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. 2018 Feb 5;8:2393. doi: 10.1038/s41598-018-20889-x

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Predicted gene gain, gene loss and recombination/mutation rates with the predicted evolutionary history of C. hyointestinalis. (a) Recombination-stripped core-gene based phylogeny, generated using BEAST2. (b) The same phylogeny as in (a), represented as two mirrored cladograms. Branch thickness denotes predicted gene gain (left) and gene loss (right) events as calculated using the Count software package⁷⁴, and expressed as a percentage of the total genomic content. Branch colour denotes the log value of the predicted recombination to mutation ratio for each corresponding branch. Reference genome sequences not generated as part of this study are referred to as REF1 (GCA000705275), REF2 (GCA001643955), REF3 (GCA900116585) and LAW (C. hyointestinalis subsp. lawsonii, GCA001643975).