A tree has been the organizing image to explain the relationships among living creatures since before Darwin's explanations for natural descent. The modern practice of comparing DNA and protein sequences to discern these relationships, however, has revealed complexities in the process of descent never before imagined. Organisms, particularly microbes, evolve by horizontal as well as vertical inheritance of traits with different groups of organisms exchanging genes, in addition to passing them down to the next generation. This research project addresses the question: Can the large scale structure of the tree/web of life be discerned? While the current data may be interpreted to mean that the depiction of life's history as a single bifurcating tree is incomplete, this should not be seen as justification to give up on reconstructing life's history. The working hypothesis underlying this research is that a reconstruction of life's early history is indeed possible, provided care is taken to guard against artifacts and that new, informative molecular characters are added to the analyses. Four complementary approaches will be used to address the question through analyses of microbial genome sequences. (1) Genome sequence data will be examined to find ancient horizontal gene transfer events that created useful taxonomic characters. An automated genome analysis pipeline will be developed to find these events, and these characters will be incorporated into new examinations of evolutionary relationships. (2) Complete genome sequences allow comparisons of all the genes of an organism with those of others to measure their evolutionary relatedness. However, the impact of horizontal acquisition of genes on these analyses is unknown. Computer simulations and genome sequences from two unrelated groups of microbes that have undergone extensive horizontal gene transfer, the Haloarchaea and the Thermotogales, will be used to gauge the extent to which different phylogenomic approaches are impacted by highways of gene sharing between different groups of organisms. (3) A public database will be constructed to store information on all putatively identified gene transfer events. This database will be a valuable resource for the wider scientific community to trace the role of gene transfer in the assembly of metabolic pathways and to examine the adaptation of organisms to new ecological niches. (4) The nature of the last common ancestor of all living creatures, the trunk of the tree of life, has been difficult to discern given all the changes in nucleotide composition that have occurred during evolutionary time. A compositional analysis will be used to detect the remaining signal of the genetic code's expansion that occurred early in life's history in order to "root" the tree of life. These in-depth analyses of several prokaryotic and eukaryotic genomes will offer insights into the impacts of horizontal gene transfer on genome evolution and phylogenetic reconstructions, as well as identify natural groups in the tree of life and help to resolve its deep structure. Unraveling the structure of the tree of life will have percussions in all fields of biology.
This research program and its associated education activities will provide an ideal training ground in which high school, undergraduate, and graduate students along with postdoctoral fellows can learn about genome and organismal evolution. Plans are for three postdoctoral fellows, nine graduate students, and about twenty undergraduate and high school students to be trained through computational and laboratory research experiences. The goal is to train computer scientists and biologists to become experts in their respective disciplines and to become effective in trans-disciplinary communication; thereby enabling successful interdisciplinary collaborations. Results from the proposed research will be introduced into related courses on three campuses and will be accessible through an integrated database, which also includes a forum for public discussions on topics related to gene transfer and organismal evolution.
