Data from: Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record

Simultaneously analysing morphological, molecular and stratigraphic data
suggests a potential resolution to a major remaining inconsistency in
crocodylian evolution. The ancient, long-snouted thoracosaurs have always
been placed near the Indian gharial Gavialis, but their antiquity (ca 72
Ma) is highly incongruous with genomic evidence for the young age of the
Gavialis lineage (ca 40 Ma). We reconcile this contradiction with an
updated morphological dataset and novel analysis, and demonstrate that
thoracosaurs are an ancient iteration of long-snouted stem crocodylians
unrelated to modern gharials. The extensive similarities between
thoracosaurs and Gavialis are shown to be an almost ‘perfect storm’ of
homoplasy, combining convergent adaptions to fish-eating, as well
resemblances between genuinely primitive traits (thoracosaurs) and
atavisms (Gavialis). Phylogenetic methods that ignore stratigraphy
(parsimony and undated Bayesian methods) are unable to tease apart these
similarities and invariably unite thoracosaurs and Gavialis. However,
tip-dated Bayesian approaches additionally consider the large temporal gap
separating ancient (thoracosaurs) and modern (Gavialis) iterations of
similar long-snouted crocodyliforms. These analyses robustly favour a
phylogeny which places thoracosaurs basal to crocodylians, far removed
from modern gharials, which accordingly are a very young radiation. This
phylogenetic uncoupling of ancient and modern gharial-like crocs is more
consistent with molecular clock divergence estimates, and also the bulk of
the crocodylian fossil record (e.g. all unequivocal gharial fossils are
very young). Provided that the priors and models attribute appropriate
relative weights to the morphological and stratigraphic signals—an issue
that requires investigation—tip-dating approaches are potentially better
able to detect homoplasy and improve inferences about phylogenetic
relationships, character evolution and divergence dates.