Scat DNA as a non-invasive method for estimating the abundance of the vulnerable mala (Lagorchestes hirsutus)

Context. Population-monitoring programs often use direct (e.g. live capture or spotlighting) or indirect (e.g. scats sightings) observations to estimate population abundance. Such methods, however, are often inadequate for rare, elusive, or cryptic species due to the difficulty in achieving sufficient encounters or detection rates. The mala (Lagorchestes hirsutus), a small native Australian macropod, listed as Vulnerable by the IUCN, is difficult to capture, susceptible to capture myopathy, and not easily sighted in their dense habitat; consequently, the population size cannot always be estimated. The use of molecular markers to identify individual genotypes from non-invasively collected samples is increasingly being used in wildlife conservation and may be an alternative approach for mala. Aim. The aim of this study was to evaluate the efficacy of noninvasive scat DNA sampling to estimate the population abundance of mala. Methods. A panel of microsatellite markers was developed for the identification of individual mala via profiling of their scats. Scats were systematically collected from a wild mala population located in an 1100-ha fenced reserve in Western Australia. Individual genotypes were determined using the microsatellite markers, and the abundance of mala was estimated using the genotypes with spatially explicit capture-recapture (SECR) and mark-resight analyses. Key results. The genetic markers proved variable and with sufficient exclusionary power to confidently identify unique individuals (mean locus genotyping error rate: 3.1%). Individual genetic identification from scat sampling, when used with traditional mark-recapture/resight analytical models, provides feasible estimates of population abundance. This is the first reliable abundance estimate of this mala population, suggesting a > 70% increase in population size since the initial reintroduction of 64 individuals in 2011-13. Conclusions. Given the inherent difficulties in surveying mala, this approach would be valuable to ensure effective monitoring of the few remaining fenced and island mala populations to prevent further decline of this vulnerable species. Implications. This is the first study to identify species-specific microsatellite markers for mala and use genetic-capture sampling with scat DNA to estimate the abundance of a mala population. The study provides an evaluation of a valuable species monitoring technique that can be applied to other rare, elusive, or cryptic threatened species.