Wednesday, February 3, 2010
If we've learned anything from US politics over the past year and half its that adding 'rogues' to an an otherwise orderly system can result in rapid descent to the lowest common denominator. In the latest issue of Systematic Biology, Thomson and Shaffer show that the same is true in phylogenetics. With the goal of reconstructing a robust phylogenetic hypothesis for turtles using existing sequence data, Thomson and Shaffer use a new pipeline and the data available via the PhyLoTA browser to assemble a dataset that is noteworthy for both its size and incompleteness: 223 taxa, 53,406 bp, 7.59% complete. Although Thomson and Shaffer explore the influence of a variety of factors on phylogenetic inference, they conclude that rogue taxa "probably represent the most insidious problem for supermatrix phylogenetics." For those unfamiliar with rogue taxa, the term is used to describe taxa whose phylogenetic position can vary dramatically without having a strong effect on a tree's overall score. Thomson and Shaffer identify rogues using the taxonomic instability index (I) calculated by Mesquite from a sample of trees generated using standard bootstrapping methods. To explore the influence of rogues on phyogenetic resolution, Thomson and Shaffer remove those taxa exhibiting the most roguish behavior and redo their analyses. The top panel of their Fig. 4 provides a compelling visual representation of the results of this exercise, with the completely unresolved tree on the left being generated before pruning rogues and the nearly fully-resolved tree on the right resulting from analysis of the same dataset subsequent to de-roguing. Although one might challenge the wisdom of deleting problematic taxa until a resolved tree is produced, this practice may be justified in some instances. How we deal with rogue taxa is sure to be a topic of debate in the years to come, but, for the time being Thomson and Shaffer's analyses suggest that simply deleting the taxa with the worst I values may be a reasonable solution.