Graphical model representations. (A) The mutation-selection model used. The four haplotypes and their respective fitnesses are depicted within circles, with the mutations rates labeling the arrows. (B) Continuous-time Markov model of the compensatory substitution process. Rates between states are shown on arrows. Each state represents the first fixation event for the given haplotype. (C) The discrete-time Markov chain, or jump chain, embedded within the continuous-time Markov chain. The relative probabilities of moving between fixed states are shown on arrows. Deleterious states are considered together for simplicity, and ab is considered an absorbing state to match the simulation procedure.