Ludvig Mortberg (Agneta.Guillemot at historia.umu.se) wrote:
: >All the data demonstrate
: >that archaebacteria are more closely related to
: >eubacteria than to eukaryota, thus supporting tha
: >classical division of living organisms into two main
: >superkingdoms, Prokaryota and Eukaryota.
: >Their seperate, reciprocally rooted trees
: >for elongation factors and ATPase subunits
: >showed Bacteria (eubacteria) as branching first from the
: >universal tree with Archaea (archaebacteria) and
: >Eukarya (eukaryotes) as sister groups.
: Who do you belive, and why? More studies? But how many?
Again, how do you propose to classify bacteria via your beloved
classical methods. What morphological characters are you going
: The idea that there is something inherrently wrong with the
: method has to be considered!
: The two "wrongs" are as follows:
: (1) A "close distance" between proteins or DNA sequences does not
: always reflect close relationship (within an organim and between
: organims). That is because mutations accumulate at different speeds at
: different loci at different times in the history of an organim.
: Selective pressure differs from time to time etc. To put it shortly;
: proteins etc., can be more similar in distantly related species than
: in closely related ones (and vice versa).
But, as the poster above has stated, if a large number of independent
trees agree with each other, then we have increasing confidence that
there is a reason for that pattern. And the most likely reason is
that the trees accurately reflect the evolutionary history.
: (2) When a cladistic approach is used, "shared derived
: sequences/mutations" have been found that apparently could be used in
: a cladogram. The problem is that of information content. A cladogram
: with morphologic characters should not be put aside for one where the
: characters are a few nucleotide substitutions.
Your statement is indicative of why you don't get many compliments around
here. Sure, some people publish junk trees. But a good tree has been
either bootstrapped or run with maximum likelihood. In either case,
if the tree is robust it means there are many more than a _few_
substitutions which distinguish clades in the tree.
Department of Cellular and Developmental Biology
Department of Genetics / HHMI
robison at mito.harvard.edu