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The posterior probabilities calculated according to Strimmer and von Haeseler did not change dramatically and each of the three tree topologies is still supported by roughly equal number of QuartOPs.
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.
The amino acid sequences for each QuartOP were retrieved from GenBank at NCBI and were aligned using ClustalW 1.8 [ 53 ] . QuartOPs were analyzed using the ML-mapping approach according to Strimmer and von Haeseler, Bayesian probabilities mapping and bootstrap support values mapping techniques (see details below).
Posterior probabilities according to Strimmer and von Haeseler
Routinely we calculated these probabilities using Strimmer's and von Haeseler's approach [ 24 ] : Using each of the three topologies as a usertree, we calculated the maximum likelihood for each of the three topologies given the data.