Additional file 1:

Alternative EF2 tree topologies. Maximum likelihood tree topologies of a) EF2 nucleotide sequence based analysis (-ln = 6943.4742, GTR + Γ + I model, α = 1.0804, pinvar = 0.2586), b) EF2 nucleotide sequence based analysis with exclusion of the third site of codon (-ln = 3280.0776, GTR + Γ + I model, α = 1.6415, pinvar = 0.4103), c) EF2 codon based analysis (-ln = 6513.1449, state frequencies f3x4 method). Bootstrap values (> 50%) are indicated at the nodes. Cnidarian Aurelia sp. was set as outgroup sequence. Scale bar is given under the tree.

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Additional file 2:

SSU and LSU rDNA tree topologies. Maximum likelihood trees constructed under a) SSU rDNA data (- ln = 6127.1469, GTR + Γ model, α = 0.3861) and b) LSU rDNA data (- ln = 8824.2894, GTR + Γ model, α = 0.317). Bootstrap values (> 50%) are indicated at the nodes. Cnidarian Aurelia sp. was set as outgroup sequence. Scale bar is given under the tree.

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Additional file 3:

Combined SSU, LSU and EF2 tree topologies. The phylogenetic trees based on Bayesian inference of combined SSU rDNA + LSU rDNA + EF2 data. a) EF2 as amino acid sequence data, b) EF2 as nucleotide sequence data, c) EF2 as nucleotide data with exclusion of the third site of codon. The Bayesian posterior probabilities are indicated at the nodes. Cnidarian Aurelia sp. was set as outgroup sequence. Scale bar is given under the tree.

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Additional file 4:

Evolution of particular myxozoan characters. Twenty cladograms show the evolutionary history of all morphological and bionomical characters under study. The balls by the nodes represent proportional likelihoods of character states. See legends for colours of particular character states.

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