The infinite-site model of a small multigene family with two duplicated genes is studied. The expectations of the amounts of nucleotide variation within and between two genes and linkage disequilibrium are obtained, and a coalescent-based method for simulating patterns of polymorphism in a small multigene family is developed. The pattern of DNA variation is much more complicated than that in a single-copy gene, which can be simulated by the standard coalescent. Using the coalescent simulation of duplicated genes, the applicability of statistical tests of neutrality to multigene families is considered.
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Hideki Innan (2003) studied this question.
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