Ancestral Legacies of an Insular Archipelago: A genomic exploration of prehistoric Japan and mainland Asia

Abstract

The objective of this thesis is to use ancient genomic data and a variety of bioinformatic approaches to explore human evolutionary history in the Japanese archipelago and mainland Asia. This thesis presents a dense genomic exploration of Japanese prehistory through the analysis of time series of ancient genomes from different cultural periods, including 12 ancient individuals which were sequenced as part of this project. This analysis reveals that the indigenous Jomon hunter-gatherer population diverged from other Asian populations ~20kya, before maintaining a small population size of ~1000 without any major significant contribution from outside of the archipelago. The isolation of the Jomon ended ~3kya with the arrival of people with northeast Asian ancestry during the Yayoi period, which is associated with the introduction of wet rice farming to the region. Surprisingly, a third wave of East Asian ancestry is observed during the imperial Kofun period. These three ancestral sources are demonstrated to characterise present-day Japanese populations, providing the first genetic evidence for a newly proposed tripartite structure for present-day Japanese populations. Subsequent chapters further explore the potential for imputation to enhance ancient genomic analysis of prehistoric Asia, and potential early connections between Asia and the Americas.