Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes.

The log 10 Bayes factors recovered under each substitution model exhibit very highly significant linear relationships ( r 2 > 0.99, p < 0.00001 in all cases) and are hence independent of the amino acid substitution model employed (electronic supplementary material, S7).

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