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Chaetognaths are traditionally classed as deuterostomes by embryologists.
Lynn Margulis and K. V. Schwartz place chaetognaths in the deuterostomes in their Five Kingdom classification.
Molecular phylogenists, however, consider them to be protostomes.
Thomas Cavalier-Smith places them in the protostomes in his Six Kingdom classification.
The similarities between chaetognaths and nematodes mentioned above may support the protostome thesis-in fact, chaetognaths are sometimes regarded as a basal ecdysozoan or lophotrochozoan.
Chaetognatha appears close to the base of the protostome tree in most studies of their molecular phylogeny.
This may explain their deuterostome embryonic characters.
If chaetognaths branched off from the protostomes before they evolved their distinctive protostome embryonic characters, they may have retained deuterostome characters inherited from early bilaterian ancestors.
Thus chaetognaths may be a useful model for the ancestral bilaterian.

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