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. 2016 Jan 26;17:79. doi: 10.1186/s12864-015-2234-5

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© Bryant et al. 2015

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 4 — Estimates of substitution rate. Coalescent analyses were implemented using the BEAST package (v1.7.5) [31] as described in the text. This was carried out both on the entire data and the Type C isolates alone, using a variety of population models as shown. The mean value represents the mean estimated substitution rate from three independent runs. The confidence intervals represent the maximum and minimum higher posterior densities obtained. As a comparison, the estimated rates are shown alongside a predicted substitution rate of M. tuberculosis in the context of transmission [49]