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Through our research focusing on genetic studies of both ancient and extant commensal animals in the Pacific for addressing issues of population origins and mobility in the region, we have been able to process a large number of archaeological faunal remains that we can compare to modern samples from the same islands. These comparisons shed light on and provide specific evidence for Rattus exulans population change through time. This information may provide a model for understanding human populations in the region and will illustrate the complexities of using data obtained from modern populations to infer prehistoric relationships. Two case studies are presented here—analyses of modern and archaeological populations of R. exulans from both Chatham Island and New Zealand. These two cases provide very different pictures regarding the relationship between the archaeological and the extant populations.