Understanding human-animal relationships is a fundamental area of archaeological research. Throughout human history, animals have been sources of food, raw materials, labor, and companionship. Humans have also had an important influence on animal populations, including extinction, domestication, and translocation. Recently, archaeological research on the interactions between humans and animals has also helped us understand the contemporary status of animal populations, providing important insights for conservation biology and establishing a new research agenda, conservation archaeogenomics. In this dissertation, I define the field of conservation of archaeogenomics and develop a case study of how archaeological, genomic, and isotope data can be integrated to inform the conservation of an endangered carnivore.

The endemic island fox (Urocyon littoralis) of California's Channel Islands is a federally listed endangered species and has been the subject of considerable conservation research, including a captive breeding program. Despite decades of research, significant questions remain about when foxes colonized the Channel Islands and the role that Native Americans may have played in their introduction and dispersal to six islands. Using mitochondrial genomes of 185 extant island and gray fox samples, I demonstrate that island and mainland lineages diverge ~9200-7100 cal BP and were quickly dispersed to the other Channel Islands, likely by humans. I also explore the possibility of a deliberate introduction by Native Americans using isotope data. I did not detect evidence of human resource provisioning of island foxes from early archaeological contexts as might be expected if they were introduced by ancient peoples. However, I did detect evidence of human resource provisioning on San Nicolas Island in the late Holocene and developed a long-term dataset documenting ~7300 years of foraging ecology in the endangered island fox. 

Archaeological investigations of human-animal relationships through time can help document the influence of Native Americans on species distribution, abundance, and ecology. Understanding how species and humans adapted to and influenced changing environments in the past will inform decisions about protecting, preserving, and restoring biodiversity in the future. This dissertation demonstrates the importance of integrating archaeology and genomics for understanding ancient and modern human environmental relationships and modern conservation biology.