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The first hypothesis corresponds to the traditional grouping Coelomata and the second corresponds to Ecdysozoa [ 3 ] .
Results and discussion Analyses of the individual protein datasets using neighbor-joining [ 16 ] show that most (62%) support Coelomata while 25% support Ecdysozoa and 13% support hypothesis III ( Supplemental Table 1, four-taxon analysis).
The four proteins showing significant support (>95%) for a hypothesis other than Coelomata were reanalyzed using maximum parsimony and maximum likelihood, bootstrap values were not significant using other methods.
To test the stability of Coelomata to taxon sampling, we included new sequences of the planarian Dugesia japonica (Phylum Platyhelminthes) in 100 five-taxon protein alignments ( Supplemental Table 1, five-taxon analysis).
The Coelomata hypothesis was significantly supported (?
97% bootstrap support, posterior probabilities = 1.
The results show support for Coelomata at all rate orders, but the support is significant with the slowest evolving proteins, regardless of rate measure or number of proteins combined (Fig.
Support for Coelomata was weakest with the fastest evolving proteins (which also showed compositional heterogeneity), indicating that Ecdysozoa, not Coelomata, may be the result of a rate bias, compositional bias, or other artifact.
Finally, the affect of lineage-specific rate variation on support for Coelomata was tested with the use of relative rate tests.
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