from experimental and field trials) impacts the accuracy of genetic measures, and also the effect of sampling intensity on these measures. We found that gNIS at small sample sizes (14% of population) can provide accurate population diversity measures, but slightly underestimated population inbreeding coefficients. Accurate measures of internal relatedness required at least 33% of the population to be sampled. Accurate geographic and genetic spatial autocorrelation analysis requires between 28% and 51% of the population to be sampled. We show that gNIS at low sample sizes can provide a powerful tool to aid conservation decision-making and provide recommendations for researchers looking to apply these techniques to free-ranging systems.

Evaluating otter reintroduction outcomes using genetic spatial capture-recapture modified for dendritic networks

Monitoring the demographics and genetics of reintroduced populations is critical to evaluating reintroduction success, but species ecology and the landscapes that they inhabit often present challenges for accurate assessments. If suitable habitats are restricted to hierarchical dendritic networks, such as river systems, animal movements are typically constrained and may violate assumptions of methods commonly used to estimate demographic parameters. Using genetic detection data collected via fecal sampling at latrines, we demonstrate applicability of the spatial capture-recapture (SCR) network distance function for estimating the size and density of a recently reintroduced North American river otter (Lontra canadensis) population in the Upper Rio Grande River dendritic network in the southwestern United States, and we also evaluated the genetic outcomes of using a small founder group (n = 33 otters) for reintroduction. Estimated population density was 0.23-0.28 otter/km, or 1 otter/3.57-4.35 km, with weak evidence of density increasing with northerly latitude (β = 0.33). Estimated population size was 83-104 total otters in 359 km of riverine dendritic network, which corresponded to average annual exponential population growth of 1.12-1.15/year since reintroduction. Growth was ≥40% lower than most reintroduced river otter populations and strong evidence of a founder effect existed 8-10 years post-reintroduction, including 13-21% genetic diversity loss, 84%-87% genetic effective population size decline, and rapid divergence from the source population (F ST accumulation = 0.06/generation). Consequently, genetic restoration via translocation of additional otters from other populations may be necessary to mitigate deleterious genetic effects in this small, isolated population. Combined with non-invasive genetic sampling, the SCR network distance approach is likely widely applicable to demogenetic assessments of both reintroduced and established populations of multiple mustelid species that inhabit aquatic dendritic networks, many of which are regionally or globally imperiled and may warrant reintroduction or augmentation efforts.

Factors influencing genotyping success and genotyping error rate of Eurasian otter (Lutra lutra) faeces collected in temperate Central Europe

The use of non-invasively collected DNA source material for genetic and genomic applications is usually characterized by low target DNA concentration and quality, genotyping errors and cost-intensive lab procedures. However, for otters (Lutrinae) as elusive species of conservation concern, genetic non-invasive sampling has become an important tool to study their ecology and demography. To increase cost-efficiency of monitoring programmes and to promote the expansion of genomic approaches to non-invasive samples, we aimed to refine sample collection and preparation. Therefore, we examined the effects of intrinsic sample characteristics (including diet), environmental conditions in the field and sample treatment in the molecular laboratory on the success of genotyping and allelic dropout (ADO) rates using microsatellite markers in 1970 fresh Eurasian otter (Lutra lutra) scats. Using fresh samples only, we probably eliminated one of the most important impediments of genotyping DNA from otter faecal samples beforehand. But, we observed higher genotyping success and lower ADO rates for anal glad secretions and faecal samples containing high proportions of mucus. Moist conditions during sample collection may promote DNA degradation and PCR inhibition, leading to decreased genotyping success rates. ADO was further affected by the type of extraction kit. However, a high proportion of variance remaining unexplained by our models implied that additional parameters were acting (amount of PCR inhibitors, non-uniform distribution of intestinal cells, efficiency of PCRs, specific microclimate at marking sites). We summarized influential factors maximizing genotyping quality of otter scats and give recommendations for sample collection, storage and DNA extraction based on our results and current literature.

Does harvest affect genetic diversity in grey wolves?

Harvest can affect vital rates such as reproduction and survival, but also genetic measures of individual and population health. Grey wolves (Canis lupus) live and breed in groups, and effective population size is a small fraction of total abundance. As a result, genetic diversity of wolves may be particularly sensitive to harvest. We evaluated how harvest affected genetic diversity and relatedness in wolves. We hypothesized that harvest would (a) reduce relatedness of individuals within groups in a subpopulation but increase relatedness of individuals between groups due to increased local immigration, (b) increase individual heterozygosity and average allelic richness across groups in subpopulations and (c) add new alleles to a subpopulation and decrease the number of private alleles in subpopulations due to an increase in breeding opportunities for unrelated individuals. We found harvest had no effect on observed heterozygosity of individuals or allelic richness at loci within subpopulations but was associated with a small, biologically insignificant effect on within-group relatedness values in grey wolves. Harvest was, however, positively associated with increased relatedness of individuals between groups and a net gain (+16) of alleles into groups in subpopulations monitored since harvest began, although the number of private alleles in subpopulations overall declined. Harvest likely created opportunities for wolves to immigrate into nearby groups and breed, thereby making groups in subpopulations more related over time. Harvest appears to affect genetic diversity in wolves at the group and population levels, but its effects are less apparent at the individual level given the population sizes we studied.

A real-time PCR assay to accurately quantify polar bear DNA in fecal extracts

DNA extracted from fecal samples contains DNA from the focal species, food, bacteria and pathogens. Most DNA quantification methods measure total DNA and cannot differentiate among sources. Despite the desirability of noninvasive fecal sampling for studying wildlife populations, low amounts of focal species DNA make it difficult to use for next-generation sequencing (NGS), where accurate DNA quantification is critical for normalization. Two factors are required prior to using fecal samples in NGS libraries: (1) an accurate quantification method for the amount of target DNA and (2) a determination of the relative amount of target DNA needed for successful single nucleotide polymorphism genotyping assays. Here, we address these needs by developing primers to amplify a 101 bp region of the nuclear F2 gene and a quantitative PCR (qPCR) assay that allows the accurate quantification of the amount of polar bear (Ursus maritimus) DNA in fecal extracts. We test the assay on pure polar bear DNA extracted from muscle tissue and find a high correlation between fluorometric and qPCR quantifications. The qPCR assay was also successfully used to quantify the amount of DNA derived from polar bears in fecal extractions. Orthologs of the F2 gene have been identified across vertebrates; thus, similar qPCR assays could be developed for other species to enable noninvasive studies.

The curse of observer experience: Error in noninvasive genetic sampling

Noninvasive genetic sampling (NGS) is commonly used to study elusive or rare species where direct observation or capture is difficult. Little attention has been paid to the potential effects of observer bias while collecting noninvasive genetic samples in the field, however. Over a period of 7 years, we examined whether different observers (n = 58) and observer experience influenced detection, amplification rates, and correct species identification of 4,836 gray wolf (Canis lupus) fecal samples collected in Idaho and Yellowstone National Park, USA and southwestern Alberta, Canada (2008-2014). We compared new observers (n = 33) to experienced observers (n = 25) and hypothesized experience level would increase the overall success of using NGS techniques in the wild. In contrast to our hypothesis, we found that new individuals were better than experienced observers at detecting and collecting wolf scats and correctly identifying wolf scats from other sympatric carnivores present in the study areas. While adequate training of new observers is crucial for the successful use of NGS techniques, attention should also be directed to experienced observers. Observer experience could be a curse because of their potential effects on NGS data quality arising from fatigue, boredom or other factors. The ultimate benefit of an observer to a project is a combination of factors (i.e., field savvy, local knowledge), but project investigators should be aware of the potential negative effects of experience on NGS sampling.

Pair bonds, reproductive success, and rise of alternate mating strategies in a social carnivore

Monogamy is commonly observed across a wide variety of species and taxa and arises when young are altricial, parental investment in young is high, and mate monopolization is generally not possible. In such species, pairs may bond for multiple breeding seasons while successfully rearing young. Individuals, however, may attempt to bypass the dominant mating strategy particularly when breeding opportunities are limited. Currently, we do not know how pair bond duration affects the efficacy of alternative mating strategies in populations with a monogamous mating system. Additionally, inferences about pair bond effects on reproductive success (i.e., both clutch size and recruitment) are largely limited to long-lived birds and little is known about effects on mammalian cooperative breeders. I used genetic sampling and pedigrees to examine the effects of pair bond duration on reproductive success (i.e., litter size, recruitment) and mating strategies in a population of gray wolves (Canis lupus) in Idaho, USA. There was a positive, marginally significant relationship between pair bond duration and apparent survival of offspring. Increased pair bond duration was also associated with a dampening in the prevalence of other alternative mating strategies such as sneaker males and polygamy. The selective advantage of alternative mating strategies is a combination of population, group (for applicable species), individual, and social influences such as pair bonds. The distribution of pair bonds in a monogamous population affects the selective advantage, and hence frequency, of various mating strategies observed.

Improving cost-efficiency of faecal genotyping: New tools for elephant species

Despite the critical need for non-invasive tools to improve monitoring of wildlife populations, especially for endangered and elusive species, faecal genetic sampling has not been adopted as regular practice, largely because of the associated technical challenges and cost. Substantial work needs to be undertaken to refine sample collection and preparation methods in order to improve sample set quality and provide cost-efficient tools that can effectively support wildlife management. In this study, we collected an extensive set of forest elephant (Loxodonta cyclotis) faecal samples throughout Gabon, Central Africa, and prepared them for genotyping using 107 single-nucleotide polymorphism assays. We developed a new quantitative polymerase chain reaction (PCR) assay targeting a 130-bp nuclear DNA fragment and demonstrated its suitability for degraded samples in all three elephant species. Using this assay to compare the efficacy of two sampling methods for faecal DNA recovery, we found that sampling the whole surface of a dung pile with a swab stored in a small tube of lysis buffer was a convenient method producing high extraction success and DNA yield. We modelled the influence of faecal quality and storage time on DNA concentration in order to provide recommendations for optimized collection and storage. The maximum storage time to ensure 75% success was two months for samples collected within 24 hours after defecation and extended to four months for samples collected within one hour. Lastly, the real-time quantitative PCR assay allowed us to predict genotyping success and pre-screen DNA samples, thus further increasing the cost-efficiency of our approach. We recommend combining the validation of an efficient sampling method, the build of in-country DNA extraction capacity for reduced storage time and the development of species-specific quantitative PCR assays in order to increase the cost-efficiency of routine non-invasive DNA analyses and expand the use of next-generation markers to non-invasive samples.

Estimating densities for sympatric kit foxes (Vulpes macrotis) and coyotes (Canis latrans) using noninvasive genetic sampling

Kit fox (Vulpes macrotis Merriam, 1888) populations in the Great Basin Desert have declined and are of increasing concern for managers. Increasing coyote (Canis latrans Say, 1823) abundance and subsequent intraguild interactions may be one cause for this decline. Concurrent monitoring of carnivores is challenging and therefore rarely conducted. One possible solution for monitoring elusive carnivores is using noninvasive genetic sampling. We used noninvasive genetic sampling to collect fecal DNA from kit foxes and coyotes and estimate their densities from 2013–2014 in Utah, USA. We identified individuals based on microsatellite genotypes and estimated density with multisession spatially explicit capture–recapture models. Mean kit fox density was 0.02 foxes·km−2, while coyote densities were up to four times greater (0.07–0.08 coyotes·km−2). Kit fox densities were significantly lower than densities in the 1950s but were comparable with estimates from the late 1990s, suggesting that populations may be stabilizing after a precipitous decline. Our kit fox density estimates were among the lowest documented for the species. Our coyote density estimate was the first reported in our region and revealed that despite seemingly high abundance, densities are low compared with other regions. Our results suggested that kit foxes may be able to coexist with coyotes.

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.

Genetic and genomic monitoring with minimally invasive sampling methods

The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.

A comparison of morphological and molecular diet analyses of predator scats

An understanding of a species’ diet is required to make sound conservation and management decisions. Traditionally, morphological analyses of undigested hard parts from food items remaining in scats have been used to assess diets. More recently, molecular analyses of scats have been used to identify plant and prey species’ DNA, but no studies have compared morphological and molecular diet analyses for large, terrestrial carnivores. We used molecular tools to determine the percentage of black bear and coyote scats that contained 3 common prey species (caribou, moose, and snowshoe hares) in Newfoundland and compared the results to a traditional morphological analysis. We found that a ranking of relative prey frequencies was consistent between the 2 methods, but molecular methods tended to detect prey species in a greater percentage of scats for all prey species. However, there were individual scats in which a prey species was detected by morphological methods only, and we provide evidence that molecular methods could result in false negatives if prey DNA is not uniformly distributed throughout a scat or as a result of PCR inconsistency. We also found that the per sample cost comparison between morphological and molecular analyses was dependent upon whether or not a molecular test was needed to identify scats to the predator species, the cost of developing molecular methods, and the number of samples being processed. We recommend that controlled feeding studies be performed to validate molecular methods and investigate the utility of molecular techniques to estimate the proportions of food items consumed.

Structural habitat predicts functional dispersal habitat of a large carnivore: how leopards change spots

Natal dispersal promotes inter-population linkage, and is key to spatial distribution of populations. Degradation of suitable landscape structures beyond the specific threshold of an individual's ability to disperse can therefore lead to disruption of functional landscape connectivity and impact metapopulation function. Because it ignores behavioral responses of individuals, structural connectivity is easier to assess than functional connectivity and is often used as a surrogate for landscape connectivity modeling. However using structural resource selection models as surrogate for modeling functional connectivity through dispersal could be erroneous. We tested how well a second-order resource selection function (RSF) models (structural connectivity), based on GPS telemetry data from resident adult leopard (Panthera pardus L.), could predict subadult habitat use during dispersal (functional connectivity). We created eight non-exclusive subsets of the subadult data based on differing definitions of dispersal to assess the predictive ability of our adult-based RSF model extrapolated over a broader landscape. Dispersing leopards used habitats in accordance with adult selection patterns, regardless of the definition of dispersal considered. We demonstrate that, for a wide-ranging apex carnivore, functional connectivity through natal dispersal corresponds to structural connectivity as modeled by a second-order RSF. Mapping of the adult-based habitat classes provides direct visualization of the potential linkages between populations, without the need to model paths between a priori starting and destination points. The use of such landscape scale RSFs may provide insight into predicting suitable dispersal habitat peninsulas in human-dominated landscapes where mitigation of human-wildlife conflict should be focused. We recommend the use of second-order RSFs for landscape conservation planning and propose a similar approach to the conservation of other wide-ranging large carnivore species where landscape-scale resource selection data already exist.

Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China

Many ecological studies and conservation management plans employ noninvasive scat sampling based on the assumption that species' scats can be correctly identified in the field. However, in habitats with sympatric similarly sized carnivores, misidentification of scats is frequent and can lead to bias in research results. To address the scat identification dilemma, molecular scatology techniques have been developed to extract DNA from the donor cells present on the outer lining of the scat samples. A total of 100 samples were collected in the winter of 2009 and 2011 in Taxkorgan region of Xinjiang, China. DNA was extracted successfully from 88% of samples and genetic species identification showed that more than half the scats identified in the field as snow leopard (Panthera uncia) actually belonged to fox (Vulpes vulpes). Correlation between scat characteristics and species were investigated, showing that diameter and dry weight of the scat were significantly different between the species. However it was not possible to define a precise range of values for each species because of extensive overlap between the morphological values. This preliminary study confirms that identification of snow leopard feces in the field is misleading. Research that relies upon scat samples to assess distribution or diet of the snow leopard should therefore employ molecular scatology techniques. These methods are financially accessible and employ relatively simple laboratory procedures that can give an indisputable response to species identification from scats.

Reading Mammal Diversity from Flies: The Persistence Period of Amplifiable Mammal mtDNA in Blowfly Guts (Chrysomya megacephala) and a New DNA Mini-Barcode Target

Most tropical mammal species are threatened or data-deficient. Data collection is impeded by the traditional monitoring approaches which can be laborious, expensive and struggle to detect cryptic diversity. Monitoring approaches using mammal DNA derived from invertebrates are emerging as cost- and time-effective alternatives. As a step towards development of blowfly-derived DNA as an effective method for mammal monitoring in the biodiversity hotspot of Peninsular Malaysia, our objectives were (i) to determine the persistence period of amplifiable mammal mtDNA in blowfly guts through a laboratory feeding experiment (ii) to design and test primers that can selectively amplify mammal COI DNA mini-barcodes in the presence of high concentrations of blowfly DNA. The persistence period of amplifiable mammal mtDNA in blowfly guts was 24 h to 96 h post-feeding indicating the need for collecting flies within 24 h of capture to detect mammal mtDNA of sufficient quantity and quality. We designed a new primer combination for a COI DNA mini-barcode that did not amplify blowfly DNA and showed 89% amplification success for a dataset of mammals from Peninsular Malaysia. The short (205 bp) DNA mini-barcode could distinguish most mammal species (including separating dark taxa) and is of suitable length for high-throughput sequencing. Our new DNA mini-barcode target and a standardized trapping protocol with retrieval of blowflies every 24 h could point the way forward in the development of blowfly-derived DNA as an effective method for mammal monitoring.

Evaluating noninvasive genetic sampling techniques to estimate large carnivore abundance

Monitoring large carnivores is difficult because of intrinsically low densities and can be dangerous if physical capture is required. Noninvasive genetic sampling (NGS) is a safe and cost-effective alternative to physical capture. We evaluated the utility of two NGS methods (scat detection dogs and hair sampling) to obtain genetic samples for abundance estimation of coyotes, black bears and Canada lynx in three areas of Newfoundland, Canada. We calculated abundance estimates using program capwire, compared sampling costs, and the cost/sample for each method relative to species and study site, and performed simulations to determine the sampling intensity necessary to achieve abundance estimates with coefficients of variation (CV) of <10%. Scat sampling was effective for both coyotes and bears and hair snags effectively sampled bears in two of three study sites. Rub pads were ineffective in sampling coyotes and lynx. The precision of abundance estimates was dependent upon the number of captures/individual. Our simulations suggested that ~3.4 captures/individual will result in a < 10% CV for abundance estimates when populations are small (23-39), but fewer captures/individual may be sufficient for larger populations. We found scat sampling was more cost-effective for sampling multiple species, but suggest that hair sampling may be less expensive at study sites with limited road access for bears. Given the dependence of sampling scheme on species and study site, the optimal sampling scheme is likely to be study-specific warranting pilot studies in most circumstances.

Balancing sample accumulation and DNA degradation rates to optimize noninvasive genetic sampling of sympatric carnivores

Noninvasive genetic sampling, or noninvasive DNA sampling (NDS), can be an effective monitoring approach for elusive, wide-ranging species at low densities. However, few studies have attempted to maximize sampling efficiency. We present a model for combining sample accumulation and DNA degradation to identify the most efficient (i.e. minimal cost per successful sample) NDS temporal design for capture-recapture analyses. We use scat accumulation and faecal DNA degradation rates for two sympatric carnivores, kit fox (Vulpes macrotis) and coyote (Canis latrans) across two seasons (summer and winter) in Utah, USA, to demonstrate implementation of this approach. We estimated scat accumulation rates by clearing and surveying transects for scats. We evaluated mitochondrial (mtDNA) and nuclear (nDNA) DNA amplification success for faecal DNA samples under natural field conditions for 20 fresh scats/species/season from <1-112 days. Mean accumulation rates were nearly three times greater for coyotes (0.076 scats/km/day) than foxes (0.029 scats/km/day) across seasons. Across species and seasons, mtDNA amplification success was ≥95% through day 21. Fox nDNA amplification success was ≥70% through day 21 across seasons. Coyote nDNA success was ≥70% through day 21 in winter, but declined to <50% by day 7 in summer. We identified a common temporal sampling frame of approximately 14 days that allowed species to be monitored simultaneously, further reducing time, survey effort and costs. Our results suggest that when conducting repeated surveys for capture-recapture analyses, overall cost-efficiency for NDS may be improved with a temporal design that balances field and laboratory costs along with deposition and degradation rates.