Search

The reionization of helium is thought to occur at $2.5\lesssim z\lesssim4$, marking the last phase transition and final global heating event of the intergalactic medium (IGM). Since it is driven by rare quasars, helium reionization should give rise to strong temperature fluctuations in the IGM between neutral and recently-ionized regions of order $\sigma (\ln T) \sim \Delta T/T = 20-50\%$. We introduce a novel method to search for reionization-induced temperature fluctuations in the IGM by using the effective optical depths of the Lyman-$\alpha$ forest towards a large number of background quasars. Higher IGM temperatures give rise to lower effective optical depths in the Lyman-$\alpha$ forest, implying that temperature fluctuations will broaden the observed optical depth distribution. We measured the distributions of effective Lyman-$\alpha$ forest optical depths across $71$ X-Shooter spectra from the XQ-100 survey in four redshift bins from $z=3.76$ to $z=4.19$ and compared them to a large-volume cosmological hydrodynamical simulation. A good agreement is found between the observations and the simulation, which does not include temperature fluctuations; therefore, we do not detect a signature of helium reionization. We then post-process the simulations to include an increasing amount of temperature fluctuations until the model becomes inconsistent with the observations. We obtain tight constraints on $\sigma (\ln T) < 0.29 \ (<0.40)$ at $2 \sigma\ (3 \sigma)$ at $z=3.76$ when averaging over scales of $100$ comoving Mpc, and weaker constraints for higher redshifts and smaller scales. Our constraints are the tightest to date, and imply that either the IGM temperature contrast caused by helium reionization is less than $\sim30\%$, or that the process has not yet significantly started at $z=3.76$., Comment: 18 pages, 6+5 figures, 3 tables, submitted to ApJ

The Lyman alpha (Lya) forest in the spectra of z>5 quasars provides a powerful probe of the late stages of the Epoch of Reionization (EoR). With the recent advent of exquisite datasets such as XQR-30, many models have struggled to reproduce the observed large-scale fluctuations in the Lya opacity. Here we introduce a Bayesian analysis framework that forward-models large-scale lightcones of IGM properties, and accounts for unresolved sub-structure in the Lya opacity by calibrating to higher-resolution hydrodynamic simulations. Our models directly connect physically-intuitive galaxy properties with the corresponding IGM evolution, without having to tune "effective" parameters or calibrate out the mean transmission. The forest data, in combination with UV luminosity functions and the CMB optical depth, are able to constrain global IGM properties at percent level precision in our fiducial model. Unlike many other works, we recover the forest observations without evoking a rapid drop in the ionizing emissivity from z~7 to 5.5, which we attribute to our sub-grid model for recombinations. In this fiducial model, reionization ends at $z=5.44\pm0.02$ and the EoR mid-point is at $z=7.7\pm0.1$. The ionizing escape fraction increases towards faint galaxies, showing a mild redshift evolution at fixed UV magnitude, Muv. Half of the ionizing photons are provided by galaxies fainter than Muv~-12, well below direct detection limits of optical/NIR instruments including JWST. We also show results from an alternative galaxy model that does not allow for a redshift evolution in the ionizing escape fraction. Despite being decisively disfavored by the Bayesian evidence, the posterior of this model is in qualitative agreement with that from our fiducial model. We caution however that our conclusions regarding the early stages of the EoR and which sources reionized the Universe are more model-dependent., Comment: 21 pages, 12 figures, 3 tables (submitted to PASA)

The recently launched James Webb Space Telescope (JWST) is opening new observing windows on the distant universe. Among JWST's instruments, the Mid Infrared Instrument (MIRI) offers the unique capability of imaging observations at wavelengths $\lambda > 5\mu$m. This enables unique access to the rest frame near infra-red (NIR, $\lambda \ge 1$\mum) emission from galaxies at redshifts $z>4$ and the visual ($\lambda \gtrsim 5000$\AA) rest frame for $z>9$. We here report on the guaranteed time observations (GTO) from the MIRI European Consortium, of the Hubble Ultra Deep Field (HUDF), forming the MIRI Deep Imaging Survey (MIDIS), consisting of an on source integration time of $\sim41$ hours in the MIRI/F560W (5.6 $\mu$m) filter. To our knowledge, this constitutes the longest single filter exposure obtained with JWST of an extragalactic field as yet., Comment: submitted to A&A on July 30, 2024

We aim to construct a machine-learning approach that allows for a pixel-by-pixel reconstruction of the intergalactic medium (IGM) density field for various warm dark matter (WDM) models using the Lyman-alpha forest. With this regression machinery, we constrain the mass of a potential WDM particle from observed Lyman-alpha sightlines directly from the density field. We design and train a Bayesian neural network on the supervised regression task of recovering the optical depth-weighted density field $\Delta_\tau$ as well as its reconstruction uncertainty from the Lyman-alpha forest flux field. We utilise the Sherwood-Relics simulation suite at $4.1\leq z \leq 5.0$ as the main training and validation dataset. Leveraging the density field recovered by our neural network, we construct an inference pipeline to constrain the WDM particle masses based on the probability distribution function of the density fields. We find that our trained Bayesian neural network can accurately recover within a $1\sigma$ error $\geq 85\%$ of the density field pixels from a validation simulated dataset that encompasses multiple WDM and thermal models of the IGM. When predicting on Lyman-alpha skewers generated using the alternative hydrodynamical code Nyx not included in the training data, we find a $1\sigma$ accuracy rate $\geq 75\%$. We consider 2 samples of observed Lyman-alpha spectra from the UVES and GHOST instruments, at $z=4.4$ and $z=4.9$ respectively and fit the density fields recovered by our Bayesian neural network to constrain WDM masses. We find lower bounds on the WDM particle mass of $m_{\mathrm{WDM}} \geq 3.8$ KeV and $m_{\mathrm{WDM}} \geq 2.2$ KeV at $2\sigma$ confidence, respectively. We are able to match current state-of-the-art WDM particle mass constraints using up to 40 times less observational data than Markov Chain Monte Carlo techniques based on the Lyman-alpha forest power spectrum., Comment: 12 pages, Submitted to A&A

Understanding when and how reionization happened is crucial for studying the early structure formation and the properties of first galaxies in the Universe. At $z>5.5$, the observed IGM optical depth shows a significant scatter, indicating an inhomogeneous reionization process. However, the nature of the inhomogeneous reionization remains debated. ASPIRE is a JWST Cycle 1 program that has spectroscopically identified $>400$ [OIII] emitters in 25 quasar fields at $z>6.5$. Combined with deep ground-based optical spectroscopy of ASPIRE quasars, ASPIRE program provides the current largest sample for IGM-galaxy connection studies during cosmic reionization. We present the first results of IGM effective optical depth measurements around [OIII] emitters using 14 ASPIRE quasar fields. We find the IGM transmission is tightly related with reionization-era galaxies to the extent that significant excess of Ly$\alpha$ transmission exists around [OIII] emitters. We measure the stacked IGM effective optical depth of IGM patches associated with [OIII] emitters and find they reach the same IGM effective optical depth at least dz~0.1 ahead of those IGM patches where no [OIII] emitters are detected, supporting earlier reionization around [OIII] emitters. Our results indicate an enhancement in IGM Ly$\alpha$ transmission around [OIII] emitters at scales beyond 25 $h^{-1}$ cMpc, consistent with the predicted topology of reionization from fluctuating UV background (UVB) models., Comment: 27 pages, 19 figures, 1 table, accepted for publication in ApJ

The escaping ionising efficiency from galaxies, $f_{\rm esc}\xi_{\rm ion}$, is a crucial ingredient for understanding their contribution to hydrogen reionisation, but both of its components, $f_{\rm{esc}}$ and $\xi_{\rm{ion}}$, are extremely difficult to measure. We measure the average escaping ionising efficiency $\langle f_{\rm{esc}} \xi_{\rm{ion}}\rangle$ of galaxies at $z=5$ implied by the mean level of ionisation in the intergalactic medium via the Lyman-$\alpha$ forest. We use the fact that $\dot{N}_{\rm{ion}} = \rho_{\rm{UV}} f_{\rm{esc}} \xi_{\rm{ion}}$, the product of the ionising output and the UV density $\rho_{\rm{UV}}$, can be calculated from the known average strength of the UV background and the mean free path of ionising photons. These quantities, as well as $\rho_{\rm{UV}}$, are robustly measured at $z\leq6$. We calculate the missing factor of $\langle f_{\rm{esc}} \xi_{\rm{ion}}\rangle$ at $z=5$, during a convenient epoch after hydrogen reionisation has completed and the intergalactic medium has reached ionisation equilibrium, but before bright quasars begin to dominate the ionising photon production. Intuitively, our constraint corresponds to the required escaping ionising production from galaxies in order to avoid over- or under-ionising the Lyman-$\alpha$ forest. We obtain a measurement of $\log \langle f_{\rm{esc}} \xi_{\rm{ion}}\rangle /$erg Hz$^{-1}$ $ = 24.28_{-0.20}^{+0.21}$ at $z=5$ when integrating $\rho_\text{UV}$ down to a limiting magnitude $M_\text{lim}=-11$. Our measurement of the escaping ionising efficiency of galaxies is in rough agreement with both observations and most models., Comment: Accepted for publication in A&A; 4 pages, 1 figure

Understanding the rapid formation of supermassive black holes (SMBHs) in the early universe requires an understanding of how stellar mass grows in the host galaxies. Here, we perform an analysis of rest-frame optical spectra and imaging from JWST of two quasar host galaxies at z>6 which exhibit Balmer absorption lines. These features in the stellar continuum indicate a lack of young stars, similar to low-redshift post-starburst galaxies whose star formation was recently quenched. We find that the stellar mass (log(M_* / M_sun) > 10.6) of each quasar host grew in a starburst episode at redshift 7 or 8. One of the targets exhibits little ongoing star formation, as evidenced by the photometric signature of the Balmer break and a lack of spatially resolved H-alpha emission, placing it well below the star formation main sequence at z = 6. The other galaxy is transitioning to a quiescent phase; together, the two galaxies represent the most distant massive post-starburst galaxies known. The maturity of these two galaxies is further supported by the stellar velocity dispersions of their host galaxies, placing them slightly above the upper end of the local M_BH - sigma_* relation. The properties of our two post-starburst galaxies, each hosting an active SMBH with log(M_BH / M_sun) > 9, suggests that black holes played a major role in shaping the formation of the first massive galaxies in the Universe., Comment: 24 pages, 7 figures, submitted to a Nature journal

The history of reionization reflects the cumulative injection of ionizing photons by sources and the absorption of ionizing photons by sinks. The latter process is traditionally described in terms of a "clumping factor" which encodes the average quadratic increase in the recombination rate of dense gas within the cosmic web. The recent measurement of a short mean free path of ionizing photons from stacked quasar spectra at $z\simeq6$ has placed the importance of sinks under increased scrutiny, but its connection to the recombination rate is not immediately obvious. Here we present analytic arguments to connect the clumping factor to the mean free path by invoking ionization equilibrium within the ionized phase of the intergalactic medium at the end of (and after) reionization. We find that the latest mean free path and hydrogen photoionization rate measurements at $z=5-6$ imply a global clumping factor $C\approx12$, much higher than previous determinations from radiation-hydrodynamic simulations of the reionization process. Similar values of $C$ are also derived when applying the same procedure to observations at $2

We present optical and near-infrared (NIR) spectroscopic observations for a sample of $45$ quasars at $6.50 < z \leq 7.64$ with absolute magnitudes at $1450$ {\AA} in the range $-28.82 \leq M_{1450} \leq -24.13$ and their composite spectrum. The median redshift and $M_{1450}$ of the quasars in the sample are $z_{\rm{median}}=6.71$ and $M_{1450,\rm{median}} \simeq -26.1$, respectively. The NIR spectra are taken with echelle spectrographs, complemented with additional data from optical long slit instruments, and then reduced consistently using the open-source Python-based spectroscopic data reduction pipeline PypeIt. The median value of the mean signal-to-noise ratios of the spectra in J, H, and K band (median $\langle \rm{SNR}_{\lambda} \rangle$) is: median $\langle \rm{SNR}_{J} \rangle=9.7$, median $\langle \rm{SNR}_{H} \rangle=10.3$, and median $\langle \rm{SNR}_{K} \rangle=11.7$; demonstrating the good data quality. This work presents the largest medium/moderate-resolution sample of quasars at $z>6.5$ from ground-based instruments. Its homogeneity and reproducibility make it ideally suited for several scientific goals, i.e., the study of the quasar proximity zones and damping wings, the Ly$\alpha$ forest, the intergalactic medium's metal content, as well as other properties such as the distribution of SMBH masses and Eddington ratios. Our composite spectrum is compared to others at both high and low-$z$ from the literature, showing differences in the strengths of many emission lines, probably due to differences in luminosity among the samples, but a consistent continuum slope, which proves that the same spectral features are preserved in quasars at different redshift ranges., Comment: 18 pages, 10 figures, submitted to MNRAS

Recent quasar absorption line observations suggest that reionization may end as late as $z \approx 5.3$. As a means to search for large neutral hydrogen islands at $z<6$, we revisit long dark gaps in the Ly$\beta$ forest in VLT/X-Shooter and Keck/ESI quasar spectra. We stack the Ly$\alpha$ forest corresponding to both edges of these Ly$\beta$ dark gaps and identify a damping wing-like extended absorption profile. The average redshift of the stacked forest is $z=5.8$. By comparing these observations with reionization simulations, we infer that such a damping wing-like feature can be naturally explained if these gaps are at least partially created by neutral islands. Conversely, simulated dark gaps lacking neutral hydrogen struggle to replicate the observed damping wing features. Furthermore, this damping wing-like profile implies that the volume-averaged neutral hydrogen fraction must be $\langle x_{\rm HI} \rangle \geq 6.1 \pm 3.9\%$ at $z = 5.8$. Our results offer robust evidence that reionization extends below $z=6$., Comment: 8 pages, 5 figures, 1 table; accepted for publication in MNRAS Letters

Recent observations have positioned the endpoint of the Epoch of Reionisation (EoR) at redshift $z \sim 5.3$. However, observations of the Lyman-$\alpha$ forest have not yet been able to discern whether reionisation occurred slowly and late, with substantial neutral hydrogen persisting at redshift $\sim 6$, or rapidly and earlier, with the apparent late end driven by the fluctuating UV background. Gunn-Peterson (GP) absorption troughs are solid indicators that reionisation is not complete until $z=5.3$, but whether they contain significantly neutral gas has not yet been proven. We aim to answer this question by directly measuring, for the first time, the neutral hydrogen fraction ($x_\mathrm{HI}$) at the end of the EoR ($5 \lesssim z \lesssim 6$) in high-redshift quasars spectra. For high neutral fractions $x_\mathrm{HI}\gtrsim0.1$, GP troughs exhibit damping wing (DW) absorption extending over $1000$ km s$^{-1}$ beyond the troughs. While conclusively detected in Lyman-$\alpha$ emission lines of quasars at $z\geq7$, DWs are challenging to observe in the general Lyman-$\alpha$ forest due to absorption complexities and small-scale stochastic transmission features. We report the first successful identification of the stochastic DW signal adjacent to GP troughs at redshifts $z=5.6$ through careful stacking of the dark gaps in Lyman-$\alpha$ forest. We use the signal to present a measurement of the corresponding global $x_\mathrm{HI}=0.19\pm0.07$ $(_{-0.16}^{+0.11})$ at $1\sigma$ $(2\sigma)$ at $z=5.6$ and a limit $x_\mathrm{HI}<0.44$ at $z=5.9$. The detection of this signal demonstrates the existence of substantially neutral islands near the conclusion of the EoR, unequivocally signaling a late-and-slow reionization scenario., Comment: 7 pages, 4 figures, published in A&A Letters, Appendix B added to address the comments of the reviewer

We present constraints on the spacetime variation of the fine-structure constant $\alpha$ at redshifts $2.5\le z<9.5$ using JWST emission-line galaxies. The galaxy sample consists of 621 high-quality spectra with strong and narrow [O III] $\lambda\lambda$4959,5007 doublet emission lines from 578 galaxies, including 232 spectra at $z>5$. The [O III] doublet lines are arguably the best emission lines to probe the variation in $\alpha$. We divide our sample into six subsamples based on redshift and calculate the relative variation $\Delta\alpha/\alpha$ for the individual subsamples. The calculated $\Delta\alpha/\alpha$ values are consistent with zero within $1\sigma$ at all redshifts, suggesting no time variation in $\alpha$ above a level of $(1-2) \times10^{-4}$ ($1\sigma$) in the past 13.2 billion years. When the whole sample is combined, the constraint is improved to be $\Delta\alpha/\alpha = (0.2\pm0.7) \times10^{-4}$. We further test the spatial variation in $\alpha$ using four subsamples of galaxies in four different directions on the sky. The measured $\Delta\alpha/\alpha$ values are consistent with zero at a $1\sigma$ level of $\sim 2\times10^{-4}$. While the constraints in this work are not as stringent as those from lower-redshift quasar absorption lines in previous studies, this work uses an independent tracer and provides the first constraints on $\Delta\alpha/\alpha$ at the highest redshifts. With the growing number of emission-line galaxies from JWST, we expect to achieve stronger constraints in the future., Comment: 15 pages, 10 figures, accepted for publication in ApJ

The attenuation of Ly$\alpha$ photons by neutral hydrogen in the intergalactic medium (IGM) at $z\gtrsim5$ continues to be a powerful probe for studying the epoch of reionisation. Given a framework to estimate the intrinsic (true) Ly$\alpha$ emission of high-$z$ sources, one can infer the ionisation state of the IGM during reionisation. In this work, we use the enlarged XQR-30 sample of 42 high-resolution and high-SNR QSO spectra between $5.8\lesssim\,z\lesssim\,6.6$ obtained with VLT/X-Shooter to place constraints on the IGM neutral fraction. This is achieved using our existing Bayesian QSO reconstruction framework which accounts for uncertainties such as the: (i) posterior distribution of predicted intrinsic Ly$\alpha$ emission profiles (obtained via covariance matrix reconstruction of the Ly$\alpha$ and N V emission lines from unattenuated high-ionisation emission line profiles; C IV, Si IV + O IV] and C III]) and (ii) distribution of ionised regions within the IGM using synthetic damping wing profiles drawn from a $1.6^3$ Gpc$^3$ reionisation simulation. Following careful quality control, we used 23 of the 42 available QSOs to obtain constraints/limits on the IGM neutral fraction during the tail-end of reionisation. Our median and 68th percentile constraints on the IGM neutral fraction are: $0.20\substack{+0.14\\-0.12}$ and $0.29\substack{+0.14\\-0.13}$ at $z = 6.15$~and 6.35. Further, we also report 68th percentile upper-limits of $\bar{x}_{\mathrm{H\,{\scriptscriptstyle I}}} < 0.21$, 0.20, 0.21 and 0.18 at $z = 5.8, 5.95, 6.05$~and 6.55. These results imply reionisation is still ongoing at $5.8\lesssim\,z\lesssim\,6.55$, consistent with previous results from XQR-30 (dark fraction and Ly$\alpha$ forest) along with other observational probes considered in the literature., Comment: 21 pages, 9 figures and 2 tables. Accepted for publication in MNRAS

Unveiling the thermal history of the intergalactic medium (IGM) at $4 \leq z \leq 5$ holds the potential to reveal early onset HeII reionization or lingering thermal fluctuations from HI reionization. We set out to reconstruct the IGM gas properties along simulated Lyman-alpha forest data on pixel-by-pixel basis, employing deep Bayesian neural networks. Our approach leverages the Sherwood-Relics simulation suite, consisting of diverse thermal histories, to generate mock spectra. Our convolutional and residual networks with likelihood metric predicts the Ly$\alpha$ optical depth-weighted density or temperature for each pixel in the Ly$\alpha$ forest skewer. We find that our network can successfully reproduce IGM conditions with high fidelity across range of instrumental signal-to-noise. These predictions are subsequently translated into the temperature-density plane, facilitating the derivation of reliable constraints on thermal parameters. This allows us to estimate temperature at mean cosmic density, $T_{\rm 0}$ with one sigma confidence $\delta T_{\rm 0} \sim 1000{\rm K}$ using only one $20$Mpc/h sightline ($\Delta z\simeq 0.04$) with a typical reionization history. Existing studies utilize redshift pathlength comparable to $\Delta z\simeq 4$ for similar constraints. We can also provide more stringent constraints on the slope ($1\sigma$ confidence interval $\delta {\rm \gamma} \lesssim 0.1$) of the IGM temperature-density relation as compared to other traditional approaches. We test the reconstruction on a single high signal-to-noise observed spectrum ($20$ Mpc/h segment), and recover thermal parameters consistent with current measurements. This machine learning approach has the potential to provide accurate yet robust measurements of IGM thermal history at the redshifts in question., Comment: 17 pages, Submitted to MNRAS

Reconstructing the intrinsic Ly$\alpha$ line flux from high-$z$ QSOs can place constraints on the neutral hydrogen content of the intergalactic medium during reionisation. There are now $\gtrsim10$ different Ly$\alpha$ reconstruction pipelines using different methodologies to predict the Ly$\alpha$ line flux from correlations with the spectral information redward of Ly$\alpha$. However, there have been few attempts to directly compare the performance of these pipelines. Therefore, we devised a blind QSO challenge to compare these reconstruction pipelines on a uniform set of objects. Each author was provided de-identified, observed rest-frame QSO spectra with spectral information only redward of 1260\AA\ rest-frame to ensure unbiased reconstruction. We constructed two samples of 30 QSOs, from X-Shooter and SDSS both spanning $3.5

We report the discovery of Cerberus, an extremely red object detected with the MIRI Deep Imaging Survey (MIDIS) observations in the F1000W filter of the Hubble Ultra Deep Field. The object is detected at $S/N\sim6$, with $\mathrm{F1000W}\sim27$ mag, and undetected in the NIRCam data gathered by the JWST Advanced Deep Extragalactic Survey, JADES, fainter than the 30.0-30.5 mag $5\sigma$ detection limits in individual bands, as well as in the MIDIS F560W ultra-deep data ($\sim$29 mag, $5\sigma$). Analyzing the spectral energy distribution built with low-$S/N$ ($<5$) measurements in individual optical-to-mid-infrared filters and higher $S/N$ ($\gtrsim5$) in stacked NIRCam data, we discuss the possible nature of this red NIRCam-dark source using a battery of codes. We discard the possibility of Cerberus being a Solar System body based on the $<0.016$" proper motion in the 1-year apart JADES and MIDIS observations. A sub-stellar Galactic nature is deemed unlikely, given that the Cerberus' relatively flat NIRCam-to-NIRCam and very red NIRCam-to-MIRI flux ratios are not consistent with any brown dwarf model. The extragalactic nature of Cerberus offers 3 possibilities: (1) A $z\sim0.4$ galaxy with strong emission from polycyclic aromatic hydrocarbons; the very low inferred stellar mass, $\mathrm{M}_\star=10^{5-6}$ M$_\odot$, makes this possibility highly improbable. (2) A dusty galaxy at $z\sim4$ with an inferred stellar mass $\mathrm{M}_\star\sim10^{8}$ M$_\odot$. (3) A galaxy with observational properties similar to those of the reddest little red dots discovered around $z\sim7$, but Cerberus lying at $z\sim15$, with the rest-frame optical dominated by emission from a dusty torus or a dusty starburst., Comment: Accepted for publication in ApJL, results unchanged, manuscript shortened to publish as a letter

The variations in Ly$\alpha$ forest opacity observed at $z>5.3$ between lines of sight to different background quasars are too strong to be caused by fluctuations in the density field alone. The leading hypothesis for the cause of this excess variance is a late, ongoing reionization process at redshifts below six. Another model proposes strong ionizing background fluctuations coupled to a short, spatially varying mean free path of ionizing photons, without explicitly invoking incomplete reionization. With recent observations suggesting a short mean free path at $z\sim6$, and a dramatic improvement in $z>5$ Ly$\alpha$ forest data quality, we revisit this latter possibility. Here we apply the likelihood-free inference technique of approximate Bayesian computation to jointly constrain the hydrogen photoionization rate $\Gamma_{\rm HI}$ and the mean free path of ionizing photons $\lambda_{\rm mfp}$ from the effective optical depth distributions at $z=5.0$-$6.1$ from XQR-30. We find that the observations are well-described by fluctuating mean free path models with average mean free paths that are consistent with the steep trend implied by independent measurements at $z\sim5$-$6$, with a concomitant rapid evolution of the photoionization rate., Comment: 23 pages, 13 figures, resubmitted to ApJ after referee's comments

The red damping wing from neutral hydrogen in the intergalactic medium is a smoking-gun signal of ongoing reionization. One potential contaminant of the intergalactic damping wing signal is dense gas associated with foreground galaxies, which can give rise to proximate damped Ly$\alpha$ absorbers. The Ly$\alpha$ imprint of such absorbers on background quasars is indistinguishable from the intergalactic medium within the uncertainty of the intrinsic quasar continuum, and their abundance at $z\gtrsim7$ is unknown. Here we show that the complex of low-ionization metal absorption systems recently discovered by deep JWST/NIRSpec observations in the foreground of the $z=7.54$ quasar ULAS~J1342$+$0928 can potentially reproduce the quasar's spectral profile close to rest-frame Ly$\alpha$ without invoking a substantial contribution from the intergalactic medium, but only if the absorbing gas is extremely metal-poor ($[{\rm O}/{\rm H}]\sim-3.5$). Such a low oxygen abundance has never been observed in a damped Ly$\alpha$ absorber at any redshift, but this possibility still complicates the interpretation of the spectrum. Our analysis highlights the need for deep spectroscopy of high-redshift quasars with JWST or ELT to "purify" damping wing quasar samples, an exercise which is impossible for much fainter objects like galaxies., Comment: 10 pages, 5 figures, submitted to ApJL

The launch of ${\it JWST}$ opens a new window for studying the connection between metal-line absorbers and galaxies at the end of the Epoch of Reionization (EoR). Previous studies have detected absorber-galaxy pairs in limited quantities through ground-based observations. To enhance our understanding of the relationship between absorbers and their host galaxies at $z>5$, we utilized the NIRCam Wide Field Slitless Spectroscopy (WFSS) to search for absorber-associated galaxies by detecting their rest-frame optical emission lines (e.g., [OIII] + H$\beta$). We report the discovery of a MgII-associated galaxy at $z=5.428$ using data from the ${\it JWST}$ ASPIRE program. The MgII absorber is detected on the spectrum of quasar J0305--3150 with a rest-frame equivalent width of 0.74$\mathring{A}$. The associated galaxy has an [OIII] luminosity of $10^{42.5}\ {\rm erg\ s^{-1}}$ with an impact parameter of 24.9 proper kiloparsecs (pkpc). The joint ${\it HST}$-${\it JWST}$ spectral energy distribution (SED) implies a stellar mass and star-formation rate of ${\rm M_* \approx 10^{8.8}}$ ${\rm M_{\odot}}$, ${\rm SFR}\approx 10\ {\rm M_{\odot}\ yr^{-1}}$. Its [OIII] equivalent width and stellar mass are typical of [OIII] emitters at this redshift. Furthermore, connecting the outflow starting time to the SED-derived stellar age, the outflow velocity of this galaxy is $\sim300\ {\rm km\ s^{-1}}$, consistent with theoretical expectations. We identified six additional [OIII] emitters with impact parameters of up to $\sim300$ pkpc at similar redshifts ($|dv|<1000\ {\rm km\ s^{-1}}$). The observed number is consistent with that in cosmological simulations. This pilot study suggests that systematically investigating the absorber-galaxy connection within the ASPIRE program will provide insights into the metal-enrichment history in the early universe., Comment: Accepted for publication in ApJL. Main text 8 pages, 4 figures. For more information of the JWST ASPIRE program please check https://aspire-quasar.github.io/index.html

Recently, the Lyman-$\alpha$ (Ly$\alpha$) forest flux auto-correlation function has been shown to be sensitive to the mean free path of hydrogen-ionizing photons, $\lambda_{\text{mfp}}$, for simulations at $z \geq 5.4$. Measuring $\lambda_{\text{mfp}}$ at these redshifts will give vital information on the ending of reionization. Here we present the first observational measurements of the Ly$\alpha$ forest flux auto-correlation functions in ten redshift bins from $5.1 \leq z \leq 6.0$. We use a sample of 35 quasar sightlines at $z > 5.7$ from the extended XQR-30 data set, this data has signal-to-noise ratios of $> 20$ per spectral pixel. We carefully account for systematic errors in continuum reconstruction, instrumentation, and contamination by damped Ly$\alpha$ systems. With these measurements, we introduce software tools to generate auto-correlation function measurements from any simulation. For an initial comparison, we show our auto-correlation measurements with simulation models for recently measured $\lambda_{\text{mfp}}$ values and find good agreements. Further work in modeling and understanding the covariance matrices of the data is necessary to get robust measurements of $\lambda_{\text{mfp}}$ from this data., Comment: 17 pages, 13 figures, submitted to MNRAS

The mean free path of ionizing photons, $\lambda_{\rm mfp}$, is a critical parameter for modeling the intergalactic medium (IGM) both during and after reionization. We present direct measurements of $\lambda_{\rm mfp}$ from QSO spectra over the redshift range $5

Proximity zones of high-redshift quasars are unique probes of their central supermassive black holes as well as the intergalactic medium in the last stages of reionization. We present 22 new measurements of proximity zones of quasars with redshifts between 5.8 and 6.6, using the enlarged XQR-30 sample of high-resolution, high-SNR quasar spectra. The quasars in our sample have UV magnitudes of $M_{1450}\sim -27$ and black hole masses of $10^9$$\unicode{x2013}$$10^{10}$ M$_\odot$. Our inferred proximity zone sizes are 2$\unicode{x2013}$7 physical Mpc, with a typical uncertainty of less than 0.5 physical Mpc, which, for the first time, also includes uncertainty in the quasar continuum. We find that the correlation between proximity zone sizes and the quasar redshift, luminosity, or black hole mass, indicates a large diversity of quasar lifetimes. Two of our proximity zone sizes are exceptionally small. The spectrum of one of these quasars, with $z=6.02$, displays, unusually for this redshift, damping wing absorption without any detectable metal lines, which could potentially originate from the IGM. The other quasar has a high-ionization absorber $\sim$0.5 pMpc from the edge of the proximity zone. This work increases the number of proximity zone measurements available in the last stages of cosmic reionization to 87. This data will lead to better constraints on quasar lifetimes and obscuration fractions at high redshift, which in turn will help probe the seed mass and formation redshift of supermassive black holes., Comment: 16 pages, 9 figures, Accepted in MNRAS

We measure the mean free path ($\lambda_{\rm mfp,HI}$), photo-ionization rate ($\langle \Gamma_{\rm HI} \rangle$) and neutral fraction ($\langle f_{\rm HI} \rangle$) of hydrogen in 12 redshift bins at $4.85

Intervening CIV absorbers are key tracers of metal-enriched gas in galaxy halos over cosmic time. Previous studies suggest that the CIV cosmic mass density ($\Omega_{\rm CIV}$) decreases slowly over 1.5 $\lesssim z\lesssim$ 5 before declining rapidly at $z\gtrsim$ 5, but the cause of this downturn is poorly understood. We characterize the $\Omega_{\rm CIV}$ evolution over 4.3 $\lesssim z\lesssim$ 6.3 using 260 absorbers found in 42 XSHOOTER spectra of $z\sim$ 6 quasars, of which 30 come from the ESO Large Program XQR-30. The large sample enables us to robustly constrain the rate and timing of the downturn. We find that $\Omega_{\rm CIV}$ decreases by a factor of 4.8 $\pm$ 2.0 over the ~300 Myr interval between $z\sim$ 4.7 and $z\sim$ 5.8. The slope of the column density (log N) distribution function does not change, suggesting that CIV absorption is suppressed approximately uniformly across 13.2 $\leq$ log N/cm$^{-2}$ < 15.0. Assuming that the carbon content of galaxy halos evolves as the integral of the cosmic star formation rate density (with some delay due to stellar lifetimes and outflow travel times), we show that chemical evolution alone could plausibly explain the fast decline in $\Omega_{\rm CIV}$ over 4.3 $\lesssim z\lesssim$ 6.3. However, the CIV/CII ratio decreases at the highest redshifts, so the accelerated decline in $\Omega_{\rm CIV}$ at $z\gtrsim$ 5 may be more naturally explained by rapid changes in the gas ionization state driven by evolution of the UV background towards the end of hydrogen reionization., Comment: 20 pages, 8 figures, 4 tables. Published in MNRAS

Over the last two decades, around 300 quasars have been discovered at $z\gtrsim6$, yet only one has identified as being strongly gravitationally lensed. We explore a new approach -- enlarging the permitted spectral parameter space, while introducing a new spatial geometry veto criterion -- which is implemented via image-based deep learning. We first apply this approach to a systematic search for reionization-era lensed quasars, using data from the Dark Energy Survey, the Visible and Infrared Survey Telescope for Astronomy Hemisphere Survey, and the Wide-field Infrared Survey Explorer.Our search method consists of two main parts: (i) the preselection of the candidates based on their spectral energy distributions (SEDs) using catalog-level photometry and (ii) relative probabilities calculation of the candidates being a lens or some contaminant, utilizing a convolutional neural network (CNN) classification. The training data sets are constructed by painting deflected point-source lights over actual galaxy images, to generate realistic galaxy-quasar lens models, optimized to find systems with small image separations, i.e., Einstein radii of $\theta_\mathrm{E} \leq 1$ arcsec. Visual inspection is then performed for sources with CNN scores of $P_\mathrm{lens} > 0.1$, which leads us to obtain 36 newly selected lens candidates, which are awaiting spectroscopic confirmation. These findings show that automated SED modeling and deep learning pipelines, supported by modest human input, are a promising route for detecting strong lenses from large catalogs that can overcome the veto limitations of primarily dropout-based SED selection approaches., Comment: 24 pages, 17 figures, and 2 tables. Accepted for publication in The Astrophysical Journal. We welcome comments from the reader

We present a new investigation of the intergalactic medium (IGM) near reionization using dark gaps in the Lyman-$\beta$ (Ly$\beta$) forest. With its lower optical depth, Ly$\beta$ offers a potentially more sensitive probe to any remaining neutral gas compared to commonly used Ly$\alpha$ line. We identify dark gaps in the Ly$\beta$ forest using spectra of 42 QSOs at $z_{\rm em}>5.5$, including new data from the XQR-30 VLT Large Programme. Approximately $40\%$ of these QSO spectra exhibit dark gaps longer than $10h^{-1}{\rm Mpc}$ at $z\simeq5.8$. By comparing the results to predictions from simulations, we find that the data are broadly consistent both with models where fluctuations in the Ly$\alpha$ forest are caused solely by ionizing ultraviolet background (UVB) fluctuations and with models that include large neutral hydrogen patches at $z<6$ due to a late end to reionization. Of particular interest is a very long ($L=28h^{-1}{\rm Mpc}$) and dark ($\tau_{\rm eff} \gtrsim 6$) gap persisting down to $z\simeq 5.5$ in the Ly$\beta$ forest of the $z_{\rm}=5.85$ QSO PSO J025$-$11. This gap may support late reionization models with a volume-weighted average neutral hydrogen fraction of $ \langle x_{\rm HI}\rangle \gtrsim 5\%$ by $z=5.6$. Finally, we infer constraints on $\langle x_{\rm HI}\rangle$ over $5.5 \lesssim z \lesssim 6.0$ based on the observed Ly$\beta$ dark gap length distribution and a conservative relationship between gap length and neutral fraction derived from simulations. We find $\langle x_{\rm HI}\rangle \leq 0.05$, 0.17, and 0.29 at $z\simeq 5.55$, 5.75, and 5.95, respectively. These constraints are consistent with models where reionization ends significantly later than $z = 6$., Comment: 17 pages, 13 figures, accepted for publication in ApJ. The Figure set and machine readable table are available at https://ydzhuastro.github.io/lyb.html

We characterize the Ly$\alpha$ halo and absorption systems toward PSO J083+11, a unique $z=6.3401$ weak-line quasar, using Gemini/GNIRS, Magellan/FIRE, and VLT/MUSE data. Strong absorptions by hydrogen and several metal lines (e.g., CII, MgII, and OI) are discovered in the spectrum, which indicates the presence of: (i) a proximate sub-damped Ly$\alpha$ (sub-DLA) system at $z=6.314$ and (ii) a MgII absorber at $z=2.2305$. To describe the observed damping wing signal, we model the Ly$\alpha$ absorption with a combination of a sub-DLA with the neutral hydrogen column density of $\log N_\mathrm{HI} = 20.03 \pm 0.30$ cm$^{-2}$ and absorption from the intergalactic medium with a neutral fraction of around 10 percent. The sub-DLA toward PSO J083+11 has an abundance ratio of [C/O] $=-0.04 \pm 0.33$ and metallicity of [O/H] $=-2.19 \pm 0.44$, similar to those of low-redshift metal-poor DLAs. These measurements suggest that the sub-DLA might truncate PSO J083+11's proximity zone size and complicate the quasar lifetime measurement. However, this quasar shows no sign of a Ly$\alpha$ halo in the MUSE data cube, where the estimated $1\sigma$ limit of surface brightness is $2.76 \times 10^{-18}$ erg s$^{-1}$ cm$^{-2}$ arcsec$^{-2}$ at aperture size of 1 arcsecond, or equivalent to a Ly$\alpha$ luminosity of $\leq 43.46$ erg s$^{-1}$. This non-detection, while being only weak independent evidence on its own, is at least consistent with a young quasar scenario, as expected for a quasar with a short accretion timescale., Comment: 22 pages, 12 figures, and 1 table. Replaced to match version accepted for publication in The Astronomical Journal. We welcome the comments from the reader. Related paper: arXiv:2009.07784

Measuring the density of the intergalactic medium using quasar sightlines in the epoch of reionization is challenging due to the saturation of Lyman-$\alpha$ absorption. Near a luminous quasar, however, the enhanced radiation creates a proximity zone observable in the quasar spectra where the Lyman-$\alpha$ absorption is not saturated. In this study, we use $10$ high-resolution ($R\gtrsim 10,000$) $z\sim 6$ quasar spectra from the extended XQR-30 sample to measure the density field in the quasar proximity zones. We find a variety of environments within $3$ pMpc distance from the quasars. We compare the observed density cumulative distribution function (CDF) with models from the $\textit{Cosmic Reionization on Computers}$ simulation, and find a good agreement between $1.5$ to $3$pMpc from the quasar. This region is far away from the quasar hosts and hence approaching the mean density of the universe, which allows us to use the CDF to set constraints on the cosmological parameter $\sigma_8=0.6\pm0.3$. The uncertainty is mainly due to the limited number of high-quality quasar sightlines currently available. Utilizing the more than $>200$ known quasars at $z\gtrsim 6$, this method will allow us in the future to tighten the constraint on $\sigma_8$ to the percent level. In the region closer to the quasar within $1.5$ pMpc, we find the density is higher than predicted in the simulation by $1.23 \pm 0.17$, suggesting the typical host dark matter halo mass of a bright quasar ($M_{\rm 1450}<-26.5$) at $z\sim 6$ is $\log_{\rm 10} (M/M_\odot)=12.5^{+0.4}_{-0.7}$., Comment: 16 pages, 11 figures, submitted to ApJ, comments are welcome

We present a new investigation of the intergalactic medium (IGM) near the end of reionization using "dark gaps" in the Lyman-alpha (Ly$\alpha$) forest. Using spectra of 55 QSOs at $z_{\rm em}>5.5$, including new data from the XQR-30 VLT Large Programme, we identify gaps in the Ly$\alpha$ forest where the transmission averaged over 1 comoving $h^{-1}\,{\rm Mpc}$ bins falls below 5%. Nine ultra-long ($L > 80~h^{-1}\,{\rm Mpc}$) dark gaps are identified at $z<6$. In addition, we quantify the fraction of QSO spectra exhibiting gaps longer than $30~h^{-1}\,{\rm Mpc}$, $F_{30}$, as a function of redshift. We measure $F_{30} \simeq 0.9$, 0.6, and 0.15 at $z = 6.0$, 5.8, and 5.6, respectively, with the last of these long dark gaps persisting down to $z \simeq 5.3$. Comparing our results with predictions from hydrodynamical simulations, we find that the data are consistent with models wherein reionization extends significantly below redshift six. Models wherein the IGM is essentially fully reionized that retain large-scale fluctuations in the ionizing UV background at $z \lesssim 6$ are also potentially consistent with the data. Overall, our results suggest that signature of reionization in the form of islands of neutral hydrogen and/or large-scale fluctuations in the ionizing background remain present in the IGM until at least $z \simeq 5.3$., Comment: 30 pages, 19 figures, 3 tables, accepted for publication in ApJ

The recent measurement of an ionising mean free path $\lambda_{\text{mfp}}<1$ pMpc at $z=6$ challenges our understanding of the small-scale structure of the intergalactic medium (IGM) at the end of reionisation. We introduce a new method to constrain \mfp at $z=6$ by using lower limits on the individual free paths of ionisation around quasars. Lyman-limit absorbers with a density sufficient to halt ionising photons produce strong absorption in the 6 lowest-energy Lyman transitions, in the absence of which a robust lower limit can be placed on the individual free path. Applying this method to a set of $26$ quasars at $5.50.31 \ (0.18)$ pMpc at $2\sigma \ (3\sigma)$: a much tighter lower bound than obtained through traditional stacking methods. Our constraints get significantly stronger for lower values of $\xi$. New constraints on \mfp and $\xi$ are crucial to our understanding of the reionisation-era IGM., Comment: Submitted to ApJ; 15 pages, 5 figures

The presence of excess scatter in the Ly-$\alpha$ forest at $z\sim 5.5$, together with the existence of sporadic extended opaque Gunn-Peterson troughs, has started to provide robust evidence for a late end of hydrogen reionisation. However, low data quality and systematic uncertainties complicate the use of Ly-$\alpha$ transmission as a precision probe of reionisation's end stages. In this paper, we assemble a sample of 67 quasar sightlines at $z>5.5$ with high signal-to-noise ratios of $>10$ per $\leq 15$ km s$^{-1}$ spectral pixel, relying largely on the new XQR-30 quasar sample. XQR-30 is a large program on VLT/X-Shooter which obtained deep (SNR $>20$ per pixel) spectra of 30 quasars at $z>5.7$. We carefully account for systematics in continuum reconstruction, instrumentation, and contamination by damped Ly-$\alpha$ systems. We present improved measurements of the mean Ly-$\alpha$ transmission over $4.93.5 \sigma$). Our results indicate that reionisation-related fluctuations, whether in the UVB, residual neutral hydrogen fraction, and/or IGM temperature, persist in the intergalactic medium until at least $z=5.3$ ($t=1.1$ Gyr after the Big Bang). This is further evidence for a late end to reionisation., Comment: Accepted for publication in MNRAS. Full measurement datasets are available on the first author's website

The reionization epoch concludes when ionizing photons reach every corner of the Universe. Reionization has generally been assumed to be limited primarily by the rate at which galaxies produce ionizing photons, but the recent measurement of a surprisingly short ionizing photon mean free path of $0.75^{+0.65}_{-0.45}$ proper Mpc at $z = 6$ by Becker et al. (2021) suggests that absorption by residual neutral hydrogen in the otherwise ionized intergalactic medium may play a much larger role than previously expected. Here we show that consistency between this short mean free path and the coeval dark pixel fraction in the Ly$\alpha$ forest requires a cumulative output of $6.1^{+11}_{-2.4}$ ionizing photons per baryon by reionization's end. This represents a dramatic increase in the ionizing photon budget over previous estimates, greatly exacerbating the tension with measurements of the ionizing output from galaxies at later times. Translating this constraint into the instantaneous ionizing production from galaxies in our model, we find $\log_{10}f_{\rm esc}\xi_{\rm ion}/\text{(erg/Hz)}^{-1} =25.02_{-0.21}^{+0.45}$ at $z\sim6$. Even with optimistic assumptions about the ionizing production efficiency of early stellar populations, and assuming the galaxy luminosity function extends to extremely faint sources ($M_{\text{UV}}\leq-11$), complete reionization requires the escape fraction of ionizing photons to exceed $20\%$ across the galaxy population. This is far larger than observed in any galaxy population at lower redshifts, requiring rapid evolution in galaxy properties after the first billion years of cosmic time. This tension cannot be completely relieved within existing observational constraints on the hydrogen neutral fraction and mean free path., Comment: 8 pages, 5 figures, submitted to ApJL

The transmission of Lyman-{\alpha} (Ly{\alpha}) in the spectra of distant quasars depends on the density, temperature, and ionization state of the intergalactic medium (IGM). Therefore, high-redshift (z > 5) Ly{\alpha} forests could be invaluable in studying the late stages of the epoch of reionization (EoR), as well as properties of the sources that drive it. Indeed, high-quality quasar spectra have now firmly established the existence of large-scale opacity fluctuations at z > 5, whose physical origins are still debated. Here we introduce a Bayesian framework capable of constraining the EoR and galaxy properties by forward-modelling the high-z Ly{\alpha} forest. Using priors from galaxy and CMB observations, we demonstrate that the final overlap stages of the EoR (when >95% of the volume was ionized) should occur at z < 5.6, in order to reproduce the large-scale opacity fluctuations seen in forest spectra. However, it is the combination of patchy reionization and the inhomogeneous UV background that produces the longest Gunn-Peterson troughs. Ly{\alpha} forest observations tighten existing constraints on the characteristic ionizing escape fraction of galaxies, with the combined observations suggesting f_{\rm esc} \approx 7^4_3%, and disfavoring a strong evolution with the galaxy's halo (or stellar) mass., Comment: 19 pages, 11 figures, submitted to MNRAS, comments are welcome

We present a computationally efficient and fast semi-numerical technique for simulating the Lyman-$\alpha$ (Ly$\alpha$) absorption optical depth in presence of neutral hydrogen "islands" left over from reionization at redshifts $5 \lesssim z \lesssim 6$. The main inputs to the analysis are (i) a semi-numerical photon-conserving model of ionized regions during reionization (named SCRIPT) along with a prescription for simulating the shadowing by neutral islands and (ii) the fluctuating Gunn-Peterson approximation to model the Ly$\alpha$ absorption. Our model is then used for simulating the large-scale fluctuations in the effective optical depth as observed along sight lines towards high$-z$ quasars. Our model is fully described by five parameters. By setting two of them to default values and varying the other three, we obtain the constraints on reionization history at $5 \lesssim z \lesssim 6$ as allowed by the data. We confirm that reionization is \emph{not} complete before $z \sim 5.6$ at $\gtrsim 2\sigma$ confidence, with the exact confidence limits depending on how the non-detections of the flux in the data are treated. We also confirm that the completion of reionization can be as late as $z \sim 5.2$. With further improvements in the model and with more sight lines at $z \sim 6$, we can take advantage of the computational efficiency of our analysis to obtain more stringent constraints on the ionization fraction at the tail-end of reionization., Comment: Accepted in MNRAS. Matches the accepted version

Observations of the redshift z=7.085 quasar J1120+0641 have been used to search for variations of the fine structure constant, alpha, over the redshift range 5.5 to 7.1. Observations at z=7.1 probe the physics of the universe when it was only 0.8 billion years old. These are the most distant direct measurements of alpha to date and the first measurements made with a near-IR spectrograph. A new AI analysis method has been employed. Four measurements from the X-SHOOTER spectrograph on the European Southern Observatory's Very Large Telescope (VLT) directly constrain any changes in alpha relative to the value measured on Earth (alpha_0). The weighted mean strength of the electromagnetic force over this redshift range in this location in the universe is da/a = (alpha_z - alpha_0)/alpha_0 = (-2.18 +/- 7.27) X 10^{-5}, i.e. we find no evidence for a temporal change from the 4 new very high redshift measurements. When the 4 new measurements are combined with a large existing sample of lower redshift measurements, a new limit on possible spatial variation of da/a is marginally preferred over a no-variation model at the 3.7 sigma level., Comment: Accepted for publication in Science Advances

We present improved results of the measurement of the correlation between galaxies and the intergalactic medium (IGM) transmission at the end of reionisation. We have gathered a sample of $13$ spectroscopically confirmed Lyman-break galaxies (LBGs) and $21$ Lyman-$\alpha$ emitters (LAEs) at angular separations $20'' \lesssim \theta \lesssim 10'$ ($\sim 0.1-4$ pMpc at $z\sim 6$) from the sightlines to $8$ background $z\gtrsim 6$ quasars. We report for the first time the detection of an excess of Lyman-$\alpha$ transmission spikes at $\sim 10-60$ cMpc from LAEs ($3.2\sigma$) and LBGs ($1.9\sigma$). We interpret the data with an improved model of the galaxy-Lyman-$\alpha$ transmission and two-point cross-correlations which includes the enhanced photoionisation due to clustered faint sources, enhanced gas densities around the central bright objects and spatial variations of the mean free path. The observed LAE(LBG)-Lyman-$\alpha$ transmission spike two-point cross-correlation function (2PCCF) constrains the luminosity-averaged escape fraction of all galaxies contributing to reionisation to $\langle f_{\rm esc} \rangle_{M_{\rm UV}<-12} = 0.14_{-0.05}^{+0.28}\,(0.23_{-0.12}^{+0.46})$. We investigate if the 2PCCF measurement can determine whether bright or faint galaxies are the dominant contributors to reionisation. Our results show that a contribution from faint galaxies ($M_{\rm UV} > -20 \, (2\sigma)$) is necessary to reproduce the observed 2PCCF and that reionisation might be driven by different sub-populations around LBGs and LAEs at $z\sim 6$., Comment: Accepted for publication in MNRAS. 17 pages, 18 figures, 3 tables + appendices. Key results: Figs. 6,13,14. Updated version matches the published one ('online' Appendices are directly in the arXiv pdf). Conclusions unchanged from earlier preprint

High-redshift QSO spectra show large spatial fluctuations in the Ly-alpha 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-alpha opacity distribution at 5~6. Reionization is complete at z=5.3 in our model, and 50% 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~6.8. The late end of reionization results in a large scatter in the photoionisation 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., Comment: 5 pages, 3 figures; accepted for publication in MNRAS

We introduce a new method for determining the influence of galaxies and active galactic nuclei (AGN) on the physical state of the intergalactic medium (IGM) at high redshift and illustrate its potential via a first application to the field of the $z=6.42$ QSO J1148+5251. By correlating the spatial positions of spectroscopically-confirmed Lyman break galaxies (LBGs) with fluctuations in the Lyman alpha forest seen in the high signal-to-noise spectrum of a background QSO, we provide a statistical measure of the typical escape fraction of Lyman continuum photons close to the end of cosmic reionisation. Here we use Keck DEIMOS spectroscopy to locate 7 colour-selected LBGs in the redshift range $5.3\lesssim z\lesssim 6.4$ and confirm a faint $z=5.701$ AGN. We then examine the spatial correlation between this sample and Ly$\alpha$/Ly$\beta$ transmission fluctuations in a Keck ESI spectrum of the QSO. Interpreting the statistical HI proximity effect as arising from faint galaxies clustered around the detected LBGs, we translate the observed mean Ly$\alpha$ transmitted flux around an average detected LBG into a constraint on the mean escape fraction $\langle f_{\rm esc}\rangle\geq0.08$ at $z\simeq6$. We also report evidence of the individual transverse HI proximity effect of a $z=6.177$ luminous LBG via a Ly$\beta$ transmission spike and two broad Ly$\alpha$ transmission spikes around the $z=5.701$ AGN. We discuss the possible origin of such associations which suggest that while faint galaxies are primarily driving reionisation, luminous galaxies and AGN may provide important contributions to the UV background or thermal fluctuations of the IGM at $z\simeq6$. Although a limited sample, our results demonstrate the potential of making progress using this method in resolving one of the most challenging aspects of the contribution of galaxies and AGN to cosmic reionisation., Comment: 21 pages, 16 figures, the version accepted in MNRAS

We present measurements of the mean and scatter of the IGM Lyman-{\alpha} opacity at 4.9 < z < 6.1 along the lines of sight of 62 quasars at z > 5.7, the largest sample assembled at these redshifts to date by a factor of two. The sample size enables us to sample cosmic variance at these redshifts more robustly than ever before. The spectra used here were obtained by the SDSS, DES-VHS and SHELLQs collaborations, drawn from the ESI and X-Shooter archives, reused from previous studies or observed specifically for this work. We measure the effective optical depth of Lyman-{\alpha} in bins of 10, 30, 50 and 70 cMpc h-1, construct cumulative distribution functions under two treatments of upper limits on flux and explore an empirical analytic fit to residual Lyman-{\alpha} transmission. We verify the consistency of our results with those of previous studies via bootstrap re-sampling and confirm the existence of tails towards high values in the opacity distributions, which may persist down to z = 5.2. Comparing our results with predictions from cosmological simulations, we find further strong evidence against models that include a spatially uniform ionizing background and temperature-density relation. We also compare to IGM models that include either a fluctuating UVB dominated by rare quasars or temperature fluctuations due to patchy reionization. Although both models produce better agreement with the observations, neither fully captures the observed scatter in IGM opacity. Our sample of 62 z > 5.7 quasar spectra opens many avenues for future study of the reionisation epoch., Comment: 23 pages, updated to match MNRAS accepted version

High-signal to noise observations of the Ly$\alpha$ forest transmissivity in the z = 7.085 QSO ULAS J1120+0641 show seven narrow transmission spikes followed by a long 240 cMpc/h trough. Here we use radiative transfer simulations of cosmic reionization previously calibrated to match a wider range of Ly$\alpha$ forest data to show that the occurrence of seven transmission spikes in the narrow redshift range z = 5.85 - 6.1 is very sensitive to the exact timing of reionization. Occurrence of the spikes requires the most under dense regions of the IGM to be already fully ionised. The rapid onset of a long trough at z = 6.12 requires a strong decrease of the photo-ionisation rate at z$\sim$6.1 in this line-of-sight, consistent with the end of percolation at this redshift. The narrow range of reionisation histories that we previously found to be consistent with a wider range of Ly$\alpha$ forest data have a reasonable probability of showing seven spikes and the mock absorption spectra provide an excellent match to the spikes and the trough in the observed spectrum of ULAS J1120+0641. Despite the large overall opacity of Ly$\alpha$ at z > 5.8, larger samples of high signal-to-noise observations of rare transmission spikes should therefore provide important further insights into the exact timing of the percolation of HII bubbles at the tail-end of reionization, Comment: 12 pages, 12 figures, published in MNRAS

Signs of damping wing absorption attenuating the Lyman-$\alpha$ emission line of the first known $z \sim 7$ quasar, ULAS J1120+0641, recently provided exciting evidence of a significantly neutral IGM. This long-awaited signature of reionization was inferred, in part, from a deficit of flux in the quasar's Lyman-$\alpha$ emission line based on predictions from a composite of lower-redshift quasars. The composite sample was chosen based on its C IV emission line properties; however, as the original study by Mortlock et al. noted, the composite contained a slight velocity offset in C IV compared to ULAS J1120+0641. Here we test whether this offset may be related to the predicted strength of the Lyman-$\alpha$ emission line. We confirm the significant ($\sim 10$ per cent at r.m.s.) scatter in Lyman-$\alpha$ flux for quasars of a given C IV velocity and equivalent width found by Mortlock et al. We further find that among lower-redshift objects chosen to more closely match the C IV properties of ULAS J1120+0641, its Lyman-$\alpha$ emission falls within the observed distribution of fluxes. Among lower-redshift quasars chosen to more closely match in C IV velocity and equivalent width, we find that ULAS J1120+0641 falls within the observed distribution of Lyman-$\alpha$ emission line strengths. This suggests that damping wing absorption may not be present, potentially weakening the case for neutral gas around this object. Larger samples of z$>$7 quasars may therefore be needed to establish a clearer picture of the IGM neutral fraction at these redshifts., Comment: 7 pages, 6 figures