In partial fulfillment of the requirements for the degree of 

Doctor of Philosophy in Quantitative Biosciences

in the School of Biological Sciences

Kai Tong

Defends his thesis:

Title: Evolution of cell differentiation and whole genome duplication in a Multicellularity Long-Term Evolution Experiment

Monday, November 28, 2022

12:30pm Eastern Time

https://gatech.zoom.us/j/97494458860 

Open to the Community

Advisor:

Dr. William Ratcliff

School of Biological Sciences

Georgia Institute of Technology

Committee Members:

Dr. Annalise Paaby

School of Biological Sciences

Georgia Institute of Technology

Dr. Alberto Stolfi

School of Biological Sciences

Georgia Institute of Technology

Dr. Peter Yunker

School of Physics

Georgia Institute of Technology

Dr. Juha Saarikangas

Helsinki Institute of Life Science 

University of Helsinki

Abstract: 

The evolution of multicellular organisms from unicellular ancestors is considered a major transition in the history of life, but significant gaps remain in our understanding of how multicellularity originates and evolves. Over the last decade, experimental evolution has emerged as a powerful approach to study multicellular evolution in real time. Our lab has been conducting a Multicellularity Long-Term Evolution Experiment (MuLTEE), evolving the simple cluster-forming yeast Saccharomyces cerevisiae (snowflake yeast) with daily selection for larger size for 1000 days (~5000 generations). In my thesis, I used the MuLTEE to explore two widespread and impactful phenomena in the evolution of multicellularity: the evolution of cell differentiation, and whole genome duplication. 

First, using single-cell RNA sequencing, I identified the evolution of three cell states within individual clusters, which differentially upregulate ribosomal processes, mitochondrial gene expression and cell wall biogenesis, and stress response and apoptosis, respectively. These cell states display conserved gene expression signatures over evolution as well as isolate-specific features, and present interesting evolutionary dynamics characterized by the broad emergence and expansion of cellular heterogeneity with isolate-specific losses. 

Second, using quantitative microscopy and whole-genome sequencing, I revealed the convergent early emergence and long-term maintenance of tetraploidy from diploid ancestors, which is in striking contrast with previous studies in yeast where diploidy is stable while nascent tetraploidy rapidly reverts to diploidy. A synthetic construction and reversion experiment showed that under selection for larger size, tetraploidy provides an immediate fitness advantage, by producing larger, more elongated cells that yield larger clusters, while evolved tetraploids rapidly underwent ploidy reduction in the absence of size selection. 

Taken together, these results shed new light on how cell differentiation can evolve from simple groups of cells, and how the emergence and maintenance of polyploidy can be driven by continuous selection on its immediate phenotypic effects, further demonstrating the power of long-term experimental evolution in understanding the processes driving multicellular evolution.