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Re: Dinofarts / Sauropod methane emissions

 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 don't think I've ever seen Bacteria and Archaea depicted as sister-groups, except maybe to illustrate an ancient classification that had "Archaebacteria" and "Eubacteria".