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

G T Lloyd,K E Davis,D W Bapst,M Friedman

doi:10.1098/rsbl.2016.0609

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.

Highlights

Divergence times are often estimated by combining fossil information with a phylogenetic hypothesis
In a classical clock-based ‘node-dating’ framework, a tree of extant taxa with branch lengths representing character changes is dated with reference to a set of fossil calibrations that constrain the minimum age for particular nodes
Divergence times were estimated for three nodes on the tree: (i) the origin of dinosaurs, (ii) the origin of Avialae and (iii) the origin of crown birds (Neornithes)

Summary

Introduction

Divergence times are often estimated by combining fossil information with a phylogenetic hypothesis. ‘tip-dating’ approaches have allowed extinct taxa to be included as terminals, with phylogenetic inference and divergence time estimation occurring simultaneously without reference to node calibrations. This opens up the possibility for using character change from molecular or morphological sources (or both) when estimating divergences between extinct and extant lineages, or even among entirely extinct lineages. Of these advancements, palaeontologists have been using stratigraphic ages to directly date divergences on existing phylogenies.

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