Extended Data Fig. 3: Average number of monophyletic (green bars), operationally monophyletic (yellow bars) and polyphyletic (orange bars) taxa across higher ranks (phylum, class, and order) in percent.

Shown are GTDB taxonomy decorated phylogenetic trees inferred with different methods, from a range of markers, from alignments trimmed to reduce compositional bias and fast evolving sites, and from alignments created as part of the simulated database expansion. Note that only taxa with two or more genomes were included, and that the data set (order representatives) used for PhyloBayes restricts the analysis to the ranks of phylum and class. Details for each inferred tree are provided in Supplementary Table 10. Percentages for all ranks are shown in Supplementary Fig. 11. Monophyly and operational monophyly was determined based on the F measure of decorated internal nodes.