  Given a sample of genome sequences from an asexual population, can one
predict its evolutionary future? Here we demonstrate that the branching
patterns of reconstructed genealogical trees contains information about the
relative fitness of the sampled sequences and that this information can be used
to predict successful strains. Our approach is based on the assumption that
evolution proceeds by accumulation of small effect mutations, does not require
species specific input and can be applied to any asexual population under
persistent selection pressure. We demonstrate its performance using historical
data on seasonal influenza A/H3N2 virus. We predict the progenitor lineage of
the upcoming influenza season with near optimal performance in 30% of cases and
make informative predictions in 16 out of 19 years. Beyond providing a tool for
prediction, our ability to make informative predictions implies persistent
fitness variation among circulating influenza A/H3N2 viruses.
