Using a sample of approximately 14,000 z > 2.1 quasars observed in the first year of the Baryon Oscillation Spectroscopic Survey (BOSS), we measure the three-dimensional correlation function of absorption in the Lyman-α forest. The angle-averaged correlation function of transmitted flux (F = e −τ ) is securely detected out to comoving separations of 60 h −1 Mpc, the first detection of flux correlations across widely separated sightlines. A quadrupole distortion of the redshift-space correlation function by peculiar velocities, the signature of the gravitational instability origin of structure in the Lyman-α forest, is also detected at high significance. We obtain a good fit to the data assuming linear theory redshiftspace distortion and linear bias of the transmitted flux, relative to the matter fluctuations of a standard ΛCDM cosmological model (inflationary cold dark matter with a cosmological constant). At 95% confidence, we find a linear bias parameter 0.16 < b < 0.24 and redshiftdistortion parameter 0.44 < β < 1.20, at central redshift z = 2.25, with a well constrained combination b (1+β) = 0.336±0.012. The errors on β are asymmetric, with β = 0 excluded at over 5σ confidence level. The value of β is somewhat low compared to theoretical predictions, and our tests on synthetic data suggest that it is depressed (relative to expectations for the Lyman-α forest alone) by the presence of high column density systems and metal line absorption. These results set the stage for cosmological parameter determinations from three-dimensional structure in the Lyman-α forest, including anticipated constraints on dark energy from baryon acoustic oscillations.

From a principal component analysis (PCA) of 78 z ∼ 3 high-quality quasar spectra in the SDSS-DR7 we derive the principal components that characterize the QSO continuum over the full available wavelength range. The shape of the mean continuum is similar to that measured at low-z (z ∼ 1), but the equivalent width of the emission lines is larger at low redshift. We calculate the correlation between fluxes at different wavelengths and find that the emission line fluxes in the red part of the spectrum are correlated with those in the blue part. We construct a projection matrix to predict the continuum in the Lyman-α forest from the red part of the spectrum. We apply this matrix to quasars in the SDSS-DR7 to derive the evolution with redshift of the mean flux in the Lyman-α forest caused by the absorption by the intergalactic neutral hydrogen. A change in the evolution of the mean flux is apparent around z ∼ 3 as a steeper decrease of the mean flux at higher redshifts. The same evolution is found when the continuum is estimated from the extrapolation of a power-law continuum fitted in the red part of the quasar spectrum if a correction derived from simple simulations is applied. Our findings are consistent with previous determinations using high spectral resolution data. We provide the PCA eigenvectors over the wavelength range 1020−2000 Å and the distribution of their weights that can be used to simulate QSO mock spectra.