  A halo merger tree forms the essential backbone of a semi-analytic model for
galaxy formation and evolution. Recent studies have pointed out that extracting
merger trees from numerical simulations of structure formation is non-trivial;
different tree building algorithms can give differing merger histories. These
differences should be carefully understood before merger trees are used as
input for models of galaxy formation. We investigate the impact of different
halo merger trees on a semi-analytic model. We find that the z=0 galaxy
properties in our model show differences between trees when using a common
parameter set. The star formation history of the Universe and the properties of
satellite galaxies can show marked differences between trees with different
construction methods. Independently calibrating the semi-analytic model for
each tree can reduce the discrepancies between the z=0 global galaxy
properties, at the cost of increasing the differences in the evolutionary
histories of galaxies. Furthermore, the underlying physics implied can vary,
resulting in key quantities such as the supernova feedback efficiency differing
by factors of 2. Such a change alters the regimes where star formation is
primarily suppressed by supernovae. Therefore, halo merger trees extracted from
a common halo catalogue using different, but reliable, algorithms can result in
a difference in the semi-analytic model. Given the uncertainties in galaxy
formation physics, however, these differences may not necessarily be viewed as
significant.
