Evolutionary ancestor inference via genome rearrangement

Zaky Adam, Université D'Ottawa / University Of Ottawa, Université D'Ottawa / University Of Ottawa
2013
Inferring ancestral gene orders in a phylgenomic tree is an important topic in comparative genomics. In this thesis, three different approaches have been used to infer ancestors, first, using common intervals in a model-free approach and extending it to using common clusters and neighbourhood parameter; second, using double cut and join operation (DCJ); third, using breakpoint distance. A statistically fair comparison between the performance of DCJ and breakpoint criteria ends the thesis. Away
more » ... rom any assumptions or considerations, probabilistic or combinatorial, about specific processes involved in rearranging genomes, we present a new phylogenetic reconstruction method based solely on common intervals. The objective function to be optimized is simply the sum over the tree branches of the symmetric difference between the two sets of intervals associated with the genomes at the two ends of the branch. To achieve this goal, we use dynamic programming optimization to determine the presence of common intervals at the ancestral nodes of the phylogeny. Noticing the drawback that the concept of common intervals suffers from, we introduce the concept of generalized adjacency to find common clusters using a neighborhood parameter that turns out to be closely related to the bandwidth parameter of a graph. Our focus will be on how this parameter affects the characteristics of clusters: how numerous they are, how large they are, how rearranged they are and to what extent they are preserved from ancestor to descendant in a phylogenetic tree. Again, we use dynamic programming optimization to determine the presence of individual edges at the ancestral nodes of the phylogeny. The DCJ (double cut and join) operation introduced by Yancopoulos et al. in 2005 is the most inclusive operation to date as it can generate all the movement rearrangements. One year later, Bergeron et al. restated the DCJ model and produced a simplified (linear) algorithm, which is now the most general existing algorithm to transform one genome into anoth [...]
doi:10.20381/ruor-13219 fatcat:6yv67zoxergghbxsyhne6gieq4