J Syst Evol ›› 2008, Vol. 46 ›› Issue (3): 239-257.DOI: 10.3724/SP.J.1002.2008.08016

• Research Articles • Previous Articles     Next Articles

Taxon sampling and the accuracy of phylogenetic analyses

Tracy A. HEATH, Shannon M. HEDTKE, David M. HILLIS*   

  1. (Section of Integrative Biology and Center for Computational Biology and Bioinformatics, One University Station C0930, The University of Texas, Austin, TX 78712, USA) dhillis@mail.utexas.edu
  • Received:2008-02-02 Published:2008-05-18

Abstract: Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phylogenetic analyses is improved significantly by thorough taxon sampling efforts. Many recent efforts to improve phylogenetic estimates have focused instead on increasing sequence length or the number of overall characters in the analysis, and this often does have a beneficial effect on the accuracy of phylogenetic analyses. However, phylogenetic analyses of few taxa (but each represented by many characters) can be subject to strong systematic biases, which in turn produce high measures of repeatability (such as bootstrap proportions) in support of incorrect or misleading phylogenetic results. Thus, it is important for phylogeneticists to consider both the sampling of taxa, as well as the sampling of characters, in designing phylogenetic studies. Taxon sampling also improves estimates of evolutionary parameters derived from phylogenetic trees, and is thus important for improved applications of phylogenetic analyses. Analysis of sensitivity to taxon inclusion, the possible effects of long-branch attraction, and sensitivity of parameter estimation for model-based methods should be a part of any careful and thorough phylogenetic analysis. Furthermore, recent improvements in phylogenetic algorithms and in computational power have removed many constraints on analyzing large, thoroughly sampled data sets. Thorough taxon sampling is thus one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracy of biological inferences that are based on these phylogenetic trees.

Key words: consistency, long-branch attraction, phylogenetic accuracy, phylogenomics, systematic error, taxon sampling, Tree of Life