Fig. 3
From: Assessment of assumptions underlying models of prokaryotic pangenome evolution
Estimation of genome intersection and gene commonality for a simulated genome dataset. a The phylogenetic tree used for generating the simulated dataset. b Genome intersections for a single turnover rate. Numbers of intersecting genomes are shown in different colors, as indicated by the color bar. The parameters used for the simulations are x = 4500 and P+ = P− = 1.5 × 103. The model prediction is obtained by substituting x and P− into Eq. 7. Model prediction is indicated by a red line. c The mean genome intersections are calculated for the tree using Eq. 9. The simulated dataset is compared to model prediction (see legend). d Gene commonality for the simulated dataset and model prediction. The model prediction for gene commonality is extracted from the mean genome intersections of b, using Eq. 3. e–g Simulations using two turnover rates. Model parameters are identical to the values that were inferred for E. coli (see Additional file 1: Table S1). Panel content is analog to b–d. Model prediction for Ik was obtained using Eq. 8