Figure 1.

Over annotation due to database bias or gene loss under equal rates of evolution Species harboring the sequences are indicated. Two cases are depicted. In A, the query sequence belongs to the "Y" subfamily which can be correctly inferred by both sequence similarity and phylogenetic tree based methods (in situation A, the query is most similar to "Y" of rat and mouse). In short, in situation A, orthology and "most similar" do (partially) overlap. In B, a situation is depicted where the query is actually a member of a third subfamily "X" but this can only be inferred by considering the evolutionary history of this sequence family. Sequence similarity based methods would misleadingly indicate that this query belongs to "Y" since it is most similar to "Y" in rat, mouse and wheat. In short, in situation B, orthology and "most similar" do not correspond. Observe that if there would have been already members of "X" in the database (no gene loss and complete sampling) the query in B could have been correctly determined to belong to a "X" subfamily (under equal rates of evolution).