The investigators will analyze the genomic DNA of bacteria in order to understand the order in which major biological innovations occurred during the last 4 billion years. They will analyze DNA insertions and deletions within genes in order to determine which bacterial groups branched first within the tree of life. This process, called rooting, allows one to date early events in the evolution of life on Earth, such as the creation of 20% of Earth's atmosphere by the oxygen producing cyanobacteria. Their lab will correlate the appearance of novel molecular and genetic mechanisms, including oxygenic photosynthesis, with geological, climatological, and other environmental changes and thereby help understand early evolutionary events.
Rooting the bacterial tree of life may contribute significantly to related scientific fields including microbiology, geology, paleontology, biochemical evolution, and genomics. The knowledge thereby obtained may also have important practical applications related to climate change and renewable energy sources. Representatives of underrepresented groups will also be involved in the research.
This project has been enormously successful, and I thank NSF for supporting it. The goals of the project are to find new methods to reconstruct the rooted history of life on Earth that accurately represents the two major mechanisms of molecular evolutionary change. Evolutionary biologists are now learning about these two major evolutionary mechanisms. In the past, evolutionary studies exclusively emphasized Darwinian (survival of the fittest) tree-like evolution, and reconstructed trees from genomic data. But today we find that evolution also has another, softer side called cooperative (endosymbiotic) evolution - which produces convergent evolution. In convergent evolution, two organisms come together to produce a new type of organism. When tree like- and convergent- evolution are both present, they produce Rings. In the past, there have been few, if any, methods for reconstructing evolutionary rings. Through this grant we have had considerable success reconstructing rings. In the first year of this project, we demonstrated that the Double Membrane Prokaryotes originated though an endosymbiotic merger of a Firmicute and an Actinobacterium (Lake, J. A., Evidence for an Early Prokaryotic Endosymbiosis, Nature, 406, 967-971, 2009). Subsequently using the presences and absences of genes in Rings analyses, similar to how nucleotides within genes are used during sequence analyses, we have developed methods to reconstruct the rooted rings of life. Recently this work, was presented at the 2013 SMBE meetings in the Session on "Large Genome Flows", and was enthusiastically received! Currently, the first methods paper is under review, and I think that we can now see our way clear to reconstructing the early evolution of life and interpreting the major changes that have occurred over the last 3.5+ Billion years. NSF support has been critical to getting to this point.
