[Taxacom] The difference

HJJACOBSON at aol.com HJJACOBSON at aol.com
Sun Oct 28 10:59:25 CDT 2007

In a message dated 10/28/2007 2:09:32 A.M. Pacific Daylight Time,  
deepreef at bishopmuseum.org writes:

As I  said before, I'm completely with you (and Don Colless) regarding the
folly  of combining morphological and molecular characters as though they
were 1:1  equivalents in terms of their phylogentically informative value. As
I said  in my first post, I'm not optimistic that we will ever have a
satisfactor  way fo quantitatively weighting them appropriatly, so I agree
with Don that  it's probably more useful to think of them as parallel means
of intrpreting  evolutioanry affinities. 

But the conclusion I've come to after  thinking about this sort of stuff is
that we have a much more fundamental  problem going on here, which is that I
believe we don't yet quite  understand evolution and phylogenies as well as
we think we do. And I  certainly don't think we've come to grips yet about
how best to  characterize our interpretations of those phylogenies (whether
through  nomenclature, or cladograms, or whatever).

In comparison to the  epiphany of seeing morphology as an extension of genome
(and of seeing the  moon as a sphere in space rather than a disk in the sky),
I don't think  we've quite yet had the epiphany that bridges the gap between
individual  reproductive events (organismal time scales) and the process of
speciation  (evolutionary time scales). This comes back to my earlier
ramblings about  all life on earth being an extremely smooth and unbroken
chain of  information flow across some 4 billion years.  That's a lot for  us
mere taxonomists to get our heads around.

This thread reminds me of a section in Sokal and Sneath 1963 "Principles of  
Numerical Taxonomy" starting on p. 111 where they were suggesting the minimum  
number of characters to use in a study. 
Here are some bit and pieces: "...characters should represent a random  
sample of the genome....." and "Imagine an organism with 10,000 gene loci ....  
assume each character yields information on 12 loci...." and " A more  realistic 
approach would be to permit the  number of genes which a  character represents 
to vary according to a plausible distribution, perhaps in  Poission fashion." 
and "To obtain information on 50% of the genes (5000 loci) we  would have to 
study 579 characters...."
After reading Carroll's "Endless forms most beautiful" and "The making of  
the fittest," I'm intrigued by his use of a whole sequences as a character  
instead of bases. Anyone care to comment?

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