Species-specific SNP arrays for non-invasive genetic monitoring of the ghost bat

This study introduced an innovative technique for individual identification of the threatened ghost bat, Macroderma gigas, by analyzing scat samples. The method involved creating specialized Single Nucleotide Polymorphism (SNP) arrays using the MassARRAY system. A total of 611 highly informative SNPs were carefully chosen from DArTseq data based on their coverage, rich information content, and compatibility with MassARRAY primer design. From this selection, three distinct panels of SNPs were crafted, each panel containing 44 to 50 SNPs. The DNA sequences of these markers have been documented and are accessible here.The application of these SNP panels was tested on 209 ghost bat scats obtained from seven caves situated in the Pilbara region of Western Australia. To identify unique genotypes, a customized R package called ScatMatch was employed. The average success rate for DNA amplification was recorded at 90%, and the rate of allelic dropout was a mere 0.03%. This precision enabled the assignment of scat samples with only one or fewer allelic mismatches to the same individual. We identified 19 distinct bats from the collected scats, including 9 confirmed or likely males and 10 confirmed or likely females. These bats were identified across a maternity roost and several transitory roosts.