In a high-resolution spectroscopic survey of rapidly oscillating Ap (roAp) stars with the Ultraviolet and Visual Echelle Spectrograph on the Very Large Telescope of the European Southern Observatory, we find that almost all stars show significant variation of the radial velocity amplitudes - on a time-scale of a few pulsation cycles - for lines of the rare earth ion Pr III and in the core of the Ha line. These variations in the radial velocity amplitudes are described by new frequencies in the amplitude spectra that are not seen in broad-band photometric studies of the same stars. The Pr III lines form high in the atmosphere of these stars at continuum optical depths of log τ 5000 < -5 and tend to be concentrated towards the magnetic poles in many stars, and the core of the Ha line forms at continuum optical depths -5 ≤ log τ 5000 ≤ -2, whereas the photometry samples the atmosphere on average at continuum optical depths closer to log τ 5000 = 0 and averages over the visible hemisphere of the star. Therefore, there are three possible explanations for the newly discovered frequencies: (1) there are modes with nodes near to the level where the photometry samples that can be easily detected at the higher level of formation of the Pr III lines; or (2) there are higher degree, l, non-radial oblique pulsation modes that are detectable in the spectroscopy because the Pr III is concentrated towards the magnetic poles where such modes have their highest amplitudes, but average out over the visible hemisphere in the photometry which samples the star's surface more uniformly; or (3) there is significant growth and decay of the principal mode amplitudes on a time-scale of just a few pulsation cycles at the high level of formation of the Pr III lines and core of the Ha line. The third hypothesis implies that this level is within the magneto-acoustic boundary layer where energy is being dissipated by both outward acoustic running waves and inward magnetic slow waves. We suggest observations that can distinguish among these three possibilities. We propose that strong changes in pulsation phase seen with atmospheric height in roAp stars, in some cases more than n rad from the top to the bottom of a single spectral line, strongly affect the pulsation phases seen in photometry in various bandpasses which explains why phase differences between bandpasses for roAp stars have never been explicable with standard theories that assume single spherical harmonics within the observable atmosphere. We also discuss the photometric amplitude variations as a function of bandpass, and suggest that these are primarily caused by continuum variations, rather than by variability in the rare earth element lines. We propose further tests of this suggestion.
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