Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach
Abstract
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 Berard 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.