RT Journal Article
SR Electronic
T1 Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 026310
DO 10.1101/026310
A1 Cedric Chauve
A1 Yann Ponty
A1 João Paulo Peirera Zanetti
YR 2015
UL http://biorxiv.org/content/early/2015/09/08/026310.abstract
AB Context The reconstruction of evolutionary scenarios for whole genomes in terms of genome rearrangements is a fundamental problem in evolutionary and comparative genomics. The DeCo algorithm, recently introduced by Bérard et al., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. However, as for many combinatorial optimization algorithms, there can exist many co-optimal, or slightly sub-optimal, evolutionary scenarios that deserve to be considered.Contribution We extend the DeCo algorithm to sample evolutionary scenarios from the whole solution space under the Boltzmann distribution, and also to compute Boltzmann probabilities for specific ancestral adjacencies.Results We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies.