Hayley Hassler, QBioS Thesis Proposal

Quantitative Biosciences Thesis Proposal
Hayley B. Hassler
School of Chemistry and Biochemistry

Phylogenomics of 3,126 archaeal and bacterial genera challenges a monophyletic origin of life
Tuesday, July 16, 2024, at 10:00 am
In Person Location: IBB 1316
Zoom Link: https://gatech.zoom.us/j/93333767189?pwd=6JCGYvd7f6Cwhhqafii91aD4O2pZg1.1
Open to the Community

Advisor: 
Dr. Loren Dean Williams (School of Chemistry and Biochemistry)

Committee Members:
Dr. William C. Ratcliff (School of Biological Sciences)
Dr. Eberhard O. Voit (Department of Biomedical Engineering)
Dr. Amit R. Reddi (School of Chemistry and Biochemistry)

Abstract:
The breadth of sequenced bacterial and archaeal genomes has increased exponentially over the past three decades. Utilizing this sequence data, previous studies have performed various comparative genomics analyses to gain insight into the genetic content, functionality, and ecology of the last universal common ancestor (LUCA). However, while more recent studies utilize ample genomes, their lack of diversity inhibits extensive identification of universal genes between the archaeal and bacterial domains. Furthermore, these studies operate under the assumption of a monophyletic origin of life, where the genetic content of LUCA is a singularity from which all extant life originated. Here, we propose an alternate hypothesis: polyphyletic origins of life. By examining the history of archaea and bacteria from this perspective, we consider their lineages as the remnants of pre-LUCA communities, redefining LUCA not as an ancestor but as the last universal exchange of genetic material. We address both origin hypotheses using all taxonomically named genera available from NCBI for archaea (n = 144) and bacteria (n = 2,982), encompassing five times the diversity of previously analyzed genomes. This extensive dataset has enabled the identification of an expanded universal gene set (n=155) and, for the first time, classification of 289 archaeal-specific and 187 bacterial-specific homologous genes. Phylogenomic comparative analyses of the evolutionary histories of these genes revealed no significant difference in their relative ages, suggesting concurrent evolution between the genes consistent with polyphyletic origins of life. Our findings challenge the conventional monophyletic paradigm, proposing a more complex evolutionary history leading to LUCA. This polyphyletic perspective has significant implications for understanding the evolutionary processes and horizontal exchanges that shaped early life, underscoring the need to re-evaluate prevailing models of early evolution and the fundamental mechanisms that have driven the diversification of life on Earth.