Darlim etal_Supp_RSBL-2021-0603.zip from The impact of molecular data on the phylogenetic position of the putative oldest crown crocodilian and the age of the clade

The use of molecular data for living groups is vital for interpreting fossils, especially when morphology-only analyses retrieve problematic phylogenies for living forms. These topological discrepancies impact on the inferred phylogenetic position of many fossil taxa. In Crocodylia, morphology-based phylogenetic inferences differ fundamentally in placing <i>Gavialis</i> basal to all other living forms, whereas molecular data consistently unite it with crocodylids. The Cenomanian <i>Portugalosuchus azenhae</i> was recently described as the oldest crown crocodilian, with affinities to <i>Gavialis</i>, based on morphology-only analyses, thus representing a potentially important new molecular clock calibration<i>.</i> Here, we performed analyses incorporating DNA data into these morphological datasets, using scaffold and supermatrix (total evidence) approaches, in order to evaluate the position of basal crocodylians including <i>Portugalosuchus</i>. Our analyses incorporating DNA data robustly recovered <i>Portugalosuchus</i> outside Crocodylia (as well as thoracosaurs, planocraniids and <i>Borealosuchus</i> spp.), questioning the status of <i>Portugalosuchus</i> as crown crocodilian and any future use as a node calibration in molecular clock studies. Finally, we discuss how, with the increasing size of phylogenomic datasets, the molecular scaffold might be an efficient (though imperfect) approximation of more rigorous but demanding supermatrix analyses.