Contrasting methods of quantifying fine structure of human recombination

There has been considerable excitement over the ability to construct linkage maps based only on genome-wide genotype data for single nucleotide polymorphic sites (SNPs) in a population sample. These maps, which are derived from estimates of linkage disequilibrium (LD), rely on population genetics theory to relate the decay of LD to the local rate of recombination, but other population processes also come into play. Here we contrast these LD maps to the classically derived, pedigree-based human recombination maps. The LD maps have a level of resolution greatly exceeding that of the pedigree maps, and at this fine scale, sperm typing allows a means of validation. While at a gross level both the pedigree maps and the sperm typing methods generally agree with LD maps, there are significant local differences between them, and the fact that these maps measure different genetic features should be remembered when using them for other genetic inferences.