Taxon sampling in phylogenetic analysis: An evalution of the basally positioned taxon

Abstract

Taxon sampling is explicitly examined using simulations and probability analyses. The simulations focus on the ability of two different sampling strategies to correctly reconstruct relationships among subgroups of taxa. One sampling strategy chooses taxa randomly, the other strategy chooses taxa to increase the phylogenetic dispersal of the taxa. Also considered is whether the inclusion of a single basal taxon will increase the frequency of correctly reconstructing the relationships among subgroups. Inclusion of the basal taxon is found to decrease success (correct subgroup relationships). The strategies are found to differ, primarily due to differing tendencies to include the basal taxon (the random strategy includes the basal taxon less frequently and outperforms the dispersed strategy). The inclusion of a basal taxon is also found to decrease the probability of correctly reconstructing ancestral character states. The probability of randomly choosing a single taxon from one side of the root is developed.