Probabilistic divergence time estimation without branch lengths: dating the origins of dinosaurs, avian flight and crown birds

Abstract

Branch lengths-measured in character changes-are an essential requirement of clock-based divergence estimation, regardless of whether the fossil calibrations used represent nodes or tips. However, a separate set of divergence time approaches are typically used to date palaeontological trees, which may lack such branch lengths. Among these methods, sophisticated probabilistic approaches have recently emerged, in contrast with simpler algorithms relying on minimum node ages. Here, using a novel phylogenetic hypothesis for Mesozoic dinosaurs, we apply two such approaches to estimate divergence times for: (i) Dinosauria, (ii) Avialae (the earliest birds) and (iii) Neornithes (crown birds). We find: (i) the plausibility of a Permian origin for dinosaurs to be dependent on whether Nyasasaurus is the oldest dinosaur, (ii) a Middle to Late Jurassic origin of avian flight regardless of whether Archaeopteryx or Aurornis is considered the first bird and (iii) a Late Cretaceous origin for Neornithes that is broadly congruent with other node- and tip-dating estimates. Demonstrating the feasibility of probabilistic time-scaling further opens up divergence estimation to the rich histories of extinct biodiversity in the fossil record, even in the absence of detailed character data.

Keywords: birds; dinosaurs; divergence time; phylogeny.

Figure 1.

Comparison of probabilistic APT dates (red bars, cal3; blue bars, Hedman; see the text) for key nodes in dinosaur phylogeny: Dinosauria I (Nyasasaurus as sister to Dinosauria), Dinosauria II (Nyasasaurus nested within Dinosauria), Avialae I (Archaeopteryx as first bird), Avialae II (Aurornis as first bird) and Neornithes (crown birds). Asterisks mark minimum bound or ‘traditional’ palaeontological estimate. Molecular and morphological clock dates for Neornithes are shown in the lower right corner (A–J; electronic supplementary material, table S3): circles indicate mean and horizontal bars the 95% HPD. Silhouettes were taken from public domain images on phylopic.org (Aurornis, Gareth Monger; Eoraptor, Scott Hartman; Vegavis, Matt Martyniuk), or modified with kind permission from works by Sergio Pérez (Archaeopteryx) and Nobu Tamura (Nyasasaurus).