The general objectives of this proposal are to relate the phylogenetic trees derived from molecular sequences from extant taxa to the geological, paleontological, and biochemical records; to changes in the atmosphere and biota; and to the origin of present day life. Three specific objectives are: (1) to test theories for the origin of the eukaryotic nucleus and to seek to identify its prokaryotic sister taxon; (2) to relate phylogenetic trees to the origin of metabolic innovations, such as the beginnings of photosynthesis, oxygen production, methanogenesis, and sulfur reduction and oxidation; and (3) to relate the phylogenetic tree to the fossil and geological records, through correlation with such factors as the time of appearance of oxygen in the atmosphere, the isotopic abundances of sulfur and carbon, the appearance of prokaryotic fossils, and with endosymbiotic events. Specific goals are to sequence three molecules (EF-Tu, Ef-G, and the trp B gene) from a diverse group of twelve taxa that exhibit metabolic innovations that are essential to understanding early events in life. Phylogenetic trees will be inferred, paying particular attention to artifacts of sequence alignment deriving unrooted phylogenetic trees from molecular sequences. The EF-Tu and trp B genes are particularly useful because they have low rates of nucleotide substitution and because EF-Tu and EF-G arose through an early gene duplication so that the tree can be rooted using these paralogous genes. Taxa have been chosen to assist in identifying the sister taxon to the eukaryotic nucleus, and to be useful in asking what were the earliest types of metabolisms.
