Any comments?

Keith Robison robison at mito.harvard.edu
Thu Oct 19 08:07:26 EST 1995

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
to use?

: 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.

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu 

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