Alleles and phylogenetic results

Richard.Zander at MOBOT.ORG Richard.Zander at MOBOT.ORG
Wed Jan 25 11:42:40 CST 2006

Check out:
Stace, C. A. 2005. Plant taxonomy and biosystematics---does DNA provide all
the answers? Taxon 54: 999--1007.
- discusses monoparental inheritance and homogenization, and effect on
phylogenetic reconstructions.

-----Original Message-----
From: Ken Kinman [mailto:kinman2 at YAHOO.COM]
Sent: Tuesday, January 24, 2006 10:30 PM
Subject: [TAXACOM] Alleles and phylogenetic results

Dear All,
     When two alleles of a gene are present in a taxon, their divergent
differences shouldn't be too problematic for phylogenetic analysis if (1)
they haven't diverged very much (differences are small in a large sequence);
and/or (2) these two alleles are actually recognized as such.

      However, what if different gene sequences deposited in the NCBI
database are different alleles, are NOT recognized as such, and are
significantly different?  Does this not have the potential to lead to false
conclusions, especially when taxon sampling is still pretty sparse?  I
wonder how widespread this problem could be.
          Ken Kinman

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