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Re: Dinofarts / Sauropod methane emissions

It seems to me that the membrane bound nucleus is a synapomorphy for Eukaryota. Maybe there 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.


On 5/8/2012 7:38 AM, Erik Boehm wrote:


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

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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