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

Proc Biol Sci. 2011 Apr 7;278(1708):1009-18. doi: 10.1098/rspb.2010.1427. Epub 2010 Sep 29.


We have developed a machine-learning approach to identify 3537 discrete orthologue protein sequence groups distributed across all available archaeal genomes. We show that treating these orthologue groups as binary detection/non-detection data is sufficient to capture the majority of archaeal phylogeny. We subsequently use the sequence data from these groups to infer a method and substitution-model-independent phylogeny. By holding this phylogeny constrained and interrogating the intersection of this large dataset with both the Eukarya and the Bacteria using Bayesian and maximum-likelihood approaches, we propose and provide evidence for a methanogenic origin of the Archaea. By the same criteria, we also provide evidence in support of an origin for Eukarya either within or as sisters to the Thaumarchaea.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Archaea / classification*
  • Archaea / genetics
  • Artificial Intelligence
  • Bacteria / classification*
  • Bacteria / genetics
  • Base Sequence
  • Bayes Theorem
  • Classification / methods*
  • Eukaryota / classification*
  • Eukaryota / genetics
  • Evolution, Molecular
  • Genome, Archaeal*
  • Likelihood Functions
  • Markov Chains
  • Phylogeny