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Re: Dinofarts / Sauropod methane emissions



http://www.pnas.org/content/105/51/20356.full

http://www.sciencemag.org/content/325/5941/666.full

I'd lean towards the Eukaryotic cell having an origin within Archaea, and thus 
Archaea being paraphyletic without including Eukaryotes (this is essentially 
the Eocyte hypothesis).

I suppose its also valid to argue that Eukaryotes are an offshoot of Eubacteria.

Then you'd have Eubacteria and Archaea as sister clades? and Eukaryotes as a 
union of them

--- On Tue, 5/8/12, David Marjanovic <david.marjanovic@gmx.at> wrote:

> From: David Marjanovic <david.marjanovic@gmx.at>
> Subject: Re: Dinofarts / Sauropod methane emissions
> To: "DML" <dinosaur@usc.edu>
> Date: Tuesday, May 8, 2012, 2:41 AM
> >  There are two main
> hypotheses: (1) That Archaea and Eukarya
> >  (=Eukaryota) are sister taxa, and form a clade to
> the exclusion of
> >  Bacteria (=Eubacteria); (2) That Eukarya arose
> from the amalgamation
> >  of an archaeon and a bacterium, and so is only a
> "secondary domain"
> >  derived from the other two.
> 
> As Erik Boehm just explained, the second hypothesis is
> indistinguishable from the endosymbiotic origin of the
> mitochondria: whenever an endosymbiote breaks up, some of
> its genes (or even all of them) can end up in the nucleus.
> Natural selection seems to have favored this for genes that
> have functions in energy metabolism; the genes that have
> functions related to DNA and RNA are homologous to archaean
> ones.
> 
> Indeed, it's likely that the nucleus, the spatial and
> temporal separation of transcription and translation in
> other words, formed as a defense mechanism against class I
> introns -- transposons introduced by mitochondria. As usual,
> I forgot where I read that; it may have been a review paper
> in Nature.
> 
> There used to be a third hypothesis, the "eocyte
> hypothesis", which said the eukaryotes arose from
> cell-wall-less archaea such as the extant *Thermoplasma*; it
> was supported by a few molecular phylogenies, IIRC, but fell
> by the wayside 15 or 20 years ago.
> 
> I do
I've ever seen Bacteria and Archaea depicted
> as sister-groups, except maybe to illustrate an ancient
> classification that had "Archaebacteria" and "Eubacteria".
>