Estimating the Abundance of a Cryptic, Endangered Marsupial, Mala (Lagorchestes hirsutus) Using Microsatellite and...

Developing high-quality, non-invasive population monitoring techniques is important for endangered species that are difficult to trap or susceptible to capture myopathy. One such species is the mala (Lagorchestes hirsutus, Central Australian subspecies), an Australian macropod that is extinct in the wild and only conserved inside four predator-free reserves and on one offshore island. DNA extracted from scat is an effective non-invasive method to 'genetically tag' individuals for capture-mark-recapture analyses to estimate population abundance. Microsatellites have previously been successfully used to identify individuals from mala scats, but are prone to genotyping errors, especially when DNA quality is low. Here, we developed an array of 50 highly informative Single Nucleotide Polymorphisms (SNPs) for targeted genotyping on the MassARRAY system to improve efficiency and confidence in individual identification. We compared the accuracy of individual identification using the SNP panel to eleven previously published microsatellite markers and compared estimates of mala abundance derived from each genotyping method. Mala scats were collected in 2020 and 2021 along nine transects within a predator-free reserve at Matuwa Kurrara Kurrara National Park, Western Australia. The SNP panel had similar amplification success to microsatellites but reduced genotyping error rates. Both genotyping methods showed a similar number of individuals identified and similar patterns in genetic diversity and relatedness across two years. Spatially explicit capture-recapture modelling using microsatellites produced an estimate of 108 (±37) mala in 2020 and 59 (±22) in 2021. Samples genotyped on the SNP panel produced an estimate of 122 (±45) individuals in 2020 and 81 (±32) in 2021. Both methods indicated a substantial decline in mala abundance from 2020 to 2021, which was likely a lag effect associated with a drought that occurred in 2019.