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Prior distributions for all parameters were the default distributions incorporated in the MrBayes software.
Posterior probabilities were also calculated with MrBayes version 2.01 [ 31 ] . Each QuartOP was analyzed with two simultaneous Markov chains for 25,000 cycles under the JTT substitution model [ 55 ] without ASRV.
1), i.e., 67% posterior probability as estimated by MrBayes and unsupported as measured by parsimony bootstrap analysis (<50%).
For the genome quartet #8 we calculated posterior probabilities under the model which takes ASRV into account with Strimmer and von Haeseler's [ 24 ] approach and with the MrBayes program version 2.01 [ 31 ] . TREE-PUZZLE 5.0 [ 56 ] was used to calculate posterior probabilities according to Strimmer and von Haeseler [ 24 ] . A discrete approximation of the gamma distribution [ 57 ] was used to describe ASRV.
Eight rate categories were used in TREE-PUZZLE [ 56 ] , and four rate categories were used in MrBayes [ 31 ] . The maps are available in the supplementary material.