Conservation genetics of Mahogany Gliders and their complex evolutionary relationship with Squirrel Gliders

These are the datasets and analysis scripts for the publication <i>"Conservation genetics of Mahogany Gliders and their complex evolutionary relationship with Squirrel Gliders"</i> submitted to Conservation Genetics 2024.<b>Abstract</b><br>Squirrel Gliders (<i>Petaurus norfolcensis</i>) are widely distributed throughout the woodlands of eastern Australia, while the similar but larger Mahogany Glider (<i>Petaurus gracilis</i>) inhabits the coastal woodlands of the Wet Tropics in northeastern Queensland. The Mahogany Glider is an Endangered species due to habitat loss and fragmentation. This study used single nucleotide polymorphism markers (SNPs) from field and museum-derived samples to investigate genetic relationships within the Squirrel/Mahogany Glider complex and conduct a conservation genetics assessment for the Mahogany Glider. Analyses of genetic structure, phylogenomics, and outlier loci identified four genetic groups: Mahogany Glider and three distinct groups in Squirrel Gliders (North Queensland, Cape Cleveland, and mid-eastern/south-eastern Queensland). We found genetic admixture between these groups, but whether the admixture is historic or current remains unclear. Squirrel Gliders from North Queensland were genetically more similar to Mahogany Gliders in some analyses than to the other two Squirrel Glider groups. Morphological analysis confirmed that Mahogany Gliders are distinguishable from other gliders primarily by their larger body size but did not provide clear differences for the other three genetic groups. We hypothesize that the four genetic groups represent four subspecies of Squirrel Glider, of which the Mahogany Glider is one. This hypothesis can be tested with further field sampling of genetics and morphology, particularly in identified areas of potential contact. When assessing Mahogany Gliders alone, we found a clear north–south split in genetic structuring, with the southern cluster being more structured than the northern cluster. Genetic diversity within Mahogany Gliders was generally comparable to that of Squirrel Gliders, but some sampling localities indicated loss of genetic diversity and low effective population size. Regardless of whether Mahogany Gliders are classified as a species or subspecies, their Endangered status underscores the need for targeted conservation efforts. The genetic findings offer practical pathways for on-ground management to enhance population recovery and connectivity.<br><b>Files in the repository</b>Data folder: data used in the analyses, including morphological data from museum and field specimens and SNPs data derived from DArT analysis.snp_filters.rmd - customized filtering steps for the glider genetics. Output different data formats and filtered status for downstream analyses.structure.rmd - Analyses of genetic structure.diversity_mgsq.rmd - Analyses of genetic diversity focused on the Mahogany and Squirrel Glider datasets.QM_SpeimenData.rmd - Analyses of morphological data from museum specimens.