Inference about recombination from haplotype data: Lower bounds and recombination hotspots

Recombination is an important evolutionary mechanism responsible for creating the patterns of haplotype variation observable in human populations. Recently, there has been extensive research on understanding the fine-scale variation in recombination across the human genome using DNA polymorphism data. Historical recombination events leave signature patterns in haplotype data. A nonparametric approach for estimating the number of historical recombination events is to compute the minimum number of recombination events in the history of a set of haplotypes. In this paper, we provide new and improved methods for computing lower bounds on the minimum number of recombination events. These methods are shown to detect a higher number of recombination events for a haplotype dataset from a region in the lipoprotein lipase gene than previous lower bounds. We apply our methods to two datasets for which recombination hotspots have been experimentally determined and demonstrate a high density of detectable recombination events in the regions annotated as recombination hotspots. The programs implementing the methods in this paper are available at www.cs.ucsd.edu/users/vibansal/RecBounds/.