The discovery of the trough in a z = 6.28 quasar, and the absence of the trough in quasars detected at redshifts just below z = 6 presented strong evidence for the hydrogen in the universe having undergone a transition from neutral to ionized around z = 6. After recombination, the universe was expected to be neutral, until the first objects in the universe started emitting light and energy which would reionize the surrounding IGM. However, as the scattering cross section of photons with energies near that of the Lyman-alpha limit with neutral hydrogen is very high, even a small fraction of neutral hydrogen will make the optical depth of the IGM high enough to cause the suppression of emission observed. Despite the fact that the ratio of neutral hydrogen to ionized hydrogen may not have been particularly high, the low flux observed past the Lyman-alpha limit indicates that the universe was in the final stages of reionization.