Can incomplete taxa rescue phylogenetic analyses from long-branch attraction?

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191 Scopus citations

Abstract

Taxon sampling may be critically important for phylogenetic accuracy because adding taxa can help to subdivide misleading long branches. Although the idea that added taxa can break up long branches was exemplified by a study of "incomplete" fossil taxa, the issue of taxon completeness (i.e., proportion of missing data) has been largely ignored in most subsequent discussions of taxon sampling and long-branch attraction. In this article, I use simulations to test the ability of incomplete taxa to subdivide long branches and improve phylogenetic accuracy in situations of potential long-branch attraction. The results show that for most methods and conditions examined, adding taxa that are only 50% complete may provide similar benefits to adding the same number of complete taxa (suggesting that the advantages of increased taxon sampling may be obtained with less data than previously considered). For parsimony, taxa that are less complete (5% to 25% complete) may often have limited ability to rescue analyses from long-branch attraction. In contrast, highly incomplete taxa can be surprisingly beneficial when using model-based methods. The results also suggest the importance of model-based methods in phylogenetic analyses that combine molecular and fossil data.

Original languageEnglish (US)
Pages (from-to)731-742
Number of pages12
JournalSystematic biology
Volume54
Issue number5
DOIs
StatePublished - Oct 1 2005

Keywords

  • Combining data
  • Fossils
  • Incomplete taxa
  • Missing data
  • Phylogenetic accuracy
  • Simulations
  • Taxon sampling

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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