Long troughs in the Lyman-$\alpha$ forest below redshift 6 due to
  islands of neutral hydrogen
  A long (110 cMpc/$h$) and deep absorption trough in the Ly$\alpha$ forest has
been observed extending down to redshift 5.5 in the spectrum of ULAS
J0148+0600. Although no Ly$\alpha$ transmission is detected, Ly$\beta$ 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 ($z \sim
5.2$), 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
Ly$\beta$. We have also modelled the Ly$\alpha$ emitter population around the
simulated troughs, and show that there is a deficit of Ly$\alpha$ emitters
close to the trough as is observed.
