Notes & References

Notes

[1] We know of two exceptions, both highly aberrant cases: in sea urchins (Echinoidea) and in vertebrates. Both are discussed later.

[2] But see the discussion by Bengston & Budd (2004), Chen et al. (2004a).

[3] Actually we still do -- but not bilaterian segmentation. However, the idea is too incomplete and too speculative to take up here.    

[4] Much of this section of the paper simply confirms earlier work by others. However, since we knew very little about either anthozoans or hox genes before starting on this piece, it was very useful to have everything in one place.

[5] Main Nematostella hox cluster, adapted from Ryan et al. (2007):

[6] The Barcelona Group apparantly uses "Bilateria" to mean some kind of stem group -- possibly Nebuchadnezzar > Nematostella. Consequently, they still refer to the Acoelomorpha as bilaterians. We will stick to the usual, crown-group definition of Bilateria.

[7] Like the echinoid hox genes, the order of the authors seems to have been altered in the course of this paper's evolution. The "suggested citation" is followed here. However, on the actual paper, the authors appear in the order: Cameron, Rowen, Nesbitt, Bloom, Rast, Berney, Arenas-Mena, Martinez, Lucas, Richardson, Davidson, Peterson & Hood.

[8] Note that the phylogenetic position of the Vetulicolia is much more debatable than our treatment might suggest. Aldridge et al. (2007) suspect that that they are basal protostomes of some kind. We have some methodological uncertainties with Aldridge et al., but they include a very useful discussion of all the possible affinities of this group.  For a contrasting view, see Shu (2005).

[9] "There is no work that affects me; nor do I aspire for the fruits of action. Who knows me acting thus unchained by action, is not tied down by actions."  Bhagavad Ghita 4:14. Actually, this is a mixed translation. It has absolutely nothing to do with hox systems. However, we can't help comparing this portion of the Ghita to the Taoist principle (or, if you're a real Taoist, non-principle) of wu-wei.   

[10] To be fair, lots of respectable people believe that rhombomeres are merely an extension of the somites, and no one doubts that the gill arch ("branchiomere") system is very closely coordinated with the rhombomeric system. Thus Liem et al. 2001), for example, treat the whole thing as one system of segmentation. We strongly disagree. More importantly, so do a lot of respectable scientists, e.g. Janvier (1996).

[11] That isn't quite right, but a more precise definition requires a lot more explanation than we can give until we've covered a lot more ground. A completely unambiguous definition is still not possible, but a better definition might be: the last common ancestor of Drosophila lab and Branchistoma hox14 and all of its descendants which (a) encode a homeodomain-containing protein and (b) whose closest homologue in Branchiostoma lies within the Branchiostoma hox cluster. The exceptions are needed to exclude pseudogenes and other non-functional riff-raff, as well as the parahox genes discussed later. It is still ambiguous because we don't define gene (introns? promoters? miRNA sequences?) and we don't say exactly what closest homologue means.

[12] Update 070712: According to a report, two recent papers in Cell by Gregor et al. emphasize how very preceise the maternal bicoid gradient is and how carefully it is maintained in early embryogenesis. Again, if so, why do flies need hox genes? We have not read the papers, but the citations are T. Gregor et al., "Stability and nuclear dynamics of the Bicoid morphogen gradient," Cell July 13, 2007 and T. Gregor et al., "Probing the limits to positional information," Cell, July 13, 2007.

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