Estimating population size of endangered brush-tailed rock-wallaby (Petrogale penicillata) colonies using faecal DNA

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.

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.

Informing the space between zero and one: a standardised, scat-based approach to monitoring changes in habitat use by brush-tailed rock-wallabies (Petrogale penicillata)

Rock-wallabies occupy outcrops, escarpments and cliffs that incorporate structurally complex refuges; because of this, local populations present methodological challenges for monitoring purposes. We describe the development and adaptive modification of a survey technique intended to measure changes in rock-wallaby activity on a site-by-site basis. Twenty spatially independent field sites were collectively sampled across two geological strata using transects consisting of regularly spaced sampling points, with concentric series of fixed-radius circular plots at each sampling point used to count numbers of fresh/recent and/or older rock-wallaby scats. The presence/absence of fresh and/or recently deposited scats was identified as likely to be the more sensitive measure of changing use. Indexes of Activity (IoA) at each field site were subsequently obtained by transect-based sampling at 10 m intervals using 2 m fixed-radius circular plots and recording the presence/absence of fresh/recent scats therein. Derived rock-wallaby IoA ranged between 0.13 and 0.94 across the 20 sites and were approximately normally distributed. Central tendency measures associated with the IoA metrics imply some potential to develop management-themed activity thresholds. Further refinement and potential applications of the approach are discussed.

Sign surveys can be more efficient and cost effective than driven transects and camera trapping: a comparison of detection methods for a small elusive mammal, the numbat (Myrmecobius fasciatus)

Abstract ContextDetermining the most efficient detection method for a target species is key for successful wildlife monitoring and management. Driven transects and sign surveys are commonly used to monitor populations of the endangered numbat (Myrmecobius fasciatus). Camera trapping is being explored as a new method. These methods were unevaluated for efficacy and cost for numbat detection. AimsTo compare efficacy and costing of driven transects, sign surveys and camera trapping for detecting numbats in the Upper Warren region, Western Australia. MethodsSeven repeat sign surveys and driven transects, as well as 4 months of camera trapping, were conducted concurrently at 50 sites along three transects. Numbat detection rates and costing of the three techniques were compared, and detection probabilities were compared between sign surveys and camera trapping. Key resultsNumbat signs were detected during 88 surveys at 39 sites, exceeding camera trapping (26 detections at 13 sites) and driven transects (seven detections near five sites). The estimated probability for detecting a numbat or a sign thereof (at a site where numbats were present) ranged from 0.21 to 0.35 for a sign survey, and 0.02 to 0.06 for 7 days of camera trapping. Total survey costs were lowest for driven transects, followed by camera trapping and sign surveys. When expressed as cost per numbat detection, sign surveys were cheapest. ConclusionsComparative studies of survey methods are essential for optimal, cost-effective wildlife monitoring. Sign surveys were more successful and cost effective than camera trapping or driven transects for detecting numbats in the Upper Warren region. Together with occupancy modelling, sign surveys are appropriate to investigate changes in occupancy rates over time, which could serve as a metric for long-term numbat monitoring. ImplicationsThere is no ‘best’ method for wildlife surveys. Case-specific comparison of animal detection methods is recommended to ensure optimal methods. For the numbat population in the Upper Warren region, further studies are needed to improve numbat detection rates from camera trapping, and to test sign surveys in autumn (March to May), when surviving juvenile numbats have established their own territory and assumptions regarding population closure are less likely to be violated.

Assessment of Male Reproductive Skew via Highly Polymorphic STR Markers in Wild Vervet Monkeys, Chlorocebus pygerythrus

Male reproductive strategies have been well studied in primate species where the ability of males to monopolize reproductive access is high. Less is known about species where males cannot monopolize mating access. Vervet monkeys (Chlorocebus pygerythrus) are interesting in this regard as female codominance reduces the potential for male monopolization. Under this condition, we assessed whether male dominance rank still influences male mating and reproductive success, by assigning paternities to infants in a population of wild vervets in the Eastern Cape, South Africa. To determine paternity, we established microsatellite markers from noninvasive fecal samples via cross-species amplification. In addition, we evaluated male mating and reproductive success for 3 groups over 4 mating seasons. We identified 21 highly polymorphic microsatellites (number of alleles = 7.5 ± 3.1 [mean ± SD], observed heterozygosity = 0.691 ± 0.138 [mean ± SD]) and assigned paternity to 94 of 97 sampled infants (96.9%) with high confidence. Matings pooled over 4 seasons were significantly skewed across 3 groups, although skew indices were low (B index = 0.023-0.030) and mating success did not correlate with male dominance. Paternities pooled over 4 seasons were not consistently significantly skewed (B index = 0.005-0.062), with high-ranking males siring more offspring than subordinates only in some seasons. We detected 6 cases of extra-group paternity (6.4%) and 4 cases of natal breeding (4.3%). Our results suggest that alternative reproductive strategies besides priority of access for dominant males are likely to affect paternity success, warranting further investigation into the determinants of paternity among species with limited male monopolization potential.

Genetic affinities of a remnant population of the brush-tailed rock-wallaby (Petrogale penicillata) in Mt Kaputar National Park, northern New South Wales

The brush-tailed rock-wallaby (Petrogale penicillata) is now extinct west of the Great Dividing Range, apart from remnant populations in the Warrumbungles and at Mt Kaputar. Previous genetic analysis has identified deep genetic subdivisions within P. penicillata, but samples from Mt Kaputar were not included. Mitochondrial DNA sequences obtained from Mt Kaputar and the Warrumbungles clustered within the Central ESU, extending its distribution north of the Hunter River onto the north-western slopes adjacent to populations of the Northern ESU. These highly threatened western populations are the only P. penicillata persisting in semiarid conditions. This makes them of particular value to the long-term survival of the species and their conservation should be a priority.

Population monitoring of small and declining brush-tailed rock wallaby (Petrogale penicillata) colonies at the extreme of their range using faecal DNA sampling

Obtaining much-needed information on population parameters such as abundance and genetic diversity can be difficult for small and declining populations. The brush-tailed rock-wallaby (Petrogale penicillata) is an endangered and cryptic species with many colonies in decline. The Warrumbungle National Park (NP) in New South Wales contains a declining metapopulation of P. penicillata at the western (inland) extreme of the species’ current range. Loss of these colonies would cause substantial range contraction and probable loss of regional genetic diversity in the Central Evolutionary Significance Unit (ESU). We used non-invasive genetic methods to identify individuals from faecal DNA from five colonies in the Warrumbungle NP. We identified a minimum of 21 individuals, with the largest colony containing seven individuals. The Warrumbungle NP colonies showed significant intercolony structuring and we were able to detect a single dispersal event. Comparison of genetic diversity to other Central ESU colonies shows that loss of the Warrumbungle NP population will result in loss of unique diversity from this region. The minimum number of animals and genetic diversity information obtained in this study was used to support management actions of herbivore control and translocation in the Warrumbungle NP population.

Breaking down scats: degradation of DNA from greater bilby (Macrotis lagotis) faecal pellets

Isolating DNA from scats (faeces) of threatened species is a valuable, non-invasive method for identifying individuals. To establish whether genotyping of greater bilby (Macrotis lagotis) individuals from faecal pellets collected in the field can be useful for population monitoring, an understanding of the DNA degradation rates is necessary. To determine the relationship between time and degradation of bilby faecal DNA, and assess whether a two-step elution process during extraction results in better-quality DNA, faecal pellets were collected from captive individuals, maintained under seminatural conditions, then harvested at known periods. DNA was amplified from faecal pellets with a 99% success rate and error rates of less than 5% up to 14 days after deposition. The amplification rate decreases, and the rate of allelic dropout increases with time, but DNA can still be amplified at rates above 60% and error rates below 15% at 90–180 days. We found that a second elution step was unnecessary, with more DNA amplified over a longer period using the first eluate. Viable DNA exists on bilby faecal pellets for a long period after deposition, which is useful for obtaining genetic samples for population monitoring programs and studies on population genetics.

Effects of natural environmental conditions on faecal glucocorticoid metabolite concentrations in jaguars (Panthera onca) in Belize

In situ studies that rely on non-invasive faecal hormone monitoring are subject to problems due to potential changes in hormone concentrations in samples exposed to field conditions. In this study, we conducted an environmental validation for measurement of faecal glucocorticoid metabolites (FGMs) in jaguars (Panthera onca). We collected fresh faeces (e.g. no older than 8 h) from jaguars (six males and four females), housed at the Belize Zoo, and exposed them randomly to two environmental conditions: shade and sun. A control (first sub-sample) was immediately frozen, after which sub-samples were frozen daily over a 5 day period in both the dry and wet seasons. We quantified FGMs using a cortisol enzyme immunoassay (EIA) and a corticosterone radioimmunoassay (RIA), both capable of identifying relevant metabolites. Results indicated that FGMs assessed with the cortisol EIA were stable for 5 days during the dry season but for <1 day during the wet season, while FGMs assessed with the corticosterone RIA were stable for 5 days during both the dry and wet seasons. Exposure of jaguar faeces to sun or shade had no effect on FGM concentrations, despite significant differences in weather parameters. Analysis of faecal morphology proved unreliable in identifying faecal age. We conclude that the corticosterone RIA is suitable for assessing FGMs in free-ranging Belizean jaguars by surveying the same transects every 3-4 days in both seasons. The cortisol EIA can be used during the dry season, but there are possible shifts in metabolite immunoactivity in wet conditions. Assessment of adrenal activity in jaguars ranging areas of varying human disturbance is a timely application of this methodology in Belize.

Estimating brush-tailed rock-wallaby population size using individual animal recognition

We undertook surveys of brush-tailed rock-wallabies (Petrogale penicillata) at four colonies in Oxley Wild Rivers National Park, north-eastern New South Wales, with the aim of developing a technique based upon individual animal recognition that could be used to obtain robust population estimates for rock-wallaby colonies. We identified individuals on the basis of distinct morphological characters in each colony using visual observations, and used the data within a ‘mark–recapture’ (or sight–resight) framework to estimate population size. More than 37 h of observations were made over 10 sampling days between 18 May and 9 June 2010. We could identify 91.7% of all rock-wallabies that were independently sighted (143 of 156 sightings of 35 animals). A small percentage of animals could not be identified during a visit because they were seen only fleetingly, were in dense cover, or were partly obscured by rock. The number of new animals sighted and photographed declined sharply at the midpoint of the survey, and there was a corresponding increase in resighting of known individuals. Population estimates using the mark–recapture methodology were nearly identical to estimates of total animals seen, suggesting that this method was successful in obtaining a complete census of rock-wallabies in each colony.

Status of warru (Petrogale lateralis MacDonnell Ranges race) in the Anangu Pitjantjatjara Yankunytjatjara Lands of South Australia. 2. Population dynamics

The population dynamics of warru (Petrogale lateralis MacDonnell Ranges race) were studied in the Anangu Pitjantjatjara Yankunytjatjara Lands, South Australia, in order to inform management and better understand the race’s conservation ecology. Mark–recapture between 2005 and 2010 at the three largest known remaining colonies, followed by POPAN modelling, indicated that population sizes were 23 at New Well and 24 at Alalka in the Musgrave Ranges, and 14 at Kalka in the Tomkinson Ranges. Taking into account recent survey results, the study confirmed that warru are ‘Endangered’ in South Australia. However, there is potential for the recovery of the race, with high average reproductive rates (in the Musgrave Ranges >90% of reproductively active females had pouch young), even sex ratios and relatively high adult survivorship (>75%). Juvenile survival (51%), however, was significantly lower than that of adults. Given that red fox (Vulpes vulpes) numbers are low at these sites, this is possibly due to predation by feral cats (Felis catus), although this needs further investigation. Juvenile survival was also positively correlated with winter rainfall, possibly indicating that access to water is important during the drier winter months. In light of these observations, it is proposed that management of remaining warru colonies focus on cat control and consider providing access to free water during winter, as well as addressing landscape-scale threats such as wildfire and the spread of exotic plants.

Molecular road ecology: exploring the potential of genetics for investigating transportation impacts on wildlife

Transportation infrastructures such as roads, railroads and canals can have major environmental impacts. Ecological road effects include the destruction and fragmentation of habitat, the interruption of ecological processes and increased erosion and pollution. Growing concern about these ecological road effects has led to the emergence of a new scientific discipline called road ecology. The goal of road ecology is to provide planners with scientific advice on how to avoid, minimize or mitigate negative environmental impacts of transportation. In this review, we explore the potential of molecular genetics to contribute to road ecology. First, we summarize general findings from road ecology and review studies that investigate road effects using genetic data. These studies generally focus only on barrier effects of roads on local genetic diversity and structure and only use a fraction of available molecular approaches. Thus, we propose additional molecular applications that can be used to evaluate road effects across multiple scales and dimensions of the biodiversity hierarchy. Finally, we make recommendations for future research questions and study designs that would advance molecular road ecology. Our review demonstrates that molecular approaches can substantially contribute to road ecology research and that interdisciplinary, long-term collaborations will be particularly important for realizing the full potential of molecular road ecology.

Field-based evaluation of scat DNA methods to estimate population abundance of the spotted-tailed quoll (Dasyurus maculatus), a rare Australian marsupial

Context. DNA extracted non-invasively from remotely collected scat samples has been used successfully to enumerate populations of a few endangered mammal species. However, scat DNA surveys relying on scent-marking behaviours need to identify if age- or sex-specific variations or seasonal changes in scat scent-marking patterns affect population estimates. Furthermore, owing to the low quantity and quality of scat DNA, a thorough assessment of the technique is needed when it is applied to different species to ensure that individual identification is reliable. Aims. In the current study, microsatellite genetic profiles derived from 208 remotely collected scats of the spotted-tailed quoll (Dasyurus maculatus), a rare Australian marsupial carnivore, were compared with DNA profiles from tissue of 22 live-trapped individuals from the same study area to critically assess the reliability of the non-invasive method to estimate population abundance. Methods. Scat samples were collected at scent-marking sites over 4 consecutive months (April–July 2005), 7 weeks of which overlapped with the trapping program to allow direct comparisons of population estimates. Key results. Combining a multiple-tubes approach with error checking analyses provided reliable genetic tags and resulted in the detection of the majority of the live-trapped population (18 of 22 individuals). Ten additional individuals not known from trapping were also observed from scat DNA. A longer-term sampling regime was required for scats than for trapping to allow direct detection of a large proportion of the population and to provide a comparable population estimate. Critically, the 4-month scat collection period highlighted the importance of performing scat surveys during the mating season when scat scent marking is more frequent, and to avoid sex and age biases in scat marking patterns. Implications. Non-invasive scat DNA sampling methods that rely on scent-marking behaviours need to consider the duration of the sampling period and temporal differences in behaviours by the sexes and age groups to ensure that meaningful population estimates are achieved.

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.

Two-step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples

Many studies in molecular ecology rely upon the genotyping of large numbers of low-quantity DNA extracts derived from noninvasive or museum specimens. To overcome low amplification success rates and avoid genotyping errors such as allelic dropout and false alleles, multiple polymerase chain reaction (PCR) replicates for each sample are typically used. Recently, two-step multiplex procedures have been introduced which drastically increase the success rate and efficiency of genotyping. However, controversy still exists concerning the amount of replication needed for suitable control of error. Here we describe the use of a two-step multiplex PCR procedure that allows rapid genotyping using at least 19 different microsatellite loci. We applied this approach to quantified amounts of noninvasive DNAs from western chimpanzee, western gorilla, mountain gorilla and black and white colobus faecal samples, as well as to DNA from ~100-year-old gorilla teeth from museums. Analysis of over 45 000 PCRs revealed average success rates of > 90% using faecal DNAs and 74% using museum specimen DNAs. Average allelic dropout rates were substantially reduced compared to those obtained using conventional singleplex PCR protocols, and reliable genotyping using low (< 25 pg) amounts of template DNA was possible. However, four to five replicates of apparently homozygous results are needed to avoid allelic dropout when using the lowest concentration DNAs (< 50 pg/reaction), suggesting that use of protocols allowing routine acceptance of homozygous genotypes after as few as three replicates may lead to unanticipated errors when applied to low-concentration DNAs.

Evaluating exotic predator control programs using non-invasive genetic tagging

Carnivorous predators are difficult to detect using conventional survey methods, especially at low levels of abundance. The introduced red fox (Vulpes vulpes) in Australia is monitored to determine the effectiveness of control programs, but assessing population parameters such as abundance and recruitment is difficult. We carried out a feasibility study to determine the effectiveness of using faecal DNA analysis methods to identify individual foxes and to assess abundance before and after lethal control. Fox faeces were collected in two sampling periods over four separate transects, and genotyped at five microsatellite loci. Two transects were subject to lethal control between collection periods. DNA was extracted from 170 fox faeces and, in total, 54 unique genotypes were identified. Fifteen biopsy genotypes from 30 foxes killed during lethal control were detected among the faecal genotypes. Overall, a similar number of genotypes were detected in both sampling periods. The number of individuals sampled in both periods was low (n = 6) and new individuals (n = 24) were detected in the second collection period. We were also able to detect animals that avoided lethal control, and movement of individuals between transects. The ability to identify individual foxes using these DNA techniques highlighted the shortcomings of the sample design, in particular the spatial scale and distances between transects. This study shows that non-invasive DNA sampling can provide valuable insight into pre and post fox abundance in relation to lethal control, individual behaviour and movement, as well as sample design. The information gained from this study will contribute to the design of future studies and, ultimately, control strategies.

Faecal DNA detection of invasive species: the case of feral foxes in Tasmania

Early detection of biological invasions is critical to reducing their impact, but because invading organisms are initially at low densities, detection and eradication can be challenging. Here, we demonstrate the utility of faecal DNA analysis for the detection of an elusive invasive species – the red fox, Vulpes vulpes, which was illegally introduced to the island of Tasmania in the late 1990s. Foxes are a devastating pest to both wildlife and agriculture on the Australian mainland, and would have a similarly serious impact in Tasmania if they became established. Attempts to eradicate foxes from Tasmania have been hampered by unreliable distribution data derived mostly from public sightings. In response, we developed a highly accurate and reliable DNA-based PCR-multiplex test that identifies foxes from field-collected faeces. We also developed a sexing test, but it was reliable only for faeces less than three weeks old. Faeces are a useful target for DNA-based diagnostics in foxes because they are deposited in prominent locations and are long-lasting. The species identification test formed a key component of a Tasmania-wide detection and eradication program. In all, 1160 geo-referenced carnivore scats were analysed; of these, 78% contained DNA of sufficient quality for species identification. A single scat from the north-east of the island was identified as belonging to fox, as was a nine-week-old roadkill carcass from the north coast, and a blood sample from near Hobart, triggering increased control and surveillance in these regions. The accuracy, reliability, and cost-effectiveness of non-invasive tests make them a critical adjunct to traditional tools for monitoring cryptic invasive species that are at low density in the early stages of invasion and when eradication is still an option.

Genotyping faecal samples of Bengal tiger Panthera tigris tigris for population estimation: a pilot study

Background

Bengal tiger Panthera tigris tigris the National Animal of India, is an endangered species. Estimating populations for such species is the main objective for designing conservation measures and for evaluating those that are already in place. Due to the tiger's cryptic and secretive behaviour, it is not possible to enumerate and monitor its populations through direct observations; instead indirect methods have always been used for studying tigers in the wild. DNA methods based on non-invasive sampling have not been attempted so far for tiger population studies in India. We describe here a pilot study using DNA extracted from faecal samples of tigers for the purpose of population estimation.

Results

In this study, PCR primers were developed based on tiger-specific variations in the mitochondrial cytochrome b for reliably identifying tiger faecal samples from those of sympatric carnivores. Microsatellite markers were developed for the identification of individual tigers with a sibling Probability of Identity of 0.005 that can distinguish even closely related individuals with 99.9% certainty. The effectiveness of using field-collected tiger faecal samples for DNA analysis was evaluated by sampling, identification and subsequently genotyping samples from two protected areas in southern India.

Conclusion

Our results demonstrate the feasibility of using tiger faecal matter as a potential source of DNA for population estimation of tigers in protected areas in India in addition to the methods currently in use.