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Darwin's Coral of Life, Gene Transfer, and Inferring Properties of the Early Biosphere

Presenter: Peter Gogarten, University of Connecticut
When: April 29, 2013 11AM PDT

Horizontal gene transfer and gene duplications play central roles in the creation of new metabolic pathways and in the adaptation of organisms to new ecological niches. While these processes constitute important evolutionary mechanisms, they also create major obstacles to reconstructing organismal evolutionary history from molecular data; however, these processes also provide an exciting opportunity to extend studies of molecular evolution to the time before the Last Universal Common Ancestor (LUCA), aka the organismal cenancestor of all life.

Horizontal Gene Transfer (HGT) plays an essential role in sharing innovations between distantly related organisms. Even multicellular organisms continue to benefit from HGT, either directly into the nuclear genome, or into the genome of symbiotic microorganisms. Pathways, such as oxygen producing photosynthesis and acetoclastic methanogenesis likely were assembled to their present form through HGT. Because of HGT the most recent common ancestors of different molecules did not all coexist in the organismal most recent common ancestor, aka the Last Universal Common Ancestor (LUCA). The molecular cenancestors existed in different lineages and at different times. Reconstructing the amino acid composition of ancestral sequences allows to root the ribosomal phylogeny (calculated from ribosomal proteins), and provides information on which amino acids were late additions to the genetic code. Despite infrequent inter domain gene transfer, the deep split in molecular phylogenies between the Archaea and Bacteria is reflected in most molecular phylogenies, confirming the fundamental division between the two domains of life.

Although the deep branches in many phylogenies derived from molecular data are occupied by extreme thermophiles, the echo from the assembly of the genetic code detectable in the early parts of the tree/web of life is not compatible with a hyperthermophilic LUCA. The compositional analysis of ancestral sequences, the late heavy bombardment (LHB) hypothesis, and consideration of tree shape suggest that the bottleneck and selection for hyperthermophyly at the base of the archaeal and bacterial domains was due to the LHB, and that life is older than the LHB.

Sequence reconstruction for enzymes that diverged before the organismal LUCA confirms some amino acids as late additions to genetic code, but also suggests that for most amino acids other tRNA charging mechanisms existed that preceded the currently known aminoacyl tRNA synthetases.

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