Reconciliation methods aim at recovering macro evolutionary events and at
localizing them in the species history, by observing discrepancies between gene
family trees and species trees. In this article we introduce an Integer Linear
Programming (ILP) approach for the NP-hard problem of computing a most
parsimonious time-consistent reconciliation of a gene tree with a species tree
when dating information on speciations is not available. The ILP formulation,
which builds upon the DTL model, returns a most parsimonious reconciliation
ranging over all possible datings of the nodes of the species tree. By studying
its performance on plausible simulated data we conclude that the ILP approach
is significantly faster than a brute force search through the space of all
possible species tree datings. Although the ILP formulation is currently
limited to small trees, we believe that it is an important proof-of-concept
which opens the door to the possibility of developing an exact, parsimony based
approach to dating species trees. The software (ILPEACE) is freely available
for download