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.
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