Large Ly α opacity fluctuations and low CMB τ in models of late reionization with large islands of neutral hydrogen extending to z < 5.5

High-redshift quasi-stellar object (QSO) spectra show large spatial fluctuations in the Ly alpha opacity of the intergalactic medium on surprisingly large scales at z greater than or similar to 5.5. We present a radiative transfer simulation of cosmic reionization driven by galaxies that reproduces this large scatter and the rapid evolution of the Ly alpha opacity distribution at 5 < z < 6. The simulation also reproduces the low Thomson scattering optical depth reported by the latest cosmic microwave background (CMB) measurement and is consistent with the observed short near-zones and strong red damping wings in the highest redshift QSOs. It also matches the rapid disappearance of observed Ly alpha emission by galaxies at z greater than or similar to 6. Reionization is complete at z = 5.3 in our model, and 50 per cent of the volume of the Universe is ionized at z = 7. Agreement with the Ly alpha forest data in such a late reionization model requires a rapid evolution of the ionizing emissivity of galaxies that peaks at z similar to 6.8. The late end of reionization results in a large scatter in the photoionization rate and the neutral hydrogen fraction at redshifts as low as z less than or similar to 5.5 with large residual neutral 'islands' that can produce very long Gunn-Peterson troughs resembling those seen in the data.