Non-invasive Genetic Sampling Research Articles

Unravelling predator–prey interactions in response to planned fire: a case study from the Tanami Desert

Context Introduced predators pose a significant threat to biodiversity. Understanding how predators interact with other threats such as fire is crucial to developing effective conservation strategies. Aims We investigated interactions between the greater bilby (Macrotis lagotis) and two introduced predators, the European red fox (Vulpes vulpes) and feral cat (Felis catus), in response to fire management in a remote part of the Tanami Desert, Australia. Methods We used motion-sensor cameras and non-invasive genetic sampling to monitor bilbies and predators. We compared activity profiles to determine the level of temporal overlap among species, and used generalised linear modelling to assess the correlation between activity and average normalised difference vegetation index (NDVI; as a proxy for fire-associated environmental change). Finally, we used spatially explicit capture–recapture modelling to estimate cat and bilby densities before and after fire. Key results Cat and bilby activity declined following fire, whereas fox activity increased (despite only a small proportion of the study area being burnt). Bilbies and foxes showed the greatest overlap in temporal activity (76%), followed by bilbies and cats (71%) and cats and foxes (68%). Bilbies and cats were more likely to be captured in areas with a lower NDVI, whereas foxes were more likely to be captured in areas with a higher NDVI. Bilby density declined significantly following fire, whereas cat density remained constant through time. Conclusions Declines in bilby activity and density following fire may be attributed to emigration from the study area and/or increases in fox activity. Post-burn emigration could be due to wide scale destruction of important food resources. However, given much of the study area where bilbies were detected remained unburnt, it is more likely that observed declines are related to increases in fox activity and associated increases in predation pressure. Improved understanding may be gained by experimentally manipulating both fire and predator densities. Implications Increases in fox activity following fire are likely to have devastating consequences for the local bilby population. It is thus vital that appropriate management activities are put in place to protect bilbies from foxes. This may be achieved through a combination of lethal control and indirect methods.

Environmental effects on faecal genotyping success in mesocarnivores

AbstractNon-invasive genetic sampling can be used in research, monitoring, and conservation of wild animals to, for example, provide insights into diets, identify individuals and estimate population sizes. Non-invasive genetic sampling may be especially useful to monitor elusive species because DNA can be derived from materials such as hairs and faeces without handling individuals. However, the reliability of the results derived from this technique is dependent on the quality of DNA obtained from samples, which can deteriorate from exposure to environmental conditions and sample age. While freshness of the sample is an important factor, the combined effect of different field conditions on the genotyping success is not fully understood. To address this gap, we systematically investigated the effects of sample age and environmental conditions on genotyping success of faeces, in an experimental setting of four treatments that combined rain and temperature conditions typical of central European climates. We compared the performance of a microsatellite marker set and a SNP panel for red fox (Vulpes vulpes), as well as a microsatellite marker set for pine marten (Martes martes) from faeces resampled over 21 days. We found that genotyping success decreased significantly with sample age, however environmental treatments did not impact the success. Furthermore, the SNPs we used amplified more successfully over time than the respective microsatellites. Therefore, the use of SNPs instead of conventional microsatellites, when using faecal samples for analysis relying on correct amplifications, could be advantageous. We recommend to prioritise the collection of fresh faeces regardless of environmental conditions.

Low signs of territorial behavior in the Eurasian otter during low-water conditions in a Mediterranean river

The Eurasian otter Lutra lutra is a territorial semi-aquatic carnivore usually found at low densities in rivers, coastal areas, and wetlands. Its diet is based on prey associated with aquatic environments. Mediterranean rivers are highly seasonal, and suffer reduced flow during the summer, resulting in isolated river sections (pools) that sometimes can be left with a minimal amount of water, leading to concentrations of food for otters. To our knowledge, this process, which was known to field naturalists, has not been accurately described, nor have otter densities been estimated under these conditions. In this study, we describe the population size and movements of an aggregation of otters in an isolated pool in the Guadiana River in the Tablas de Daimiel National Park (central Spain), which progressively dried out during the spring–summer of 2022, in a context of low connectivity due to the absence of circulating water in the Guadiana and Gigüela rivers. Using non-invasive genetic sampling of 120 spraints collected along 79.4 km of sampling transects and spatial capture-recapture methods, we estimated the otter density at 1.71 individuals/km of river channel length (4.21 individuals/km2) in a progressively drying river pool, up to five times higher than previously described in the Iberian Peninsula. The movement patterns obtained with the spatial capture-recapture model are not quite different from those described in low density, which seems to indicate a wide home range overlap, with low signs of territoriality.

Estimating distribution and abundance of wide-ranging species with integrated spatial models: Opportunities revealed by the first wolf assessment in south-central Italy.

Estimating demographic parameters for wide-ranging and elusive species living at low density is challenging, especially at the scale of an entire country. To produce wolf distribution and abundance estimates for the whole south-central portion of the Italian wolf population, we developed an integrated spatial model, based on the data collected during a 7-month sampling campaign in 2020-2021. Data collection comprised an extensive survey of wolf presence signs, and an intensive survey in 13 sampling areas, aimed at collecting non-invasive genetic samples (NGS). The model comprised (i) a single-season, multiple data-source, multi-event occupancy model and (ii) a spatially explicit capture-recapture model. The information about species' absence was used to inform local density estimates. We also performed a simulation-based assessment, to estimate the best conditions for optimizing sub-sampling and population modelling in the future. The integrated spatial model estimated that 74.2% of the study area in south-central Italy (95% CIs = 70.5% to 77.9%) was occupied by wolves, for a total extent of the wolf distribution of 108,534 km2 (95% CIs = 103,200 to 114,000). The estimate of total population size for the Apennine wolf population was of 2557 individuals (SD = 171.5; 95% CIs = 2127 to 2844). Simulations suggested that the integrated spatial model was associated with an average tendency to slightly underestimate population size. Also, the main contribution of the integrated approach was to increase precision in the abundance estimates, whereas it did not affect accuracy significantly. In the future, the area subject to NGS should be increased to at least 30%, while at least a similar proportion should be sampled for presence-absence data, to further improve the accuracy of population size estimates and avoid the risk of underestimation. This approach could be applied to other wide-ranging species and in other geographical areas, but specific a priori evaluations of model requirements and expected performance should be made.

Fecal genotyping to estimate small mammal population size, with a comparison to live mark-recapture estimates

Live capture-recapture is often considered the gold standard for estimating wildlife population size or density, but the approach can be limited by permitting requirements, required labor, welfare concerns, and biased estimates resulting from heterogeneity in individual behavior. Noninvasive genetic sampling (e.g., from fecal pellets) offers a powerful alternative approach, but this method’s success varies among taxa, with little research available on its use in rodents. Here, we addressed a series of questions to develop a noninvasive genetic sampling approach for the endangered giant kangaroo rat (Dipodomys ingens): (1) how quickly does DNA degrade in natural conditions, (2) how many pellets are required to recover a genotype, (3) how often do multiple individuals contaminate a pooled sample from a single sampling location, and (4) how do variable and parameter estimates from noninvasive genetic sampling compare to live-trapping mark-recapture estimates? We found that fecal pellets were successfully genotyped up to 9 days (estimated probability of recovery = 0.78) after exposure to hot, arid conditions, but that rate fell precipitously soon after. Although giant kangaroo rats are territorial, multiple individuals deposited fecal pellets at the same sampling locations; however, single pellets contained sufficient DNA to recover genotypes and to identify individuals, so contamination was not a problem for this approach. Capture probabilities were lower using noninvasive genetic sampling ( = 0.26, SE = 0.01) than live trapping ( = 0.40, SE = 0.06). Population estimates were generally similar using noninvasive genetic sampling, although they were quite a bit higher ( = 64 , = 38) on one grid. Noninvasive genetic sampling can overcome many of the limitations of live-trapping for small mammals, but the approach should be tested in additional taxa and systems to provide more generalizable recommendations for sampling schemes.

Development of a non-invasive method for species and sex identification of rare forest carnivores using footprint identification technology

Many wildlife species have sex specific habitat requirements. Due to the unique requirements for birthing and raising offspring, female reproductive habitat is often a limiting factor for a population and has been identified as a priority for conservation. Therefore, the ability to detect where females persist on the landscape and identify these potential reproductive areas is essential in creating effective conservation strategies. Here we describe the development of a non-invasive method to identify species and sex based on track images collected at track plate stations using footprint identification technology (FIT). We developed this technique using data from the southern Sierra Nevada fisher (Pekania pennanti) population and a co-occurring species of conservation concern the Pacific marten (Martes caurina). We coupled track plate footprints with non-invasive genetic samples and camera trap images to create a reference dataset of known species for fisher and marten and known sex for fisher. We used FIT to geo-reference 167 marten and 367 fisher tracks (34 males, 27 females) using 7 landmark points and then extracted 124 morphometric variables (distances, angles, and areas) for use in identifying species and sex for fisher using linear discriminant analyses. Using a single variable, we found species classification accuracy >99% in distinguishing fisher from marten. For fisher sex identification our most parsimonious model consisting of only 2 variables achieved an accuracy of 94.0% for the training set and 89.4% for the test set. We also report a method to quantify classification uncertainty for each track. This method provides a rapid, cost effective, entirely non-invasive method to accurately identify sex that can easily be implemented in field studies.

Novel multilayer network analysis to assess variation in the spatial co-occurrences of close kin in wild caribou populations

Understanding how individuals within populations are connected genetically and through shared space-use is critical to understanding the demographic patterns of at-risk populations. In recent years, non-invasive genetic sampling methods have allowed us to begin addressing these questions. Using a network analysis framework, we examined the spatial co-occurrence and genetic relatedness of boreal and central mountain caribou (Rangifer tarandus) in populations varying in sizes and trend from across western Canada. Using 15 microsatellites loci and a sex-specific marker, we developed pedigree networks for each population, including first to third order relationships. We constructed networks of individual spatial co-occurrence, and using multilayer network analysis, we determined the degree to which caribou that co-occurred spatially were related. Caribou populations varied in the extent and classes of familial relationships which co-occurred in space. In most populations, spatial co-occurrences were greater than expected only for parent-offspring relationships. A sex-specific analysis of the longest sampled population revealed that this was driven by a significant overlap between mothers and their offspring. Whereas in populations where very few parent-offspring relationship were detected, no significant overlap was found between any relationship categories. The lack of overlap in these populations may be an indication of poor calf survival. On the other hand, the higher degree of overlap with more distant relations (i.e., grandparents) seen in some populations may indicate a population that lacks mobility. Our research presents a new approach to explore both spatial and genetic overlap at the individual level in support of the conservation of threatened populations.

Density and genetic diversity of grizzly bears at the northern edge of their distribution

AbstractSpecies at the periphery of their range are typically limited in density by poor habitat quality. As a result, the central–marginal hypothesis (CMH) predicts a decline in genetic diversity of populations toward the periphery of a species' range. Grizzly bears (Ursus arctos) once ranged throughout most of North America but have been extirpated from nearly half of their former range, mainly in the south. They are considered a species at risk even in Canada's remote North, where they occupy the northernmost edge of the species' continental distribution in a low‐productivity tundra environment. With climate change, one of their main prey species in the tundra (caribou), which has always shown yearly fluctuations, is declining, but simultaneously, grizzlies appear to be expanding their range northward in the same tundra environment. Yet, a lack of population density estimates across the North is hindering effective conservation action. The CMH has implications for the viability of peripheral populations, and the links between population fluctuations, potential bottlenecks, and genetic diversity need to be determined to contribute to species' conservation. Using noninvasive genetic sampling from 2012 to 2014 and autosomal DNA genotyping (via microsatellites), we estimated bear density using a spatial capture–recapture framework and analyzed genetic diversity using observed heterozygosity (Ho), allelic richness (AR), and expected heterozygosity (He). We compared our findings to other studies that used comparable methodologies on grizzly bears and a related species (black bears; Ursus americanus). We found densities of grizzly bears that were low for the species but characteristic for the region (5.9 ± 0.4 bears/1000 km2), but with high Ho (0.81 ± 0.05), AR (7 ± 0.78), and He (0.71 ± 0.03), despite a signal of recent bottlenecks. In both species, peripherality was not correlated with Ho but was negatively correlated with density. We suggest that the apparent growth of this expanding population of grizzlies offsets the negative impacts of recent bottlenecks on Ho. Indigenous knowledge provides historical context (on the order of centuries, e.g., arctic large mammal fluctuations, grizzly bear bottlenecks) for the current bear population dynamics (on the order of decades, e.g., climate change, northern grizzly bear expansion).

Development of short-target primers for species identification in biological studies of Carnivora.

Noninvasive genetic sampling greatly facilitates studies on the genetics, ecology, and conservation of threatened species. Species identification is often a prerequisite for noninvasive sampling-based biological studies. Due to the low quantity and quality of genomic DNA from noninvasive samples, high-performance short-target PCR primers are necessary for DNA barcoding applications. The order Carnivora is characterized by an elusive habit and threatened status. In this study, we developed three pairs of short-target primers for identifying Carnivora species. The COI279 primer pair was suitable for samples with better DNA quality. The COI157a and COI157b primer pairs performed well for noninvasive samples and reduced the interference of nuclear mitochondrial pseudogenes (numts). COI157a could effectively identify samples from Felidae, Canidae, Viverridae, and Hyaenidae, while COI157b could be applied to samples from Ursidae, Ailuridae, Mustelidae, Procyonidae, and Herpestidae. These short-target primers will facilitate noninvasive biological studies and efforts to conserve Carnivora species.

How to Choose? Comparing Different Methods to Count Wolf Packs in a Protected Area of the Northern Apennines.

Despite a natural rewilding process that caused wolf populations in Europe to increase and expand in the last years, human-wolf conflicts still persist, threatening the long-term wolf presence in both anthropic and natural areas. Conservation management strategies should be carefully designed on updated population data and planned on a wide scale. Unfortunately, reliable ecological data are difficult and expensive to obtain and often hardly comparable through time or among different areas, especially because of different sampling designs. In order to assess the performance of different methods to estimate wolf (Canis lupus L.) abundance and distribution in southern Europe, we simultaneously applied three techniques: wolf howling, camera trapping and non-invasive genetic sampling in a protected area of the northern Apennines. We aimed at counting the minimum number of packs during a single wolf biological year and evaluating the pros and cons for each technique, comparing results obtained from different combinations of these three methods and testing how sampling effort may affect results. We found that packs' identifications could be hardly comparable if methods were separately used with a low sampling effort: wolf howling identified nine, camera trapping 12 and non-invasive genetic sampling eight packs. However, increased sampling efforts produced more consistent and comparable results across all used methods, although results from different sampling designs should be carefully compared. The integration of the three techniques yielded the highest number of detected packs, 13, although with the highest effort and cost. A common standardised sampling strategy should be a priority approach to studying elusive large carnivores, such as the wolf, allowing for the comparison of key population parameters and developing shared and effective conservation management plans.

Individuality matters in human–wildlife conflicts: Patterns and fraction of damage‐making brown bears in the north‐eastern Carpathians

Abstract Effective, evidence‐based management is required to ensure long‐term coexistence between people and wildlife in an increasingly humanized world. Although behavioural individuality is recognized as a key factor affecting evolutionary and ecological processes, it has rarely been explicitly assessed in relation to human–wildlife conflicts. The ‘problem individual’ paradigm states that some conspecifics within a given population have a disproportionately large contribution to conflicts. To the best of our knowledge, no studies have so far systematically tested this assumption in large carnivores. Here, we investigated the variation in conflict behaviour among brown bears Ursus arctos within the population inhabiting the Polish Eastern Carpathians. We inspected all sites notified as damaged by bears in 2014–2017 to determine the number and sex of the individuals involved. We conducted systematic noninvasive genetic sampling to estimate the size of the local population by spatially explicit capture–recapture models. We assessed the fraction and sex ratio of damage‐making bears in relation to the population, as well as the behavioural patterns by classifying and differentiating between occasional and repetitive damage‐makers. Approximately one‐third of the estimated 72 (95% CI 45.2–115.5) brown bears inhabiting the Polish Eastern Carpathians were responsible for damage occurrence in the region. The majority of damage‐makers were female (65% vs. 35% of male), which reflected the sex ratio of the local population (0.57). Thirty‐three per cent of the damage‐making bears (i.e. nine individuals) were classified as ‘problem individuals’, exhibiting repetitive conflict behaviour. Synthesis and applications. This study provides evidence of intraspecific differences in conflict behaviour in a large carnivore species, the brown bear, and indicates that damage‐making behaviour is not exhibited with the same frequency by all individuals within a population. Managers and policy‐makers should be aware that targeting individuals involved in conflicts without reference to the whole population may lead to misleading conclusions or an incomplete picture of the mechanisms underlying the conflicts, and thus, to mismanagement. Unravelling the behavioural patterns of individual engagement in damage through large‐scale and population‐wide studies is needed to accurately assess the magnitude of damage and enhance human–wildlife coexistence in areas experiencing conflicts.

Identification of familial networks reveals sex-specific density dependence in the dispersal and reproductive success of an endangered ungulate

Density is an important demographic parameter that is commonly overlooked in studies of wild populations. Here, we examined the effects of variable spatially explicit density on a range of demographic parameters in a wild population of a cryptic ungulate, boreal woodland caribou (Rangifer tarandus caribou). Using non-invasive genetic sampling, we applied spatial capture–recapture methods with landscape covariates to estimate the density of boreal woodland caribou across a 108,806 km2 study area. We then created a familial network from the reconstructed parent–offspring relationships to determine whether spatial density influenced sex-specific individual reproductive success, female pregnancy status, and dispersal distance. We found that animal density varied greatly in response to land cover types and disturbance; animal density was most influenced by landscape composition and distance to roads varying from 0 in areas with >20% deciduous cover to 270 caribou per 1,000 km2 in areas presenting contiguous older coniferous cover. We found that both male and female reproductive success varied with density, with males showing a higher probability of having offspring in higher-density areas, and the opposite for females. No differences were found in female pregnancy rates occurring in high- and low-density areas. Dispersal distances varied with density, with offspring moving shorter distances when parents were found in higher-density areas. Familial networks showed lower-closeness centrality and lower-degree centrality for females in higher-density areas, indicating that females found in higher-density areas tend to be less broadly associated with animals across the range. Although high-density areas do reflect good-quality caribou habitat, the observed decreased closeness and degree centrality measures, dispersal rates, and lower female recruitment rates suggest that remnant habitat patches across the landscape may create population sinks.

Identification of three Asian otter species (Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata) using a novel noninvasive PCR-RFLP analysis.

Four species of otters occur in tropical Asia, and all face multiple threats to their survival. Studies of distribution and population trends of these otter species in Asia, where they occur sympatrically, are complicated by their elusive nature and difficulties with reliable identification of species in field surveys. In Malaysia, only three species, the smooth-coated otter, Asian small-clawed otter, and hairy-nosed otter have been reliably reported as residents. We designed a replicable and cost-efficient PCR-RFLP protocol to identify these three species. Using published reference sequences of mitochondrial regions, we designed and tested three PCR-RFLP protocols on DNA extracted from reference samples and 33 spraints of wild otters collected along the North Central Selangor Coast of Malaysia. We amplified and sequenced two fragments (450 and 200 bp) of the mt D-loop region and a 300-bp fragment of the mt ND4 gene using primer sets TanaD, TanaD-Mod, and OTR-ND4, respectively. Amplification products were digested with restriction enzymes to generate species-specific RFLP profiles. We analyzed the costs of all three protocols and compared these with the costs of sequencing for species identification. Amplification success was highest for the smallest PCR product, with the TanaD-Mod primer amplifying DNA from all 33 spraints. TanaD and OTR-ND4 primers amplified DNA from 60.6% and 63.6% spraints, respectively. PCR products of TanaD-Mod provided the expected species-specific RFLP profile for 32 (97%) of the spraints. PCR products of OTR-ND4 provided the expected RFLP profile for all 21 samples that amplified, but TanaD produced spurious bands and inconsistent RFLP profiles. The OTR-ND4 primer-enzyme protocol was the least expensive (437 USD) for processing 100 samples, followed by TanaD-Mod (455 USD). We suggest the use of both OTR-ND4 and TanaD-Mod protocols that show potential for highly efficient and reliable species identification from noninvasive genetic sampling of three Asian otter species. We expect our novel noninvasive PCR-RFLP analysis methods to facilitate population monitoring, ecological and behavioral studies on otters in tropical and subtropical Asia.

A flexible and efficient Bayesian implementation of point process models for spatial capture-recapture data.

Spatial capture-recapture (SCR) is now routinely used for estimating abundance and density of wildlife populations. A standard SCR model includes sub-models for the distribution of individual activity centers (ACs) and for individual detections conditional on the locations of these ACs. Both sub-models can be expressed as point processes taking place in continuous space, but there is a lack of accessible and efficient tools to fit such models in a Bayesian paradigm. Here, we describe a set of custom functions and distributions to achieve this. Our work allows for more efficient model fitting with spatial covariates on population density, offers the option to fit SCR models using the semi-complete data likelihood (SCDL) approach instead of data augmentation, and better reflects the spatially continuous detection process in SCR studies that use area searches. In addition, the SCDL approach is more efficient than data augmentation for simple SCR models while losing its advantages for more complicated models that account for spatial variation in either population density or detection. We present the model formulation, test it with simulations, quantify computational efficiency gains, and conclude with a real-life example using non-invasive genetic sampling data for an elusive large carnivore, the wolverine (Gulo gulo) in Norway.

"Guess Who's Coming to Dinner": Molecular Tools to Reconstruct multilocus Genetic Profiles from Wild Canid Consumption Remains.

Simple SummaryWolves and European wildcats are two iconic predator species that can live in overlapping ecological contexts and also share their habitats with their domestic free-ranging relatives, increasing the risk of anthropogenic hybridisation and its possible deleterious consequences. By applying a multidisciplinary approach, we morphologically and molecularly analysed the cat remains found in a canid faecal sample collected in a forested area of central Italy. Individual multilocus genotypes of both predator and prey were identified turning out to be, respectively, a wolf showing traces of dog ancestry at autosomal microsatellite loci and a domestic cat.Non-invasive genetic sampling is a practical tool to monitor pivotal ecological parameters and population dynamic patterns of endangered species. It can be particularly suitable when applied to elusive carnivores such as the Apennine wolf (Canis lupus italicus) and the European wildcat (Felis silvestris silvestris), which can live in overlapping ecological contexts and sometimes share their habitats with their domestic free-ranging relatives, increasing the risk of anthropogenic hybridisation. In this case study, we exploited all the ecological and genetic information contained in a single biological canid faecal sample, collected in a forested area of central Italy, to detect any sign of trophic interactions between wolves and European wildcats or their domestic counterparts. Firstly, the faecal finding was morphologically examined, showing the presence of felid hair and claw fragment remains. Subsequently, total genomic DNA contained in the hair and claw samples was extracted and genotyped, through a multiple-tube approach, at canid and felid diagnostic panels of microsatellite loci. Finally, the obtained individual multilocus genotypes were analysed with reference wild and domestic canid and felid populations to assess their correct taxonomic status using Bayesian clustering procedures. Assignment analyses classified the genotype obtained from the endothelial cells present on the hair sample as a wolf with slight signals of dog ancestry, showing a qi = 0.954 (C.I. 0.780–1.000) to the wolf cluster, and the genotype obtained from the claw as a domestic cat, showing a qi = 0.996 (95% C.I. = 0.982–1.000) to the domestic cat cluster. Our results clearly show how a non-invasive multidisciplinary approach allows the cost-effective identification of both prey and predator genetic profiles and their taxonomic status, contributing to the improvement of our knowledge about feeding habits, predatory dynamics, and anthropogenic hybridisation risk in threatened species.

AGEING AND THE AMOUNT OF DNA EXTRACTED FROM BAWEAN DEER (A xis kuhlii ) FECES

Noninvasive genetic sampling is the most reliable approach to collect endangered species which are typically rare and elusive. However, the approach is hampered by poor quality and quantity of DNA amount, and therefore, a pilot study is required. Our current short communication article reports the first noninvasive genetic sampling approach using feces of critically endangered Bawean deer (Axis kuhlii) to test the effect of aging on the amount of DNA extraction. Fecal samples of the Bawean deer were collected from the Bawean Deer Captive Unit in Sangkapura Village, Bawean Island, East Java. The samples were grouped into two different categories, namely: 1) New samples: for feces that had just been expelled for less than a day and 2) Old samples: for feces that were estimated to have been expelled for more than a day. There were 11 New samples and 16 Old samples. The samples were extracted using the QIAGEN Mini Stool Kit. The DNA quantification was carried out by using a fluorometer. The results of the extraction between the two categories were analyzed by the Kruskal Wallis test. The results showed that the mean rank value of the New samples was better (15.27) than the Old samples (13.13). The P value of the Kruskal Wallis test, however, was higher than the Asymp significant value, indicating that there was no meaningful differences (P = 0.49) between the two samples categories. The work described in this short communication article is a preliminary result and an important step in the study of Bawean deer population genetic.

Noninvasive genetic sampling with a spatial capture‐recapture analysis to estimate abundance of Roosevelt elk

AbstractPrecise abundance estimates of large mammals are important for effective conservation, harvest, and conflict management. Determining abundance of wide‐ranging, herding ungulate species has presented a unique challenge to wildlife managers because of factors such as dense forest, elusive behavior, and heterogeneity in density across the landscape. Roosevelt elk (Cervus canadensis roosevelti) populations in Northern California, USA, are no exception to these challenges, and as the elk population has grown, so has human–wildlife conflict, necessitating the need for efficient and repeatable methods to determine population abundance for management decisions. We explored non‐invasive genetic sampling combined with spatial capture‐recapture (SCR) as an alternative for monitoring populations that are difficult to observe directly. We combined an SCR model with a binomial point process and an unstructured single survey search method to estimate elk abundance in Northern California via Bayesian inference. We searched open grassy hillsides for female‐calf groups and used a detection dog team to search forested areas to increase the number of detections of males and other solitary individuals. For the SCR analysis, we used sex and survey effort as detection covariates, and used a trap‐level random effect to account for overdispersion in the count data from the herding behavior of elk. Our population estimate (N ± SD) for the study area was 618 ± 36.34 individuals (95% Bayesian credible interval = 551–693) with a mean density of 1.09 ± 0.06 elk/km2. Our work demonstrates a potential method to estimate population size of ungulates in an area that is not conducive to traditional monitoring methods.

A genotyping-in-thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples.

Studies in ecology, evolution, and conservation often rely on noninvasive samples, making it challenging to generate large amounts of high‐quality genetic data for many elusive and at‐risk species. We developed and optimized a Genotyping‐in‐Thousands by sequencing (GT‐seq) panel using noninvasive samples to inform the management of invasive Sitka black‐tailed deer (Odocoileus hemionus sitkensis) in Haida Gwaii (Canada). We validated our panel using paired high‐quality tissue and noninvasive fecal and hair samples to simultaneously distinguish individuals, identify sex, and reconstruct kinship among deer sampled across the archipelago, then provided a proof‐of‐concept application using field‐collected feces on SGang Gwaay, an island of high ecological and cultural value. Genotyping success across 244 loci was high (90.3%) and comparable to that of high‐quality tissue samples genotyped using restriction‐site associated DNA sequencing (92.4%), while genotyping discordance between paired high‐quality tissue and noninvasive samples was low (0.50%). The panel will be used to inform future invasive species operations in Haida Gwaii by providing individual and population information to inform management. More broadly, our GT‐seq workflow that includes quality control analyses for targeted SNP selection and a modified protocol may be of wider utility for other studies and systems where noninvasive genetic sampling is employed.

Wolf Dispersal Patterns in the Italian Alps and Implications for Wildlife Diseases Spreading.

Simple SummaryWildlife dispersal directly influences population expansion patterns, and may have indirect effects on the spread of wildlife diseases. For many species, little is known about dispersal, despite its importance to conservation. We documented the natural dispersal processes of an expanding wolf (Canis lupus) population in the Italian Alps to understand the dynamics of the recolonization pattern and identify diseases that might be connected with the process through the use of non-invasive genetic sampling over a 20-year period. By documenting 55 dispersal events, with an average minimum straight dispersal distance of 65.8 km (±67.7 km), from 7.7 km to 517.2 km, we discussed the potential implications for maintaining genetic diversity of the population and for wildlife diseases spreading.Wildlife dispersal directly influences population expansion patterns, and may have indirect effects on the spread of wildlife diseases. Despite its importance to conservation, little is known about dispersal for several species. Dispersal processes in expanding wolf (Canis lupus) populations in Europe is not well documented. Documenting the natural dispersal pattern of the expanding wolf population in the Alps might help understanding the overall population dynamics and identifying diseases that might be connected with the process. We documented 55 natural dispersal events of the expanding Italian wolf alpine population over a 20-year period through the use of non-invasive genetic sampling. We examined a 16-locus microsatellite DNA dataset of 2857 wolf samples mainly collected in the Western Alps. From this, we identified 915 individuals, recaptured 387 (42.3%) of individuals, documenting 55 dispersal events. On average, the minimum straight dispersal distance was 65.8 km (±67.7 km), from 7.7 km to 517.2 km. We discussed the potential implications for maintaining genetic diversity of the population and for wildlife diseases spreading.

Identifying individual ungulates from fecal DNA: a comparison of field collection methods to maximize efficiency, ease, and success

Non-invasive genetic sampling can facilitate the identification of individual animals across a landscape, with applications to management and conservation. Fecal material is a readily available source of DNA, and various methods exist for collecting fecal samples for DNA preservation. In particular, swab methods offer considerable promise, but their utility in real-world field contexts remains relatively untested. We systematically compared multiple genetic fecal sampling methods across all stages of data collection and analysis, including sampling in the field, DNA extraction in the lab, and identification of individuals using microsatellite genotyping. We collected 112 fecal samples from black-tailed deer (Odocoileus hemionus columbianus) in the field in Mendocino County, California, across a range of sample conditions of unknown age. We systematically compared the efficiency, ease, and genotyping success of three methods for field collection and storage of ungulate fecal samples: whole pellets in ethanol, whole dry pellets in paper envelopes, and cotton swabs in buffer. Storage method, sample condition, and their interaction predicted genotyping success in the top binomial GLMMs. We found that swabbing pellets resulted in the greatest percentage of individually identifiable genotypes (81%, compared to 60% for dry samples and 56% for ethanol), despite lower DNA concentrations. While swabbing pellets requires a greater time investment in the field, the samples are easier and safer to store and transport, and subsequent labwork is more efficient as compared to whole-pellet collection methods. We, therefore, recommend the swab method for most contexts. We provide additional recommendations and field protocols based on subsequent collection of 2284 swab samples for a larger monitoring study of the deer population, given that this large number of samples spanned a range of sample conditions and time spent in storage.