Table 1.

Maximum likelihood bootstrap values (ML) and bayesian posterior probabilities (Bayes) of the Eukaryote Supergroups in the Phylogenomic Trees.

		79 Taxa				74 Taxaa	77 Taxab				72 Taxac
		All Sites		20% Removedd		All Sites	All Sites		20% Removedd		All Sites
Nodee	Groups	ML	Bayes	ML	Bayes	ML	ML	Bayes	ML	Bayes	ML
A	Opisthokonta	100	1.00	100	1.00	100	100	1.00	100	1.00	100
B	Unikonts	79	0.99	99	1.00	87	57	0.99	96	1.00	58
C	Amoebozoa	86	1.00f	100	1.00	100	84	1.00f	100	1.00	100
D	Collodictyon + Malawimonas	86	0.79	98	0.63	94	NA	NA	NA	NA	NA
E	Excavata	100	1.00	100	1.00	100	100	1.00	100	1.00	100
F	Bikonts	98	1.00	98	1.00	95	98	1.00	100	1.00	93
G	Archaeplastida	-	0.98	63	0.84	-	-	0.99	71	0.95	-
H	Archaeplastida + CCTH + SAR	-	1.00	81	1.00	-	-	1.00	88	1.00	-
I	CCTH	-	*	54	*	-	50	*	60	*	-
J	SAR	98	1.00	100	1.00	96	99	1.00	100	1.00	96

NOTE.—“-” indicate bootstrap values < 50% or PP < 0.5; “*” indicate that CCTH (Cryptophyta, Centrohelida, Telonemia, and Haptophyta) is not monophyletic.

^aFive taxa (Leishmania, Trypanosoma, Sawyeria, Entamoeba, and Breviata) were removed.

^bTwo Malawimonas taxa were removed.

^cTwo Malawimonas taxa and five taxa (Leishmania, Trypanosoma, Sawyeria, Entamoeba, and Breviata) were removed.

^dRemoval of the 20% fastest evolving sites from the alignment.

^eThe capital letters correspond to supergroups marked in figure 3.

^fBreviata is sister to Opisthokonta (fig 3).