Figure 2

Three phylogenetic trees of the Hmd protein family. Each phylogeny was calculated independently using different software, tree calculation algorithms, and amino acid substitution models, which are displayed to the upper left of each tree. Archaeal prephenate dehydrogenase is used as an outgroup in each tree. The trees have differing branch lengths, but almost identical topologies. The Phylip tree differs from the other two at three leaf nodes highlighted in red. In these trees, Hmd enzymes and paralogs form two distinct monophyletic groups. Only two species with complete genome sequences, M. smithii and M. labraenum, have an Hmd enzyme and do not have an Hmd paralog. The phylogenies indicate that three independent duplications of the Hmd paralog took place in the lineage leading to M. jannaschii, the lineage leading to M. kandleri, and the lineage of the last common ancestor of M. marburgensis and M. thermoauotrophicum. This analysis suggests that Hmd paralogs have a conserved functional role in class I hydrogenotrophic methanogens.