The Gunn-Peterson trough is a spectral feature in electromagnetic radiation (EMR) from beyond approximately redshift 6, a time prior to the full effects of the epoch of reionization (EOR). The effect was predicted by James Gunn and Bruce Peterson in the 1960s and first observed around 40 years later when quasars at that distance were observed. It is a means of studying the universe at that time, e.g., to identify the EOR's redshift and to observe its progress. The phenomenon of the trough's creation is termed the Gunn-Peterson effect.
The feature is an EMR reduction over a spectral band with its longer-wavelength edge at the redshifted Lyman alpha (Ly-α) wavelength. From the sufficiently distant quasar, EMR toward us first passes through intergalactic medium (IGM) which still includes significant neutral hydrogen, and the wavelengths of this traveling EMR that are somewhat shorter than Ly-α are at some point redshifted to the Ly-α wavelength at which point the neutral hydrogen that it is passing through absorbs some of it. The degree of absorption at any particular wavelength can be characterized by an optical depth, termed its Gunn-Peterson optical depth.
At later stages in the path of the EMR (and that of EMR from nearer quasars), there is a relatively small amount of Ly-α absorption which is greater where the IGM is denser and greater within any less-ionized clouds along the way, forming the Lyman-alpha forest.