© 2005 Society of Systematic Biologists
The Shape of Supertrees to Come: Tree Shape Related Properties of Fourteen Supertree Methods
1 Department of Zoology, The Natural History Museum London SW7 5BD United Kingdom E-mail: marw{at}nhm.ac.uk (M.W.)
2 Department of Biology, National University of Ireland Maynooth, County Kildare, Ireland
3 Department of Computer Science, Iowa State University Ames, Iowa, 50011–1040, USA
4 Department of Earth Sciences, University of Bristol Bristol BS8 1RJ, United Kingdom
5 Département de sciences biologiques, Université de Montréal C.P. 6128, Succ. Centre-ville, Montréal (Québec), H3C 3J7, Canada
6 Fisheries Research Services, Freshwater Laboratory Faskally, Pitlochry, Perthshire PH16 5LB, United Kingdom
Edited by Olaf Bininda-Emonds: Associate Editor
 |
Abstract |
|---|
Using a simple example and simulations, we explore the impact of input tree shape upon a broad range of supertree methods. We find that input tree shape can affect how conflict is resolved by several supertree methods and that input tree shape effects may be substantial. Standard and irreversible matrix representation with parsimony (MRP), MinFlip, duplication-only Gene Tree Parsimony (GTP), and an implementation of the average consensus method have a tendency to resolve conflict in favor of relationships in unbalanced trees. Purvis MRP and the average dendrogram method appear to have an opposite tendency. Biases with respect to tree shape are correlated with objective functions that are based upon unusual asymmetric tree-to-tree distance or fit measures. Split, quartet, and triplet fit, most similar supertree, and MinCut methods (provided the latter are interpreted as Adams consensus-like supertrees) are not revealed to have any bias with respect to tree shape by our example, but whether this holds more generally is an open problem. Future development and evaluation of supertree methods should consider explicitly the undesirable biases and other properties that we highlight. In the meantime, use of a single, arbitrarily chosen supertree method is discouraged. Use of multiple methods and/or weighting schemes may allow practical assessment of the extent to which inferences from real data depend upon methodological biases with respect to input tree shape or size.
Keywords: Consensus; parsimony; phylogeny; tree similarity; Tree of Life
Received April 15, 2004; Revised June 8, 2004; Accepted January 12, 2005
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  W. J. Baker, V. Savolainen, C. B. Asmussen-Lange, M. W. Chase, J. Dransfield, F. Forest, M. M. Harley, N. W. Uhl, and M. Wilkinson Complete Generic-Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches Syst Biol, May 30, 2009; (2009) syp021v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Torices and A. A. Anderberg Phylogenetic analysis of sexual systems in Inuleae (Asteraceae) Am. J. Botany, May 1, 2009; 96(5): 1011 - 1019. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. T Lloyd, K. E Davis, D. Pisani, J. E Tarver, M. Ruta, M. Sakamoto, D. W.E Hone, R. Jennings, and M. J Benton Dinosaurs and the Cretaceous Terrestrial Revolution Proc R Soc B, November 7, 2008; 275(1650): 2483 - 2490. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Steel and A. Rodrigo Maximum Likelihood Supertrees Syst Biol, April 1, 2008; 57(2): 243 - 250. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Ruta, D. Pisani, G. T Lloyd, and M. J Benton A supertree of Temnospondyli: cladogenetic patterns in the most species-rich group of early tetrapods Proc R Soc B, December 22, 2007; 274(1629): 3087 - 3095. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Pisani, J. A. Cotton, and J. O. McInerney Supertrees Disentangle the Chimerical Origin of Eukaryotic Genomes Mol. Biol. Evol., August 1, 2007; 24(8): 1752 - 1760. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Cotton and M. Wilkinson Majority-Rule Supertrees Syst Biol, June 1, 2007; 56(3): 445 - 452. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Wilkinson, J. A. Cotton, F.-J. Lapointe, and D. Pisani Properties of Supertree Methods in the Consensus Setting Syst Biol, April 1, 2007; 56(2): 330 - 337. [Full Text] [PDF]
|
|
|
|
|
|
O. Gauthier and F.-J. Lapointe Seeing the Trees for the Network: Consensus, Information Content, and Superphylogenies Syst Biol, April 1, 2007; 56(2): 345 - 355. [Full Text] [PDF]
|
|
|
|
|
|
B. Holland, G. Conner, K. Huber, and V. Moulton Imputing Supertrees and Supernetworks from Quartets Syst Biol, February 1, 2007; 56(1): 57 - 67. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. M. McMahon and M. J. Sanderson Phylogenetic Supermatrix Analysis of GenBank Sequences from 2228 Papilionoid Legumes Syst Biol, October 1, 2006; 55(5): 818 - 836. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Bertrand and M. Harlin Stability and Universality in the Application of Taxon Names in Phylogenetic Nomenclature Syst Biol, October 1, 2006; 55(5): 848 - 858. [Full Text] [PDF]
|
|
|
|
|
|
S. Joly and A. Bruneau Incorporating Allelic Variation for Reconstructing the Evolutionary History of Organisms from Multiple Genes: An Example from Rosa in North America Syst Biol, August 1, 2006; 55(4): 623 - 636. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. R. Moore, S. A. Smith, and M. J. Donoghue Increasing Data Transparency and Estimating Phylogenetic Uncertainty in Supertrees: Approaches Using Nonparametric Bootstrapping Syst Biol, August 1, 2006; 55(4): 662 - 676. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. G. Burleigh, A. C. Driskell, and M. J. Sanderson Supertree Bootstrapping Methods for Assessing Phylogenetic Variation among Genes in Genome-Scale Data Sets Syst Biol, June 1, 2006; 55(3): 426 - 440. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Morrison Book-Review Syst Biol, June 1, 2006; 55(3): 530 - 532. [Full Text] [PDF]
|
|
|
|
|
|
J. A. Cotton, C. S. C. Slater, and M. Wilkinson Discriminating Supported and Unsupported Relationships in Supertrees Using Triplets Syst Biol, April 1, 2006; 55(2): 345 - 350. [Full Text] [PDF]
|
|
|
|
|
|
M. Wilkinson, D. Pisani, J. A. Cotton, and I. Corfe Measuring Support and Finding Unsupported Relationships in Supertrees Syst Biol, October 1, 2005; 54(5): 823 - 831. [Full Text] [PDF]
|
|