Message 2005-08-0004: Fwd: Great example of the problems with redundant codes

Fri, 29 Jul 2005 14:52:00 -0400

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Date: Fri, 29 Jul 2005 14:52:00 -0400
From: Philip Cantino <>
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
>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 M. Hillis
>Alfred W. Roark Centennial Professor of Natural Sciences
>Section of Integrative Biology
>University of Texas
>One University Station C0930
>Austin, TX 78712


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