Palaeogenomics of animal domestication: computational modelling of ancestry, demography and selection

• Main Author: Irving-Pease, EK
• Other Authors: Larson, G
• Format: Thesis
• Language: English
• Published: 2020
• Subjects: palaeogenomics; domestication; Arctic; Siberia
• Online Access: https://ora.ox.ac.uk/objects/uuid:7f196cb1-4331-44fa-8878-b29b793810d9

The study of animal domestication is in the midst of a genomic revolution, as technological advances dramatically increase the availability of DNA sequence data from ancient and modern domestic populations. For the first time, palaeogenomic datasets are being produced of sufficient size and scope to directly observe anthropological and evolutionary processes through time; from the emergence of domestic animals in the Neolithic, to the formation of modern breeds in the Victorian era. This thesis applies computational modelling of ancient and modern DNA to infer ancestry, demography, and selection in domestic cattle (Bos taurus), horses (Equus ferus caballus), and dogs (Canis familiaris). Chapter 1 reviews the substantial contribution palaeogenomics has made to the study of animal domestication, and details the latest theoretical and empirical advances, alongside individual profiles of sixteen major domestic species. Chapter 2 reconstructs the allele frequency trajectories of genetic variants linked to quantitative traits in genome-wide associations studies (GWAS) of cattle and horses. Using a Bayesian modelling approach, and a dataset of more than 350 ancient genomes spread across the last 10,000 years, the age of the allele under selection for thousands of GWAS variants is inferred, along with the selection coefficients for hundreds of polygenic traits. Chapter 3 analyses the first ancient genome-wide DNA from pre-contact North American dogs. Admixture analyses show that the earliest American dogs were not independently domesticated, and originated from a population of arctic dogs in Eastern Siberia. These dogs likely accompanied humans during the peopling of the continent, and rapidly diversified after their arrival, until their sudden replacement following the arrival of European colonists. Remarkably, their most closely related living relatives are now an 8,000-year-old contagious cancer clone known as Canine Transmissible Venereal Tumour (CTVT). Chapter 4 presents an ancestry analysis of a rare breed of ...