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A long (110 cMpc/$h$) and deep absorption trough in the Ly$\alpha$ forest hasbeen observed extending down to redshift 5.5 in the spectrum of ULASJ0148+0600. Although no Ly$\alpha$ transmission is detected, Ly$\beta$ spikesare present which has led to claims that the gas along this trough must beionized. Using high resolution cosmological radiative transfer simulations inlarge volumes, we show that in a scenario where reionization ends late ($z \sim5.2$), our simulations can reproduce troughs as long as observed. In thismodel, we find that the troughs are caused by islands of neutral hydrogen.Small ionized holes within the neutral islands allow for the transmission ofLy$\beta$. We have also modelled the Ly$\alpha$ emitter population around thesimulated troughs, and show that there is a deficit of Ly$\alpha$ emittersclose to the trough as is observed.

Long troughs in the Lyman-$\alpha$ forest below redshift 6 due to islands of neutral hydrogen