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. 2009 May 21;58(1):130–145. doi: 10.1093/sysbio/syp017

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FIGURE 8. — Ambiguous characters interact with model misspecification to produce misleading branch-length estimates. A data set is simulated using an ultrametric tree. Some sites evolve under a slow rate, whereas others evolve under a fast rate. Ambiguous characters are introduced nonrandomly with respect to rate and taxon. If rate variation is correctly modeled, the estimated tree is ultrametric. If rate variation is not correctly modeled, the estimated tree is non-ultrametric. The interaction between ambiguous characters and model misspecification causes among-site rate variation to be manifested as among-branch rate variation. Note that the pattern of branch lengths inferred depend on the taxonomic distribution of the ambiguous characters, even though the ambiguous sites contain no topological information.