| Summary: | For more than 20 years, a model for the colonisation ofIsland Southeast Asia (ISEA), involving as two waves of dispersal, has assumed the ~status of near-consensus. The first colonisation of the region by modem humans occurred around 50,000 years ago, but according to the 'Out of Taiwan' model, these populations were assimilated or replaced in the mid-Holocene by rice agriculturists from China, who moved to Taiwan and from there into ISEA and later the Pacific. This theory originated in the analysis of the tree of the Austronesian language family, spoken by most of these populations. In this thesis, mitochondrial DNA variation was analysed using a phylogeographic approach in order to test this hypothesis against other proposed models for the colonization of ISEA. Two improved analytical tools were employed to do this. One was an upgrade of the previously used founder analysis approach, and the second a reassessment of human mitochondrial DNA clock. I developed a time-dependent mutation rate that allows for the effect of purifying selection on the more recent nodes of the human complete mitochondrial tree (control region as well as coding region), increasing both the accuracy and precision of the age estimates. The founder analysis revealed that the Late Pleistocene and Early Holocene were the key periods that shaped the mitochondrial diversity of ISEA, possibly due to events related to climate change and sea-level rise, and that the mid-Holocene Neolithic signal traces mainly to Mainland Southeast Asia, rather than Taiwan. The analysis of complete mitochondrial geno~es suggested a first arrival of modem humans 50,000-60,000 years ago, confmned the importance of sea-level rises in the region, and highlighted the significance of interaction networks in establishing current genetic patterns in ISEA, the Pacific and Taiwan. The analysis offers little support for 'the 'Out of Taiwan' model, pointing to a more complex demographic history for the region in which climatic change appears to have played a crucial role.
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