  We show how to incorporate fluctuations of the recombination rate along the
chromosome into standard gene-genealogical models for the decorrelation of gene
histories. This enables us to determine how small-scale fluctuations
(Poissonian hot-spot model) and large-scale variations [Kong et al. (2002)] of
the recombination rate influence this decorrelation. We find that the
empirically determined large-scale variations of the recombination rate give
rise to a significantly slower decay of correlations compared to the standard,
unstructured gene-genealogical model assuming constant recombination rate. A
model with long-range recombination-rate variations and with demographic
structure (divergent population) is found to be consistent with the empirically
observed slow decorrelation of gene histories. Conversely, we show that
small-scale recombination-rate fluctuations do not alter the large-scale
decorrelation of gene histories.
