The transition probabilities between ancestry pairs.

If Ak represent a specific ancestry and θk represents the admixture proportion of that ancestry in the admixed population, then these equations are the transition probabilities for all possible types of transitions given a probability rj of one or more recombinations occurring between the previous informative CSV and the jth informative CSV. The rows represent the ancestry state at the previous CSV and the columns the ancestry state being transitioned into at the jth CSV.