Additional file 1 of A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea
Creators: name: Aouad, Monique
name: Flandrois, Jean-Pierre
name: Jauffrit, Frédéric
name: Gouy, Manolo
name: Gribaldo, Simonetta
name: Brochier-Armanet, Céline
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 1: Figure S1. Unrooted Bayesian phylogeny of Archaea. The tree corresponds to the A supermatrix (72 protein families, 218 taxa, 16,006 amino acids positions). The tree was inferred with PHYLOBAYES using the CAT+GTR+G4 model. Values at branch correspond to branch lengths (top) and posterior probabilities (bottom). The scale bar indicates the average number of substitutions per site. Figure S2. Unrooted Maximum Likelihood phylogeny of Archaea. The tree corresponds to the A supermatrix (72 protein families (218 taxa, 16,006 amino acids positions). The tree was inferred with IQ-TREE using the LG+C20+G4 model. Values at branch correspond to branch lengths (top) and bootstrap values (bottom). The scale bar indicates the average number of substitutions per site. Figure S3. Unrooted Bayesian phylogeny of Archaea inferred through the Slow-Fast procedure. Starting from the A supermatrix (72 protein families, 218 taxa, 16,006 amino acids positions), the fastest evolving sites were removed progressively. At each step, a Bayesian tree was inferred with PHYLOBAYES using the CAT+GTR+G4 model. Values at branch correspond to posterior probabilities. The scale bars indicate the average number of substitutions per site. Figure S4. Unrooted Bayesian phylogeny of Archaea inferred through the Slow-Fast procedure by excluding the DPANN. Starting from the A supermatrix (72 protein families, 199 taxa, 15,430 amino acids positions), the fastest evolving sites were removed progressively. At each step, a Bayesian tree was inferred with PHYLOBAYES using the CAT+GTR+G4 model. Values at branch correspond to posterior probabilities. The scale bars indicate the average number of substitutions per site. Figure S5. Unrooted Bayesian phylogeny of Archaea and Eucarya. The tree corresponds to the AE supermatrix (61 protein families, 236 taxa, 13,468 amino acids positions). The tree was inferred with PHYLOBAYES using the CAT+GTR+G4 model. Values at branch correspond to branch lengths (top) and posterior probabilities (bottom). The scale bar indicates the average number of substitutions per site. Figure S6. Unrooted maximum likelihood phylogeny of Archaea and Eucarya. The tree corresponds to the AE supermatrix (61 protein families, 236 taxa, 13,468 amino acids positions). The tree was inferred with IQ-TREE using the LG+C20+G4 model. Values at branch correspond to branch lengths (top) and bootstrap values (bottom). The scale bar indicates the average number of substitutions per site. Figure S7. Phylogenetic position of the Eucarya relatively to Cluster I lineages by Dayhoff4 recoding. Unrooted Bayesian phylogenetic tree built using the AE supermatrix (64 protein families, 114 taxa, 13,468 amino acids positions). The tree was inferred with PHYLOBAYES using the CAT+GTR+G4 model and the amino acid recoding scheme Dayhoff4. The length of the branches corresponds to evolutionary distances. Supports at branch correspond to posterior probabilities. Figure S8. Phylogenetic position of the Eucarya relatively to Cluster I lineages by Dayhoff6 recoding. Unrooted Bayesian phylogenetic tree built using the AE supermatrix (64 protein families, 114 taxa, 13,468 amino acids positions). The tree was inferred with PHYLOBAYES using the CAT+GTR+G4 model and the amino acid recoding scheme Dayhoff6. The length of the branches corresponds to evolutionary distances. Supports at branch correspond to posterior probabilities. Figure S9. Rooted Bayesian phylogeny of the Archaea. The tree corresponds to the AB supermatrix (41 protein families, 285 taxa, 7,853 amino acids positions). The tree was inferred with PHYLOBAYES using the CAT+GTR+G4 model. Values at branch correspond to branch lengths (top) and posterior probabilities (bottom). The scale bar indicates the average number of substitutions per site. Figure S10. Rooted maximum likelihood phylogeny of Archaea. The tree corresponds to the AB supermatrix (41 protein families, 285 taxa, 7,853 amino acids positions). The tree was inferred with IQ-TREE using the LG+C20+G4 model. Values at branch correspond to branch lengths (top) and bootstrap values (bottom). The scale bar indicates the average number of substitutions per site. Figure S11. Rooted Bayesian phylogeny of Archaea without DPANN and Altiarchaea. The tree corresponds to a version AB supermatrix built without DPANN and Altiarchaea (41 protein families, 261 taxa, 7,952 amino acids positions). Values at branch correspond to branch lengths (top) and posterior probabilities (bottom). The scale bar indicates the average number of substitutions per site. Table S1. List of the taxa used in the study (435 archaea, 67 bacteria, and 18 eukaryotes). The 42 archaeal species useid in the study by Raymann et al. (2015) are indicated. The 218 representative archaeal species kept for phylogenetic analyses are in green. Their presence in the 72 archaeal protein families used in this study is indicated. Representative species kept for the Slow-Fast analysis are in dark green. Table S2. List of markers from Raymann et al. (2015) used in this study. For each marker, the corresponding COG name and general description are also indicated. The nine markers displaying complex evolutionary histories are indicated in red. These markers were not retained for supermatrices construction.