Markov Jump Processes in Estimating Sharing of Identity by Descent

Identity by descent (IBD) sharing is a very important genomic feature in population genetics which can be used to reconstruct recent demographic history. In this paper we provide a framework to estimate IBD sharing for a demographic model called two-population model with migration. We adopt the structured coalescent theory and use a continuous-time Markov jump process {X(t), t >= 0} to describe the genealogical process in such model. Then we apply Kolmogorov backward equation to calculate the distribution of coalescence time and develop a formula for estimating the IBD sharing. The simulation studies show that our method to estimate IBD sharing for this demographic model is robust and accurate.