Is It Better to Add Taxa or Characters to a Difficult

TLDR: In this paper, the effects of adding characters and/or taxa on phylogenetic accuracy were explored using data generated by computer simulation using a four-taxon tree in the "Felsenstein zone/7".

Abstract: The effects on phylogenetic accuracy of adding characters and/or taxa were explored using data generated by computer simulation. The conditions of this study were constrained but allowed for systematic investigation of certain parameters. The starting point for the study was a four-taxon tree in the "Felsenstein zone/7 representing a difficult phylogenetic problem with an extreme situation of long branch attraction. Taxa were added sequentially to this tree in a manner specifically designed to break up the long branches, and for each tree data matrices of different sizes were simulated. Phylogenetic trees were reconstructed from these data using the criteria of parsimony and maximum likelihood. Phylogenetic accuracy was measured in three ways: (1) proportion of trees that are completely correct, (2) proportion of correctly reconstructed branches in all trees, and (3) proportion of trees in which the original four-taxon statement is correctly reconstructed. Accuracy improved dramatically with the addition of taxa and much more slowly with the addition of characters. If taxa can be added to break up long branches, it is much more preferable to add taxa than characters. (Long branch attraction; parsimony; phylogenetic recon? struction; simulation; taxon sampling.) It is obvious that the successful recon? struction of phylogenetic relationships re? quires some amount of data sampling from relevant taxa and informative char? acters. Far less clear, however, is how much of each data type is required, and whether one of those sources of data has a greater impact on accuracy than the other. Given limited time and resources, it is important to explore the costs and benefits to phylo? genetic accuracy of adding taxa versus in? creasing the number of characters. For ex? ample, given that one has sufficient time and resources to sequence 10 kilobases (kb) of DNA, would it be better to se? quence, say, 2.5 kb from each of 4 taxa, or 1 kb from each of 10, or 0.25 kb from each of 40?