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Bootstrap resampling of the data set revealed that estimates of variability and power were associated with considerable uncertainty.
Stress orientation uncertainty was estimated using 2000 bootstrap resampling of the entire data (Hardebeck and Michael, 2006).
Bootstrap resampling of the NJ and P trees (1,000 and 100 replicates, respectively) was performed to provide statistical confidence to the topologies inferred.
Parametric bootstrap resampling of the reference matrix yielded a 95% confidence interval range for λ of 0.990 to 1.012 with an average of 1.0008.
This result is also robust to the underlying sampling variance of the diversity estimates, because bootstrap resampling of the individual bases in the sequence data also demonstrates a significant correlation (median rs = −0.61; 95% CI: −0.87, −0.17).
A customized routine for bootstrap resampling of the sequence data was compiled using Absoft Pro Fortran 8.0 (Rochester Hills, MI). Individual bases in the sequence data were sampled with replacement, and the Spearman Rank Correlation (rs) was obtained from the standardized diversities (divided by FP) of the three northern samples (HI, IR, SB) against chromosomal position.
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As recommended by Preacher and Hayes [52], we set 95% as the value for the confidence interval and 5000 bootstrap resamples of the indirect effects.
These p-values for shifts in correlation were estimated using 20,000 bootstrap resamples of the raw data, at which point p-values were stable.
The analysis of 100 bootstrap resamples of the alignment data sets was performed using PHYLIP.
The strength of support for relationships was assessed by using 1,000 bootstrap resamples of the dataset.
Forty thousand bootstrap resamples of the discretized weights were obtained by randomly weighting each sample according to the Bayesian bootstrap distribution [ 62], and a high-scoring network was found for each resample using greedy hill-climbing with random restarts and the sparse candidate algorithm [ 63].
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