Selection of evolutionary models for phylogenetic hypothesis testing usingparametric methods

Recent molecular studies have incorporated the parametric bootstrap method to test a priori hypotheses when the results of molecular based phylogenies are in conflict with these hypotheses. The parametric bootstrap requires t he specification of a particular substitutional model, the parameters of wh ich will be used to generate simulated, replicate DNA sequence data sets. I t has been both suggested that, (a) the method appears robust to changes in the model of evolution, and alternatively that, (b) as realistic model of DNA substitution as possible should be used to avoid false rejection of a n ull hypothesis. Here we empirically evaluate the effect of suboptimal subst itution models when testing hypotheses of monophyly with the parametric boo tstrap using data sets of mtDNA cytochrome oxidase I and II (COI and COII) sequences for Macaronesian Calathus beetles, and mitochondrial 16S rDNA and nuclear ITS2 sequences for European Timarcha beetles. Whether a particular hypothesis of monophyly is rejected or accepted appears to be highly depen dent on whether the nucleotide substitution model being used is optimal. It appears that a parameter rich model is either equally or less likely to re ject a hypothesis of monophyly where the optimal model is unknown. A compar ison of the performance of the Kishino-Hasegawa (KH) test shows it is not a s severely affected by the use of suboptimal models, and overall it appears to be a less conservative method with a higher rate of failure to reject n ull hypotheses.