Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

Overview & Synopsis

We consider a recently introduced dynamic programming scheme to compute parsimonious evolutionary scenarios for gene adjacencies. We extend this scheme to sample evolutionary scenarios from the whole solution space under the Boltzmann distribution. We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic inconsistencies observed in the resulting ancestral gene adjacencies.