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Open Access Publications from the University of California

Reconstructing Phylogenetic Rings and Their Application

  • Author(s): Larsen, Joseph Robert
  • Advisor(s): Sinsheimer, Janet S
  • et al.

Phylogenetic rings represent evolution on a taxanomic scale through convergent ( genome fusion events) and divergent (phylogenetic tree-like events) gene flows. Rings have the potential to reconcile the inconsistent phylogenetic tree models that have been constructed from phenotypic evidence versus genotypic evidence. In order to exemplify this potential phylogenetic rings were applied here to investigate the origins of photosynthesis in the Proteobacteria. Another opportunity with-in phylogenetic ring research is developing a quantitative method to reconstruct the rings. The two methods explored here are Occam’s Ring, the simplest ring reconstruction, and the Ring Identification for Non-Generalized Structures (R.I.N.G.S.) method, a more in-depth ring reconstruction based on quantitative methods. Phylogenetic rings have the potential to help resolve many of the conundrums in modeling evolution, which phylogenetic trees have been unable to address. This thesis is another step in solving these issues by further developing phylogenetic rings.

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