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. 2018 Jul 24;4(9):e000201. doi: 10.1099/mgen.0.000201

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© 2018 The Authors

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 4. — beast reconstruction of the tip-dated phylogenetic tree of R. salmoninarum clade 1 using a relaxed-clock model. Short reads were mapped against reference genome ATCC 33209 and consensus sequence alignments were passed to beast for phylogenetic reconstruction. Left panel: phylogenetic tree of all R. salmoninarum clade 1 isolates. Chilean isolates are highlighted in red. Chilean multi-isolate lineages are labelled. Tip labels of Chilean isolates are highlighted in red. Right panel: phylogenetic trees of the three Chilean multi-isolate lineages (1a, 1b, 1c). Tips are coloured by host species (Atlantic salmon, blue; rainbow trout, orange; coho salmon, red). Estimated divergence dates are annotated at each node and 95 % CIs indicated (red bar).