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Biochemistry, Biophysics, and Structural Biology Commons

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Retrospective Theses and Dissertations

2003

Evolution and organismal biology

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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Protein Structure, Distribution Of Homoplasy And Phylogenetic Inference , Olivier Fedrigo Jan 2003

Protein Structure, Distribution Of Homoplasy And Phylogenetic Inference , Olivier Fedrigo

Retrospective Theses and Dissertations

All molecular phylogenetic methods are based on two assumptions: independence of characters and constant selective pressure. It is well known that these assumptions are often violated, but it is assumed that the methods are robust to such violations. However, the increase of unorthodox phylogenies makes us wonder about their reliability. None of the currently used phylogenetic methods and models account for a change of functional/structural constraint at the protein level. In order to understand the consequences on the phylogenetic inference, I studied the distribution of the structural/functional misleading phylogenetic signal in the tree and described the effect of ...