Fig. (2).

Example of a false mosaic sequence caused by plesiomorphies. A) Alignment of sequences with a potential recombinant sequence (Strain 3). Note that the midpoint-rooted Neighbour Joining tree cluster such sequence with strains 4 and 5 (distance from strain 3 to strains 4 and 5 is shorter than distance to strains 1 and 2). B) The same alignment than in A but including an outgroup strain. Note that only sinapomorphies are highlighted and there is no SNP supporting the clustering of strain 3 with strains 4 and 5. Instead, there are five SNPs supporting the clustering of Strain 3 with strains 1 and 2. In addition, a rooted Neighbour Joining tree (right) show the clustering of Strain 3 with strains 1 and 2.