  We compare the shapes and intrinsic alignments of galaxies in the
MassiveBlack-II cosmological hydrodynamic simulation (MBII) to those in a dark
matter-only (DMO) simulation performed with the same volume
(100$h^{-1}$Mpc)$^{3}$, cosmological parameters, and initial conditions.
Understanding the impact of baryonic physics on galaxy shapes and alignments
and their relation to the dark matter distribution should prove useful to map
the intrinsic alignments of galaxies from hydrodynamic to dark matter-only
simulations. We find that dark matter subhalos are typically rounder in MBII,
and the shapes of stellar matter in low mass galaxies are more misaligned with
the shapes of the dark matter of the corresponding subhalos in the DMO
simulation. At $z=0.06$, the fractional difference in the mean misalignment
angle between MBII and DMO simulations varies from $\sim 28 \% - 12 \%$ in the
mass range $10^{10.8} - 6.0 \times 10^{14} h^{-1}M_{\odot}$. We study the dark
matter halo shapes and alignments as a function of radius, and find that while
galaxies in MBII are more aligned with the inner parts of their dark matter
subhalos, there is no radial trend in their alignments with the corresponding
subhalo in the DMO simulation. This result highlights the importance of
baryonic physics in determining the alignment of the galaxy with respect to the
inner parts of the halo. Finally, we compare the ellipticity-direction (ED)
correlation for galaxies to that for dark matter halos, finding that it is
suppressed on all scales by stellar-dark matter misalignment. In the projected
shape-density correlation ($w_{\delta+}$), which includes ellipticity
weighting, this effect is partially canceled by the higher mean ellipticities
of the stellar component, but differences of order $30-40\%$ remain on scales
$> 1$ Mpc over a range of subhalo masses, with scale-dependent effects below
$1$ Mpc.
