Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes.
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.
Kelly
S
S
Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. steven.kelly@plants.ox.ac.uk
Wickstead
B
B
Gull
K
K
D000595:Amino Acid Sequence; D001105:Archaea / Q000145:classification* / Q000235:genetics; D001185:Artificial Intelligence; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D001483:Base Sequence; D001499:Bayes Theorem; D002965:Classification / Q000379:methods*; D056890:Eukaryota / Q000145:classification* / Q000235:genetics; D019143:Evolution, Molecular; D020745:Genome, Archaeal; D016013:Likelihood Functions; D008390:Markov Chains; D010802:Phylogeny