>1. they used a subset of available glutamine synthetase genes;
>2. they "rooted" their rRNA tree based on a so-called molecular clock
>that is known not to exist, dismissing the contradictions with the
>fossil record that this "clock" implies;
>3. they presented bootstrap values without emphasizing that these values
>are inflated (relative to standard bootstraps) by their procedure of
>treating a string of related sequences as a 'supersequence' (sometimes
>even repeating the same sequence to make a supersequence);
>4. in drawing conclusions about the relationships of organisms (as
>opposed to genes) they did not take seriously enough the possible
>confounding effects of gene duplication and lateral transfer. Some of
>these effects had been suggested previously be other groups.
>>Although the abstract seemed to state very clearly that a group
>"archaebacteria" was a sister to "eubacteria", there were not coherent
>groups of either in the glutamine synthetase tree, and in the rRNA tree,
>the statement is unreliable because it is based on the clock-rooted
>tree.
>
We believe there are several points to be clarified. Just reading more
carefully the paper of Saccone et al. it is clear that we state clearly
that different genes give different trees and thus the question of the
rooting of the tree of life is still unsolved (in our opinion!). Of course
a single-gene phylogeny does not solve definitely the issue.
However, Glutamine synthetase and SSU and LSU rRNAs - under the Molecular
Clock assumption - put the root on the Eukariotic branch. Dr Stoltzfus
state that the Clock does not exists! Is this a novel dogma? We have never
said that the rate of evolution is invariably constant in all lineages, but
there are cases - may be a few - in which an almost linear relationship
between genetic distance and time is observed. One of these is represented
by second codon, positions of GS when distant relationships are considered.
To justify the eubacterial rooting in the case of rRNAs and GS you need to
impose another equally unproven assumption, i.e. that eukaryotic GS evolve
much faster than prokariotic ones.
The boostrap problem related to supergenes is not relevant as the
eukariotic rooting is equally strongly supported also by single-genes
phylogeny.
The effects of eventual gene duplication and lateral gene transfers are of
course to be taken into account. This is the reason why we clearly state in
the paper to be cautious with phylogenies based on a few genes.
Cecilia Saccone, Graziano Pesole
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Dept. of Biochemistry and Molecular Biology phone: +39-80-5443305
University of Bari fax: +39-80-5443317
via Orabona, 4 -5484467
70125 Bari - Italy E-mail:
graziano at area.ba.cnr.it
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