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Partial vs. whole trees

aroger at ac.dal.ca aroger at ac.dal.ca
Mon Mar 15 19:55:49 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)?

I just thought it might be worth pointing out that one can hardly grow a
tree as suggested above when there is a single taxon whose complete genome
has been sequenced.  The essence of tree building is comparing homologous
sequences from a variety of taxa.  So perhaps the question should be:
has anyone tried building a tree of several genome sequences (or several
sub-genomic sequences) from taxa whose genomic sequences can be align
ed with confidence.  I think the answer is then obvious.  We simply don't
have enough genome sequences to be able to test phylogenetic hypotheses.
The problem with doing it in eukaryotes is also that the majority of 
nuclear DNA is non-coding or highly repetitive and so the sequences are 
likely to change very quickly (in the former case) or be vastly rearranged
(what with all of those retroviruses and transposons inserting, 
mediating recombination and generally having a good time at the 
expense of the genes that are there to maintain organismal fitness).  The
question, though, does raise a very important and relevant point and that
is that phylogenies based on several genes combined (that is putting a
handfull of genes end to end in the multiple alignment) might provide
enough informative sites so that very small branchlengths may be resolved.
This technique may be extremely useful in attacking such problems as
elucidating the relationships between metazoan phyla.  A classic problem
that has come up recently in the rRNA phylogeny literature is the 
question of whether the animal kingdom is holophyletic or polyphyletic.
In a Science paper in 1988, Field et al., suggested that SSUrRNA phylogenies
of metazoans suggested that Cnidarians evolved separately from the Bilateral
animals.  A reanalysis of the data by Lake in 1990 using a different
tree-building algorithm contradicted this result.  De Wachter's group
sequenced the SSUrRNA gene from another Cnidarian and their tree showed
a holophyletic Metazoa.  What all of this suggests to me is that the
branchlength connecting the Cnidaria to the other Bilateral animals is 
very small and perhaps not enough time elapsed before after the origin of
the Metazoa and before their divergence to accumulate synapomorphous change
in their rRNA sequences.  However, if multiples of genes were analysed
enough synapomorphies would be present to resolve this shared branch.  Here
I find myself far from the topic at hand.....I am also assuming a particular
phylogeny, that is that the Metazoa are holophyletic and then arguing why
the data don't support it....I'm prepared to defend this though, so
sharks are welcomed...

Andrew Roger
aroger at ac.dal.ca

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