Path: utzoo!utgpu!water!watmath!uunet!ig!lanl.gov!dbd%benden
From: dbd%benden@LANL.GOV (Dan Davison)
Newsgroups: bionet.molbio.evolution
Subject: More DNA hybridization discussion
Message-ID: <8810101524.AA06838@benden.lanl.gov>
Date: 10 Oct 88 15:24:34 GMT
Sender: daemon@presto.ig.com
Lines: 45

Some more points about the Sarich, Sibley, Ahlquist saga:

Joe Felsenstein writes:
      Dan -- care to expand on your remarks?

OK, here goes.

  (2)[An open question is] Whether DNA hybridization data on relationships
     is fatally flawed owing to presence of some repeated sequences.[...]
     Here I would ask Dan Davison for some details on why he thinks
     "fractured, highly repetitive elements" would cause trouble.  If 
     there are enough different repeated sequences involved, then we
     should still be able to use them to measure average divergence
     of sequences.

Before presenting my reasons, a bit of background.  I was a grad student
at SUNY Stony Brook and that is the home of Ferris, Rohlf, and Sokol
(although I was not in that department [whew!]).  Therefore I was
frequently around the cladist vs. pheneticist (sp?) discussions/wars.
I also was in laboratories that were doing DNA hybridization of the
Britten (Cot) type, although I did *not* do any of that myself.  I then
went to the U of Houston, where I spent two years looking at small
small ribosomal RNA sequences and constructing phylogenetic trees from
sequence distance data.

Now to the meat of the subject.  I do not specifically believe that DNA
hybridization data on relationships is fatally flawed owing to the presence
of some repeated sequences.  This certainly is not the case in enterobacteria
and the fruit fly, the only systems in which I have any experience.



  (3) Whether there is a fatal flaw in the use of any data like
      DNA hybridization which must be analyzed as distances rather than
      by reference to individual sites.  Sarich is NOT raising this issue
      -- he is a long-term DEFENDER of use of distance measures and methods.
      But without knowing Marks, I get the impression that he comes from
      the "phylogenetic systematics" tradition which considers that there
      is something fatally wrong with distances.  In any case, although the
      issue is not being raised by Sarich and Marks, it is clear that many
      phylogenetic systematists consider this to be the issue and that any
      discomfiture of Sibley reinforces this position.  Even if everything
      Sarich and Marks say is accepted I don't see that this point follows
      at all.  I have argued (in papers controversying with Farris) that
      there is not a fatal flaw in distance methods.