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

Abstract

The brush-tailed rock-wallaby (Petrogale penicillata) is an endangered species in southeastern Australia and many of the remaining populations are declining. The steep rocky habitat and shy nature of the species make it difficult to obtain data on population parameters such as abundance and recruitment. Faecal pellet counts from scat plots are commonly used to monitor population trends but these are imprecise and difficult to relate to absolute population size. We conducted a noninvasive genetic sampling 'mark-recapture' study over a 2-year period to identify individuals from faecal DNA samples and estimate the population size of four brush-tailed rock-wallaby colonies located in Wollemi National Park, New South Wales. Scat plots in rock-wallaby colonies were used as sample collection points for this study. Two separate population estimates were carried out for three of the colonies to determine if we could detect recruitment and changes in population size. We determined that there was one large colony of an estimated 67 individuals (95% confidence interval: 55-91) and three smaller colonies. Monitoring of the smaller colonies also detected possible population size increases in all three. Our results indicate that faecal DNA analysis may be a promising method for estimating and monitoring population trends in this species particularly when used with a traditional field survey method.

Non-Invasive Genetic Identification of the Red FoxVulpes vulpesin the Shiretoko National Park, Eastern Hokkaido, Japan

“…Frantz et al 2003;Piggott et al 2006), indicating the difficulty of genetic analysis using fecal samples. The genotyping reproducibility values (53.5-88.4%, Table 1) show the unavoidable risks for genotyping errors.…”

“…In non-invasive DNA analysis, in general, feces are newly and systematically collected only for the purpose of genetic study (e.g. Banks et al 2002;Lucchini et al 2002;Flagstad et al 2004;Bellemain et al 2005;Piggott et al 2006). For example, Shimatani et al (2008Shimatani et al ( , 2010 analyzed DNA of fecal samples younger than 24 hours, which were collected from field everyday in one sampling period.…”

Habitat connectivity, more than species’ biology, influences genetic differentiation in a habitat specialist, the short-eared rock-wallaby (Petrogale brachyotis)

“…To ensure duplicate samples of faecal DNA or samples from trapped animals were not included in the analysis, only unique multilocus genotypes were used for population analyses. Following Piggott et al (2006b) we accepted a heterozygous genotype if each allele was present in two out of three replicates and only accepted a homozygous allele if only one allele was identified in all three replicates. A post hoc method was implemented, whereby samples that matched at all but four alleles were assigned the same identity (one individual removed from further analyses).…”

“…We therefore replicated all PCRs three times, according to Piggott et al (2006b), to control for allelic dropout (stochastic non-amplification of one allele), the occurrence of false alleles and ensure reduction in type 1 errors (novel genotypes which are incorrect). The microsatellite DNA fragments were scored using GENEMAPPER v4.0 (Applied Biosystems) for allele size and quantification.…”

Genetic monitoring as a promising tool for conservation and management

“…Box 1; [13,14]). For example, in Australia, microsatellite DNA and CMR analysis has provided a feasible and cost-effective strategy for monitoring long-term changes in brush-tailed rock-wallaby Petrogale penicillata abundance [15].…”