Sequence-Length Requirements for Phylogenetic Methods

We study the sequence lengths required by neighbor-joining, greedy parsimony, and a phylogenetic reconstruction method (DCMNJ+MP) based on disk-covering and the maximum parsimony criterion. We use extensive simulations based on random birth-death trees, with controlled deviations from ultrametricity, to collect data on the scaling of sequence-length requirements for each of the three methods as a function of the number of taxa, the rate of evolution on the tree, and the deviation from ultrametricity. Our experiments show that DCMNJ+MP has consistently lower sequence-length requirements than the other two methods when trees of high topological accuracy are desired, although all methods require much longer sequences as the deviation from ultrametricity or the height of the tree grows. Our study has significant implications for large-scale phylogenetic reconstruction (where sequence-length requirements are a crucial factor), but also for future performance analyses in phylogenetics (since deviations from ultrametricity are proving pivotal).