Extremely low genetic diversity and small Ne in the Critically Endangered Nangur Spiny Skink (Nangura spinosa) of eastern Australia

Abstract Globally, many species have small, fragmented populations and hence genetic factors become a primary threat to their persistence. The Critically Endangered Nangur Spiny Skink ( Nangura spinosa ) inhabits vine thicket in Nangur and Oakview National Parks in south-east Queensland, Australia. The two populations are naturally isolated and are now very small, with census estimates of < 50 in the Nangur population and ~ 1000 at Oakview. Using a genome-wide SNP dataset, we conducted a genetic health assessment to provide management actions for species recovery. The populations form two distinct genetic groups, with high genetic differentiation. In contrast, there is high connectivity within each population, likely driven by regular dispersal over very short distances and infrequent movements over longer distances. The Oakview population had low heterozygosity (H obs = 0.139; H exp = 0.142; mean individual F = 0.116) and contained 72% of the SNPs. The Nangur population had very low heterozygosity (H obs = 0.114; H exp = 0.112; mean individual F = 0.289). N e estimates for the populations were very small: ~16–43 for Nangur and ~ 66–179 for Oakview. Genetic health metrics for the Oakview population are comparable to other Critically Endangered Australian skinks, but are much worse for Nangur. The results for the Nangur population indicate high levels of inbreeding, high relatedness, and very low individual heterozygosity. Poor genetic health is likely already contributing to fitness loss and declines, especially for the Nangur population. We recommend within-population translocations and/or managed breeding in captivity to slow genetic erosion. Additionally, genetic rescue is urgently required, via crosses between the populations. This study is a clear example of how genetic data can assist species recovery.