Table 1.
Approximately Unbiased Tests of Alternate Topologies.
| Hypothesis tested | AU test P-value |
|---|---|
| [FeFe]-hydrogenase and NARF-like (NARFL) proteins | |
| ML tree under the LG4X+Gamma model | 0.744 |
| ML tree under the C20+Gamma model | 1e−09b |
| Monophyly of eukaryotic hydrogenases and NARFL proteins; Thalassiosira and Nyctotherus unconstrained | 2e−10b |
| Monophyly of eukaryotic hydrogenases; NARFL proteins unconstrained; Thalassiosira and Nyctotherus unconstrained | 0.001b |
| Monophyly of eukaryotic non-periplasmic-like hydrogenases; eukaryotic periplasmic-like hydrogenases and NARFL proteins unconstrained; Thalassiosira and Nyctotherus unconstrained | 0.504 |
| Monophyly of eukaryotic non-periplasmic-like hydrogenases and Clade 1 and 2 alphaproteobacteria; eukaryotic periplasmic-like hydrogenases and NARFL proteins unconstrained; all other alphaproteobacteria unconstrained; Thalassiosira and Nyctotherus unconstrained | 0.266 |
| Monophyly of eukaryotic non-periplasmic-like hydrogenases, and Clade 1 alphaproteobacteria basal to eukaryotic non-periplasmic-like hydrogenases; eukaryotic periplasmic-like hydrogenases and NARFL proteins unconstrained; all other alphaproteobacteria unconstrained; Thalassiosira and Nyctotherus unconstrained | 0.459 |
| [FeFe]-hydrogenase | |
| ML tree under the LG4X+Gamma model | 0.704 |
| ML tree under the C20+Gamma model | 5e−08b |
| Monophyly of eukaryotic hydrogenases; Thalassiosira and Nyctotherus unconstrained | 0.002b |
| Monophyly of eukaryotic non-periplasmic-like hydrogenases; Thalassiosira and Nyctotherus and periplasmic hydrogenases unconstrained | 0.555 |
| Monophyly of eukaryotic non-periplasmic-like hydrogenases and Clade 1 and 2 alphaproteobacteria; Thalassiosira and Nyctotherus unconstrained; eukaryotic periplasmic hydrogenases unconstrained; all other alphaproteobacteria unconstrained | 0.042a |
| Clade 1 alphaproteobacteria basal to eukaryotic non-periplasmic-like hydrogenases; Thalassiosira and Nyctotherus unconstrained; Clade 2 eukaryotes unconstrained; all other alphaproteobacteria unconstrained | 0.504 |
| [FeFe]-hydrogenase (non-periplasmic-like) | |
| ML tree under the LG4X+Gamma model | 0.680 |
| ML tree under the C20+Gamma model | 0.016a |
| Eukaryote monophyly; Thalassiosira unconstrained | 0.627 |
| Monophyly of eukaryotes and Clade 1 and 2 alphaproteobacteria; Thalassiosira and Nyctotherus unconstrained; all other alphaproteobacteria unconstrained | 0.406 |
| Clade 1 alphaproteobacteria basal to eukaryotes; Thalassiosira and Nyctotherus unconstrained; all other alphaproteobacteria unconstrained | 0.576 |
| Clade 2 alphaproteobacteria basal to eukaryotes; Thalassiosira and Nyctotherus unconstrained; all other alphaproteobacteria unconstrained | 0.362 |
| PFO | |
| ML tree under the LG4X+Gamma model | 1.000 |
| ML tree under the C20+Gamma model | 0.057 |
| Monophyly of eukaryotes and alphaproteobacteria | 1e−05b |
| Alphaproteobacteria basal to eukaryotes | 1e−05b |
| PFO+sulfite reductase | |
| ML tree under the LG4X+Gamma model | 0.999 |
| ML tree under the C20+Gamma model | 0.003b |
| Monophyly of eukaryotes and alphaproteobacteria | 0.013a |
| Alphaproteobacteria basal to eukaryotes | 0.035a |
| ASCT1B | |
| ML tree under the LG4X+Gamma model | 0.734 |
| ML tree under the C20+Gamma model | 0.036a |
| Eukaryote monophyly | 1e−33b |
| Monophyly of Clade 1 eukaryotes and Clade 2 eukaryotes; other eukaryotes unconstrained | 0.716 |
| Monophyly of Clade 1, 2 and 3 eukaryotes; other eukaryotes unconstrained | 0.601 |
| Monophyly of Clade 2 and Clade 3 eukaryotes; other eukaryotes unconstrained | 0.549 |
| Monophyly of Clade 2 and Clade 4 eukaryotes; other eukaryotes unconstrained | 8e−07b |
| Monophyly of Clade 1, 2 and 4 eukaryotes; other eukaryotes unconstrained | 7e−06b |
| Monophyly of Clade 1 eukaryotes and alphaproteobacteria; other eukaryotes unconstrained | 0.548 |
| Monophyly of Clade 2 eukaryotes and alphaproteobacteria; other eukaryotes unconstrained | 0.525 |
| Flavodiiron protein | |
| ML tree under the LG4X+Gamma model | 0.702 |
| ML tree under the C20+Gamma model | 1e−06b |
| T. vaginalis sequence 2 constrained with Mastigamoeba, Entamoeba, Sawyeria and Stygiella | 0.521 |
| Eukaryote monophyly; T. vaginalis 2 unconstrained | 0.001b |
aRejected with P-value <0.05.
bRejected with P-value <0.01.