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The number of populations that best represents the observed data under the model implemented was determined by maximizing the estimated Ln likelihood of the data for different values of K. Third, we used the Bayesian clustering algorithm implemented in Baps 4 [71] to identify the optimal number K of partitions among groups of samples.

The model implemented was similar to that of single-trait BayesA analyses described previously.

For the analysis of each species, the nucleotide substitution model implemented was the one suggested by Modeltest [ 64] based on the Akaike Information Criterion (AIC) [ 65].

The user's guide for SPICE2.G with BSIM model implemented is also included.

The channel models implemented are AWGN, Rician and Rayleigh channels.

Second, our data show that, in practice, the models implemented were generally hybrids of the two types presented here.

The PAML models implemented here are sensitive to low numbers of sequences [ 45].

The models implemented so far were very diverse.

The model framework was implemented using MASON Version 11.

The mixed model approach was implemented with MrBayes.

Our generative model was implemented in WebPPL.