Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets

J. Gordon Burleigh, Amy C. Driskell, Michael J. Sanderson

Research output: Contribution to journalArticlepeer-review

41 Scopus citations


Nonparamtric bootstrapping methods may be useful for assessing confidence in a supertree inference. We examined the performance of two supertree bootstrapping methods on four published data sets that each include sequence data from more than 100 genes. In "input tree bootstrapping," input gene trees are sampled with replacement and then combined in replicate supertree analyses; in "stratified bootstrapping," trees from each gene's separate (conventional) bootstrap tree set are sampled randomly with replacement and then combined. Generally, support values from both supertree bootstrap methods were similar or slightly lower than corresponding bootstrap values from a total evidence, or supermatrix, analysis. Yet, supertree bootstrap support also exceeded supermatrix bootstrap support for a number of clades. There was little overall difference in support scores between the input tree and stratified bootstrapping methods. Results from supertree bootstrapping methods, when compared to results from corresponding supermatrix bootstrapping, may provide insights into patterns of variation among genes in genome-scale data sets.

Original languageEnglish (US)
Pages (from-to)426-440
Number of pages15
JournalSystematic biology
Issue number3
StatePublished - Jun 2006
Externally publishedYes


  • Nonparametric bootstrapping
  • Phylogenetics
  • Supermatrix
  • Supertree
  • Supertree bootstrapping

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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