SCOL Project: Genome Stratigraphy:Physiological and Temporal Reconstruction of Early Life
Life has been present on Earth for most of its 4.5 billion year history. However, the geological record of a living planet becomes increasingly scant as it progresses backwards through time. Biology-associated rock signatures such as fossils, geochemical changes, and lipid biomarkers become scarcer and more ambiguous with increased age; few rocks even remain from before 3.8 billion years ago. Because of this lack of geological evidence, we have a very limited understanding of the conditions on the early Earth under which life originally evolved and diversified. Consequently, from this record alone we can directly infer little about the physiological nature of life during its origin and earliest evolution, or the timing of these events. Finding answers to these questions requires another planetary record that has not yet been fully utilized, the record preserved within the inherited genomes of organisms living today.
The proposed work will probe this genomic record in order to develop a more comprehensive understanding of life’s beginnings. This will be accomplished by developing novel computational techniques for analyzing and comparing genome sequence data across the Tree of Life. The projects described in the major aims of this work will each investigate a distinct line of evidence using these techniques. These investigations will include reconstructing the ancient functions of proteins involved in the founding of the genetic code before the common ancestor of extant life; mapping the histories and origins of genes responsible for primitive metabolisms and ecologies in ancient lineages; and using changes in gene sequences over time as a “molecular clock”, cross-calibrated by horizontal gene transfers across the Tree of Life. A more accurate dating of events in early evolution is an especially important result of this work, as it is necessary for understanding the causal relationships between the genomic and geological records, and the significance of major planetary events in life’s origins, such as the Late Heavy Bombardment.
Taken together, these investigations promise to further constrain our temporal, ecological, and mechanistic understandings of the earliest events in Earth’s history, firmly rooted in both geological and biological perspectives.
Greg Fournier holds a B.A. in Genetics from Dartmouth College (2001) and a Ph.D. in Genetics and Genomics from the University of Connecticut (2009), where his thesis work focused on the early evolution of the genetic code. Following his graduate work, he was awarded a NASA Astrobiology Institute postdoctoral fellowship, which he brought to the Department of Biological Engineering at the Massachusetts Institute of Technology. During his postdoctoral fellowship he investigated the role of horizontal gene transfer in early protein evolution, and the reconstruction of ancient protein sequences. He is currently an Assistant Professor of Geobiology in the Department of Earth, Atmospheric and Planetary Sciences at the Massachusetts Institute of Technology, and holds joint appointments with both Woods Hole Oceanographic Institute and the interdepartmental MIT Microbiology Program. His current research focuses on integrating the genomic and geochemical records of life on Earth, and dating early events in microbial evolution. Ongoing projects in the lab include using horizontal gene transfer events and phylometabolomics to better constrain microbial molecular clock studies, exploring the role of recombination in ancient gene transfer events and phylogenies, and dating the origins of methanogenesis, bacterial phototrophy, and the major Domains of life.