An Analysis of Alu Elements in Baboons

Transposable elements compose a large portion of mammalian genomes and are estimated to make up anywhere from ~45% - ~70% of the human genome. Alu elements are primate-specific retrotransposons that are found in high copy number (\u3e 1 million copies) and are spread throughout the genome. These elements are the most commonly repeated sequence in the human genome and have contributed to a number of disease states in humans. Alu elements are useful markers for population genetics and phylogenetics and have proven valuable in understanding difficult to determine relationships between species and within populations. Baboons (genus Papio) are spread throughout sub-Saharan Africa and are commonly used in cardiovascular studies due to their physiological and anatomical similarity to humans. Six species compose genus Papio, all differentiated by morphological features (primarily size and color). While each species appears to be distinct, a number of studies report regular interbreeding between them. Recent work on the genome of baboons has found that they possess the highest rate of Alu element mobilization of any primate genome studied thus far. This dissertation utilizes Alu elements that have recently inserted in the baboon genome to determine population structure within different baboon species. Using these elements, we are also able to determine if a specified individual is the product of hybridization between two parents from different baboon species or if they are potentially individuals that have migrated from their natal troop. This dissertation also examines subfamilies of Alu elements that are lineage-specific to baboons. These insertion events have occurred since the baboon and macaque lineages diverged about 8.5 million years ago. Over 100 novel Alu subfamilies were uncovered during these experiments, supporting the work of the baboon genome consortium, which found that there is a rapid mobilization rate of Alu elements in the baboon lineage. This work on a model organism for cardiovascular disease continues to expand our knowledge in the field of comparative genomics