Thanks for the heads up.
I would suspect that given greater importance of horizontal gene transfer
(HGT) in bacteria that the signal would be more blurred in bacteria rather
than in higher organisms. So your skepticism of the application of
phylogenies based on sequence data is unfounded.
Of course, the fact that HGT is so important and evident in bacteria
provides for non-Darwinian evolutionary mechanisms that produce complex
systems.
TG
>Teichmann, SA and Mitchison, G. "Is there a phylogenetic signal in
>prokaryote proteins?" J. Molec. Evol. 49:98-107
>
>Abstract
>
>Using the sequence information from nine completely sequence bacterial
>genomes, we extract 32 protein families that are thought to contain
>orthologous proteins from each genome. The alignments of these 32 families
>are used to construct a phylogeny with the neighbor-joining algorithm. This
>tree has several topological features that are different from the
>conventional phylogeny, yet it is highly reliable according to its bootstrap
>values. Upon closer study of the individual families used, it is clear that
>the strong phylogenetic signal comes from three families, at least two of
>which are good candidates for horizontal transfer. The tree from the
>remaining 29 families consists almost entirely of noise at the level of
>bacterial phylum divisions, indicating that even with large amounts of data,
>it MAY NOT BE POSSIBLE TO RECONSTRUCT THE PROKARYOTE PHYLOGENY USING
>STANDARD SEQUENCE BASED METHODS. (Emphasis mine)
>
>If it won't work in bacteria, what hope is there for higher organisms??? I
>predict that the signals will become less and less clear, the more we know.
>Art
>http://geology.swau.edu
_________________
Terry M. Gray, Ph.D., Computer Support Scientist
Chemistry Department, Colorado State University
Fort Collins, Colorado 80523
grayt@lamar.colostate.edu http://www.chm.colostate.edu/~grayt/
phone: 970-491-7003 fax: 970-491-1801