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Full sensitivity analyses will be conducted with bootstrapping to provide confidence intervals around cost and effect estimates and to produce cost acceptability curves.
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All runs were conducted with 100 bootstrap replicates, and majority-rule consensus trees with bootstrap branch support were calculated by PHYML.
A rapid bootstrap analysis and search for the best-scoring ML tree was conducted with 1,000 bootstrap replicates.
The statistical analysis of the trees was conducted with the bootstrap test (1,000 replicates).
A single run was conducted with 1000 bootstrap replicates followed by a full maximum likelihood search, using the partitioned data with the GTR+G+I model selected for each partition and the Oregon Cave sample selected as an out-group.
We conducted fast bootstrapping with 100 replicates as described above, and the resulting best-scoring ML tree was considered as the constrained ML tree.
Bootstrapping was conducted with the "resample" command, using 100 bootstrap replicates.
Mean cost comparisons were conducted with paired t-tests and bootstrapping methods.
Bootstrapping was conducted with 1000 replicates with 10 random taxon additions and heuristic research options.
Bootstrapping was conducted with 1,000 replicates.
Parsimony bootstrapping was conducted with 1000 replicates and NNI branch swapping.
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