Isolated on sky islands: genetic diversity and population structure of an endangered mountain lizard

Sky island species face climate-driven and anthropogenic habitat loss and population fragmentation, and are therefore vulnerable to genetic erosion. We conducted a genetic study of the cryptic and threatened alpine she-oak skink ( Cyclodomorphus praealtus ) throughout its range, across two regions of the mainland Australian Alps; an extensive high elevation plateau in the north (‘Kosciuszko Plateau’) and several smaller plateaus in the south (‘southern plateaus’). We investigated whether extensive potential habitat across Kosciuszko Plateau supported larger, connected populations with better genetic health than more fragmented southern plateaus. Our analyses of genome-wide markers confirmed effective isolation of the two regions. We identified three populations from the southern plateaus, largely aligning with discrete landforms, and four populations on Kosciuszko Plateau. Only one individual, from the southern-most population, showed evidence of admixture between the two regions. Across its range, C. praealtus populations had low genetic diversity and small effective population sizes. In contrast to our expectations, Kosciuszko Plateau populations were smaller, with greater genetic differentiation and a higher degree of inbreeding than the southern populations. We detected admixture between populations on Kosciuszko Plateau, while the southern plateaus had limited admixture. We found no evidence of local adaptation, suggesting plateaus represent interglacial refugia. Our results suggest that C. praealtus has little capacity to withstand further disturbance or rapid environmental changes. Maintaining or restoring habitat quality in occupied and suitable connecting habitats across the species’ range is paramount. ‘Genetic rescue’ should be investigated as an option to mitigate the effects of isolation and improve population resilience.