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

Journal article

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.

Authors: Kelly, S; Wickstead, W; Gull, K; Kelly, S

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Royal Society
• Journal: Proceedings. Biological sciences / The Royal Society
• Volume: 278
• Issue: 1708
• Pages: 1009-1018
• Publication date: 2011-04-01
• DOI: 10.1098/rspb.2010.1427
• EISSN: 1471-2954
• ISSN: 0962-8452
• Language: English
• Keywords: Amino Acid Sequence; Likelihood Functions; Bayes Theorem; Eukaryota; Base Sequence; Artificial Intelligence; Phylogeny; Genome, Archaeal; Archaea; Bacteria; Evolution, Molecular; Markov Chains; Classification