Doctor of Philosophy (PhD)


Biological Sciences

Document Type



Alu elements are primate specific retrotransposons that have remained active throughout the course of primate evolution. As a result of this sustained mobilization. Alu elements are present in greater copy number in primate genomes than any other transposable element. An average of over one million Alu elements has been identified in every sequenced haplorrhine genome to date. These characteristics qualify Alu elements as ideal characters for studying evolutionary relationship among primates.

The increasing availability of whole genome sequencing data presents novel challenges and opportunities for comparative genomic analyses. Genomic data is now publicly available for most primate species. Such an abundance of resources allows researchers to re-examine previously unresolved or unexplored evolutionary relationships applying a comprehensive whole genome approach. The implications of such research models for studying human biology and evolution. Historically, the Old World monkey primate models has been a popular choice for investigating the human condition. More specifically, no catarrhine taxon has been exploited more extensively than those belonging to the Papionini tribe.

This dissertation describes an innovation computational method suitable for examining complex phylogenetic relationships among primates. Furthermore, it utilizes a quickly expanding database of publicly available whole genome sequencing data to perform phylogenetic and population genetic analyses. Through an integrative approach, the reported algorithm can identify Alu insertions indicative of hybridization and admixture. In addition, this method can be used to construct fully resolved cladograms despite well-documented histories of admixture and hybridization.



Committee Chair

Batzer, Mark