Unringing a bell: metazoan phylogenomics and the partition bootstrap

Several large phylogenomic analyses have recently cast doubt on long-held beliefs about early metazoan phylogenetic patterns. Those data sets, and the relative bootstrap support for various controversial clades, are reanalysed in the context of parsimony, yielding results that are at considerable odds with the original likelihood or Bayesian findings. Discrepancies are considered in light of the tendency of RAxML to overestimate support values by virtue (sic) of its lazy search algorithm and its autocorrelated pseudoreplication as well as the extraordinary ability for Bayesian analyses to be led astray by missing data. In addition to standard nonparametric bootstrapping as a measure of support, a new strategy involving resampling loci as units, partition bootstrap support, is introduced as a more defensible alternative to resampling nonindependent sites.