A population genetics model with recombination hotspots that are heterogeneous across the population

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Abstract
Both sperm typing and linkage disequilibrium patterns from large population genetic data sets have demonstrated that recombination hotspots are responsible for much of the recombination activity in the human genome. Sperm typing has also revealed that some hotspots are heterogeneous in the population; and linkage disequilibrium patterns from the chimpanzee have implied that hotspots change at least on the separation time between these species. We propose a population genetics model, inspired by the double-strand break model, which features recombination hotspots that are heterogeneous across the population and whose population frequency changes with time. We have derived a diffusion approximation and written a coalescent simulation program. This model has implications for the “hotspot paradox.”