Frontiers in paleogenomics: Methodological challenges and multidisciplinary studies of human past in South America

Abstract

The study of the past through the examination of preserved genetic material from ancient remains has revolutionised the fields of archaeology, anthropology, and evolutionary biology. The ancient DNA revolution was made possible both by advancements in laboratory techniques to retrieve degraded DNA, as well as the advent of next-generation sequencing. As a result, over 10,000 genomes from ancient human beings have been sequenced since 2010. However, as a young research field, human paleogenomics is still growing in many ways, including integration with adjacent disciplines that study similar questions, overcoming methodological challenges, and exploring understudied regions of the world. In Part 1 of this thesis, I review multidisciplinary evidence in support of the hypothesis of a state-wide resettlement policy enforced by the elites of the South American Inka empire upon the peoples they colonised in the Andes. I combine evidence from paleogenomics, archaeology, isotopic studies, radiocarbon dating and ethnohistory to broadly characterise the resettlement practice. I provide recommendations for the integration of multidisciplinary evidence into future studies of similarly anthropological research questions. In Part 2 of this thesis, I investigate methodological challenges currently facing the human paleogenomics field. In 2021 two commercial laboratory kits were released that allow insolution enrichment of 1.2 million nuclear single nucleotide polymorphisms (SNPs) in DNA sequencing libraries from ancient human specimens. In Chapter 2 I investigate the strong allelic bias revealed in the data generated by one of these kits, from Daicel Arbor Biosciences. I present 20 attempted strategies to reduce the allelic bias, with none satisfactorily successful. However, I present specific guidelines to allow for the data to be safely included in analyses. In Chapter 3, I similarly benchmark the second kit, released by Twist Bioscience, and select this as the data generation method to be used in the final part of the thesis. In Part 3 of this thesis, I investigate the demographic history of the ancient Indigenous inhabitants of the Chonos Archipelago, Chile. I contribute to the anthropological understanding of these ancient people whose culture is now extinct. I situate the ancestry of the Chonos people in the known context of the Southern Cone of South America and gain demographic insights into interactions with neighbouring cultures through time in ancient South America.