Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material

The availability of many assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context. The DeCo algorithm, recently introduced by Bérard et al., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. Following the approach pioneered by Sturmfels and Pachter, we describe how to modify the DeCo dynamic programming algorithm to identify classes of cost schemes that generate similar parsimonious evolutionary scenarios for gene adjacencies. We also describe how to assess the robustness, again to changes of the cost scheme, of the presence or absence of specific ancestral gene adjacencies in parsimonious evolutionary scenarios. We apply our method to six thousands mammalian gene families, and show that computing the robustness to changes of cost schemes provides interesting insights on the DeCo model.