Fig 1.
Phylogeny of VNTR-1 and -10 isolates (from [3]) showing the distribution of SNPs in sampled cattle.
In this paper we have ignored the samples from badgers but show them here to indicate the close phylogenetic relatonship to the cattle isolates.
Fig 2.
Comparison of the pairwise distribution of SNP differences for observed cases in Northern Ireland and in our simulations.
The yellow boxes on the right hand plot indicate the number of SNP differences associated with each point.
Table 1.
Summary of the priors used in the model.
In the cases of β, αRC, αCR, μ we used non-informative priors whereas in the case of σ, γ, Ω the priors were chosen on the basis of existing field and experimental estimates [3, 15, 16].
Table 2.
AIC scores for the various models investigated.
The best model is one in which we have a reservoir population that does not actively contribute to pathogen diversity the minimal diversity model).
Table 3.
Summary of the posterior estimates for the minimal diversity model which best fits the data from our calculations, (see Table 2 for the AIC scores for each model).
95% credible intervals are given in square braces.
Fig 3.
Comparison of the pairwise distribution of SNP differences for the four rejected models.
(a) A single reservoir connecting every farm (top left), (b) Maximum diversity model (top right), (c) Intermediate diversity model (bottom left), (d) No Connecting Reservoirs (bottom right).