Hybridization and the Evolution of Reef Coral Diversity Steven V. Vollmer and Stephen R. Palumbi

The estimated rates of introgression presented in the paper (Table 1) are derived from a Bayesian coalescent model employing Markov chain Monte Carlo (MCMC) methods, which can be sensitive to priors for the migration parameter [M in units of 2N_em) and the time of divergence (T in units of t/2N)(1). To ensure that the model converged on consistent estimates of M and produced approximately the same LRT statistics, we ran multiple simulations for each gene in which the priors of M and T, and the starting seeds were varied. Results of five independent replicate simulations for each gene (Fig. 1) show good convergence of the model with consistent estimates of M and LRT statistics achieved for each dataset. The estimated rates of introgression, presented in Table 1 of the paper, are from simulations with the priors M = 0-10 and T = 0-10.

*The Bayesian coalescent model (MDIV) used in this study is provided by R. Nielson at the link: http://www.bscb.cornell.edu/Homepage/Rasmus_Nielson/files.html.

References:

1. R. Nielson, J. Wakeley, Genetics 158, 885-896 (2001).

Supplemental Figure 1. Plots of the likelihood surfaces for the migration parameter (M in units of 2N_em) from 5 independent replicates for each gene: A) Mini-collagen, B) Calmodulin, C) Pax-C, and D) Mitochondrial putative control region, showing the convergence of the likelihood ratio test (LRT) statistic.

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