Cold, creeping things: deep phylogeographic structure in a naturally fragmented cool-adapted skink (Scincidae; Anepischetosia) from south-eastern Australia

Abstract The temperate forests of eastern Australia have been extensively fragmented over the last 200 years and are now increasingly threatened by fire and climate change. To understand and manage the impacts of these threats, there is a need to understand patterns of endemism and diversity across an array of ecologically divergent taxa. Anepischetosia is a monotypic genus of scincid lizards that is adapted to cool, wet forest habitats in far south-eastern mainland Australia. Here we use reduced representation genomic data and sequencing of the mitochondrial ND4 locus from museum tissue samples to characterise phylogeographic structure and population-level genetic diversity in this taxon. These data reveal novel patterns of deep and geographically localised genetic structuring, including at least six ESUs spanning several candidate species. Many divergent lineages are associated with localised patches of mesic habitat, especially in the north of the range, suggesting long histories of persistence through major environmental change across the Plio-Pleistocene, similar to that observed in some mesic and temperate taxa from non-glaciated landscapes in the northern hemisphere. Two putative ESUs, whose ranges overlap areas impacted by recent high-intensity bushfires, have low genetic diversity and may be of conservation concern. Additional seemingly isolated and divergent populations in western Victoria remain poorly sampled and may comprise yet further ESUs or candidate species. These results highlight how genomic analyses can reveal overlooked patterns of diversity and populations of conservation concern by leveraging museum collections – as long as these are well-sampled and accessible – even in landscapes that are considered comparatively “well known”.