In partial fulfillment of the requirements for the degree of

Doctor of Philosophy in Biology

In the

School of Biological Sciences

Autumn Peterson

Will defend her dissertation

Using synthetic biology and experimental evolution to reconstruct major evolutionary innovations

19, November 2025 at 2:30 PM ET

Engineered Biosystems Building (EBB), CHOA seminar room EBB 1005

Meeting link: https://gatech.zoom.us/j/94935218803?pwd=mhRaWhhZYhUNXKs0Mi7LbuCqrvNayd.1

 Thesis Advisor:

William Ratcliff, Ph.D.

School of Biological Sciences

Georgia Institute of Technology

Committee Members:

Ozan Bozdag, Ph.D.

School of Biological Sciences

Georgia Institute of Technology

Annalise Paaby, Ph.D.

School of Biological Sciences

Georgia Institute of Technology

Frank Rozenweig, Ph.D.

School of Biological Sciences

Georgia Institute of Technology

John Blazeck, Ph.D.

School of Chemical and Biomolecular Engineering

Georgia Institute of Technology

ABSTRACT: Evolutionary innovations have shaped the history of life on Earth. This thesis uses synthetic biology and experimental evolution to explore the origin of phototrophic metabolism and the evolution of multicellularity in yeast. 

The first part of this work examines whether a retinalophototrophic system can be readily acquired by an organism with no prior history of phototrophy. We transformed unicellular Saccharomyces cerevisiae into a facultative photoheterotroph by inserting a rhodopsin into the yeast vacuole, allowing light to translocate protons into the vacuolar compartment, a function typically driven by consuming ATP. We show that yeast-bearing rhodopsins gain a selective advantage when grown under green light, growing more rapidly than their non-phototrophic ancestor. This work demonstrates the remarkable ease with which rhodopsins may be horizontally transferred, providing novel biological function without the need for prior evolutionary optimization. 

                Next, we explored the role of nascent life cycle structures on the evolution of collective-level adaptations. All complex multicellular lineages (animals, plants, brown algae, red algae and fungi) develop clonally and are obligately multicellular. We used S. cerevisiae to engineer a facultative life cycle (alternating between single cell and multicellular clusters) and compared it to obligate multicellularity. Using experimental evolution, we found that all obligately multicellular populations evolved larger multicellular size and tetraploidy, a known multicellular trait. These traits were severely constrained in facultative populations, despite tetraploidy being strongly beneficial across the full life cycle. We show that facultative life cycles create an establishment barrier through population asymmetries due to group formation reducing the number of units of selection, coupled with cell-level selection dominating group-level selection. These findings demonstrate that the presence of a unicellular stage creates genetic barriers to multicellular adaptations, which may explain why facultatively multicellular organisms have remained simple compared to complex multicellularity seen only in obligately multicellular organisms. 

Together, this thesis advances our understanding of early steps in evolutionary innovations, with a focus on the origin of phototrophy and the role of obligate life cycles during the transition to multicellularity.