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. Author manuscript; available in PMC: 2019 Oct 7.
Published in final edited form as: Mol Ecol. 2019 Jul 9;28(13):3241–3256. doi: 10.1111/mec.15120

Fig. 3.

Fig. 3.

Patterns of effective population size and migration through time of Mycobacterium tuberculosis lineages 1-4. Bayesian skyline plots (top panels) show inferred changes in effective population size (Ne) through time deduced from lineage specific analyses. Black lines denote median Ne and gray shading the 95% highest posterior density. Estimated migration through time for each lineage is shown in the bottom panels (see Methods). Grey shading depicts the rates inferred after the addition or subtraction of a single migration event, and demonstrate the uncertainty of rate estimates, particularly from the early history of each lineage where branches are coalescing towards the MRCA. (Data omitted where less that 4 branches of the phylogeny are represented.) Dates are shown in years and are based on scaling the phylogeny of the Old World collection with a substitution rate of 5 × 10−8 substitutions/site/year (Kay et al. 2015).