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Guy A. Hoelzer hoelzer at med.unr.edu
Thu Aug 20 16:33:54 EST 1998

In article <6rhk8p$2d8 at net.bio.net>, Claudio Slamovits
<claudio at bg.fcen.uba.ar> wrote:

> I'm working on a phylogenetic analysis using a DNA sequence that show
> different bases in some positions for the same taxon. I use the standard
> IUPAC code for the ambiguities in those positions (Y, R, W, etc) but in most
> cases there is a base more represented than the others (e.g. for Y, C
> appears more than T). I'd like to take advantage of this "extra" information
> in the analysis but I don't know how to manage it.
> I'd appreciate any suggestion.

Intraspecific polymorphism is not a problem.  It is a reality that has
important implications in phylogenetic analysis.  Real problems can arise
when intraspecific polymorphism has not been adequately sampled and
included in the analysis.  The best way to deal with it is to include each
different sequence as a separate "operational taxonomic unit" (OTU) in the
analysis.  That way you use all of the information and you have the chance
to detect intraspecific para(poly)phyly when it occurs.

Guy Hoelzer                              e-mail:  hoelzer at med.unr.edu
Department of Biology                    phone:   702-784-4860
University of Nevada Reno                fax:     702-784-1302
Reno, NV  89557

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