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95% confidence intervals of mean of r2 and |D'| were constructed for each bin by a bootstrap analyses [ 24]. 1,000 samples of the same size as the original sample were randomly sampled with replacement for each bin.
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The confidence values of the internal nodes were calculated by performing bootstrap analyses with 1,000 replicates.
Robustness of resulting topologies was examined by using bootstrap analyses (10 ).
For all analyses involving brood size, reported P-values were obtained from percentiles of the bootstrap distributions generated by the bootstrap analyses described above.
In case of severely skewed distribution of cost variables, we will check the robustness of results by applying transformations or by performing bootstrap analyses.
The significance of the included covariates was further supported by the bootstrap analyses, as none of the 95% CIs for the covariate effects included zero.
This was also substantiated by the bootstrap analyses in which four of the six mutations remaining in the final genotypic score had been selected in over 95% of the bootstrap samples.
The timing of the transfer of the priS gene is more difficult to pinpoint since the separation of the Entamoeba and Mastigamoeba sequences is only weakly supported by the bootstrap analyses.
Thus, on one hand, branches used to establish the proteins that belong to a subfamily must be significantly supported by bootstrap analyses.
A fast-evolving position removal series followed by rapid ML bootstrap analyses was repeated on the 157-protein data set without the 12 long-branched taxa.
Relative support of internal nodes was performed by bootstrap analyses with 1,000 replications (MP, NJ), or by the quartet puzzling support values on the basis of 1,000 puzzling steps (ML).
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