Fig. 3

Distribution of gene functions in the core genome of the last bacterial common ancestor. a Size and functions of the last bacterial common ancestor (LBCA) core genome as the gain/loss penalty ratio (g) is increased during ancestral reconstruction through asymmetric Wagner parsimony. Functional categories comprising at least 5% of the core genome at g = 2.0 are shown. b Distribution of LBCA core orthogroups by biological system and minimum gain/loss penalty to be observed. Systems with at least 10 orthogroups of which at least 50% are present in the LBCA core genome at g = 2.0 and at least one at g = 1.0 are shown. c Distribution of LBCA core orthogroups related to ribosomal proteins (RPs), aminoacyl-tRNA synthetases (AARSs), and translation factors. d Jaccard similarity between modern and LBCA core genomes at g = 1.0 and g = 2.0, by species phylogenetic class. The core genomes least and most similar to that of the LBCA for g = 1.0 and g = 2.0 are labeled