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
Gavialis basal to all other living forms, whereas molecular data
consistently unite it with crocodylids. The Cenomanian Portugalosuchus
azenhae was recently described as the oldest crown crocodilian, with
affinities to Gavialis, based on morphology-only analyses, thus
representing a potentially important new molecular clock calibration. 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
Portugalosuchus. Our analyses incorporating DNA data robustly recovered
Portugalosuchus outside Crocodylia (as well as thoracosaurs, planocraniids
and Borealosuchus spp.), questioning the status of Portugalosuchus a 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.