NEW HORIZONS IN ANCIENT DNA RESEARCH: OVERCOMING PRESERVATION CHALLENGES TO STUDY ANCIENT HUMAN AND ANIMAL INTERACTIONS

Abstract

The reconstruction and understanding of past environments is essential to anthropological research, as humanity and the environment have shaped and been shaped by each other. Anthropological questions—such as human land use (Ellis et al., 2010, 2021) or responses to environmental changes (Islebe et al., 2022; Jeong et al., 2014)—utilize paleoecological data and approaches. Similarly, archaeological data is critical for paleoecological research (Crabtree & Dunne, 2022; Crumley, 2021; O’Brien, 2001), firmly intertwining the two disciplines. Paleoecological research employs numerous methodological approaches, and paleogenomics has become a critical aspect of paleoecology in recent years as the development of novel laboratory and bioinformatic approaches has led to an exponential increase in production of paleogenomic data. In this dissertation, I optimize cutting-edge laboratory and bioinformatic to maximize the paleogenomic potential of these faunal remains and address diverse, human-focused paleoecological questions. The first chapter provides background concerning the challenges and advancements of ancient DNA research and the value of faunal genomics in anthropology. Chapter two uses paleogenomics to question how sacrificed golden eagles (Aquila chrysaetos) were procured in the Mesoamerican city of Teotihuacan before sacrificial events. This chapter also features extensive laboratory experimentation to maximize aDNA yields. Chapter three is methodologically focused and is an attempt to recover DNA from late Pleistocene asphaltic remains from the La Brea Tar Pits in Los Angeles, California. Here we explore the taphonomic conditions in asphalt seeps and excavation methods that can affect the preservation and recovery of DNA. The fourth chapter is a genomic identification of rockfish from archaeological contexts along the Pacific coast, from the Aleutian Islands to Southern California. With remains spanning the last 5,000 years, this project features an iterative approach to species identification. The final chapter unpacks the broader conclusions and future directions of these projects. It recenters this research in the wider fields of ancient DNA, paleoecology, anthropology; and proposes new paths for future research. Taken together this research explores what can be learned at the outer limits of DNA preservation, and the breadth of research possible in anthropology