Extended Data Fig. 3: Convergence and prior sensitivity analyses for the HR4-ARD model in African cichlids.

Posterior distribution of estimated transition rates under the HR4-ER model for three different priors (50, 100, 150) on the total number of transitions; a, very low lability, b, low lability, c, high lability, and d, very high lability. e, Posterior probability distribution of four replicate MCMC runs of the HR4-ER model; two chains ran for 50,000 generations and two chains ran for 500,000 generations. f, Histogram of Kolmogorov-Smirnov (KS) scores for model parameters. The grey dotted line marks the threshold for the KS test of 0.0921 (α = 0.01, ESS > 625), indicating that the model parameters were drawn from the same distribution for all replicate runs. Running the chain longer resulted in the same posterior probability distribution and transition rate estimates despite ESS scores <625 for some parameters for 50,000 generations. Posterior distribution of transition rates across replicate MCMC runs for g, very low lability h, low lability i, high lability and j, very high lability.