1. Shimodaira H (2002) an Approximately Unbiased Test of Phylogenetic Tree Selection. Syst

Table S4. HpsN tree topological comparison using the Approximately Unbiased (AU) test [1] and the more conservative Shimodaira-Hasegawa (SH) test [2] implemented in the Consel software [3], with the site-wise log-likelihood estimated using the RAxML pthread v7.3.0 [4]. The two trees under comparison are those reconstructed using composition-homogeneous (Fig. 3) and composition-heterogeneous (Fig. S3A) models using the P4 Bayesian phylogenetic software, and they mainly differ in the position of the SAR11 clade sequences. Both tests consistently show that there is approximately equal probability for the trees, and neither could be rejected. Therefore, the phylogenetic position of the SAR11 HpsN cannot be resolved. The third tree, reconstructed with PhyloBayes (Fig. S3B), is nearly identical to Fig. S3A in its topology.

Hypothesis AU test SH test Composition-homogeneous tree (Fig. 3) 0.535 0.537 Composition-heterogeneous tree (Fig. S3A) 0.465 0.463

1. Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51(3):492–508. 2. Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16:1114–1116. 3. Shimodaira H, Hasegawa M (2001) CONSEL: For assessing the confidence of phylogenetic tree selection. Bioinformatics 17(12):1246–1247. 4. Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688– 2690.