For phylogenomic analyses, only single-copy core genes were used. Codon-based alignments for each OGs were obtained by aligning the translated protein with MAFFT [84] and back-translating with PAL2NAL [85]. Poorly aligned regions were filtered by Gblocks [86], with default parameters except for option -t = c. The aligned sequences were concatenated as a single data set using homemade Python scripts. The approximately-maximum-likelihood phylogenetic tree was built using the generalized time-reversible model implemented in FastTree [87] and visualized using the Interactive Tree of Life [88]. In addition, we used R function pvclust [89] to perform a hierarchical cluster analysis, based on an absence/presence (0/1) matrix of dispensable genes according to GET_HOMOLOGUES results. To further elucidate the population structure of M. luteus, we used Fastbaps [35] with default parameters based on the core genome alignment. We also used the model-based Bayesian method implemented in Structure 2.3.4 [36], in which the admixture model was used with a varying K from 2 to 10, and the optimal value for K was obtained by STRUCTURE HARVESTER [90]. The pangenome matrix and the rooted species tree were used as inputs for COUNT [91] to calculate posterior probabilities for gain and loss of each OG across all nodes during the evolution of M. luteus.

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