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Partial vs. whole trees

Ron DeBry debry at dirac.scri.fsu.edu
Sat Mar 13 11:19:21 EST 1993

In article <9303121847.AA05027 at net.bio.net> preissj at CLVAX1.CL.MSU.EDU ("J Preiss--Seq Anal") writes:
>With all this discussion about the merits of using partial trees, and warnins
>about the dangers of using only 300bp from a 3,000bp viral genome, I am 
>begining to wonder what this means for us eukaryotic biologists.  Has anyone
>made a tree of a eukaryote from a complete sequence (of the entire genome)?
>Sorry, obviously a retorical question.  But, what about 10% of a genomic 
>sequence as with viral work.  What does this mean for the confidence levels
>of all those phylogenies based on 0.0001% (ie a single gene)?

The problem with using only 300bp of viral sequence isn't that it is
only a small fraction of the genome, but that it is a small number of
bases on an absolute scale.  

Not all sequences are created equal, for example sequence of the entire
mitochondrial genome probably wouldn't shed much light on the
relationships among metazoan phyla, but other factors being equal more
sequence information is much better than less.  Also, it would be best
to have sequence from different regions of the genome.  This would help
identify cases where the "gene tree" is not the same as the species tree
(although in practice this is rarely done).

Ron DeBry
Dept. of Biological Sciences
debry at sb.fsu.edu

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