Response to Comment on "Hexapod Origins: Monophyletic or Paraphyletic?"

Open Access
Publisher Website
Google Scholar
Abstract
Despite the correct placement of the honeybee and louse, it is not clear that the Delsuc et al. method performs better generally. In fact, one might expect that reducing nucleotide sequence data set to only two states (R and Y) might exacerbate saturation at many sites, and be more susceptible to problems of nonstationarity of substitutions than an amino acid data set (8). In the latter, the model of substitution reflects the probability of a replacement to be fixed, and the use of 20-state characters decreases the possibility of overlooking convergence. The inference of phylogenies based on amino acid sequences is common practice and is generally accepted as among the most reliable of methods (8–10). Although the matrix of amino acid change used in the first of our two analyses was based on vertebrate sequences, it has been extensively used to study relationships among invertebrates with no reports of significant flaws (1, 6).