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. 2016 Mar 11;17:222. doi: 10.1186/s12864-016-2426-7

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© Warne et al. 2016

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. 6 — Evidence of recombination in the essD gene. On the left is a maximum likelihood phylogeny constructed with essD gene sequences from isolates containing the essC1 subtype. To the right, each vertical colored line represents a SNP position in the essD sequence, top. Colored vertical lines along the tracks represent bases that differ from the ancestral sequence: grey = non-homoplastic change; colored lines represent homoplastic bases: red = A, blue = T, green = C, orange = G. The pattern of lines provide a barcode of essD similarity between strains and identifies regions containing homoplasies that are incongruent with the phylogeny and are associated with recombination