© 2007 Society of Systematic Biologists
Alignment and Topological Accuracy of the Direct Optimization approach via POY and Traditional Phylogenetics via ClustalW + PAUP*
1 Idaho State University, Department of Biological Sciences Pocatello, Idaho 83209, USA E-mail: ogdet{at}isu.edu
2 Center for Evolutionary Functional Genomics, The Biodesign Institute, and the School of Life Sciences, Arizona State University Tempe, Arizona 85287-4501, USA E-mail: msr{at}asu.edu (M.S.R.)
Edited by Karl Kjer: Associate Editor
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Abstract |
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Direct optimization frameworks for simultaneously estimating alignments and phylogenies have recently been developed. One such method, implemented in the program POY, is becoming more common for analyses of variable length sequences (e.g., analyses using ribosomal genes) and for combined evidence analyses (morphology + multiple genes). Simulation of sequences containing insertion and deletion events was performed in order to directly compare a widely used method of multiple sequence alignment (ClustalW) and subsequent parsimony analysis in PAUP* with direct optimization via POY. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (clocklike, non-clocklike, and ultrametric). Alignment accuracy scores for the implied alignments from POY and the multiple sequence alignments from ClustalW were calculated and compared. In almost all cases (99.95%), ClustalW produced more accurate alignments than POY-implied alignments, judged by the proportion of correctly identified homologous sites. Topological accuracy (distance to the true tree) for POY topologies and topologies generated under parsimony in PAUP* from the ClustalW alignments were also compared. In 44.94% of the cases, Clustal alignment tree reconstructions via PAUP* were more accurate than POY, whereas in 16.71% of the cases POY reconstructions were more topologically accurate (38.38% of the time they were equally accurate). Comparisons between POY hypothesized alignments and the true alignments indicated that, on average, as alignment error increased, topological accuracy decreased.
Keywords: ClustalW; direct optimization; multiple sequence alignment; parsimony; phylogenetics; POY; sensitivity analysis; simulation; tree reconstruction
Received November 17, 2005; Revised February 26, 2006; Accepted October 19, 2006
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