Combining genetic non-invasive sampling with spatially explicit capture-recapture models for density estimation of a patchily distributed small mammal

From species detection to population size indexing: the use of sign surveys for monitoring a rare and otherwise elusive small mammal

Monitoring the occupancy and abundance of wildlife populations is key to evaluate their conservation status and trends. However, estimating these parameters often involves time and resource-intensive techniques, which are logistically challenging or even unfeasible for rare and elusive species that occur patchily and in small numbers. Hence, surveys based on field identification of signs (e.g. faeces, footprints) have long been considered a cost-effective alternative in wildlife monitoring, provided they produce reliable detectability and meaningful indices of population abundance. We tested the use of sign surveys for monitoring rare and otherwise elusive small mammals, focusing on the Cabrera vole (Microtus cabrerae) in Portugal. We asked how sampling intensity affects true positive detection of the species, and whether sign abundance is related to population size. We surveyed Cabrera voles’ latrines in 20 habitat patches known to be occupied, and estimated ‘true’ population size at each patch using DNA-based capture-recapture techniques. We found that a searching rate of ca. 3 min/250m2 of habitat based on adaptive guided transects was sufficient to provide true positive detection probabilities > 0.85. Sign-based abundance indices were at best moderately correlated with estimates of ‘true’ population size, and even so only for searching rates > 12 min/250m2. Our study suggests that surveys based on field identification of signs should provide a reliable option to estimate occupancy of Cabrera voles, and possibly for other rare or elusive small mammals, but cautions should be exercised when using this approach to infer population size. In case of practical constraints to the use of more accurate methods, a considerable sampling intensity is needed to reliably index Cabrera voles’ abundance from sign surveys.

A novel noninvasive genetic survey technique for small mammals

Noninvasive genetic surveys, often conducted by collecting fecal samples, have become a popular tool for surveying wildlife, but have primarily been applied to species with large and conspicuous scat. Although many small mammals are threatened, endangered, or data deficient, noninvasive genetic surveys have rarely been applied due to the challenges of detecting their inconspicuous fecal pellets. As part of a broader study of the endangered salt marsh harvest mouse (Reithrodontomys raviventris), we developed a noninvasive genetic survey technique for the community of small mammals in their putative range. We designed bait stations to passively collect fecal samples from rodents, and developed a multiplex primer set that amplified unique fragment sizes for salt marsh harvest mice and four other sympatric species. We tested the primer set on positive controls and on fecal pellets collected from bait stations at two regularly monitored field sites known to have very different densities of salt marsh harvest mice. The multiplex amplified DNA from all five species, even when all five species were present in a single sample. A positive species identification was made for all field-collected samples, and 43% of these field-collected samples had multispecies detections. The combination of bait stations and genetic species identification proved to be an effective means of noninvasively surveying small mammals in potential salt marsh harvest mouse habitat. The sampling technique should be applicable to a wide variety of small mammals in other systems.

Non-invasive monitoring and reintroduction biology of the brush-tailed rock-wallaby (

Thirty-nine endangered brush-tailed rock-wallabies (Petrogale penicillata) were reintroduced to Grampians National Park, western Victoria, between 2008 and 2012. Subsequent high mortality, low breeding, and no recruitment were linked to fox predation and physical disturbance during monitoring. From 2014 to 2017, the colony was left undisturbed and monitored only by remote camera. Five adult animals were identified across this period (1 ♂ and 3 ♀s – all tagged; and one untagged female), and an average of 0.7 pouch young were birthed per tagged female per year. In 2019, camera-monitoring and non-invasive genetic monitoring (faecal) were used to identify colony members, genetic diversity, and breeding. Camera monitoring in 2019 identified the same five individuals, whereas genetic monitoring using 12 microsatellites identified eight individuals (two male and six female genotypes). Genetic diversity within the colony was moderate (expected heterozygosity (He) = 0.655, observed heterozygosity (Ho) = 0.854). Leaving the colony undisturbed after 2013 correlated with improved adult survival, increased breeding, and successful recruitment of young to the population. Recommendations for the Grampians colony include continuation of regular camera- and scat monitoring to improve our understanding of the reintroduction biology of P. penicillata and other marsupials in open, unfenced landscapes.

Novel microsatellites and investigation of faecal DNA as a non-invasive population monitoring tool for the banded hare-wallaby (

Monitoring programs for populations of small or medium-sized animals often use live-capture or photo-monitoring trapping methods to estimate population size. The banded hare-wallaby (Lagostrophus fasciatus), a small macropodiform marsupial, does not readily enter traps or have individually unique distinguishing physical features and is consequently difficult to monitor using these methods. Isolating DNA from faecal material to obtain individual genotypes is a promising monitoring technique and may present an alternative approach for this species. We developed novel species-specific microsatellite markers and undertook trials to assess faecal DNA degradation in ambient environmental conditions at two locations where this species has been translocated. The quality of DNA yielded from faecal pellets was evaluated through amplification failure and genotyping error rates of microsatellite markers. Error rates were compared for different treatments and exposure duration across multiple individuals. DNA was successfully obtained from all samples and error rates increased with exposure duration, peaking after 14–30 days depending on the site and treatment. The level of solar exposure was the most significant factor affecting degradation rate but both this and exposure duration had significant effects on amplification failure. Analysing DNA obtained from faecal pellets may represent a practical non-invasive method of deriving population estimates for this species and warrants further development.

Landscape Characteristics Affecting Small Mammal Occurrence in Heterogeneous Olive Grove Agro-Ecosystems

Understanding how small mammals (SM) are associated with environmental characteristics in olive groves is important to identify potential threats to agriculture and assess the overall conservation value and functioning of agro-ecosystems. Here, we provide first insights on this topic applied to traditional olive groves in northeast (NE) Portugal by assessing the landscape attributes that determine SM occurrence, focusing on one species of conservation concern (Microtus cabrerae Thomas 1906) and one species often perceived as a potential pest of olives (Microtus lusitanicus Gerbe 1879). Based on SM genetic non-invasive sampling in 51 olive groves and surrounding habitats, we identified seven rodent species and one insectivore. Occupancy modelling indicated that SM were generally less detected within olive groves than in surrounding habitats. The vulnerable M. cabrerae reached a mean occupancy (95% CI) of 0.77 (0.61–0.87), while M. lusitanicus stood at 0.37 (0.24–0.52). M. cabrerae was more likely to occur in land mosaics with high density of agricultural field edges, while M. lusitanicus was more associated with high density of pastureland patches. Overall, our study suggests that the complex structure and spatial heterogeneity of traditionally managed olive grove agro-ecosystems may favor the occurrence of species-rich SM communities, possibly including well-established populations of species of conservation importance, while keeping potential pest species at relatively low occupancy rates.

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.

Noninvasive Genetic Assessment Is an Effective Wildlife Research Tool When Compared with Other Approaches

Wildlife research has been indispensable for increasing our insight into ecosystem functioning as well as for designing effective conservation measures under the currently high rates of biodiversity loss. Genetic and genomic analyses might be able to yield the same information on, e.g., population size, health, or diet composition as other wildlife research methods, and even provide additional data that would not be possible to obtain by alternative means. Moreover, if DNA is collected non-invasively, this technique has only minimal or no impact on animal welfare. Nevertheless, the implementation rate of noninvasive genetic assessment in wildlife studies has been rather low. This might be caused by the perceived inefficiency of DNA material obtained non-invasively in comparison with DNA obtained from blood or tissues, or poorer performance in comparison with other approaches used in wildlife research. Therefore, the aim of this review was to evaluate the performance of noninvasive genetic assessment in comparison with other methods across different types of wildlife studies. Through a search of three scientific databases, 113 relevant studies were identified, published between the years 1997 and 2020. Overall, most of the studies (94%) reported equivalent or superior performance of noninvasive genetic assessment when compared with either invasive genetic sampling or another research method. It might be also cheaper and more time-efficient than other techniques. In conclusion, noninvasive genetic assessment is a highly effective research approach, whose efficacy and performance are likely to improve even further in the future with the development of optimized protocols.

Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity

The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.