Date of Award


Document Type

Honors Thesis

Degree Name

Bachelor of Science


Biological Science


Despite the close relationship humans share with chimpanzees, the evolutionary history of this species is relatively unknown. Due to its high copy number and high mutation rate, population genetic analyses of chimpanzees have focused on a 1.1 kilo-­‐base segment of mitochondrial DNA (mtDNA) known as the control region. Earlier work based on analyses of the hypervariable region 1 (HVR-­‐1), one of two fragments that make up the control region, support the separation of Upper Guinea and Gulf of Guinea chimpanzees into a monophyletic group separate from Central and East African chimpanzees. I aimed to compare and contrast the chimpanzee mtDNA coding region phylogeny to the mtDNA complete genome phylogeny to analyze the effects of removing the control region. Through this investigation it can be inferred whether analysis of the coding region maintains the relationships between taxa without losing substantial resolution. The second goal of this research was to identify fixed differences outside the control region. In the present study, 59 chimpanzee and bonobo mtDNA genomes were analyzed. Alignments were generated in preparation for the creation of four phylogenies, (complete genome, coding region, entire control region, hyper variable region 1), using the program Geneious. The program Network was also applied to examine the patterns of diversity within each subspecies and to identify fixed differences. The mtDNA coding region tree inferred the same general relationships between taxa as that proposed by the mtDNA complete genome. The branches of the mtDNA complete genome tree, however, are slightly better resolved due to the high mutation rate of the control region. Although previous and current analysis of mtDNA yields informative phylogenies, the conclusions drawn from this research and past investigations is limited to the relationship between females of this species as mtDNA is maternally inherited. Through subsequent studies of several types of molecular data, a better understanding of the chimpanzee lineage can be achieved. In addition 143 fixed differences were identified that could aid in subspecies classification in future investigations of chimpanzee fecal samples.