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insertion/deletion:how to weigh in a DNA sequence matrix?

Arlin Stoltzfus arlin at is.dal.ca
Tue Nov 11 22:53:40 EST 1997

Zhang Daming wrote:
> Dear colleagues,
> I have a data matrix of ITS sequences in a tribe of Liliaceae, in which
> several insertion/deletions, 4-16 bp long, appear informative (existed
> in several taxa, seemingly as synapomorphis ). Unfortunately, when I
> applied PAUP to them , aligned each single base involved as either "-"
> or "?",  I found that  the ins/dels were apparently un-informative and
> somewhat homoplasy. Comparing to base substitution, "structural
> variations", like ins/del, inversion or translocation, would be much
> rarer, and should be somehow weighed over other characters. I tried
> weighing them in different quantity, and even treating them as extra
> characters at the matrix before using PAUP program. But the results
> looked not improved. Could anyone tell me how to deal with such 
> problem?

Its not safe simply to assume that indel characters are more informative
than nucleotide characters.  One should reduce the weight of indels 
to the extent that there is greater variation in mutation rates 
for different specific indels than in mutation rates for different 
specific nucleotide substitutions.  On the other hand, one should 
increase the weight of indels to the extent that they are much 
rarer evolutionary changes than nucleotide substitutions.  That is, 
the weighting must be some point of balance between conflicting 
factors.  Unless one has a highly sophisticated model of evolution 
that allows one to calculate a weighting, or very extensive 
analyses of the consistency of indels with other characters that 
gives one an empirically estimated weighting, then one can't 
know where this point of balance lies.

For some work on how parallel mutations may influence evolution, 

  Macey, et al., 1997.  Mol. Biol. Evol. 14(1): 20-39.

  Cunningham, et al., 1997. Mol. Biol. Evol. 14(1):113-116.

  Foster, et al., 1997.  J. Mol. Evol. 44: 282-288.

  Gu, et al., 1997, Genetica, in press, cited in Wen-Hsiung Li's book

  Golding, 1987, Ch. 8 in "Genetic Constraints on Adaptive Evolution", 
  ed. V. Loeschke (Springer-Verlag, Berlin)

Arlin Stoltzfus, Ph.D. (arlin at is.dal.ca)
Department of Biochemistry, Dalhousie University
Halifax, Nova Scotia B3H 4H7 CANADA
phone: 902-494-2968     fax: 902-494-1355

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