A method for noninvasive individual genotyping of black-footed cat (Felis nigripes)

The black-footed cat (Felis nigripes) is endemic to the arid regions of southern Africa. One of the world's smallest wild felids, the species occurs at low densities and is secretive and elusive, which makes ecological studies difficult. Genetic data could provide key information such as estimates on population size, sex ratios, and genetic diversity. In this study, we test if microsatellite loci can be successfully amplified from scat samples that could be noninvasively collected from the field. Using 21 blood and scat samples collected from the same individuals, we statistically tested whether nine microsatellites previously designed for use in domestic cats can be used to identify individual black-footed cats. Genotypes recovered from blood and scat samples were compared to assess loss of heterozygosity, allele dropout, and false alleles resulting from DNA degradation or PCR inhibitors present in scat samples. The microsatellite markers were also used to identify individuals from scats collected in the field that were not linked to any blood samples. All nine microsatellites used in this study were amplified successfully and were polymorphic. Microsatellite loci were found to have sufficient discriminatory power to distinguish individuals and identify clones. In conclusion, these molecular markers can be used to monitor populations of wild black-footed cats noninvasively. The genetic data will be able to contribute important information that may be used to guide future conservation initiatives.

National eDNA-based monitoring of Batrachochytrium dendrobatidis and amphibian species in Norway

Freshwaters represent the most threatened environments with regard to biodiversity loss and, therefore, there is a need for national monitoring programs to effectively document species distribution and evaluate potential risks for vulnerable species. The monitoring of species for effective management practices is, however, challenged by insufficient data acquisition when using traditional methods. Here we present the application of environmental DNA (eDNA) metabarcoding of amphibians in combination with quantitative PCR (qPCR) assays for an invasive pathogenic chytrid species (Batrachochytrium dendrobatidis -Bd), a potential threat to endemic and endangered amphibian species. Statistical comparison of amphibian species detection using either traditional or eDNA-based approaches showed weak correspondence. By tracking the distribution of Bd over three years, we concluded that the risk for amphibian extinction is low since Bd was only detected at five sites where multiple amphibians were present over the sampled years. Our results show that eDNA-based detection can be used for simultaneous monitoring of amphibian diversity and the presence of amphibian pathogens at the national level in order to assess potential species extinction risks and establish effective management practices. As such our study represents suggestions for a national monitoring program based on eDNA.

The dispersion and detection patterns of mtDNA-assigned red fox Vulpes vulpes scats in Tasmania are anomalous

Models used for resource allocation in eradication programmes must be based on replicated data of known quality and have proven predictive accuracy, or they may provide a false indication of species presence and/or distribution. In the absence of data corroborating the presence of extant foxes Vulpes vulpes in Tasmania, a habitat-specific model based upon mtDNA data (Sarre et al. 2012. Journal Applied Ecology, 50, 459-468) implied that foxes were widespread. Overall, 61 of 9940 (0·6%) surveyed scats were assigned as mtDNA fox positive by the fox eradication programme (FEP). We investigated the spatiotemporal distribution of the 61 mtDNA-assigned fox scats and modelled the probability of replicating scat detection in independent surveys using detection dogs based upon empirically derived probabilities of scat detection success obtained by the FEP using imported fox scats. In a prior mainland study, fox genotypes were recurrently detected in a consecutive four-day pool of scats. In Tasmania, only three contemporaneously collected scat pairs of unknown genotype were detected by the FEP within an area corresponding to a conservatively large mainland fox home range (639 ha) in a decade. Nearest neighbour pairs were widely spaced (mean = 7·0 km; circular area = 153 km2) and generated after a mean of 281 days. The majority of assigned mtDNA positive scats were found in urban and peri-urban environments corresponding to small mainland fox home ranges (30-45 ha) that imply higher scat density and more certain replication. Using the lowest empirically determined scat detection success for dogs, the failure to replicate fox scat detection on 34 of 36 occasions in a large (639 ha) home range is highly improbable (P = 0·00001) and suggestive of Type I error. Synthesis and applications. Type I error, which may have various sources, should be considered when scat mtDNA data are few, accumulated over many years, uncorroborated by observations of extant specimens, inadequately replicated in independent surveys within an expected spatiotemporal scale and reported in geographically isolated environments unlikely to have been colonized.

Lessons from long-term predator control: a case study with the red fox

Context Predator-control aims to reduce an impact on prey species, but efficacy of long-term control is rarely assessed and the reductions achieved are rarely quantified. Aims We evaluated the changing efficacy of a 58-year-long campaign against red foxes (Vulpes vulpes) on Phillip Island, a 100-km2 inhabited island connected to the Australian mainland via a bridge. The campaign aimed to eliminate the impact of foxes on ground-nesting birds, particularly little penguins (Eudyptula minor). Methods We monitored the success rate of each fox-control technique employed, the level of effort invested if available, demographics of killed foxes, the numbers of penguins killed by foxes and penguin population size. Key results The campaign began as a bounty system that ran for 30 years and was ineffective. It transitioned into a coordinated, although localised, control program from 1980 to 2005 that invested considerable effort, but relied on subjective assessments of success. Early during the control period, baiting was abandoned for less effective methods that were thought to pose fewer risks, were more enjoyable and produced carcasses, a tangible result. Control was aided by a high level of public awareness, by restricted fox immigration, and by a clear, achievable and measurable target, namely, to prevent little penguin predation by foxes. Carcasses did prove valuable for research, revealing the genetic structure and shifts in fox demographics. The failure of the program was evident after scientific evaluation of fox population size and ongoing fox impacts. In 2006, the campaign evolved into an eradication attempt, adopting regular island-wide baiting, and since then, has achieved effective knock-down of foxes and negligible predation on penguins. Conclusions Effective predator control was achieved only after employing a dedicated team and implementing broad-scale baiting. Abandoning widespread baiting potentially delayed effective control for 25 years. Furthermore, both predator and prey populations should be monitored concurrently because the relationship between predator abundance and impact on prey species is not necessarily density dependent. Implications Critical to adopting the best management strategy is evaluating the efficacy of different methods independently of personal and public biases and having personnel dedicated solely to the task.

Slow recruitment in a red-fox population following poison baiting: a non-invasive mark–recapture analysis

Context Optimal management of invasive species should determine the interval between lethal-control operations that will sustain a desired population suppression at minimum cost. This requires an understanding of the species’ rate of recruitment following control. These data are difficult to acquire for vertebrate carnivores such as the red fox (Vulpes vulpes), which are not readily trapped or observed. Aims To provide a long-term evaluation of the effects of 1080 poison baiting on the abundance and extent of movement of red foxes in a semiarid environment. Methods We used non‐invasive DNA sampling of fox hairs in semi-arid Western Australia where the population was subject to two episodes of aerially delivered sodium fluoroacetate (1080) poison baits within 12 months. Sampling took place at ~45-day intervals and individual foxes were identified by genotyping eight microsatellite DNA markers and a gender-specific marker. Open-population and spatially explicit mark–recapture models were used to estimate the density, apparent survival and movements of foxes before and following baiting. Key results Following a severe reduction in density after baiting, fox density during the ensuing 12 months increased slowly (0.01 foxes km–2 month–1), such that density had only reached 22% of pre-baiting levels ~10 months after the initial baiting. Moreover, recovery was non‐linear as population growth was negligible for 6 months, then exhibited a nine-fold increase 7–9 months after control, coincident with the dispersal of juveniles in autumn. Fox movements between recaptures were on average 470% greater after baiting than before, in line with expectations for low-density populations, suggesting that the probability of encountering baits during this period would be higher than before baiting. Conclusions Baiting with 1080 poison significantly reduced the density of foxes, and the low density was sustained for more than 6 months. Foxes moved significantly further between recaptures after baiting when at low densities. Implications Control programs in this region may be carried out at low frequency to suppress fox density to a fraction of unbaited levels. The intensity of follow-up baiting may also be adjusted downwards, to take account of an increased probability of bait encounter in more mobile foxes.

The impact of fox control on the relative abundance of forest mammals in East Gippsland, Victoria

Predation by European red foxes is believed to be the major cause of the extinction and decline of a large number of native medium-sized terrestrial mammals in Australia. We examined the impact of poisoning of foxes on the relative abundance of a group of medium-sized mammals in an experiment conducted in three large forest blocks in south-eastern Australia. The blocks consisted of paired sites, as follows: one site where poison baiting was used to control foxes (treatment site) and one where foxes were not controlled (non-treatment site). At all six sites, the population responses of a range of mammals were measured, and compared between treatment and non-treatment sites. The relative fox abundance, as indexed by bait-take, declined during the course of the study at treatment sites and to a lesser extent at non-treatment sites. The decline in bait-take at non-treatment sites was most likely due to treatment sites acting as ecological traps, so that reduced intra-specific competition attracted foxes from non-treatment to treatment sites, where they were subsequently poisoned. There was a significant treatment effect for the abundances of total mammals, long-nosed potoroos, southern brown bandicoots and common brushtail possums, with higher abundances at treatment sites than at non-treatment sites. Common ringtail possums increased in abundance during the course of the study, with no significant difference between treatment and non-treatment sites. There was no significant effect of time or treatment on the abundance of long-nosed bandicoots. The increase in the abundance of native mammals at treatment sites was most likely due to a lower predation pressure by foxes brought about by fox control, and the smaller increase in abundance in non-treatment blocks was likely due to the ecological-trap effect because of fox baiting at treatment sites. The present study demonstrated that broad-scale fox control can lead to increases in the abundance of native mammals in forested habitats, without recourse to aerial baiting or fences. The study also demonstrated that the influence of fox control on the fox abundance can extend well beyond the perimeter of the area baited.

Comparison of methods to detect rare and cryptic species: a case study using the red fox (Vulpes vulpes)

Choosing the appropriate method to detect and monitor wildlife species is difficult if the species is rare or cryptic in appearance or behaviour. We evaluated the effectiveness of the following four methods for detecting red foxes (Vulpes vulpes) on the basis of equivalent person hours in a rural landscape in temperate Australia: camera traps, hair traps (using morphology and DNA from hair follicles), scats from bait stations (using DNA derived from the scats) and spotlighting. We also evaluated whether individual foxes could be identified using remote collection of their tissues. Genetic analysis of hair samples was the least efficient method of detection among the methods employed because of the paucity of samples obtained and the lack of follicles on sampled hairs. Scat detection was somewhat more efficient. Scats were deposited at 17% of bait stations and 80% of scats were amplified with a fox-specific marker, although only 31% of confirmed fox scats could be fully genotyped at all six microsatellite loci. Camera trapping and spotlighting were the most efficient methods of detecting fox presence in the landscape. Spotlighting success varied seasonally, with fox detections peaking in autumn (80% of spotlighting transects) and being lowest in winter (29% of transects). Cameras detected foxes at 51% of stations; however, there was limited seasonality in detection, and success rates varied with camera design. Log-linear models confirmed these trends. Our results showed that the appropriate technique for detecting foxes varies depending on the time of the year. It is suggested that wildlife managers should consider both seasonal effects and species biology when attempting to detect rare or elusive species.

DNA genotypes reveal red fox (Vulpes vulpes) abundance, response to lethal control and limitations of contemporary survey techniques

Context. Scat genotyping has not been routinely used to measure fox (Vulpes vulpes) abundance and our study sought to provide a benchmark for further technique development and assessment of field methods. Aims. This study sought to provide a comparative assessment of some common methods used to determine fox density and contrast their success with scat DNA genotyping. Methods. DNA recovered from fox scats was used to genotype individual red foxes and determine their abundance at four transects. Population indices were also developed from bait take, scat counts and sand plot tracks using index-manipulation-index (IMI) procedures on the same transects. Known samples of foxes were taken from two treatment transects using cyanide delivered in the M-44 ejector to manipulate the population and to recover foxes at the end of the trial. Key results. Replicated counts on a 41-km-spotlight transect at the field site before and after the population manipulation had low variance and good correlation (r2 = 0.79, P < 0.01). Scat genotypes revealed 54 foxes in eight days and, when combined with biopsy DNA from recovered foxes, a minimum known to be alive (KTBA) density of between 1.6 and 5 foxes km–1 was calculated for the transects. Overall, 15/30 (50%) of all recovered foxes had not been detected by scat genotyping, 23/53 (49%) of KTBA genotypes were detected only once and 5/54 (9.5%) of foxes were found to have moved between two transects. Conclusions. At transects where population manipulation occurred, surviving individuals contributed significantly more scats than at the control transects and some individuals were detected at bait stations at a much greater frequency. This strongly suggested that they had contributed disproportionately to some IMI density estimates that were probably influenced by a change in the activity of some individuals rather than changes in population density alone. At one transect, eight foxes were confirmed to be present by spotlight surveys and were detected by scat and KTBA genotypes, yet were undetected by scat, bait station and sand plot indices. Implications. Scat and other DNA-based survey techniques provide a great deal of information about the identification and movement of individuals and if DNA sampling methods can be made more efficient they have the potential to provide accurate abundance estimates that are independent of the control technique.