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Article
How should gaps be treated in parsimony? A comparison of approaches using simulation
Molecular Phylogenetics and Evolution (2007)
  • T. Heath Ogden, Utah Valley University
Abstract
Simulation with indels was used to produce alignments where true site homologies in DNA sequences were known; the gaps from these datasets were removed and the sequences were then aligned to produce hypothesized alignments. Both alignments were then analyzed under three widely used methods of treating gaps during tree reconstruction under the maximum parsimony principle. With the true alignments, for many cases (82%), there was no diVerence in topological accuracy for the diVerent methods of gap coding. However, in cases where a diVerence was present, coding gaps as a Wfth state character or as separate presence/absence characters outperformed treating gaps as unknown/missing data nearly 90% of the time. For the hypothesized alignments, on average, all gap treatment approaches performed equally well. Data sets with higher sequence divergence and more pectinate tree shapes with variable branch lengths are more aVected by gap coding than datasets associated with shallower non-pectinate tree shapes.
Keywords
  • Clustal; DNA sequence alignment; Evolutionary distance; Gap character coding; Homology; Indel; Parsimony; Simulation; Tree reconstruction
Publication Date
2007
Citation Information
T. Heath Ogden. "How should gaps be treated in parsimony? A comparison of approaches using simulation" Molecular Phylogenetics and Evolution Vol. 42 (2007)
Available at: http://works.bepress.com/heath_ogden/7/