In Part 1 of What the Hell is a Chaetognath?! we learned from a study by Matus et al. using a consensus tree built from many genes, that Chaetognaths are the sister-taxon to the protostomes. This was surprising because Chaetognaths have long been classified as deuterostomes. The molecular evidence is strong even if I bitched about a few technicalities in their tree-building process (i.e. exluding taxa to get a different tree). A complimentary study in the same issue directly after the Matus et al. article, Marlétaz et al. consider the phylogeny of the Cheatognaths... again.
Before I delve into the science, a bit of an aside. Both studies analyzed genes of Chaetognaths and BLASTed the database of model organisms with those genes (mostly expressed sequence tags or ESTs). Each study had a different set of authors (no overlap) and came to the same conclusion, namely that Chaetognaths are protostomes. That is fine, I think the science is there. But 2 2-page articles saying the same thing with essentially the same method, published in the same issue of the same journal!? Come on people, lets work together. This is a little ridiculous. My guess it is political. One group found out what the other was doing. So as not to step on anyone's toes, they make an agreement to publish together, but separately. It happens. Just a little pointless is all.
Back to science! The Marlétaz et al. paper actually did find something new and interesting though. They sequences over 11,000 ESTs of a juvenile Chaetognath (Spadella cephaloptera, below).
In their prodding around they found the gene for Guanidinoacetate N-methyltransferase. This gene is interesting because it is only found in Deuterostomes and Cnidarians, lost in the Protostomes. It catalyzes the final step towards creatine synthesis, which is an important compound in energy metabolism of brain and muscle. Interesting that this is derived from a Cnidarian ancestor! Maybe that is why our brains look like jelly? Anyways, this provides striking evidence for their placement as a sister taxon to the Protostomes. Hence the common ancestor is not between a Protostome and Deuterostome, but between a Chaetognath and a deuterostome. May I remind you that Chaetognaths share the same embryological characteristics as Deuterostomes, plus now a Deuterostome-specific gene carried down from the Cnidarians and lost to the Protostomes. The phylogeny below (reprinted here without permission) from the Marlétaz et al. paper says it all.
Problems? Well, like I mentioned in Part 1, they exclude the Platyhelminthes from analysis. What is about flatworms that confuses Chaetognath phylogeny?? For one, they were the previous occupants of the sister-clade-to-Protostomes position, otherwise known as the position between Cnidarians and protostomes. Figure S2 from the online supplementary material shows the effects of this analysis. Fig. S2A includes Chaetognaths, while Fig S2B excludes them (reprinted without permission).
As you can see, Platyhelminthes was excluded based on the weak bootstrap support either way. This begs the question about why are Chaetognaths and Platyhelminthes so closely related (potentially), while only Chaetognaths retain deuterostomy characteristics? Thats another topic for another day though. I'll leave you with the concluding sentences:
"It confirms, on a genomic basis, that deuterostomy in an embryological sense is not a decisive character for the classification of animals. Some animals, like the chaetognaths, can be protostomes and yet show features of a deuterostome-like embryology. Nevertheless, the position of chaetognaths as a sistergroup of protostomes prompts us to propose that their development could be reminiscent of the bilaterian ancestor and testify that chaetognaths are a landmark phylum for addressing hypotheses about the origins of bilaterians."