Estimating time to the common ancestor for a beneficial allele

The haplotypes of a beneficial allele carry information about its history that can shed light on its age and putative cause for its increase in frequency. Specifically, the signature of an alleles age is contained in the pattern of local ancestry that mutation and recombination impose on its haplotypic background. We provide a method to exploit this pattern and infer the time to the common ancestor of a positively selected allele following a rapid increase in frequency. We do so using a hidden Markov model which leverages the length distribution of the shared ancestral haplotype, the accumulation of derived mutations on the ancestral background, and the surrounding background haplotype diver