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Fig. 2 | BMC Ecology and Evolution

Fig. 2

From: A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

Fig. 2

Support of the archaeal topology by the different supermatrices and desaturation analyses. A The topology corresponds to the Bayesian tree shown in Fig. 1. Dots correspond to the support of each node by the different analyses. Top dots represent, from left to right, posterior probabilities (PP) of BI trees built with the A, AE, and AB supermatrices, respectively. Bottom dots represent, from left to right, bootstrap values (BV) of ML trees built with the A, AE, and AB supermatrices, respectively. Green signifies branches supported by a PP ≥ 0.95 or a BV ≥ 95%, light green signifies branches supported by a PP < 0.95 or a BV < 95%, light red signifies alternative branching supported by a PP < 0.95 or a BV < 95%, red signifies alternative branching supported by a PP ≥ 0.95 or a BV ≥ 95%. The corresponding ML and BI trees are provided as Additional file 1: Figs. S1, S2, S5, S6, S9, and S10. B Results of the slow-fast procedure to the A supermatrix displayed as supports for the main internal branches of the archaeal phylogeny shown in panel (A). The percentage of positions kept for tree inferences is indicated. For instance, S82 indicates that 82% of the amino acid positions of the A supermatrix were kept, while the 18% fastest evolving sites were removed. Green squares: branches supported by a PP ≥ 0.95 or a BV ≥ 95%, light green squares: branches supported by a PP < 0.95 or a BV < 95%, light red squares: alternative branching supported by a PP < 0.95 or a BV < 95%, red squares: alternative branching supported by a PP ≥ 0.95 or a BV ≥ 95%. Full trees are provided as Additional file 1: Fig. S3. C Identical to B, except that the DPANN sequences were removed from the A supermatrix. Full trees are provided as Additional file 1: Fig. S4

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