testing if seqs. are in same phylo. tree?

Kent E. Holsinger kent at darwin.darwin.eeb.uconn.edu
Fri Nov 10 09:02:56 EST 1995

>>>>> "David" == David Maddison <beetle at ag.arizona.edu> writes:
In article <beetle-0911952139530001 at bembidion.agforbes.arizona.edu> beetle at ag.arizona.edu (David Maddison) writes:

    David> Another way to put it is that I would like to know if this
    David> collection of sequences is monophyletic on the grand tree
    David> of all gene trees, or if it is para/polyphyletic with the
    David> intervening sequences being of different function.  While
    David> this is fundamentally a phylogenetic question (presuming
    David> such a grand tree of all gene trees exists), it is a
    David> horrendous one to answer in that the sequences are so
    David> divergent that one can't do a normal phylogenetic analysis
    David> on them - there's just nothing to get a hold of.

    David> So has anyone written about possible methods of coping with
    David> such problems?  (Obviously some of the general literature
    David> on phylogenetic inference has some applicable stuff, but I
    David> want to know if anyone has anyone has talked about this
    David> specific problem, even if they have done so without
    David> presenting it fully as a phylogenetics problem.)

This probably isn't quite what you're looking for either, but Sam
Karlin has done quite a bit of work on statistical comparison of DNA
sequences. He has developed fast computer algorithms for determining
whether observed sequence similarities are greater than might be
expected by chance. I think W. Ford Doolittle has proposed similar
methods. He may even have suggested them as a way of determining
whether genes (or pieces of genes) are homologous. I don't have the
references handy, but let me know if these sound like what you're
looking for and you have trouble finding them. I think I have copies
of at least a couple of them somewhere in my files that you could use
as the basis of a Science Citation Index search.

-- Kent


Kent E. Holsinger                
Department of Ecology &          
   Evolutionary Biology          
University of Connecticut, U-43                                       
Storrs, CT   06269-3043                                               
Kent at Darwin.EEB.UConn.Edu

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