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Date: Fri, 29 Jul 2005 14:52:00 -0400
From: Philip Cantino <cantino@ohiou.edu>
To: phylocode@ouvaxa.cats.ohiou.edu
Subject: Fwd: Great example of the problems with redundant codes
I am posting an interesting message from David Hillis. Phil Cantino >I'm not a member of the PhyloCode discussion group any more, and I >don't know if it is even still in existence. But if it is, this >might make an interesting posting. > >Some people claim that the redundant codes (Botanical, Zoological, >etc.) never cause real world problems. Recently a graduate student >in my lab was comparing a large phylogenetic analysis of many >thousands of taxa from throughout life. Looking at such a large tree >is very difficult, and he needed a way to see if the tree matched >the major taxonomic groups that have been proposed over time. So, he >downloaded the GenBank taxonomy for all the sequences, and used that >to filter the results for the tree and look for conflicts. He was >troubled as to why many groups, such as Insecta, were not supported >in the tree, and found that one sequence that GenBank was listed as >an insect (Stilbum vulgare, whose taxonomy is listed as Eukaryota; >Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; >Endopterygota; Hymenoptera; Apocrita; Aculeata; Chrysidoidea; >Chrysididae; Chrysidinae; Chrysidini; Stilbum; see >http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=38532133) >was deeply embedded in Fungi. > >Why does the sequence of Stilbum vulgare fall out with the Fungi? >Because it is a duplicated name, and the sequence associated with >that name IS of a fungus (which is clear in the original >publication). That is the correct name for the fungus. But, there it >is in GenBank, happily organized with the insects (and other insect >species of Stilbum). So much for he problem of duplicated names >never causing problems! > > > >David >-- >David M. Hillis >Alfred W. Roark Centennial Professor of Natural Sciences >Section of Integrative Biology >University of Texas >One University Station C0930 >Austin, TX 78712