  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.
