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. 2020 Sep 2;10:14428. doi: 10.1038/s41598-020-71344-9

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© The Author(s) 2020

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Most parsimonious acquisition and loss of selected genomic elements and predicted biological processes, superimposed on a maximum clade credibility phylogeny of 13 Lineage II S. Typhimurium isolates from New York State. A gain or loss of a genomic element or biological process is indicated by a purple box with green or red text, respectively, with gene names and plasmid replicons in boldfaced text. Strains were isolated from bovine or human clinical sources (blue and magenta tip labels, respectively) from 1999 to 2016. The time scale in years is plotted along the x-axis of the phylogeny. Branch labels correspond to posterior probabilities.