Figure 1. Hypothetical DNA barcode sequences where tree-based and similarity methods produce incorrect identifications.

A. Alignment where two recently diverged sister species (species1 and species2) have only one diagnostic nucleotide differentiating them from each other (position 1) and at the same time share two polymorphisms (positions 2 and 3). Species3 is included as outgroup; B. Pairwise uncorrected similarities based on the alignment with highest pairwise similarities in boldface; C. Neighbor joining tree; D. Strict consensus of all maximum parsimony trees.