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. 2016 Nov 30;2(11):e000095. doi: 10.1099/mgen.0.000095

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© 2016 The Authors

This is an open access article under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited.

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Fig. 1. — ML phylogenetic tree of 58 Y. ruckeri isolates. The tree was based on alignment of 11 715 non-recombinant core genome SNPs with branch lengths corrected for ascertainment bias using RAxML. Branch support was estimated by performing 1000 bootstrap replicates. Metadata show host, geographical origin and serotype where known. Bar, estimated substitution rate. + Isolate collected from Atlantic salmon (S. salar) reared concurrently with rainbow trout (O. mykiss) in the same hatchery. # Isolated from brook trout (Salvelinus fontinalis) reared alongside Atlantic salmon in the same hatchery. Arrows indicate independent losses of the LPS O-antigen cluster and O-antigen-deficient isolates are indicated by O-.