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RE: A plea to theropod workers- Code the Taxa in Your Analyses

Very well ...

To wit:


  It doth be true then, speaking a'fore the highest in the heavens, that yon 
etymology doth spake most true of thine most simplistic interpretations.

...err ... aside from the horribly bad prose:

David wrote:

<That would make every phylogenetic tree a cladogram.

We have two terms, and we have two meanings that often need to be 

I replied:

<Based solely on the etymology, one would have to side with Tom and Brad: 
Mickey's preferential analysis is preferrable, in my opinion, to precede the 
formation of a cladogram through a phylogenetic matrix, but it is hardly 
synonymous to have a thourough analytical process to both preceed and follow 
the formation of a tree (especially when TNT [which is FREE, Brad] and PAUP 
create THOUSANDS of cladograms) and be identical to said formation.>

  This single, whole sentence is utter garbage, and I shouldn't have composed 
it this way. I think I left a few things out, and the parsing in my head was 
much cleaner, but of course like most ideas, pick and choose when you think 
them. Sometimes I'm more cohesive, but in other times I am very jumbled 
depending on how fast I'm thinking (my fingers are not as fast as my thoughts, 
and I hardly look at what I'm typing when I do.

  So ... "cladogram" and "phylogenetic tree" are not synonymous. They are 
certainly not even the product of the same analysis (in the strictest sense, it 
takes a second analysis to combine all resultant trees, and an additional one 
to pare it back for parsimony, and another one to jackknife it, etc. even 
though some systems separate these as functions and others do not but automate 
it in the main function).

  As noted before, one is a stylized idea of the other, and the former is often 
based only on parts of the results of a single phylogenetic analysis, usually 
the consensus tree -- which is not itself the product of any single analysis 
but a combination of thousands of different analyses, each with its own end 
tree. When you replied with the above to Tom's support of Brad (based on my 
reading -- you never cite your respondents), you conflated these without 
distinguishing the two ideas you note above:

<Who cares about dictionaries? :-) A cladogram is the result of a 
cladistic analysis. Not every representation of a phylogenetic 
hypothesis is a cladogram.>

  Tom, who was contesting the idea of these two terms being similar, is correct 
here, as I see it. Textbook defintions also separate the two terms (at least 
the two I recall reading do, but now cannot remember the authors of as they 
were years ago).


Jaime A. Headden

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