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Core genome phylogenetic tree of MAP. The innermost circle shows the host from which the strain was isolated. The next five circles indicate the presence/absence pattern of cattle-specific essential colonization factors identified by Eshraghisamani et al. [41]. The outermost circle indicates which strains were identified as autochthonous (black) and allochthonous (blank) by aurora. The arrowheads point to empirically identified allochthonous strains in the dataset.

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