The fragile alpine freshwater ecosystems of Australia are threatened by historic land use and projected climate change, yet little is known about the fauna of these environments. The aim of this research is to analyse the diversity of two important crustaceans found in these ecosystems, the neoniphargid amphipods and phreatoicid isopods. Preliminary phylogenetic analyses using DNA barcoding techniques, found deep divergences in both taxa, leading to the definition of six amphipod and two isopod Evolutionary Significant Units in the Bogong High Plains. Subsequent next generation sequencing, allowing the analysis of a greater proportion of the genome, has shown that these ESUs represent different species. Next-generation analysis of two of the six amphipod lineages has shown further deep lineage divergence, suggesting the presence of cryptic hyper-diversity with the amphipods of alpine Australia. The majority of amphipod species exhibited highly restricted distributions, while both isopod species had overlapping distributions across the entire sample area.
This study suggests that there is a high level of undiscovered biodiversity within Australian alpine aquatic crustaceans. The highly number of species and restricted distributions have important consequences for the conservation of the headwaters of Australia’s major river system. Habitat loss and/or fragmentation associated with environmental change is likely to result in biodiversity reductions, with species unlikely to shift their ranges in response to future climate change, or recover from localised extinction events.