Fig 1.
Median network displaying diversity of Mycobacterium bovis in Africa using 48 markers (43 spoligotype spacers and 5 VNTRs).
The genotypes of M. tuberculosis, M. caprae, M. africanum, M. canetti and M. pinnipedii strains were included as outgroups. Samples were coloured according to the geographic location (in the case of M. bovis strains) or according to the strains (in the case of other M. tuberculosis complex strains). Figure was made using freely available phylogenetic software network (http://www.fluxus-engineering.com).
Fig 2.
Geographic distribution of diversity of Mycobacterium bovis in Africa using the Kriging algorithm of Surfer 8 software for four diversity estimators (haplotype diversity Hd, the average number of differences K, the nucleotide diversity Pi and ρ).
Map outline was adapted from https://commons.wikimedia.org/wiki/Atlas_of_the_world.
Table 1.
Diversity measures obtained from the sample of Mycobacterium bovis genotypes in different countries.
Diversity indices were not calculated for locations with low sample size (n<20).
Fig 3.
Neighbour-joining population tree based on a matrix of Fst values between populations.
A dataset of European M. tuberculosis (Mtb) was used as an outgroup. Sample sets indicated as (*) have a low sample size and their placement in the tree is possibly uncertain.
Fig 4.
Comparison between hypothetical time of introduction of dairy animals across Africa from the archaeological record (A.) and genetic diversity statistics, ρ (B.) and Pi (C.). Colour of data points in (B) and (C) correspond to the regions of the same colour in the map (A). Map was adapted from https://commons.wikimedia.org/wiki/Atlas_of_the_world.