Fig 1.
Maximum likelihood phylogenetic tree of sequenced MAP isolates.
Phylogenetic tree of global (n = 26, labeled with a black dot (•)) and Canadian (n = 182) isolates based on 9,670 variant sites using the TPM1uf nucleotide substitution model. The tree is rooted to the Type I sequence. A magnification of the phylogeny excluding the Type I, III, and B isolates is outlined in dotted lines. The dominant subtype is shaded in grey. Bootstrap values with branch support ≥ 70% are displayed.
Fig 2.
Maximum likelihood phylogenetic trees of Canadian and global MAP isolates.
A) Phylogenetic tree of one Canadian and ten global Type III isolates based on 5,416 concatenated variant sites. B) Phylogenetic tree of six Canadian and four global “Bison type” isolates based on 403 concatenated variant sites. The global sequences are shaded in grey and branches are labeled according to the isolate ID.
Fig 3.
Rarefaction curves indicating the mean subtype richness of each region at different sampling efforts.
Rarefaction curves were generated using the function rarefy in the R package Vegan using A) a strict subtype definition (9 total subtypes) and B) a relaxed subtype definition (32 total subtypes). 95% confidence intervals are indicated by a dotted line. The 7 regions are labeled with shapes indicated in the key at the bottom of the figure. Regions are abbreviated as follows: Québec = QC, Alberta = AB, Ontario = ON, the Atlantic region = AT, Manitoba = MB, British Columbia = BC, and Saskatchewan = SK.
Fig 4.
Phylogenetic clustering of MAP isolates among Canadian regions.
A) Circularized maximum likelihood phylogenetic tree of 182 Canadian MAP isolates, rooted to the Type III isolate. Tips are colored according to province of origin (Alberta = blue, Ontario = light blue, British Colombia = red, Québec = orange, Saskatchewan = yellow, the Atlantic provinces = pink, Manitoba = purple). The branches leading to the nine subtypes are labeled with a square. Dotted lines indicate the threshold for the different subtype definitions used in the rarefaction analysis. B) Map of the 7 Canadian regions in which MAP isolates were obtained. C) The statistics (AI = association index, PS = parsimony score, MC = monophyletic clade size statistic), number of samples from each of the 7 regions, observed mean, null mean, and significance (p-value) are presented. Low AI and PS scores indicate a strong association, whereas high MC scores indicate a strong association.
Fig 5.
Phylogenetic clustering of MAP isolates in three regions in Alberta.
A) Circularized maximum likelihood phylogenetic tree of 58 Alberta MAP isolates. Tips are colored according to the geographical location of originating farms (Region 1 = light blue, Region 2 = dark blue, Region 3 = blue). B) Map of Alberta with the three regions indicated by their respective colors. C) BaTS analysis of the phylogeny-region association. The statistics (AI = association index, PS = parsimony score, MC = monophyletic clade size statistic), number of samples from each region, observed mean, null mean, and significance (p-value) are presented. Low AI and PS scores indicate a strong association, whereas high MC scores indicate a strong association.