<< 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)>>
Which is what we would expect if extant bacteria do not
stem from a single common ancestor, but instead emerged
from a set of distinct ancestors (which could cross talk through
lateral transfer).
Mike