  Turbulence is the leading candidate for angular momentum transport in
protoplanetary disks and therefore influences disk lifetimes and planet
formation timescales. However, the turbulent properties of protoplanetary disks
are poorly constrained observationally. Recent studies have found turbulent
speeds smaller than what fully-developed MRI would produce (Flaherty et al.
2015, 2017). However, existing studies assumed a constant CO/H2 ratio of 0.0001
in locations where CO is not frozen-out or photo-dissociated. Our previous
studies of evolving disk chemistry indicate that CO is depleted by
incorporation into complex organic molecules well inside the freeze-out radius
of CO. We consider the effects of this chemical depletion on measurements of
turbulence. Simon et al. (2015) suggested that the ratio of the peak line flux
to the flux at line center of the CO J=3-2 transition is a reasonable
diagnostic of turbulence, so we focus on that metric, while adding some
analysis of the more complex effects on spatial distribution. We simulate the
emission lines of CO based on chemical evolution models presented in Yu et al.
(2016), and find that the peak-to-trough ratio changes as a function of time as
CO is destroyed. Specifically, a CO-depleted disk with high turbulent velocity
mimics the peak-to-trough ratios of a non-CO-depleted disk with lower turbulent
velocity. We suggest that disk observers and modelers take into account the
possibility of CO depletion when using line peak-to-trough ratios to constrain
the degree of turbulence in disks. Assuming that CO/H2 = 0.0001 at all disk
radii can lead to underestimates of turbulent speeds in the disk by at least
0.2 km/s.
