Bootstrap Support Is Not First-Order Correct

The appropriate interpretation of bootstrap support for splits and the question of what constitutes large bootstrap support have received considerable attention. One desirable interpretation, indeed the interpretation that was put forward when bootstrap support for splits was first introduced, is that 1-minus bootstrap support is a P value for the hypothesis that the split is not well resolved. As a P value, bootstrap support has been argued to be first-order correct. By obtaining the limiting distribution of bootstrap support for a split when maximum likelihood estimation is conducted, it is shown that bootstrap support is not first-order correct and insight is provided into the nature of the problem. Borrowing from earlier results, it is also shown that similar results hold when the neighbor-joining algorithm is used. Examples suggest that bootstrap support is generally conservative as a P value and give insight as to why this is usually the case. The analysis indicates that the problem is largely due to the unusual nature of tree space where boundary trees always have at least 2 neighbors.