The abundance and structure of dark matter subhalos has been analyzed
extensively in recent studies of dark matter-only simulations, but
comparatively little is known about the impact of baryonic physics on halo
substructures. We here extend the SUBFIND algorithm for substructure
identification such that it can be reliably applied to dissipative
hydrodynamical simulations that include star formation. This allows, in
particular, the identification of galaxies as substructures in simulations of
clusters of galaxies, and a determination of their content of gravitationally
bound stars, dark matter, and hot and cold gas. Using a large set of
cosmological cluster simulations, we present a detailed analysis of halo
substructures in hydrodynamical simulations of galaxy clusters, focusing in
particular on the influence both of radiative and non-radiative gas physics,
and of non-standard physics such as thermal conduction and feedback by galactic
outflows. We also examine the impact of numerical nuisance parameters such as
artificial viscosity parameterizations. We find that diffuse hot gas is
efficiently stripped from subhalos when they enter the highly pressurized
cluster atmosphere. This has the effect of decreasing the subhalo mass function
relative to a corresponding dark matter-only simulation. These effects are
mitigated in radiative runs, where baryons condense in the central subhalo
regions and form compact stellar cores. However, in all cases, only a very
small fraction, of the order of one percent, of subhalos within the cluster
virial radii preserve a gravitationally bound hot gaseous atmosphere.
(abridged)Comment: improved manuscript, to appear in MNRA