Abstract
Supertree methods comprise one approach to reconstructing large molecular phylogenies given estimated source trees for overlapping subsets of the entire set of taxa. These source trees are combined into a single supertree on the full set of taxa using various algorithmic techniques, with the most common being matrix representation with parsimony (MRP). When the data allow, the competing approach is a combined analysis (also known as a “supermatrix” or “total evidence” approach) whereby the different sequence data matrices for each of the different subsets of taxa are concatenated into a single supermatrix, and a tree is estimated on that supermatrix. In this paper, we report an extensive simulation study comparing the supertree methods MRP and weighted MRP against combined analysis methods on large model trees, using a novel simulation methodology (Super-Method Input Data Generator, or SMIDGen), which better reflects biological processes and the practices of systematists. This study shows that combined analysis based upon maximum likelihood outperforms all the other methods, giving especially big improvements when the largest subtree does not contain most of the taxa.
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References
Sanderson, M.J., Purvis, A., Henze, C.: Phylogenetic supertrees: Assembling the trees of life. Trends Ecol. Evol. 13, 105–109 (1998)
Bininda-Emonds, O.R.P., Gittleman, J.L., Steel, M.A.: The (super) tree of life: Procedures, problems, and prospects. Annu. Rev. Ecol. Syst. 33, 265–289 (2002)
Bininda-Emonds, O.R.P.: The evolution of supertrees. Trends in Ecology and Evolution 19, 315–322 (2004)
Bininda-Emonds, O.R.P.: Phylogenetic Supertrees: Combining Information To Reveal The Tree Of Life. Computational Biology (2004)
Baum, B.R.: Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41, 3–10 (1992)
Ragan, M.A.: Phylogenetic inference based on matrix representation of trees. Mol. Phylo. Evol. 1, 53–58 (1992)
Ronquist, F.: Matrix representation of trees, redundancy, and weighting. Syst. Biol. 45, 247–253 (1996)
Bininda-Emonds, O.R.P., Sanderson, M.J.: Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. Syst. Biol. 50, 565–579 (2001)
Chen, D., Diao, L., Eulenstein, O., Fernández-Baca, D., Sanderson, M.J.: Flipping: A supertree construction method. In: Bioconsensus. DIMACS: Series in Discrete Mathematics and Theoretical Computer Science, vol. 61, pp. 135–160. American Mathematical Society-DIMACS, Providence (2003)
Burleigh, J.G., Eulenstein, O., Fernández-Baca, D., Sanderson, M.J.: MRF supertrees. In: Bininda-Emonds, O.R.P. (ed.) Phylogenetic Supertrees: Combining Information To Reveal The Tree Of Life, pp. 65–86. Kluwer Academic, Dordrecht (2004)
Eulenstein, O., Chen, D., Burleigh, J.G., Fernández-Baca, D., Sanderson, M.J.: Performance of flip supertree construction with a heuristic algorithm. Syst. Biol. 53, 299–308 (2004)
Lapointe, F.J., Levasseur, C.: Everything you always wanted to know about average consensus and more. In: Bininda-Emonds, O.R.P. (ed.) Phylogenetic Supertrees: Combining Information To Reveal The Tree Of Life, pp. 87–106. Kluwer Academic, Dordrecht (2004)
Piaggio-Talice, R., Burleigh, J.G., Eulenstein, O.: Quartet supertrees. In: Bininda-Emonds, O.R.P. (ed.) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 173–191. Kluwer Academic, Dordrecht (2004)
Ross, H.A., Rodrigo, A.G.: An assessment of matrix representation with compatibility in supertree construction. In: Bininda-Emonds, O.R.P. (ed.) Phylogenetic Supertrees: Combining Information To Reveal The Tree Of Life, pp. 35–64. Kluwer Academic, Dordrecht (2004)
Chen, D., Eulenstein, O., Fernández-Baca, D., Burleigh, J.G.: Improved heuristics for minimum-flip supertree construction. Evol. Bioinform. 2, 401–410 (2006)
Criscuolo, A., Berry, V., Douzery, E., Gascuel, O.: SDM: A fast distance-based approach for (super) tree building in phylogenomics. Syst. Biol. 55, 740–755 (2006)
Soltis, D.E., Soltis, P.S., Nickrent, D.L., Johnson, L.A., Hahn, W.J., Hoot, S.B., Sweere, J.A., Kuzoff, R.K., Kron, K.A., Chase, M.W.: Angiosperm phylogeny inferred from 18S Ribosomal DNA sequences. Ann. Mo. Bot. Garden 84, 1–49 (1997)
Glenner, H., Hansen, A.J., Sørensen, M.V., Ronquist, F., Huelsenbeck, J.P., Willerslev, E.: Bayesian inference of the metazoan phylogeny: A combined molecular and morphological approach. Current Biology 14, 1644–1649 (2004)
Dunn, C.W., Hejnol, A., Matus, D.Q., Pang, K., Browne, W.E., Smith, S.A., Seaver, E., Rouse, G.W., Obst, M., Edgecombe, G.D., Sorensen, M.V., Haddock, S.H.D., Schmidt-Rhaesa, A., Okusu, A., Kristensen, R.M., Wheeler, W.C., Martindale, M.Q., Giribet, G.: Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452(7188), 745–749 (2008)
Swofford, D.L., Olson, G.J., Waddell, P.J., Hillis, D.M.: Phylogenetic Inferrence, 2nd edn., pp. 407–425. Sinauer Associates, Sunderland (1996)
Stamatakis, A.: RAxML-NI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690 (2006)
Swofford, D.L.: PAUP*: Phylogenetic analysis using parsimony (* and other methods). Ver. 4. Sinauer Associates, Sunderland (2002)
Ganapathy, G.: Algorithms and Heuristics for Combinatorial Optimization in Phylogeny. PhD thesis, University of Texas at Austin (2006)
Brauer, M.J., Holder, M.T., Dries, L.A., Zwickl, D.J., Lewis, P.O., Hillis, D.M.: Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference. Mol. Biol. Evol. 19, 1717–1726 (2002)
Baldwin, J., Fitch, D., De Ley, P., Nadler, S.: The Nematode Branch of the Assembling the Tree of Life Project: NemATOL (2008), http://nematol.unh.edu
Chase, M.W., Soltis, D.E., Olmstead, R.G., Morgan, D., Les, D.H., Mishler, B.D., Duvall, M.R., Price, R.A., Hills, H.G., Qiu, Y.L.: Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Ann. Mo. Bot. Garden 80, 528–580 (1993)
Rambaut, A., Grassly, N.C.: Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13, 235–238 (1997)
Page, R.D.M.: Taxonomy, supertrees, and the tree of life. In: Bininda-Emonds, O.R.P. (ed.) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 247–265. Kluwer Academic, Dordrecht (2004)
Thain, D., Tannenbaum, T., Livny, M.: Distributed computing in practice: the condor experience. Concurrency and Computation: Practice and Experience 17, 323–356 (2005)
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Swenson, M.S., Barbançon, F., Linder, C.R., Warnow, T. (2009). A Simulation Study Comparing Supertree and Combined Analysis Methods Using SMIDGen. In: Salzberg, S.L., Warnow, T. (eds) Algorithms in Bioinformatics. WABI 2009. Lecture Notes in Computer Science(), vol 5724. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04241-6_28
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DOI: https://doi.org/10.1007/978-3-642-04241-6_28
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