The forest of Lyman-alpha absorption lines seen in the spectra of distant quasars has become an important probe of the distribution of matter in the Universe. We use large, hydrodynamical simulations from the OWLS project to investigate the effect of feedback from galaxy formation on the probability distribution function and the power spectrum of the Lyman-alpha transmitted flux. While metal-line cooling is unimportant, both galactic outflows from massive galaxies driven by active galactic nuclei and winds from low-mass galaxies driven by supernovae have a substantial impact on the flux statistics. At redshift z=2.25, the effects on the flux statistics are of a similar magnitude as the statistical uncertainties of published data sets. The changes in the flux statistics are not due to differences in the temperature-density relation of the photo-ionised gas. Instead, they are caused by changes in the density distribution and in the fraction of hot, collisionally ionised gas. It may be possible to disentangle astrophysical and cosmological effects by taking advantage of the fact that they induce different redshift dependencies. In particular, the magnitude of the feedback effects appears to decrease rapidly with increasing redshift. Analyses of Lyman-alpha forest data from surveys that are currently in process, such as BOSS/SDSS-III and X-Shooter/VLT, must take galactic winds into account.
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