Abstract
BACKGROUND: Descriptive hierarchical Poisson models and population-genetic coalescent mixture models are used to describe the observed variation in single-nucleotide polymorphism (SNP) density from samples of size two across the human genome. RESULTS: Using empirical estimates of recombination rate across the human genome and the observed SNP density distribution, we produce a maximum likelihood estimate of the genomic heterogeneity in the scaled mutation rate theta. Such models produce significantly better fits to the observed SNP density distribution than those that ignore the empirically observed recombinational heterogeneities. CONCLUSION: Accounting for mutational and recombinational heterogeneities can allow for empirically sound null distributions in genome scans for "outliers", when the alternative hypotheses include fundamentally historical and unobserved phenomena.