Diachonic DNA Analyses of Animal Breeds and Populations

Abstract

Humans are dependent on the animals they raise and breed for food and secondary products. Archaeological and genetic investigations can provide critical insights into the history and development of these breeds and help understand human activities in the past. Furthermore, many well-adapted breeds are endangered and archaeological and genetic data can help inform future breed conservation choices. Utilising ancient DNA data could potentially permit detailed diachronic analyses of the development of animal breeds. Ancient DNA analyses have typically focussed on large-scale biogeographic patterns in time and space, such as the spread of domesticates or the movements of peoples. Few studies have attempted fine-scale diachronic analysis within single animal populations or breeds. This is largely due to restricted sample availability and the limited phylogenetic resolution provided by the mitochondrial genome, the most commonly used ancient DNA marker. In this thesis, I demonstrate that fine-scale diachronic analyses within single animal populations and breeds over short time scales are feasible. First, in order to address the limitations of sample size, I assessed three sample screening methods’ abilities (maximum mitochondrial DNA amplicon length, NanoDrop® spectrometry and collagen preservation) to select samples in which DNA was preserved and analysed the utility of parchment as a novel source of ancient and historic DNA. None of the screening methods accurately predicted DNA preservation, but collagen preservation was able to weed out extremely poorly preserved samples from further analysis. All but one of the tested parchments produced multiple sequences matching several different species. Parchment therefore was not appropriate for fine-scale diachronic analyses. Next, I assessed whether analysing the nuclear genome could permit fine-resolution diachronic genetic studies. Since single nucleotide polymorphisms are ideal candidate nuclear markers for diachronic DNA analyses, I assessed the accuracy of the nuclear SNP-typing methodology, SNaPshot™, by genotyping three coat colour markers for a sample of historic Thoroughbred horses for which both phenotypic and correct genotypic information were known from pedigree information in the General Stud Book. The SNaPshot™ protocol was found to provide accurate genotypic information in all cases. Finally, as a proof of method, I compared the diachronic information provided by the mitochondrial and nuclear genomes in Icelandic and Thoroughbred horses. Specifically, in the Icelandic horse, I analysed the mitochondrial D-loop and three coat colour genes in modern and historic populations. In the Icelandic horse, I found statistically significant evidence for genetic change in the mitochondrial genome over the last 150 years. I found no evidence for change in coat colour allele frequencies. Conversely, in the biased and small historic Thoroughbred dataset, the mitochondrial genome was insufficient to provide population-level information, but I was able to show that allele frequencies in the nuclear MSTN gene, a gene previously shown to influence racing performance, have changed significantly in the past century.