The analysis for the history of gene gain and loss was done by a stochastic mapping method implemented using the gainLoss program32. The program takes the patterns of absence or presence of gene clusters and analyzes the evolution of such observed phyletic patterns within the likelihood framework using a probabilistic evolutionary model that assumes the gain and loss of genes along the phylogeny that follow a Markovian continuous process, and infers probabilities and expectations for all gain and loss events in a per site per branch manner. The core genome phylogeny was used as the reference tree. The probabilistic evolutionary model used here assumed that the gain/loss ratio varies among sites (variable gain/loss ratio (mixture)). The total number of gains/losses for each branch was calculated as the probability of gain/loss for each gene cluster, summed across all the genes. The probability cutoff implemented to call a gene gained/lost at a branch of the phylogenetic tree was >0.98.