Electronic Thesis and Dissertation Repository

Thesis Format

Integrated Article


Master of Science




Organelle genomes are known to have large sizes and substantial non-coding content, despite conserved coding regions and low substitution rates. Notably, volvocine green algae exhibit significant variation in plastid genome size, with some species harboring ptDNA ten times larger than the average. To explain this variability, my thesis explores two hypotheses. The first proposes that genetic divergence accumulates due to weak negative selection and genetic drift, resulting in similar evolution rates for coding and non-coding regions. The second suggests high evolution rates in non-coding sequences are due to error-prone repair mechanisms. Analyzing new plastid genomes from volvocine green algae, I found a potential for high silent-site substitution rates in intergenic regions. My analysis shows that these hypotheses can be applied to plastid genomes of close relatives to advance our understanding of the mechanisms of sequence evolution specific to non-coding DNA accumulation within the volvocine green algae.

Summary for Lay Audience

Scientists have been studying how the genetic code of species known as DNA can change. DNA is found in a cellular structure known as the nucleus and consists of a coding region and non-coding region. DNA can also be found in other special structures such as the mitochondrion and the plastid known as organelles. These organelles have different kinds of DNA and their DNA can change in different ways. My thesis is focusing on a group of green algae called Chlamydomonadales to understand why their organelle DNA varies so much in size. These algae have more DNA in their plastids compared to others in their group. I wanted to know why, so I looked at how their plastid DNA changes over time. I used two ideas to explain it. One idea was that the non-coding parts of the DNA change a lot because of how they're repaired. The other idea was that the changes happen at a slower rate overall. I compared the DNA of closely related species and found that the non-coding parts were changing faster than the coding parts, supporting the repair idea. By understanding these changes, we can learn more about why the DNA in these algae is so big and different.