Fig. 3: Maximum likelihood phylogenetic tree based on the concatenated sequences of 16 ribosomal proteins of Proteobacteria.
From: A human respiratory tract-associated bacterium with an extremely small genome
The tree includes 451 species belonging to phylum Proteobacteria, two species of Actinobacteria (used as outgroups) and IOLA (listed in Supplemental Data 2). A total of 454 sets of the 16 ribosomal proteins (RpL2, 3, 4, 5, 6, 14, 15, 16, 18, 22, and 24 and RpS3, 8, 10, 17, and 19) were used. Species belonging to the same class are presented in the same color. The tree was constructed using the 1895-position alignment by the maximum likelihood method with the LG + R10 model and 1000 ultrafast bootstrap replicates. The scale bar indicates substitutions per site. Black dots indicate divergence episodes with bootstrap values greater than 80%. Four species that have a small genome (<1.0 Mb) with a low GC content (<30%), such as IOLA, are indicated.
