Table 1. Approximately unbiased (AU) tests of alternate topologies.

Hypothesis tested	AU testP-value
[FeFe]-hydrogenase
ML tree	0.952
Eukaryote monophyly	0.094
Acanthamoeba+Mastigamoeba monophyly	3e-41
Acanthamoeba+short-branching Entamoeba monophyly	4e-06
Acanthamoeba+long-branching Entamoeba monophyly	0.004
(Acanthamoeba, α-prot.s1), other eukaryotes, (bacteria)	0.015
[FeFe]-hydrogenase (long branches removed)
ML tree	0.921
Eukaryote monophyly	0.547
Acanthamoeba+Entamoeba monophyly	0.003
(Acanthamoeba, α-prot.s1), other eukaryotes, (bacteria)	2e-05
PFO
ML tree	0.707
Eukaryote monophyly	0.674
Acanthamoeba+Mastigamoeba monophyly	0.181
Acanthamoeba+Entamoeba monophyly	0.059
Acanthamoeba+Mastigamoeba+Entamoeba monophyly	0.045
(Acanthamoeba, α-prot.s1), other eukaryotes, (bacteria)	2e-37
ASCT
ML tree	0.803
Eukaryote monophyly	0.002
(Acanthamoeba, Euk clade 12), other eukaryotes (bacteria)	0.625
(Acanthamoeba, Malawimonas, Capsaspora, Euk clade 12), other euks, (bacteria)	0.452
(Euk clade 12, α-prot.s1), other eukaryotes Pseudovibrio Commensalibact., (bacteria)	0.036
(Euk clade 23, α-prot.s1), other eukaryotes, Pseudovibrio, Commensalibact., (bacteria)	0.032
(Acanthamoeba, α-prot.s1), other eukaryotes, Pseudovibrio, Commensalibacter, (bacteria)	0.032
HydE
ML tree	0.848
Eukaryote monophyly	0.866
Acanthamoeba+Mastigamoeba monophyly	0.948
((Eukaryotes, α-prot.s1), β-prot.s4), Spironucleus, (bacteria)	0.605
HydF
ML tree	0.757
Eukaryote monophyly	0.758
Acanthamoeba+Mastigamoeba monophyly	0.678
HydG
ML tree	0.985
Eukaryote monophyly	0.944
Acanthamoeba+Mastigamoeba monophyly	0.880

¹α-proteobacteria.

²Euk clade 1: opisthokonts+Blastocystis.

³Euk clade 2: Thecamonas+Salpingoeca+Monosiga.

⁴β-proteobacteria.