Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Theses & dissertations (Interdisciplinary)


Genetics; Ecology and Evolutionary Biology;

First Advisor

Gavin J. P. Naylor


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 change of constraint at the protein level on the DNA substitution pattern.;While randomly distributed, homoplastic changes cancel "each other" and can be considered as background noise. However, homoplastic events due to independent change in hydrophobic constraint tend to accumulate in some parts of the tree and can be misleading. A method has been implemented (DISECT) to estimate the distribution of such homoplasies and to improve the tree inference with a partial down-weighting scheme.;Change of constraint at the protein level can influence the DNA substitution pattern. The software program DRUIDS has been designed to detect anomalies in substitution pattern due to a change of constraint. Analysis of four cytochrome b datasets shows that the same regions exhibit a deviation from stationarity in amino acid hydrophobicity and volume and have a high substitution rate. In addition, these regions fail the HKY model of evolution and cluster in areas that interact with neighboring proteins in the bc1 complex. Local constraints change frequently in interacting areas and compensatory substitutions occur to maintain the fitness of the bc1 complex phenotype. Similar study of a protein that interacts with cytochrome b (Subunit 7) confirms these results. A close look at the genetic code structure shows an asymmetry of nucleotide substitutions when there is a change of residue hydrophobicity and volume and current molecular model of evolution do not accommodate such biases.;The results of this dissertation suggest that molecular phylogenetic models and methods should account for more biology to be more reliable.



Digital Repository @ Iowa State University,

Copyright Owner

Olivier Fedrigo



Proquest ID


File Format


File Size

163 pages