Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling

Background: Phylogenies are essential to many areas of biology, but phylogenetic methods may give incorrect estimates under some conditions. A potentially common scenario of this type is when few taxa are sampled and terminal branches for the sampled taxa are relatively long. However, the best solution in such cases (i.e., sampling more taxa versus more characters) has been highly controversial. A widespread assumption in this debate is that added taxa must be complete (no missing data) in order to save analyses from the negative impacts of limited taxon sampling. Here, we evaluate whether incomplete taxa can also rescue analyses under these conditions (empirically testing predictions from an earlier simulation study). Methodology/Principal Findings: We utilize DNA sequence data from 16 vertebrate species with well-established phylogenetic relationships. In each replicate, we randomly sample 4 species, estimate their phylogeny (using Bayesian, likelihood, and parsimony methods), and then evaluate whether adding in the remaining 12 species (which have 50, 75, or 90% of their data replaced with missing data cells) can improve phylogenetic accuracy relative to analyzing the 4 complete taxa alone. We find that in those cases where sampling few taxa yields an incorrect estimate, adding taxa with 50% or 75% missing data can frequently (>75% of relevant replicates) rescue Bayesian and likelihood analyses, recovering accurate phylogenies for the original 4 taxa. Even taxa with 90% missing data can sometimes be beneficial. Conclusions: We show that adding taxa that are highly incomplete can improve phylogenetic accuracy in cases where analyses are misled by limited taxon sampling. These surprising empirical results confirm those from simulations, and show that the benefits of adding taxa may be obtained with unexpectedly small amounts of data. These findings have important implications for the debate on sampling taxa versus characters, and for studies attempting to resolve difficult phylogenetic problems.