What the hell is a chaetognath?! Part 1

So I thought they were deuterostomes, but apparently thats only half the story. Lynn Margulis classified the arrow worms as deuterostomes in her 5-kingdom classfication (after Whittaker). Their deuterostome characteristics include radial, indeterminate cleavage, a posterior position of the blastopore (deuterostomy), enterocoelous coelom formation and a tripartite adult body plan with a post-anal tail. At least this is what I was taught "growing up". Three papers in Current Biology last year showed that while they have developmental patterns like deuterostomes, their genes tell another story!

The first paper by Matus et al. sampled several phyla and used several genes. A consensus tree built from 72 EST genes grouped them within the Lophotrochozoa. They also constructed a tree using tropomyosin genes showing Chaetognaths as the sister taxon to all the Lophotrochozoa. One thing that bugged about the EST tree is that when they included the Priapulida, Chaetognaths grouped with them in the Ecdysozoa. When the data were reanalyzed without the Priapulids, Chaetognaths grouped with the last common ancestor of the molluscs and annelids. The authors argued that

"The association with the Ecdysozoa, therefore, depends on a single taxon and is not likely to reflect a general affinity for the group."

But shouldn't you use total evidence? Can you really justify leaving out data because it doesn't fit your expectations? In their supplementary material, they show three trees with three different conclusions.
The first tree:

"Bayesian tree based on the analysis of RY-coded concatenated SSU and LSU rRNA genes shows a relationship between the chaetognaths Paraspadella and Sagitta with priapulids."

Conclusion: Chaetognaths are sister-taxon to Priapulids, well situated within the Ecdysozoa.

The second tree:

"Bayseian analysis of Ribosomal SSU and LSU data, excluding priapulids from RY re-coded data... The maximum likelihood bootstrap tree had very low support values."

Conclusion: Chaetognaths are sister-taxon to Platyhelminthes, well situated within the Lophotrochozoa.

The third tree:

"Bayesian analysis of Ribosomal SSU and LSU data excluding long branch platyhelminths and priapulids from RY re-coded data."

Conclusion: Chaetognaths are sister-taxon to all the Lophotrochozoa, occupying a basal position to the clade. This is the tree they liked and went with for their main article.



Don't get me wrong, I (think) I believe them. Their maximum likelihood studies show best support for Tree #3 and fits nicely into a story, keeps everything monophyletic and stable. For instance they state:

"To eliminate long branch attraction artefacts, we analyzed subsets of taxa to determine the effects of taxon sampling (Supplemental data). Regardless of the taxa removed (nematodes, platyhelminths or tardigrades) the chaetognaths remained as sister to annelids and molluscs with varying degrees of support in Bayesian analyses and as sister to the Ecdysozoa (arthropods, nematodes and tardigrades) with weak bootstrap support in likelihood analyses."

I (think) I believe their analysis and conclusions, but I'm just concerned about the structure of the tree. There are profound evolutionary differences between protostomes and deuterostomes or between Lophotrochozoans and Ecdysozoans. One day I will go into detail about the different clades. Either way, the molecular data say Chaetognaths are definitely Protostomes. It disturbs me though that most of the developmental and morphological similarities to deuterostomes, as the authors stated, may be the result of convergent evoluton. In my opinion, convergent evolution tends to destabilize tree topology by decreasing parsimony. Sometimes I feel that when you invoke convergent evolution too much you might as well through up your hands and proclaim the magnificence of the grand designer...