Table 3. Verticality of prokaryotic taxa across protein families with at least two taxonomic groups.

The list of bacterial (top) and archaeal (bottom) taxa occurring in all trees (right) and only trees that were filtered for conservation (average branch length in the tree ≤ 0.1) (left). Archaeal and bacterial phyla with less than 5 representative species in the dataset were excluded. P_mono refers the proportion of monophyletic trees. N_mono indicates the number of trees in which this taxon is monophyletic whereas N_trees shows the number of occurrences of the phyla in the respective dataset.

		All trees– 101,423				Conserved trees– 8,547
	Taxon	Pmono	Nmono	Ntrees		Pmono	Nmono	Ntrees
Bacteria
	Acidithiobacillia	0.81	1,677	2,067		0.91	629	688
	Chlamydiae	0.74	1,378	1,867		0.75	482	642
	Tenericutes	0.68	2,770	4,076		0.50	391	776
	Actinobacteria	0.60	30,050	49,958		0.37	1,214	3,293
	Bacilli	0.59	24,365	41,526		0.25	1,017	3,997
	Chlorobi	0.59	1,728	2,946		0.80	494	619
	Thermotogae	0.57	2,252	3,937		0.65	495	764
	Cyanobacteria	0.56	8,655	15,446		0.64	843	1,319
	Deinococcus-Thermus	0.54	3,156	5,858		0.63	705	1,113
	Synergistetes	0.53	1,001	1,872		0.70	484	692
	Epsilonproteobacteria	0.52	3,815	7,270		0.37	513	1,397
	Fusobacteria	0.51	1,805	3,516		0.60	717	1,194
	Spirochaetes	0.50	5,063	10,130		0.44	683	1,564
	Bacteroidetes	0.49	11,677	23,755		0.40	759	1,879
	Gammaproteobacteria	0.48	29,439	61,803		0.18	1,078	5,874
	Negativicutes	0.45	1,892	4,170		0.59	804	1,371
	Nitrospirae	0.43	1,377	3,180		0.47	359	762
	Alphaproteobacteria	0.43	18,086	41,953		0.35	1,312	3,735
	Aquificae	0.43	1,210	2,826		0.43	290	672
	Planctomycetes	0.40	1,755	4,399		0.55	533	961
	Chloroflexi	0.39	2,349	6,003		0.46	521	1,141
	Acidobacteria	0.38	1,789	4,666		0.58	625	1,077
	Betaproteobacteria	0.38	14,203	37,225		0.34	1,601	4,775
	Deltaproteobacteria	0.37	8,512	23,013		0.38	1,005	2,618
	Verrucomicrobia	0.36	1,146	3,152		0.56	601	1,067
	Clostridia	0.32	7,481	23,638		0.34	1,084	3,196
	Erysipelotrichia	0.17	344	2,001		0.43	451	1,058
Archaea
	Thermococcales	0.73	2,482	3,380		0.79	271	341
	Methanococcales	0.73	1,612	2,220		0.83	236	283
	Methanobacteriales	0.68	1,949	2,857		0.79	282	356
	Sulfolobales	0.66	2,223	3,387		0.75	280	374
	Archaeoglobales	0.62	1,415	2,286		0.79	252	318
	Methanomicrobiales	0.60	1,616	2,693		0.74	301	406
	Methanosarcinales	0.60	3,392	5,654		0.63	318	503
	Thermoproteales	0.55	1,537	2,775		0.61	257	420
	Thermoplasmatales	0.49	662	1,364		0.58	212	366
	Desulfurococcales	0.41	852	2,072		0.44	130	298
	Natrialbales	0.32	1,459	4,503		0.42	246	588
	Haloferacales	0.27	980	3,593		0.40	205	513
	Halobacteriales	0.20	1,024	5,057		0.30	178	591