[Taxacom] Molluscan phylogeny (overview)

[Dr. David Campbell]

> This sounds awfully like data manipulation. As for groups being
> probably real because they are consistently' supported across 
multiple data sets, this is problematic because it depends on what kind 
of data.  Phenetic methods, for example, consistently supported 
reptiles as a natural group, but cladistic methodology showed that the 
group was not 'real' at all. That is particularly pertinent given that 
aligned homologies do not exist in nature and that the individual 
homologies are determined as a consequence of an overall similarity 
algorithm that somehow balances gaps and substitutions. I'm not sure I 
would like to rest a phylogenetic reality on imaginary homologies.<

I failed to specify that I did not mean to work the data until it gives 
a particular result that you want; rather, look at whatever comes out 
of multiple analyses and do not be quick to assume that an interesting 
pattern in your latest analysis is the final answer.  

DNA alignment ranges from highly confident to probably imaginary, but 
again this is best determined by trying various parameters and/or 
attempting alignment by hand and seeing whether your results change.  
Any hints from structure, codons, etc. will help as well.  All analysis 
of DNA sequences involves some assumptions of homology; methods that do 
not use an explicit alignment nevertheless are internally making 
assumptions about the homology of different sequences.    

"Real" is of course a problematic term.  Reptilia is a paraphyletic 
group of organisms with certain similarities that provide or exclude 
certain ecological options, so in one sense it is "real"; however, 
almost all phylogenetic analyses do not support it as monophyletic, and 
those that have can readily be explained as being misled by 
plesiomorphic or convergent features.


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