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