  Consider a genetic locus carrying a strongly beneficial allele which has
recently fixed in a large population. As strongly beneficial alleles fix
quickly, sequence diversity at partially linked neutral loci is reduced. This
phenomenon is known as a selective sweep. The fixation of the beneficial allele
not only affects sequence diversity at single neutral loci but also the joint
allele distribution of several partially linked neutral loci. This distribution
can be studied using the ancestral recombination graph for samples of partially
linked neutral loci during the selective sweep. To approximate this graph, we
extend recent work by Schweinsberg & Durrett 2005 and Etheridge, Pfaffelhuber &
Wakolbinger 2006 using a marked Yule tree for the genealogy at a single neutral
locus linked to a strongly beneficial one. We focus on joint genealogies at two
partially linked neutral loci in the case of large selection coefficients
\alpha and recombination rates \rho = O(\alpha/\log\alpha) between loci. Our
approach leads to a full description of the genealogy with accuracy of O((\log
\alpha)^{-2}) in probability. As an application, we derive the expectation of
Lewontin's D as a measure for non-random association of alleles.
