DNA and pacific commensal models : applications, construction, limitations, and future prospects

Components of the Pacific transported landscape have been used as proxies to trace the prehistoric movement of humans across the Pacific for almost two decades. Analyses of archaeological remains and DNA sequences of plants, animals, and microorganisms moved by or with humans have contributed to understanding prehistoric migration, trade, exchange, and sometimes revealed the geographic origins of particular plants and animals. This paper presents the basic elements of a DNA-based commensal model and discusses the phylogenetic and population genetic approaches these models employ. A clear delineation of the underlying assumptions of these models and the background information required to construct them have yet to appear in the literature. This not only provides a framework with which to construct a commensal model but also highlights gaps in current knowledge. The ways in which commensal models have enriched archaeological reconstructions will be highlighted, as will their current limitations. With these limitations in mind, options will be outlined for augmenting commensal models through the application of established techniques and new technologies in order to provide the best tools for reconstructing ancient human mobility and behavior in the Pacific and beyond

Chatham Island mitogenome Ion Torrent NGS raw sequences

Chatham Island mitogenome Ion Torrent NGS raw sequence

BEAST mitogenome phylogenetic analysis with Yule speciation prior

BEAST mitogenome phylogenetic analysis with Yule speciation prio

BEAST Dloop phylogenetic analysis with Yule speciation prior

BEAST Dloop phylogenetic analysis with Yule speciation prio

Sequence alignment of Chatham Island sea lions

Sequence alignment of Chatham Island sea lion mtDNA D-loop including all Chatham Islands individuals (NRO number, location, haplotype - C1 to 9), exemplar haplotype sequences of subantarctic individuals (SA1-3), exemplar haplotype sequences of prehistoric New Zealand individuals (NZ1-14), and outgroups (Australian sea lion, South American sea lion, New Zealand furseal). Please see Suppl. Info. Table S1 for numbers of New Zealand and subantarctic individuals for each haplotype

BayeSSC .par files

BayeSSC .par file

Pinniped whole mitogenome phylogenetic alignment

Pinniped whole mitogenome phylogenetic alignmen

Individual Based Model for anthropogenic mortality estimates

Individual Based Model for anthropogenic mortality estimate