The human genome evolved over millions of years towards its current form. Despite this long time its base composition did not reach a stationary state yet. Instead one observes long range correlated fluctuations of the Guanine-Cytosine (GC) content. This so called isochore structure of the genome is found in almost all warm-blooded vertebrates. The origin, timing, and functional implications of this structure are still controversial. We introduce a dynamical model, which could explain the emergence of long-range correlations along chromosomes through DNA sequence duplications. Based on this model we identify the evolutionary signatures of such duplications and discuss possible biological mechanisms.