Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies [article]

Ashok Rajaraman, Cedric Chauve, Yann Ponty (INRIA Saclay Ile de France, LIX)
2015 arXiv   pre-print
The availability of a large number of 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. allows the computation of 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 generates
more » ... imilar parsimonious evolutionary scenarios for gene adjacencies, as well as the robustness to changes to the cost scheme of evolutionary events of the presence or absence of specific ancestral gene adjacencies. We apply our method to six thousands mammalian gene families, and show that computing the robustness to changes to cost schemes provides new and interesting insights on the evolution of gene adjacencies and the DeCo model.
arXiv:1503.05292v2 fatcat:ympjtt44rnbdxhennuqbjekcma