Mitchell, KierenAustin, JeremyHeiniger, HollyMudge, Caitlin Simone2024-07-262024-07-262024https://hdl.handle.net/2440/141679Australia has undergone severe ecosystem modifications within the last 200 years since European colonisation. The ongoing impacts of European colonisation have contributed to the rapid extinction of nearly 10% of terrestrial endemic mammalian fauna in Australia (~30 species). The biodiversity present prior to European arrival was vastly different to what is present today. Similarly, the distribution and ecology of modern animal populations does not represent their historical distribution and ecology prior to population declines and extinctions. The major ecosystem modifications seen in Australia cause issues with resolving taxonomy of extinct and extant species, establishing historical distributions, understanding biodiversity prior to European arrival, determining accurate extinction estimates, and assessing genetic changes through time. However, we are unable to use data from modern specimens and the fossil record alone as proxies for understanding the effects of major past events in Australia. Elsewhere in the world, ancient DNA has proven to be a powerful source of data to compliment data from modern specimens and the fossil record, but until recently it has been challenging to undertake ancient DNA studies on Australian species. Recent advances have allowed us to analyse smaller quantities of DNA from lower quality fossils like those typically found in Australia. Additionally, museum collections are increasingly being used as sources of historical DNA, which is advantageous as many Australian species that became extinct soon after European arrival are only represented in these museum collections. In this thesis I used ancient DNA and museum collections to resolve outstanding questions regarding taxonomy, genetic diversity, phylogeography, and demography of four distinct taxa that experienced severe range contractions or extinctions since European arrival. This thesis provides a framework for producing large genetic datasets for other Australian taxa. With advances in ancient DNA techniques, we are able to use museum collections in population studies and identify cryptic diversity. Future studies should focus on developing nondestructive methods to recover genetic material from small specimens and incorporating radiocarbon analyses. My results suggest that biodiversity has fluctuated substantially since the Late Pleistocene in response to major climate events and biogeographic changes. I also argue that ancient DNA studies should not be carried out in isolation but should be part of a holistic approach that considers ancient biogeography.enAncient DNAAustralian mammalsPhylogeneticsEvolutionary geneticsPleistoceneThesis