Title: Exploring the human past during the ancient DNA revolution
Comittee: John Wakeley and David Reich (HMS Genetics) (Advisors), Daniel Hartl, Hopi Hoekstra
Abstract:Over the last decade, advances in ancient DNA sequencing technology have made it possible to study the genomes of ancient humans on a large scale. Genome-wide information is now available from several thousand ancient humans, enabling researchers to explore questions about the demography of ancient human populations, such as the genetic relationships between members of ancient groups and patterns of migration between groups. As the field of ancient DNA has developed, it has become essential to critically examine the tools that we use to study this growing source of data and to consider the scope of questions that it can be used to answer. In this dissertation, I directly address both of these aims.
In Chapter 1, I assess the performance of qpAdm, a statistical tool for modeling population admixture that is often used in ancient DNA analyses, but its performance has not previously been rigorously tested. Using simulated data, I show that qpAdm is a robust tool that can accurately identify plausible admixture models and estimate admixture proportions, even in cases where data quality is limited. Further, I highlight several potential cases where users should exercise caution when using qpAdm, and create an updated user guide, making the tool more accessible to future users.
In Chapter 2, I present the first of two novel applications of ancient DNA to the study of the human past, highlighting the information that can be learned from in-depth analysis of multiple individuals from specific archaeological sites. Here I examine ancient DNA from 22 individuals from Peqi’in Cave, a Chalcolithic period burial site in present-day Israel. By modeling the ancestry of these individuals, I help to resolve an ongoing debate about the cause of cultural changes associated with the Chalcolithic period in the Levant, suggesting that these changes are the result of migration into the region, rather than cultural diffusion.
In Chapter 3, I use ancient DNA and other biomolecular tools to explore the origins of the mysterious skeletons of Roopkund Lake in the Indian Himalayas. I analyze ancient DNA from 38 individuals from this high-altitude lake site and identify multiple distinct genetic groups that were deposited approximately 1000 years apart. This chapter highlights the ability of ancient DNA to study highly disturbed archaeological sites that are difficult to examine using traditional archaeological methods and to identify entirely unanticipated historical migrations.