Abstract
Remote Oceania is a vast region comprising many islands in the Pacific Ocean. Human settlement occurred relatively recently, dating from ~3000–2800 BP in western Remote Oceania (WRO) and ~1200–800 BP in eastern Remote Oceania (ERO). The origins of people moving into WRO are relatively well understood, but questions remain about the dispersal into ERO. Various approaches have been used to study dispersal routes and settlement patterns, but the rapid and recent nature of colonisation poses challenges. Ancient DNA analysis of commensal animals, known as the commensal model, has been used as a proxy for human movement and interactions, and has provided additional insights into the complex settlement of the broader Pacific region. However, poor sample coverage, alongside low mitochondrial diversity, often restricts its resolution in Remote Oceania.
This thesis advances our understanding of Remote Oceania’s settlement history by applying the commensal model to archaeological pig (Sus scrofa) and dog (Canis lupus familiaris) remains and by investigating how emerging DNA technologies can extend its scope, focusing on three different genetic markers: mitogenomes, genomic data, and the gut microbiome. Two key periods are examined: the expansion into WRO by Lapita peoples (~3000 BP), and the expansion into and within ERO by Polynesian peoples (~1200 BP onwards).
Pigs are important in Remote Oceanic cultures, but existing data are sparse, and the short mitochondrial COI region has proven insufficient for tracing regional movement. Newly generated whole mitogenomes from archaeological pigs spanning the Lapita to historic periods across several archipelagos show that all pre-contact pigs belong to a single lineage consistent with the "Pacific Clade". Greater mitochondrial diversity in WRO compared to ERO suggests a bottleneck during the East Polynesian expansion and limited movement of pigs between these regions post-settlement. Furthermore, the lack of diversity in ERO prevents finer-scale interpretations and underscores the need for more comprehensive datasets.
Similarly, dogs also experienced a severe bottleneck during Polynesian expansion, with kurī (Polynesian dogs) in Aotearoa New Zealand displaying minimal mitochondrial diversity. To test whether genomic data can overcome this, genome-wide data from 16 kurī palaeofaeces with a high endogenous DNA content is presented. Both the extended mitogenome dataset and the genome-wide data suggests a potential north-south separation. This aligns with archaeological evidence of a Middle Period (1450-1650 AD) shift away from long-distance voyaging to extended use of local resources. However, small sample sizes, limited geographical coverage, and sequencing depth prevent firm conclusions about whether this reflects true population structure or mere kinships.
The kurī gut microbiome, reconstructed from the same palaeofaeces, provides further resolution into human, animal, and environmental interactions. Differences are observed between pre- and post-contact samples, partly due to the loss of specific species. Significant north-south differences are also detected, however these are driven by the presence of fish-spoiling bacteria in southern samples. By integrating these findings with Māori subsistence patterns, they suggest an association with traditional barracouta preservation practises. Furthermore, several pathogens are detected, but interestingly, these primarily affect other species, such as fish.
Overall, this thesis demonstrates both the potential and limitations of the commensal model when incorporated with emerging DNA technologies. By integrating ancient DNA from pigs and dogs with other disciplines, it provides new insights into the settlement history of Remote Oceania, while also significantly contributing to the growing field of palaeofaecal metagenomics.