Genetic tagging from scats is one of the minimally invasive sampling (MIS) monitoring approaches commonly used to guide management decisions and evaluate conservation efforts. Microsatellite markers have traditionally been used but are prone to genotyping errors. Here, we present a novel method for individual identification in the Threatened ghost bat Macroderma gigas using custom-designed Single Nucleotide Polymorphism (SNP) arrays on the MassARRAY system. We identified 611 informative SNPs from DArTseq data from which three SNP panels (44-50 SNPs per panel) were designed. We applied SNP genotyping and molecular sexing to 209 M. gigas scats collected from seven caves in the Pilbara, Western Australia, employing a two-step genotyping protocol and identifying unique genotypes using a custom-made R package, ScatMatch. Following data cleaning, the average amplification rate was 0.90 ± 0.01 and SNP genotyping errors were low (allelic dropout 0.003 ± 0.000) allowing clustering of scats based on one or fewer allelic mismatches. We identified 19 unique bats (9 confirmed/likely males and 10 confirmed/likely females) from a maternity and multiple transitory roosts, with two male bats detected using roosts, 9 km and 47 m apart. The accuracy of our SNP panels enabled a high level of confidence in the identification of individual bats. Targeted SNP genotyping is a valuable tool for monitoring and tracking of non-model species through a minimally invasive sampling approach.
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