Fig. 3.

Examination of evolutionary relationships between genes in the Thermotogales genomes and their homologs in the Archaea, Aquificales, and Clostridia. For each scenario, all embedded quartets in a tree made from Thermotogales, 2 Archaea, 2 Aquificales, and 2 Clostridia homologs were evaluated. A score per scenario was calculated as the ratio of the number of embedded quartets significantly supporting the scenario to the total number of evaluated quartets (for more details see SI Methods). Numbers in parentheses refer to subsets of data from the “Information Storage and Processing” functional supercategory. A quartet topology is unrooted and does not allow distinguishing which 2 taxa are responsible for the observed relationship (i.e., the inferred topology could be because of gene flow either to/from Thermotogales or to/from Aquificales); analyses in Table 1 provide some evidence for directionality. Abbreviations: T, Thermotogales genome; C, Clostridiales; Aq, Aquificales; Ar, Archaea.