Deciphering the mtDNA record of prehistoric population movements in Oceania

This thesis uses mitochondrial DNA (mtDNA) phylogenies to explore patterns of past human mobility in Oceania. To extend the current knowledge of mtDNA variation in Oceania, 20 entire mt genomes were sequenced and analysed in a data set of more than 144 sequences from Australia, Oceania, Island Southeast Asia and Taiwan. The MinMax Squeeze method enabled this large data set to be analysed with an optimality criterion (Pierson et al. 2006). The analysis revealed two major groups of haplogroups in Oceania, distinguished by the relationships to others outside of the region: an 'ancient' set of types whose phylogenies and distributions suggest they are descended from the Pleistocene-era settlers of Near Oceania, and a second 'young' group whose presence in Oceanic populations may reflect more recent movements into Near Oceania. The detailed phylogenies of these haplogroups presented here will aid in future investigations of human mtDNA in Oceania, allowing samples to be screened by defining mutations to target haplogroups of interest. A large data set of global entire human mt DNA sequences was assembled from public data bases and tested for evidence of selection and recombination. These tests, and phylogenetic analyses of random subsets of the data set, found high levels of homoplasy in the sequences. Homoplasy in the control region of the mtDNA molecule was examined in particular, resulting in a relative scale of mutability at each position of the ~1kb sequence. Subsequent phylogenetic tests of weighting schemes derived from this analysis for the control hypervariable region I (HVR-I) did not show demonstrable improvements over the unweighted examples, but did highlight instances in which the HVR-I sequence failed to predict the more robust trees generated by the coding region. Finally, the HVR-I and diagnostic SNPs were sequenced in a set of 46 Polynesian samples from Auckland, and this data was analysed within a large set of HVR-I sequences (more than 4000) from Oceanic, Asian and the American populations available from public data bases. These analyses were informed by the whole mtDNA phylogenies generated earlier in the project, and add population level data to the emerging picture of prehistoric female mobility gained from entire mtDNA analyses