Table 1.

Prokaryote Monophyly in Eukaryote Monophyly Trees

	Degree of Prokaryote Monophyly
Group	Stricta	Outerb	Innerc
Chlamydiae	0.844	0.856	0.962
Chlorobi	0.672	0.695	0.893
Deinococcus	0.654	0.693	0.882
Thermotogae	0.579	0.635	0.851
ε-Proteobacteria	0.534	0.583	0.785
Cyanobacteria	0.473	0.557	0.760
Crenarchaeota	0.341	0.598	0.660
Chloroflexi	0.286	0.364	0.665
Spirochaetes	0.249	0.298	0.641
β-Proteobacteria	0.237	0.415	0.501
Bacteroidetes	0.214	0.334	0.642
Euryarchaeota	0.200	0.476	0.505
α-Proteobacteria	0.194	0.398	0.499
Actinobacteria	0.170	0.359	0.534
Archaea, otherd	0.092	0.159	0.486
γ-Proteobacteria	0.090	0.382	0.325
Firmicutes	0.080	0.310	0.345
δ-Proteobacteria	0.056	0.152	0.361
Bacteria, other	0.038	0.099	0.292

^aThe proportion of trees in which the group is monophyletic.

^bThe proportion of the members of the given group that are present in the tree and contained within the smallest clade containing all members of the group (and members of other groups); n_group/n_clade, where n_group is the number of members of the group in the clade and n_clade is the number of OTUs in that clade. Value shown is the mean across all trees.

^cThe proportion of the members of the given group that are present in the tree and contained within the group’s largest monophyletic clade; n_group{clade}/n_group{tree}, where n_group{clade} is the number of members of the group in the clade and n_group{tree} is the number of group members in the tree. Value shown is the mean across all trees.

^dDesignates a grouping of Nanoarchaea, Thaumarchaea, and Korarchaeota lumped together, the individual samples of which are either one or too small to consider monophyly.