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We present a data reduction pipeline (DRP) for Keck/NIRSPEC built as an addition to the PypeIt Python package. The DRP is capable of reducing multi-order echelle data taken both before and after the detector upgrade in 2018. As part of developing the pipeline, we implemented major improvements to the capabilities of the PypeIt package, including manual wavelength calibration for multi-order data and new output product that returns a coadded spectrum order-by-order. We also provide a procedure for correcting telluric absorption in NIRSPEC data by using the spectra of telluric standard stars taken near the time of the science spectra. At high resolutions, this is often more accurate than modeling-based approaches., Comment: 2 pages, 1 figure, accepted to RNAAS

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

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 introduce a new approach for analyzing the IGM damping wings imprinted on the proximity zones of quasars in the epoch of reionization (EoR). Whereas past work has typically forgone the additional constraining power afforded by the blue side continuum ($1216\,\r{A} \lesssim \lambda \lesssim 1280\,\r{A}$) and/or opted not to model the large correlated IGM transmission fluctuations in the proximity zone ($\lambda \lesssim 1216\,\r{A}$), we construct a generative probabilistic model for the entire spectrum accounting for all sources of error - the stochasticity induced by patchy reionization, the impact of the quasar's ionizing radiation on the IGM, the unknown intrinsic spectrum of the quasar, and spectral noise. This principled Bayesian method allows us to marginalize out nuisance parameters associated with the quasar's radiation and its unknown intrinsic spectrum to precisely measure the IGM neutral fraction, $\langle x_{\rm HI}\rangle$. A key element of our analysis is the use of dimensionality reduction (DR) to describe the intrinsic quasar spectrum via a small number of nuisance parameters. Using a large sample of $15,559$ SDSS/BOSS quasars at $z \gtrsim 2.15$ we trained and quantified the performance of six distinct DR methods, and find that a six parameter PCA model (five coefficients plus a normalization) performs best, with complex machine learning approaches providing no advantage. By conducting statistical inference on 100 realistic mock EoR quasar spectra, we demonstrate the reliability of the credibility contours that we obtain on $\langle x_{\rm HI}\rangle$ and the quasar lifetime, $t_{\rm Q}$. The new method introduced here will transform IGM damping wings into a precision probe of reionization, on the same solid methodological and statistical footing as other precision cosmological measurements., Comment: Submitted to MNRAS

We investigate the precision with which the Lyman-$\alpha$ damping wing signature imprinted on the spectra of high-redshift quasars (QSOs) by the foreground neutral intergalactic medium (IGM) can measure the history of cosmic reionization. We leverage a novel inference pipeline based on a generative probabilistic model for the entire spectrum (both red- and blueward of the Lyman-$\alpha$ line), accounting for all relevant sources of uncertainty - the stochasticity caused by patchy reionization, the impact of the quasar's ionizing radiation on the IGM, it's unknown intrinsic spectrum, and spectral noise. Performing fast JAX-based Hamiltonian Monte-Carlo (HMC) parameter inference, we precisely measure the underlying global IGM neutral fraction as well as the lifetime of the quasar. Running a battery of tests on over a thousand mocks, we find optimal precision when running the pipeline with a six parameter PCA continuum model (five coefficients and a normalization) on $\mathrm{S}/\mathrm{N} \sim 10$ spectra, binned to a $\sim 500\,\mathrm{km}/\mathrm{s}$ velocity pixel scale, and extending at least out to the C IV $\lambda\,1549\,\text{\r{A}}$ emission line. After marginalizing out nuisance parameters associated with the quasar continuum, a single spectrum constrains the IGM neutral fraction to $28.0_{-8.8}^{+8.2}\,\%$ and the quasar lifetime to $0.80_{-0.55}^{+0.22}\,\mathrm{dex}$, improving notably towards spectra with a stronger IGM damping wing imprint. Higher precision can be achieved by averaging over statistical quasar samples. We identify two primary sources of uncertainty that contribute approximately equally to the total error budget: the uncertain quasar continuum model and the stochastic distribution of neutral regions arising from both the reionization topology and the location of the quasar's ionization front., Comment: Submitted to MNRAS

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

The [CII] 158 $\mu$m emission line and the underlying far-infrared (FIR) dust continuum are important tracers for studying star formation and kinematic properties of early galaxies. We present a survey of the [CII] emission lines and FIR continua of 31 luminous quasars at $z>6.5$ using the Atacama Large Millimeter Array (ALMA) and the NOrthern Extended Millimeter Array (NOEMA) at sub-arcsec resolution. This survey more than doubles the number of quasars with [CII] and FIR observations at these redshifts and enables statistical studies of quasar host galaxies deep into the epoch of reionization. We detect [CII] emission in 27 quasar hosts with a luminosity range of $L_{\rm [CII]}=(0.3-5.5)\times10^9~L_\odot$ and detect the FIR continuum of 28 quasar hosts with a luminosity range of $L_{\rm FIR}=(0.5-13.0)\times10^{12}~L_\odot$. Both $L_{\rm [CII]}$ and $L_{\rm FIR}$ are correlated ($\rho\simeq0.4$) with the quasar bolometric luminosity, albeit with substantial scatter. The quasar hosts detected by ALMA are clearly resolved with a median diameter of $\sim$5 kpc. About 40% of the quasar host galaxies show a velocity gradient in [CII] emission, while the rest show either dispersion-dominated or disturbed kinematics. Basic estimates of the dynamical masses of the rotation-dominated host galaxies yield $M_{\rm dyn}=(0.1-7.5)\times10^{11}~M_\odot$. Considering our findings alongside those of literature studies, we found that the ratio between $M_{\rm BH}$ and $M_{\rm dyn}$ is about ten times higher than that of local $M_{\rm BH}-M_{\rm dyn}$ relation on average but with substantial scatter (the ratio difference ranging from $\sim$0.6 to 60) and large uncertainties., Comment: 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

Protoclusters, the progenitors of galaxy clusters, trace large scale structures in the early Universe and are important to our understanding of structure formation and galaxy evolution. To date, only a handful of protoclusters have been identified in the Epoch of Reionization (EoR). As one of the rarest populations in the early Universe, distant quasars that host active supermassive black holes are thought to reside in the most massive dark matter halos at that cosmic epoch, and could thus potentially pinpoint some of the earliest protoclusters. In this letter, we report the discovery of a massive protocluster around a luminous quasar at $z=6.63$. This protocluster is anchored by the quasar, and includes three [CII] emitters at $z\sim6.63$, 12 spectroscopically confirmed Ly$\alpha$ emitters (LAEs) at $6.5430$ in its central region (i.e., $R\lesssim2$ cMpc). We estimate that this protocluster will collapse into a galaxy cluster with a mass of $6.9^{+1.2}_{-1.4}\times10^{15}~M_\odot$ at the current epoch, more massive than the most massive clusters known in the local Universe such as Coma. In the quasar vicinity, we discover a double-peaked LAE which implies that the quasar has a UV lifetime greater than 0.8 Myrs and has already ionized its surrounding intergalactic medium., Comment: Accepted for publication in ApJL

Blazars are radio-loud Active Galactic Nuclei (AGN) whose jets have a very small angle to our line of sight. Observationally, the radio emission are mostly compact or a compact-core with a 1-sided jet. With 2.5$^{\prime\prime}$ resolution at 3 GHz, the Very Large Array Sky Survey (VLASS) enables us to resolve the structure of some blazar candidates in the sky north of Decl. $-40$ deg. We introduce an algorithm to classify radio sources as either blazar-like or non-blazar-like based on their morphology in the VLASS images. We apply our algorithm to three existing catalogs, including one of known blazars (Roma-BzCAT) and two of blazar candidates identified by WISE colors and radio emission (WIBRaLS, KDEBLLACS). We show that in all three catalogs, there are objects with morphology inconsistent with being blazars. Considering all the catalogs, more than 12% of the candidates are unlikely to be blazars, based on this analysis. Notably, we show that 3% of the Roma-BzCAT "confirmed" blazars could be a misclassification based on their VLASS morphology. The resulting table with all sources and their radio morphological classification is available online., Comment: 21 pages, 11 figures, accepted for publication in The Astrophysical Journal

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 small-scale structure of baryons in the intergalactic medium is intimately linked to their past thermal history. Prior to the $\gtrsim10^4$ K photoheating during the epoch of reionization, cold baryons may have closely traced the clumpy cosmic web of dark matter down to scales as low as $\lesssim1$ comoving kpc, depending on the degree of heating by the X-ray background. After the passage of the ionization front, this clumpy structure can persist for $\sim10^{8}$ years. The strong Ly$\alpha$ damping wings detected towards a few of the highest redshift quasars, in addition to their smaller-than-expected Ly$\alpha$-transmissive proximity zones, suggest that they have ionized and heated the foreground intergalactic medium less than $10^7$ years ago. Signatures of the pre-reionization small-scale structure should thus persist in their intergalactic surroundings. Here we explore how the persistence of this clumpy structure can affect the statistics of Ly$\alpha$ transmission inside the transparent proximity zones of $z\gtrsim7$ quasars by post-processing a suite of small-volume hydrodynamical simulations with 1D ionizing radiative transfer. We find that the Ly$\alpha$ flux power spectrum and flux PDF statistics of ten $z=7.5$ proximity zones, with realistic observational parameters, could distinguish the gaseous structure of a $T_{\rm IGM}\sim2$ K CDM model from warm dark matter models with particle masses $m_{\rm WDM}>10$ keV and X-ray heated models with $f_{\rm X}f_{\rm abs}>0.1$ ($T_{\rm IGM}(z=7.5)\gtrsim275$ K) at the $2\sigma$ level., Comment: 18 pages, 17 figures, submitted to ApJ

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 epoch of hydrogen reionization is complete by $z=5$, but its progression at higher redshifts is uncertain. Measurements of Ly$\alpha$ forest opacity show large scatter at $z<6$, suggestive of spatial fluctuations in neutral fraction ($x_\mathrm{HI}$), temperature, or ionizing background, either individually or in combination. However, these effects are degenerate, necessitating modeling these physics in tandem in order to properly interpret the observations. We begin this process by developing a framework for modeling the reionization history and associated temperature fluctuations, with the intention of incorporating ionizing background fluctuations at a later time. To do this, we generate several reionization histories using semi-numerical code AMBER, selecting histories with volume-weighted neutral fractions that adhere to the observed CMB optical depth and dark pixel fractions. Implementing these histories in the \texttt{Nyx} cosmological hydrodynamics code, we examine the evolution of gas within the simulation, and the associated metrics of the Ly$\alpha$ forest opacity. We find that the pressure smoothing scale within the IGM is strongly correlated with the adiabatic index of the temperature-density relation. We find that while models with 20,000 K photoheating at reionization are better able to reproduce the shape of the observed $z=5$ 1D flux power spectrum than those with 10,000 K, they fail to match the highest wavenumbers. The simulated autocorrelation function and optical depth distributions are systematically low and narrow, respectively, compared to the observed values, but are in better agreement when the reionization history is longer in duration, more symmetric in its distribution of reionization redshifts, or if there are remaining neutral regions at $z<6$. The systematically low variance likely requires the addition of a fluctuating UVB., Comment: To be submitted to MNRAS. Comments welcome

The auto-correlation function of the Lyman-$\alpha$ (Ly$\alpha$) forest flux from high-z quasars can statistically probe all scales of the intergalactic medium (IGM) just after the epoch of reionization. The thermal state of the IGM, which is determined by the physics of reionization, sets the amount of small-scale power seen in the \lya forest. To study the sensitivity of the auto-correlation function to the thermal state of the IGM, we compute the auto-correlation function from cosmological hydrodynamical simulations with semi-numerical models of the thermal state of the IGM. We create mock data sets of 20 quasars to forecast constraints on $T_0$ and $\gamma$, which characterize a tight temperature-density relation in the IGM, at $5.4 \leq z \leq 6$. At $z = 5.4$ we find that an ideal data set constrains $T_0$ to 29\% and $\gamma$ to 9\%. In addition, we investigate four realistic reionization scenarios that combine temperature and ultra-violet background (UVB) fluctuations at $z = 5.8$. We find that, when using mock data generated from a model that includes temperature and UVB fluctuations, we can rule out a model with no temperature or UVB fluctuations at $>1\sigma$ level 50.5\% of the time., Comment: 18 pages, 13 figures, comments welcome. arXiv admin note: text overlap with arXiv:2208.09013

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

Observed scatter in the Lyman-alpha opacity of quasar sightlines at $z<6$ has motivated measurements of the correlation between Ly$\alpha$ opacity and galaxy density, as models that predict this scatter make strong and sometimes opposite predictions for how they should be related. Our previous work associated two highly opaque Ly$\alpha$ troughs at $z\sim5.7$ with a deficit of Lyman-$\alpha$ emitting galaxies (LAEs). In this work, we survey two of the most highly transmissive lines of sight at this redshift, towards the $z=6.02$ quasar SDSS J1306+0356 and the $z=6.17$ quasar PSO J359-06. We find that both fields are underdense in LAEs within 10 $h^{-1}$ Mpc of the quasar sightline, somewhat less extensive than underdensities associated with Ly$\alpha$ troughs. We combine our observations with three additional fields from the literature, and find that while fields with extreme opacities are generally underdense, moderate opacities span a wider density range. The results at high opacities are consistent with models that invoke UV background fluctuations and/or late reionization to explain the observed scatter in IGM Ly$\alpha$ opacities. There is tension at low opacities, however, as the models tend to associate lower IGM Ly$\alpha$ opacities with higher densities. Although the number of fields surveyed is still small, the low-opacity results may support a scenario in which the ionizing background in low-density regions increases more rapidly than some models suggest after becoming ionized. Elevated gas temperatures from recent reionization may also be making these regions more transparent., Comment: 20 pages, 17 figures. Accepted to ApJ

In the process of producing the roughly three ionizing photons per atom required to reionize the IGM, the same massive stars explode and eject metals into their surroundings. While the overly sensitive Lya transition makes Gunn-Peterson absorption of background quasar light an ineffective probe of reionization at z > 6, strong low-ionization transitions like the MgII doublet will give rise to a detectable "metal-line forest", if metals pollute the neutral IGM. We measure the auto-correlation of the MgII forest transmission using a sample of ten ground based z >= 6.80 quasar spectra probing the redshift range 5.96 < z_MgII < 7.42 (z_MgII,median = 6.47). The correlation function exhibits strong small-scale clustering and a pronounced peak at the doublet velocity (768 km/s) arising from strong absorbers in the CGM of galaxies. After these strong absorbers are identified and masked the signal is consistent with noise. Our measurements are compared to a suite of models generated by combining a large hydrodynamical simulation with a semi-numerical reionization topology, assuming a simple uniform enrichment model. We obtain a 95% credibility upper limit of [Mg/H] < -3.73 at z_MgII,median = 6.47, assuming uninformative priors on [Mg/H] and the IGM neutral fraction x_HI. Splitting the data into low-z (5.96 < z_MgII < 6.47; z_MgII,median = 6.235) and high-z (6.47 < z_MgII < 7.42; z_MgII,median = 6.72) subsamples again yields null-detections and 95% upper limits of [Mg/H] < -3.75 and [Mg/H] < -3.45, respectively. These first measurements set the stage for an approved JWST Cycle 2 program (GO 3526) targeting a similar number of quasars that will be an order of magnitude more sensitive, making the Mgii forest an emerging powerful tool to deliver precision constraints on the reionization and enrichment history of the Universe., Comment: Submitted to MNRAS; 23 pages, 21 figures, 1 table

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

The Ly$\alpha$ forest (LAF) at $z>5$ probes the thermal and reionization history of the intergalactic medium (IGM) and the nature of dark matter, but its interpretation requires comparison to cosmological hydrodynamical simulations. At high-$z$, convergence of these simulations is more exacting since transmission is dominated by underdense voids that are challenging to resolve. With evidence mounting for a late end to reionization, small structures down to the sub-kpc level may survive to later times than conventionally thought due to the reduced time for pressure smoothing to impact the gas, further tightening simulation resolution requirements. We perform a suite of simulations using the Eulerian cosmological hydrodynamics code Nyx, spanning domain sizes of 1.25-10 $h^{-1}$ Mpc and 5-80 $h^{-1}$ kpc cells, and explore the interaction of these variables with the timing of reionization on the properties of the matter distribution and the simulated LAF at $z=5.5$. In observable Ly$\alpha$ power, convergence within 10% is achieved for $k< 0.1$ s/km, but larger $k$ shows deviation of up to 20 percent. While a later reionization retains more small structure in the density field, because of the greater thermal broadening there is little difference in the convergence of LAF power between early ($z=9$) and later ($z=6$) reionizations. We conclude that at $z\sim5.5$, resolutions of 10 kpc are necessary for convergence of LAF power at $k<0.1$ s/km, while higher-$k$ modes require higher resolution, and that the timing of reionization does not significantly impact convergence given realistic photoheating., Comment: Submitted to MNRAS. Comments welcome

We present the first results from the JWST ASPIRE program (A SPectroscopic survey of biased halos In the Reionization Era). This program represents an imaging and spectroscopic survey of 25 reionization-era quasars and their environments by utilizing the unprecedented capabilities of NIRCam Wide Field Slitless Spectroscopy (WFSS) mode. ASPIRE will deliver the largest ($\sim280~{\rm arcmin}^2$) galaxy redshift survey at 3-4 $\mu$m among JWST Cycle-1 programs and provide extensive legacy values for studying the formation of the earliest supermassive black holes (SMBHs), the assembly of galaxies, early metal enrichment, and cosmic reionization. In this first ASPIRE paper, we report the discovery of a filamentary structure traced by the luminous quasar J0305-3150 and ten [OIII] emitters at $z=6.6$. This structure has a 3D galaxy overdensity of $\delta_{\rm gal}=12.6$ over 637 cMpc$^3$, one of the most overdense structures known in the early universe, and could eventually evolve into a massive galaxy cluster. Together with existing VLT/MUSE and ALMA observations of this field, our JWST observations reveal that J0305-3150 traces a complex environment where both UV-bright and dusty galaxies are present, and indicate that the early evolution of galaxies around the quasar is not simultaneous. In addition, we discovered 31 [OIII] emitters in this field at other redshifts, $5.3

Studies of rest-frame optical emission in quasars at $z>6$ have historically been limited by the wavelengths accessible by ground-based telescopes. The James Webb Space Telescope (JWST) now offers the opportunity to probe this emission deep into the reionization epoch. We report the observations of eight quasars at $z>6.5$ using the JWST/NIRCam Wide Field Slitless Spectroscopy, as a part of the ''A SPectroscopic survey of biased halos In the Reionization Era (ASPIRE)" program. Our JWST spectra cover the quasars' emission between rest frame $\sim$ 4100 and 5100 \r{A}. The profiles of these quasars' broad H$\beta$ emission lines span a FWHM from 3000 to 6000 $\rm{km~s^{-1}}$. The H$\beta$-based virial black hole (BH) masses, ranging from 0.6 to 2.1 billion solar masses, are generally consistent with their MgII-based BH masses. The new measurements based on the more reliable H$\beta$ tracer thus confirm the existence of billion solar-mass BHs in the reionization epoch. In the observed [OIII] $\lambda\lambda$4960,5008 doublets of these luminous quasars, broad components are more common than narrow core components ($\le~1200~\rm{km~s^{-1}}$), and only one quasar shows stronger narrow components than broad. Two quasars exhibit significantly broad and blueshifted [OIII] emission, thought to trace galactic-scale outflows, with median velocities of $-610~\rm{km~s^{-1}}$ and $-1430~\rm{km~s^{-1}}$ relative to the [CII] $158\,\mu$m line. All eight quasars show strong optical FeII emission, and follow the Eigenvector 1 relations defined by low-redshift quasars. The entire ASPIRE program will eventually cover 25 quasars and provide a statistical sample for the studies of the BHs and quasar spectral properties., Comment: 13 pages, 4 figures, accepted for publication in ApJL

We test the impact of gravitational lensing on the lifetime estimates of seven high-redshift quasars at redshift $z\gtrsim6$. The targeted quasars are identified by their small observed proximity zone sizes, which indicate extremely short quasar lifetimes $(t_Q\lesssim10^5 \text{ yrs})$. However, these estimates of quasar lifetimes rely on the assumption that the observed luminosities of the quasars are intrinsic and not magnified by gravitational lensing, which would bias the lifetime estimates towards younger ages. In order to test possible effects of gravitational lensing, we obtain high-resolution images of the seven quasars with the {\em Hubble Space Telescope (HST)} and look for signs of strong lensing. We do not find any evidence of strong lensing, i.e., all quasars are well-described by point sources, and no foreground lensing galaxy is detected. We estimate that the strong lensing probabilities for these quasars are extremely small $(\sim1.4\times10^{-5})$, and show that weak lensing changes the estimated quasar lifetimes by only $\lesssim0.2$ dex. We thus confirm that the short lifetimes of these quasars are intrinsic. The existence of young quasars indicates a high obscured fraction, radiatively inefficient accretion, and/or flickering light curves for high-redshift quasars. We further discuss the impact of lensing magnification on measurements of black hole masses and Eddington ratios of quasars., Comment: 14 pages, 4 figures, 3 tables. Accepted by the Astrophysical Journal

Koptelova et al. 2022 (K22) recently claimed a new quasar discovery at $z=7.46$. After careful consideration of the publicly-available data underlying K22's claim, we find that the observations were contaminated by a moving Solar System object, likely a main-belt asteroid. In the absence of the contaminated photometry, there is no evidence for the nearby, persistent WISE source being a high-redshift object; in fact, a detection of the source in DELS $z$-band rules out a redshift $z>7.3$. We present our findings as a cautionary tale of the dangers of passing asteroids for photometric selections., Comment: RNAAS; 2 pages, 1 figure. The asteroid has been conclusively identified as (43838) 1993 FW49

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

Cosmic reionization was the last major phase transition of hydrogen from neutral to highly ionized in the intergalactic medium (IGM). Current observations show that the IGM is significantly neutral at $z>7$, and largely ionized by $z\sim5.5$. However, most methods to measure the IGM neutral fraction are highly model-dependent, and are limited to when the volume-averaged neutral fraction of the IGM is either relatively low ($\bar{x}_{\rm HI} \lesssim 10^{-3}$) or close to unity ($\bar{x}_{\rm HI}\sim 1$). In particular, the neutral fraction evolution of the IGM at the critical redshift range of $z=6-7$ is poorly constrained. We present new constraints on $\bar{x}_{\rm HI}$ at $z\sim5.1-6.8$, by analyzing deep optical spectra of $53$ quasars at $5.736.1$ are consistent with the redshift evolution of the neutral fraction of the IGM derived from the Planck 2018., Comment: 13 pages, 6 figures, 2 tables, accepted for publication in ApJ

Lyman-alpha emitters (LAEs) are excellent probes of the reionization process, as they must be surrounded by large ionized bubbles in order to be visible during the reionization era. Large ionized regions are thought to correspond to over-dense regions and may be protoclusters, making them interesting test-beds for early massive structures. Close associations containing several LAEs are often assumed to mark over-dense, ionized bubbles. Here, we develop the first framework to quantify the ionization and density fields of high-z galaxy associations. We explore the interplay between (i) the large-scale density of a survey field, (ii) Poisson noise due to the small number density of bright sources at high redshifts (z~7), and (iii) the effects of the ionized fraction on the observation of LAEs. We use Bayesian statistics, a simple model of reionization, and a Monte-Carlo simulation to construct a more comprehensive method for calculating the large-scale density of LAE regions than previous works. We find that Poisson noise has a strong effect on the inferred density of a region and show how the ionized fraction can be inferred. We then apply our framework to the strongest association yet identified: Hu et al. (2021) found 14 LAEs in a volume of ~50,000 cMpc^3 inside the COSMOS field at z~7. We show that this is most likely a 2.5-sigma over-density inside of an ionized or nearly ionized bubble. We also show that this LAE association implies that the global ionized fraction is Q = 0.60 (+0.08,-0.09), within the context of a simple reionization model., Comment: 14 pages, 14 figures, submitted to MNRAS

We build a multi-output generative model for quasar spectra and the properties of their black hole engines, based on a Gaussian process latent-variable model. This model treats every quasar as a vector of latent properties such that the spectrum and all physical properties of the quasar are associated with non-linear functions of those latent parameters; the Gaussian process kernel functions define priors on the function space. Our generative model is trained with a justifiable likelihood function that allows us to treat heteroscedastic noise and missing data correctly, which is crucial for all astrophysical applications. It can predict simultaneously unobserved spectral regions, as well as the physical properties of quasars in held-out test data. We apply the model to rest-frame ultraviolet and optical quasar spectra for which precise black hole masses (based on reverberation mapping measurements) are available. Unlike reverberation-mapping studies, which require multi-epoch data, our model predicts black hole masses from single-epoch spectra, even with limited spectral coverage. We demonstrate the capabilities of the model by predicting black hole masses and unobserved spectral regions. We find that we predict black hole masses at close to the best possible accuracy., Comment: accepted for publication in ApJ

Fluctuations in Lyman-$\alpha$ (Ly$\alpha$) forest transmission towards high-$z$ quasars are partially sourced from spatial fluctuations in the ultraviolet background (UVB), the level of which are set by the mean free path of ionizing photons ($\lambda_{\text{mfp}}$). The auto-correlation function of Ly$\alpha$ forest flux characterizes the strength and scale of transmission fluctuations and, as we show, is thus sensitive to $\lambda_{\text{mfp}}$. Recent measurements at $z \sim 6$ suggest a rapid evolution of $\lambda_{\text{mfp}}$ at $z>5.0$ which would leave a signature in the evolution of the auto-correlation function. For this forecast, we model mock Ly$\alpha$ forest data with properties similar to the XQR-30 extended data set at $5.4 \leq z \leq 6.0$. At each $z$ we investigate 100 mock data sets and an ideal case where mock data matches model values of the auto-correlation function. For ideal data with $\lambda_{\text{mfp}}=9.0$ cMpc at $z=6.0$, we recover $\lambda_{\text{mfp}}=12^{+6}_{-3}$ cMpc. This precision is comparable to direct measurements of $\lambda_{\text{mfp}}$ from the stacking of quasar spectra beyond the Lyman limit. Hypothetical high-resolution data leads to a $\sim40\%$ reduction in the error bars over all $z$. The distribution of mock values of the auto-correlation function in this work is highly non-Gaussian for high-$z$, which should caution work with other statistics of the high-$z$ Ly$\alpha$ forest against making this assumption. We use a rigorous statistical method to pass an inference test, however future work on non-Gaussian methods will enable higher precision measurements., Comment: Accepted for publication in MNRAS, 16 pages, 11 figures

We present measurements of black hole masses and Eddington ratios for a sample of 38 bright (M$_{1450}$ < -24.4 mag) quasars at 5.8 < z < 7.5, derived from VLT/X-shooter near-IR spectroscopy of their broad CIV and MgII emission lines. The black hole masses (on average M$_{BH}$ ~ 4.6 x 10$^9$ M$_{\odot}$) and accretion rates (with Eddington ratios ranging between 0.1 and 1.0) are broadly consistent with that of similarly luminous 0.3 < z < 2.3 quasars, but there is evidence for a mild increase in the median Eddington ratio going towards z > 6. Combined with deep ALMA observations of the [CII] 158 $\mu$m line from the quasar host galaxies and VLT/MUSE investigations of the extended Ly$\alpha$ halos, this study provides fundamental clues to models of the formation and growth of the first massive galaxies and black holes. Compared to local scaling relations, z > 5.7 black holes appear to be over-massive with respect to their host galaxies, and their accretion properties do not change with host galaxy morphology. Under the assumption that the kinematics of the T ~ 10$^4$ K gas, traced by the extended Ly$\alpha$ halos, are dominated by the gravitational potential of the dark matter halo, we report a similar relation between the black hole mass and circular velocity to the one reported for z ~ 0 galaxies. These results paint a picture where the first supermassive black holes reside in massive halos at z > 6 and lead the first stages of galaxy formation by rapidly growing in mass with a duty cycle of order unity. However, this duty cycle needs to drastically drop towards lower redshifts, while the host galaxies continue forming stars at a rate of hundreds of solar masses per year, sustained by the large reservoirs of cool gas surrounding them., Comment: Accepted for publication on AAS journals. 24 pages + appendices, 15 figures, 5 tables (including full list of z>5.7 quasars with MgII based black hole mass estimates). For access to the data and codes used in this work, please contact the authors

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

We present statistics of HeII Lya transmission spikes and large-scale absorption troughs using archival high-resolution ($R=\lambda /\Delta \lambda \simeq 12,500$-$18,000$) far-UV spectra of eight HeII-transparent quasars obtained with the Cosmic Origins Spectrograph on the Hubble Space Telescope. The sample covers the redshift range 2.5100cMpc at z>3 to L~30cMpc at z~2.7, signaling a significant progression of HeII reionization at these redshifts. Furthermore, unexpectedly long L~65cMpc troughs detected at z~2.9 suggest that the UV background fluctuates at larger scales than predicted by current models. By comparing the measured incidence of transmission spikes to predictions from forward-modeled mock spectra created from the outputs of a (146cMpc)^3 optically thin Nyx hydrodynamical simulation employing different UV background models, we infer the redshift evolution of the HeII photoionization rate $\Gamma_\mathrm{He\,II}(z)$. The photoionization rate decreases with increasing redshift from $\simeq 4.6\times 10^{-15}\mathrm{\,s^{-1}}$ at z~2.6 to $\simeq 1.2 \times 10^{-15}\mathrm{\,s^{-1}}$ at z~3.2, in agreement with previous inferences from the HeII effective optical depth, and following expected trends of current models of a fluctuating HeII-ionizing background., Comment: Accepted for publication in ApJ following minor revision (added 2 new figures); 16 pages, 14 figures

Bright, high redshift ($z>6$) QSOs are powerful probes of the ionisation state of the intervening intergalactic medium (IGM). The detection of Ly$\alpha$ damping wing absorption imprinted in the spectrum of high-z QSOs can provide strong constraints on the epoch of reionisation (EoR). In this work, we perform an independent Ly$\alpha$ damping wing analysis of two known $z>7$ QSOs; DESJ0252-0503 at $z=7.00$ (Wang et al.) and J1007+2115 at $z=7.51$ (Yang et al.). For this, we utilise our existing Bayesian framework which simultaneously accounts for uncertainties in: (i) the intrinsic Ly$\alpha$ emission profile (reconstructed from a covariance matrix of measured emission lines; extended in this work to include NV) and (ii) the distribution of ionised (H\,{\scriptsize II}) regions within the IGM using a $1.6^3$ Gpc$^3$ reionisation simulation. This approach is complementary to that used in the aforementioned works as it focuses solely redward of Ly$\alpha$ ($1218 < \lambda < 1230$\AA) making it more robust to modelling uncertainties while also using a different methodology for (i) and (ii). We find, for a fiducial EoR morphology, $\bar{x}_{\rm HI} = 0.64\substack{+0.19 \\ -0.23}$ (68 per cent) at $z=7$ and $\bar{x}_{\rm HI} = 0.27\substack{+0.21 \\ -0.17}$ at $z=7.51$ consistent within $1\sigma$ to the previous works above, though both are slightly lower in amplitude. Following the inclusion of NV into our reconstruction pipeline, we perform a reanalysis of ULASJ1120+0641 at $z=7.09$ (Mortlock et al.) and ULASJ1342+0928 at $z=7.54$ (Ba\~nados et al.) finding $\bar{x}_{\rm HI} = 0.44\substack{+0.23 \\ -0.24}$ at $z=7.09$ and $\bar{x}_{\rm HI} = 0.31\substack{+0.18 \\ -0.19}$ at $z=7.54$. Finally, we combine the QSO damping wing constraints for all four $z\gtrsim7$ QSOs to obtain a single, unified constraint of $\bar{x}_{\rm HI} = 0.49\substack{+0.11 \\ -0.11}$ at $z=7.29$., Comment: 15 pages, 9 figures. Submitted to MNRAS, comments welcome

The thermal state of the intergalactic medium (IGM) contains vital information about the epoch of reionization, one of the most transformative yet poorly understood periods in the young universe. This thermal state is encoded in the small-scale structure of Lyman-$\alpha$ (Ly$\alpha$) absorption in quasar spectra. The 1D flux power spectrum measures the average small-scale structure along quasar sightlines. At high redshifts, where the opacity is large, averaging mixes high signal-to-noise ratio transmission spikes with noisy absorption troughs. Wavelet amplitudes are an alternate statistic that maintains spatial information while quantifying fluctuations at the same spatial frequencies as the power spectrum, giving them the potential to more sensitively measure the small-scale structure. Previous Ly$\alpha$ forest studies using wavelet amplitude probability density functions (PDFs) used limited spatial frequencies and neglected strong correlations between PDF bins and across wavelets scales, resulting in sub-optimal and unreliable parameter inference. Here we present a novel method for performing statistical inference using wavelet amplitude PDFs that spans the full range of spatial frequencies probed by the power spectrum and that fully accounts for these correlations. We applied this procedure to realistic mock data drawn from a simple thermal model parameterized by the temperature at mean density, $T_0$, and find that wavelets deliver 1$\sigma$ constraints on $T_0$ that are on average 7% more sensitive at $z=5$ (12% at $z=6$) than those from the power spectrum. We consider the possibility of combing wavelet PDFs with the power, but find that this does not lead to improved sensitivity., Comment: Accepted for publication in MNRAS, 22 Pages, 16 Figures

We report the results of near-infrared spectroscopic observations of 37 quasars in the redshift range $6.3< z\le7.64$, including 32 quasars at $z>6.5$, forming the largest quasar near-infrared spectral sample at this redshift. The spectra, taken with Keck, Gemini, VLT, and Magellan, allow investigations of central black hole mass and quasar rest-frame ultraviolet spectral properties. The black hole masses derived from the MgII emission lines are in the range $(0.3-3.6)\times10^{9}\,M_{\odot}$, which requires massive seed black holes with masses $\gtrsim10^{3-4}\,M_{\odot}$, assuming Eddington accretion since $z=30$. The Eddington ratio distribution peaks at $\lambda_{\rm Edd}\sim0.8$ and has a mean of 1.08, suggesting high accretion rates for these quasars. The CIV - MgII emission line velocity differences in our sample show an increase of CIV blueshift towards higher redshift, but the evolutionary trend observed from this sample is weaker than the previous results from smaller samples at similar redshift. The FeII/MgII flux ratios derived for these quasars up to $z=7.6$, compared with previous measurements at different redshifts, do not show any evidence of strong redshift evolution, suggesting metal-enriched environments in these quasars. Using this quasar sample, we create a quasar composite spectrum for $z>6.5$ quasars and find no significant redshift evolution of quasar broad emission lines and continuum slope, except for a blueshift of the CIV line. Our sample yields a strong broad absorption line quasar fraction of $\sim$24%, higher than the fractions in lower redshift quasar samples, although this could be affected by small sample statistics and selection effects., Comment: Accepted for publication in ApJ. 26 pages, 9 figures

The observed large-scale scatter in Lyman $\alpha$ opacity of the intergalactic medium at $z<6$ implies large fluctuations in the neutral hydrogen fraction that are unexpected long after reionization has ended. A number of models have emerged to explain these fluctuations that make testable predictions for the relationship between Ly$\alpha$ opacity and density. We present selections of $z=5.7$ Ly$\alpha$-emitting galaxies (LAEs) in the fields surrounding two highly opaque quasar sightlines with long Ly$\alpha$ troughs. The fields lie towards the $z=6.0$ quasar ULAS J0148+0600, for which we re-analyze previously published results using improved photometric selection, and towards the $z=6.15$ quasar SDSS J1250+3130, for which results are presented here for the first time. In both fields, we report a deficit of LAEs within 20 $h^{-1}$ Mpc of the quasar. The association of highly opaque sightlines with galaxy underdensities in these two fields is consistent with models in which the scatter in Ly$\alpha$ opacity is driven by large-scale fluctuations in the ionizing UV background, or by an ultra-late reionization that has not yet concluded at $z=5.7$., Comment: Accepted to ApJ. 17 pages, 13 figures

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 lifetime of quasars can be estimated by means of their proximity zone sizes, which are regions of enhanced flux bluewards of the Lyman-$\alpha$ emission line observed in the rest-frame UV spectra of high-redshift quasars, because the intergalactic gas has a finite response time to the quasars' radiation. We estimate the effective lifetime of the high-redshift quasar population from the composite transmitted flux profile within the proximity zone region of a sample of $15$ quasars at $5.8\leq z\leq 6.6$ with precise systemic redshifts, and similar luminosities, i.e. $-27.6\leq M_{1450}\leq-26.4$, and thus a similar instantaneous ionizing power. We develop a Bayesian method to infer the effective lifetime from the composite spectrum, including robust estimates of various sources of uncertainty on the spectrum. We estimate an effective lifetime of the quasar population as a whole of $\log_{10}(t_{Q}/{yr}) = 5.7^{+0.5 (+0.8)}_{-0.3 (-0.5)}$ given by the median and $68$th ($95$th) percentile of the posterior probability distribution. While our result is consistent with previous quasar lifetime studies, it poses significant challenges on the current model for the growth of supermassive black holes (SMBHs) located in the center of the quasars' host galaxies, which requires that quasar lifetimes are more than an order of magnitude longer., Comment: 15 pages, 7 figures, accepted by ApJ

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 extents of proximity zones of high-redshift quasars enable constraints on the timescales of quasar activity, which are fundamental for understanding the growth of the supermassive black holes (SMBHs) that power the quasars' emission. In this study, we obtain precise estimates for the ultraviolet (UV) luminous lifetimes of ten quasars at $5.8< z< 6.5$. These objects were pre-selected to have short lifetimes based on preliminary measurements of their proximity zone sizes, and were then targeted for high quality follow-up sub-mm, optical, and infrared observations required to increase the measurements' precision and securely determine their lifetimes. By comparing these proximity zone sizes to mock quasar spectra generated from radiative transfer simulations at a range of different lifetimes, we deduce extremely short lifetimes $t_{\rm Q}<10^4$ yr for four objects in our sample, whereas the remaining quasars are consistent with longer lifetimes of $t_{\rm Q}\gtrsim 10^5$ yr. These young objects with small proximity zones represent $\lesssim10\%$ of the quasar population as a whole. We compare our results in detail to other studies on timescales of quasar activity, which point towards an average lifetime of $t_{\rm Q}\sim10^6$ yr for the quasar population. This is consistent with finding newly turned on quasars approximately $\sim 1-10\%$ of the time. These young quasars represent an unique opportunity to study triggering and feedback mechanisms of SMBHs, since the onset of their UV luminous quasar phase happened only recently, and therefore traces of this process might still be observable., Comment: re-submitted to ApJ

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

Efficient and accurate simulations of the reionization epoch are crucial to exploring the vast uncharted parameter space that will soon be constrained by measurements of the 21 cm power spectrum. One of these parameters, $R_{\rm max}$, is meant to characterize the absorption of photons by residual neutral gas inside of ionized regions, but has historically been implemented in a very simplistic fashion acting only as a maximum filtering scale. We leverage the correspondence between excursion set methods and the integrated flux from ionizing sources to define two physically-motivated prescriptions of the mean free path of ionizing photons that smoothly attenuate the contribution from distant sources. Implementation of these methods in semi-numerical reionization codes requires only modest additional computational effort due to the fact that spatial filtering is still performed on scales larger than the characteristic absorption distance. We find that our smoothly-defined mean free path prescriptions more effectively suppress large-scale structures in the ionization field in semi-numerical reionization simulations compared to the standard $R_{\rm max}$ approach, and the magnitude of the mean free path modulates the power spectrum in a much smoother manner. We show that this suppression of large-scale power is significant enough to be relevant for upcoming 21 cm power spectrum observations. Finally, we show that in our model the mean free path plays a larger role in regulating the reionization history than in models using $R_{\rm max}$., Comment: 13 pages, 12+2 figures, accepted for publication in MNRAS