[Taxacom] Eukaryotic origins: the debate continues but narrows

[Kenneth Kinman]

Dear All,
       The origins of Eukaryota clearly involve the Metabacteria (a.k.a.
"Archaebacteria" or even a.k.a. "Archaea").  The debate has heated up
and narrowed in the last several years whether the first eukaryote was
sister to the most basal metabacteria, or whether it evolved from within
the metabacteria/archaebacteria.       
       Even if the first eukaryote split off within the
metabacteria/archaebacteria, it apparently happened so deeply within
(near the base) of that group that it is difficult to decide one way or
the other.  So much so, that it may actually depend on how one precisely
defines Metabacteria/Archaebacteria.   
       The taxon which muddies these waters the most is Thaumarchaeota
(named back in 2008), members of which tended to be previously regarded
as primitive members of Crenarchaeota (a.k.a. "eocytes"), which I have
long favored as the most likely ancestors of Eukaryota. If they are
basal Crenarchaeotes, then I see no reason to abandon that long-held
belief.   
      However, since Thaumarchaeota was split off as a separate taxon,
there are clearly those who suspect that it split off before either
Crenarchaeota or Euryachaeota (the two major taxa of
Metabacteria/Archaebacteria).  In any case, we are dealing with the most
basal known branchings of these taxa from one another, so the debate is
really no big surprise.     
      Today, I discovered a recently published (April 2011) paper which
weighs in on this debate (Kelly, Wicksead, and Gull, 2011).  Their
conclusion is that Eukaryota evolved from within Thaumarchaeota, or is
its sister group.  So if Thaumarchaeota compromise the sole basal taxon
of Metabacteria/Archaebacteria, AND if Eukaryota is sister group to them
and other metabacteria, then Cavalier-Smith is correct in predicting
that Eurkaryota and Metabacteria/Archaebacteria are sister groups.  But
if Eukaryota arose from within Thaumarchaeota, or from within
Crenarchaeota, within Euryarchaeota, or even within some combination of
those clades, then Metabacteria (a.k.a. Archaebacteria) is clearly
paraphyletic.                
      In any case, I strongly suspect that Thaumarchaeota would make
Metabacteria/Archaebacteria paraphyletic, and that strict cladists would
then be tempted to split it off (in toto or in part), in order to
eliminate that paraphyly.  That is what some of them often tend to do
when paraphyly crops up once again.  Anyway, below is the citation to
the 2011 paper by Kelly, et al. and the abstract of that paper.    
           ------------Ken Kinman

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Archaeal phylogenomics provides evidence in support of a methanogenic
origin of the Archaea and a thaumarchaeal origin for the eukaryotes 
S. Kelly, B. Wickstead, and 
K. Gull (2011)

Abstract
We have developed a machine-learning approach to identify 3537 discrete
orthologue protein sequence groups distributed across all available
archaeal genomes. We show that treating these orthologue groups as
binary detection/non-detection data is sufficient to capture the
majority of archaeal phylogeny. We subsequently use the sequence data
from these groups to infer a method and substitution-model-independent
phylogeny. By holding this phylogeny constrained and interrogating the
intersection of this large dataset with both the Eukarya and the
Bacteria using Bayesian and maximum-likelihood approaches, we propose
and provide evidence for a methanogenic origin of the Archaea. By the
same criteria, we also provide evidence in support of an origin for
Eukarya either within or as sisters to the Thaumarchaea.