Herding Ancient Domesticates: From Bones to Genomes

Abstract

This thesis demonstrates the power of the analysis of ancient domesticate genomes of cattle and sheep in order to analyse past population dynamics of the two species. In total 113 whole genomes and 127 mitogenomes of wild and domestic cattle, and 28 whole genomes of sheep, are analysed with respect to domestication and subsequent European migration events. The successes and failures of recovering ancient DNA from archaeological specimens using NGS are discussed, with results supporting previous claims of the prowess of the petrous bone for the preservation of ancient DNA. The analysis of ancient mitogenomes demonstrates a reduction in haplotype diversity as cattle migrated west into Europe, supporting previous publications. Bayesian analysis of modern and ancient mitogenomes demonstrates the divergence of some of the major haplogroups could have been linked to environmental conditions, with the dating of some of these branches occurring for the first time. While the formation of the macro haplogroup T likely coincided with the beginnings of domestication. Whole genome analysis of Near Eastern and European taurine cattle and European auroch, builds upon the mitogenomes analysis. It demonstrates support for the domestication of taurine cattle in the Near East and the subsequent migration into Europe. Migrations, population bottlenecks and admixture with European auroch all contributed to the genetic structure present in ancient and modern day cattle. A transect through the Atlantic Edge of Europe, formed of 77 genomes, suggests cattle population history of this region does not mirror that of the contemporary human population. Additionally, preliminary results of allele frequencies suggest selection for increase milk yields occurring post the appearance of lactose tolerance in European humans. Finally, the demonstration of genetic structure in sheep indicates geographic structure similar to that of modern breeds existed in the ancient Eurasian sheep population, while tentative conclusions are formed regarding subsequent sheep migrations post-Bronze Age.