We analyze sensitive, sub-arcsecond resolution ALMA Science Verification observations of CO emission lines in the protoplanetary disk hosted by the young, isolated Ae star HD 163296. The observed spatial morphology of the 12CO J=3-2 emission line is asymmetric across the major axis of the disk; the 12CO J=2-1 line features a much less pronounced, but similar, asymmetry. The J=2-1 emission from 12CO and its main isotopologues have no resolved spatial asymmetry. We associate this behavior as the direct signature of a vertical temperature gradient and layered molecular structure in the disk. This is demonstrated using both toy models and more sophisticated calculations assuming non-local thermodynamic equilibrium (non LTE) conditions. A model disk structure is developed to reproduce both the distinctive spatial morphology of the 12CO J=3-2 line as well as the J=2-1 emission from the CO isotopologues assuming relative abundances consistent with the interstellar medium. This model disk structure has tau=1 emitting surfaces for the 12CO emission lines that make an angle of about 15 degrees with respect to the disk midplane. Furthermore, we show that the spatial and spectral sensitivity of these data can distinguish between models that have sub-Keplerian gas velocities due to the vertical extent of the disk and its associated radial pressure gradient (a fractional difference in the bulk gas velocity field of approximately greater than 5%).
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