[Taxacom] Paralogous genes (was: Mayr's criticism of the worst cladification)

[Kenneth Kinman]

Hi Curtis,
      Don't laugh too hard.  Some people have been rooting "life" with
paralogous gene sequences.  Lake et al. have been making a lot of
progress, and the root doesn't have anything to do with Archaebacteria
(a.k.a. Archaea).  Archaebacteria is a terrible misnomer, because
Eubacteria are much older.  As Mayr mentions, the name Metabacteria
(proposed in 1989) is far more appropriate.  But at least Archaebacteria
is better than Domain Archaea.  Many years were virtually wasted doing
cladistic analyses using Archaebacteria as outgroup to Eubacteria.  When
you use an ingroup as an outgroup, it totally distorts the results.  The
paraphyly of Metabacteria (Archaebacteria) is actually a minor problem
in comparison.                    
        One problem I see with using paralogous gene sequences as
outgroups is that one can't be completely sure that they are truly
paralogous.  But the evidence for a eubacterial root for the tree of
life keeps mounting, and the real question now is what subclade of
Eubacteria is sister group to all other life forms on Earth.  And
Curtis, you should know by now that I love cladistics (and
classifications that are mostly cladistic), and that it is just strict
cladism (and its paraphylophobia) that I object to.   Anyway, below is a
weblink to Lake, 2008, on his continued attempts to root the real Tree
of Life (and hopefully people will stop printing those Three Domain
Trees):        
        ---------Ken Kinman

http://astrobiology.nasa.gov/articles/evidence-for-a-new-root-of-the-tree-of-life/

-----------------------------------------------------
Curtis Clark wrote:
On 2009-04-03 09:36, Kenneth Kinman wrote: 
>       Of course the Three Domain tree is well-supported
>cladistically. 

ROTFLMAO! What's the outgroup to life? 
Almost from the moment the "three domain" scheme came out, cladists were
pointing out that the Archaea were paraphyletic, based on the
understanding of that time. 
How far will you go with your attempts to link things you don't like
with cladistics? IF the former CEO of General Motors had accepted
paraphyletic groups, would the company still be solvent?