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

Abstract.—Nonparamtric bootstrapping methods may be useful for assessing confidence in a supertree inference. We ex-amined 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) boot-strap 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 superma-trix, 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. [Nonparametric bootstrapping; phylogenetics; supermatrix; supertree; supertree bootstrapping.] Large data sets derived from whole genomes or from sequence databases are becoming more commonplace in phylogenetic studies. Numerous phylogenetic anal-yses have used data sets that include sequences from more than 100 loci (e.g., Daubin et al., 2001; Baptest