In article <badger.766075571 at phylo>, badger at phylo.life.uiuc.edu (Jonathan Badger) writes:
> As a microbiology graduate student at the University of Illinois (Woese's
> home turf), I'm curious as how the detractors of the Three Kingdoms
> explain evidence such as the presence of TATA-binding proteins in the Archea
> that appear to be part of a eukaryotic-style TF IID complex (Marsh, et al.,
> 1994). If the Archea are not more closely related to eukaryotes than bacteria,
> what do you suppose occurred? Horizontal gene transfer?
>There is no need to propose special explanations. Lets suppose that archaes,
euks, and eubs really are three clades, but we don't know how they are
related. Finding a pattern of [ + , + , - ] for some character, such as
the presence or absence of TFIID, is not usable phylogenetic information
(unless the character states are ordered). If the ancestral state is
[ + ], then loss in any of the groups can occur, regardless of the
phylogeny, leaving two [ + ]'s and one [ - ].