Fig. 2: Difference in transition matrices for matched structured and unstructured models.

a, Matching coalescence rate profiles for a structured and unstructured model. The blue line indicates the theoretical inverse coalescence rate for the structured model, where populations A and B are of constant size, the split and admixture times are given by the vertical, dashed green lines and the admixture fraction is 30%. The orange line indicates an unstructured model with size changes that generate a coalescence rate equal exactly to the structured model. b, A visualization of ξ = (Q^U − Q^S)/Q^S, the relative difference between the transition matrices for the structured and unstructured models in a. Q^U and Q^S are row stochastic matrices, where Q(α∣β) describes the probability of transitioning from discretized time β to time α, conditional on recombination having occurred. The dashed green lines indicate the split and admixture times as in a.