High-redshift quasi-stellar object (QSO) spectra show large spatial fluctuations in the Ly α opacity of the intergalactic medium on surprisingly large scales at $z$ ≳ 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 α 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 α emission by galaxies at $z$ ≳ 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 α forest data in such a late reionization model requires a rapid evolution of the ionizing emissivity of galaxies that peaks at $z$ ∼ 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 $z$ ≲ 5.5 with large residual neutral ‘islands’ that can produce very long Gunn–Peterson troughs resembling those seen in the data.

A long (110 cMpc/h) and deep absorption trough in the Lyα forest has been observed extending down to redshift 5.5 in the spectrum of ULAS J0148+0600. Although no Lyα transmission is detected, Lyβ spikes are present which has led to claims that the gas along this trough must be ionized. Using high resolution cosmological radiative transfer simulations in large volumes, we show that in a scenario where reionization ends late (z ∼ 5.2), our simulations can reproduce troughs as long as observed. In this model, we find that the troughs are caused by islands of neutral hydrogen. Small ionized holes within the neutral islands allow for the transmission of Lyβ. We have also modelled the Lyα emitter population around the simulated troughs, and show that there is a deficit of Lyα emitters close to the trough as is observed.

We present the Technicolor Dawn simulations, a suite of cosmological radiationhydrodynamic simulations of the first 1.2 billion years. By modeling a spatiallyinhomogeneous UVB on-the-fly with 24 frequencies and resolving dark matter halos down to 10 8 M ⊙ within 12h −1 Mpc volumes, our simulations unify observations of the intergalactic and circumgalactic media, galaxies, and reionization into a common framework. The only empirically-tuned parameter, the fraction f esc,gal (z) of ionizing photons that escape the interstellar medium, is adjusted to match observations of the Lyman-α forest and the cosmic microwave background. With this single calibration, our simulations reproduce the history of reionization; the stellar mass-star formation rate relation of galaxies; the number density and metallicity of damped Lyman-α absorbers (DLAs) at z ∼ 5; the abundance of weak metal absorbers; the ultraviolet background (UVB) amplitude; and the Lyman-α flux power spectrum at z = 5.4. The galaxy stellar mass and UV luminosity functions are underproduced by ≤ 2×, suggesting an overly vigorous feedback model. The mean transmission in the Lyman-α forest is underproduced at z < 6, indicating tension between measurements of the UVB amplitude and Lyman-α transmission. The observed Si IV column density distribution is reasonably well-reproduced (∼ 1σ low). By contrast, C IV remains significantly underproduced despite being boosted by an intense > 4 Ryd UVB. Solving this problem by increasing metal yields would overproduce both weak absorbers and DLA metallicities. Instead, the observed strength of high-ionization emission from high-redshift galaxies and absorption from their environments suggest that the ionizing flux from conventional stellar population models is too soft.