Inferring the Characteristics of Ancient Populations using Bioinformatic Analysis of Genome-wide DNA Sequencing Data

Abstract

In this thesis, I apply, evaluate, and develop methods for learning about past populations from genome-wide sequencing data. Specifically, I: • apply methods based on random genetic drift between populations, to determine that pre-Holocene gene flow occurred between the ancestors of domestic cattle (Bos primigenius) and European bison (Bison priscus), and that the contribution of Bos genealogy to the bison lineage was less than 10 %; • use simulations to assess the impact of short genomic scaffolds when inferring past populations sizes with the pairwise sequentially Markov coalescent, and show that population size inferences can be robust for scaffold lengths as short as 100 kb; • perform genetic sex determination of ancient DNA specimens to show that bison (Bison spp.) and brown bear (Ursus arctos) specimens are approximately 75% male, and that male-biased observations likely stem from the ecological and social structures of the populations; • and develop a suite of software tools for processing hairpin bisulfite sequencing data, which can be used to investigate genome-wide DNA methylation levels in ancient DNA.