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Re: Dinofarts / Sauropod methane emissions



> It seems to me that the membrane bound nucleus is a synapomorphy for 
> Eukaryota.
> Having organelles that originate from archaea and bacteria downs not
> mean there is a polyphyletic origin for eukaryotes 

I'm not disputing that Eukaryotes are monophyletic.
I'm disputing that Archaea are monophyletic if you exclude Eukaryotes, and this 
has nothing to do with endosymbiosis, as the endosymbionts (mitochondria or 
chloroplasts) were Eubacteria.

However, its more complicated than just having a cyanobacteria or a alpha 
proteobacteria living inside the Eukaryotic cell.
Through unclear mechanisms (we have candidates and can speculate), genes from 
the ancestor of mitochondria have been moved to the nucleus.
For example, the human mitochondria today has less than 17kbp.
No "true" bacteria has less than about 500 kbp.
While many of the "core" RNAs, genes, and proteins that seem to define 
Eukaryotes appear to be of Archaeal origin, many genes (perhaps the majority) 
also appear to be of Eubacterial origin - they may have come from lateral gene 
unrelated to symbiosis transfer when Archaea and Eubacteria were closer, or 
from endosymbionts themselves (or both).

The point is that Eukaryotes definitely seem to be a hybrid between archaea and 
Eubacteria. It seems it would thus be paraphyletic to define either an Archaea 
or Eubacteria that does not include Eukaryotes.

An analogy: Occasionally mules, hybrids of Horses and Donkeys, are fertile.
If one were to establish a breeding population of mules (lets assume it 
happened, its not out of the realm of possibility) - would you group mules in 
the Horse clade, or the Donkey clade?
Could you define either clade without including mules, and still have it be 
monophyletic?

--- On Tue, 5/8/12, Dan Chure <danchure@easilink.com> wrote:

> From: Dan Chure <danchure@easilink.com>
> Subject: Re: Dinofarts / Sauropod methane emissions
> To: erikboehm07@yahoo.com
> Cc: "DML" <dinosaur@usc.edu>, david.marjanovic@gmx.at
> Date: Tuesday, May 8, 2012, 10:09 AM
> It seems to me that the membran
are endosymbiotic relationships
> that further 
> define the Eukaryota, but they would not elucidate Eukaryote
> 
> relationships. Having a cyanobacterial origin for
> chloroplasts does not 
> mean that cyanobacteria and plants are sister groups. 
> Plants could be 
> the sistergroup of Archaea and still have an endosymbiotic
> relationship 
> with cyanobacteria. Having organelles that originate from
> archaea and 
> bacteria downs not mean there is a polyphyletic origin for
> eukaryotes 
> per se. The eukaryotes still might be more closely related
> to archeaea 
> than bacteria or the other way around.  However, I am
> now swimming in 
> the deep side of the pool and may be over my head.
> 
> D
> 
> 
> 
> 
> On 5/8/2012 7:38 AM, Erik Boehm wrote:
> > 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 endosy
> 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".
> >>
> >
> >
> > -----
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> 
> 
>