A new test of phylogenetic model fitness addresses the issue of the basal angiosperm phylogeny

We readdress the issue of phylogeny of the basal extant angiosperms employing a source previously not systematically investigated, specifically, the non-coding sequences of cpDNA. Comparison of trees with and without grasses or the outgroup (Pinus) in our analyses revealed no rearrangements in tree topology that might be expected if LBA were distorting the position of the magnoliids. For each model applied, irrespective of whether monocots or ANITA members appeared basally divergent, the orchid Phalaenopsis assumed the same position on the trees with the reduced taxon set as did the branch bearing the orchid plus the grasses in the full alignment. However, our new test of model fitness revealed a different flaw influencing the placement of monocots, which is related to model mis-specification. This flaw similarly affects the full alignment and the alignment with grasses removed. In both cases the models favouring a relatively derived position for the monocots and basal placement of the branch of Amborella plus Nymphaea provide better overall prediction of the observed data structure. In the view of apparent unsuitability of the bootstrap method for large data sets, our novel test provides a new means of exploring conflicts caused by systematic errors in phylogenetic analyses.