The study of human demographic history in the Pacific is currently entering a new era. New sequencing technologies, improved techniques to retrieve DNA from subfossil remains and new data analysis approaches will most likely revolutionize our understanding of this complex human achievement. Enabled by these new technical advances, researchers can now draw information from genetic markers such as complete genomes and extensive genome-wide re-sequencing data along with an improved modern and ancient DNA sampling of uniparental inherited markers such as mtDNA and NRY. However, the availability of these new data require new methods of analysis. 2nd generation sequencing platforms such as 454 (ROCHE), MiSeq and HiSeq (Illumina) or IonTorrent and IonProton (Life Technologies) generate huge amounts of data, which cannot be processed by hand. Improvements in ancient DNA technologies allow us to investigate demographic changes through time and thus overcome shortfalls of modern DNA data such as genetic drift or recent migrations, but standard analysis tools are not made for heterogeneous DNA data and thus might not be appropriate for the analysis of this type of data. In this thesis I focus on addressing some of the issues discussed above, as well as the implementation of newly emerging analysis methods, such as model-based analysis, into the study of human colonization of Polynesia.