[Taxacom] Mollusk phylogeny

[Dr. David Campbell]

> The reference is P.A. Goloboff et al. Phylogenetic analysis of 73
> 060
> taxa corroborates major eukaryotic groups. Cladistics 25 (2009)
> 211-230.

Another relevant quote is 

"The least accurate parts of the tree were in the invertebrates and 
protozoans"

The results also address another issue recently discussed on this list:
"In our trees, Johnius belangerii (a percomorph fish) is the sister 
group of Homo sapiens".  They do note that this is an example of 
contamination.  

Being personally aware of several erroneous sequences on GenBank 
(parasites or other contaminants from the wrong phylum-try blasting 
some parasitic nematodes and you can get several phyla), I would like 
to see more detail.  I also note that bivalve cox1 sequences are pretty 
saturated by the time you go back to the mid-Mesozic (unless you look 
at indels rather than third position bases), and do not know what 
effect such issues might have.  

The most important part of the paper in this regard is 

"The full data set and the trees found (in TNT format), as well as the 
C scripts used to donwnload GenBank sequences, can be obtained from 
http://www.zmuc.dk/public/phylogeny/TNT/More/Supp_Data_Set.tgz"

Anyone with plenty of spare time can take a look.

They analyze the entire Eukaryota, so not having appropriate outgroup 
is not one of their problems (having adequate genetic data for the 
outgroup might be, however).

Sequencing complete genomes of representative mollusks and other 
lophotrochozoans would indeed be helpful to our understanding of the 
group.  However, hints from assorted sequences suggest that there may 
be a lot of duplications in many species, causing problems with the 
shotgun-type approach.  

-- 
Dr. David Campbell
425 Scientific Collections Building
Department of Biological Sciences
Biodiversity and Systematics
University of Alabama, Box 870345
Tuscaloosa AL 35487-0345  USA