Tip dating with fossil sites and stratigraphic sequences.

Benedict King,Martin Rücklin

doi:10.7717/peerj.9368

Abstract

Tip dating, a method of phylogenetic analysis in which fossils are included as terminals and assigned an age, is becoming increasingly widely used in evolutionary studies. Current implementations of tip dating allow fossil ages to be assigned as a point estimate, or incorporate uncertainty through the use of uniform tip age priors. However, the use of tip age priors has the unwanted effect of decoupling the ages of fossils from the same fossil site. Here we introduce a new Markov Chain Monte Carlo (MCMC) proposal, which allows fossils from the same site to have linked ages, while still incorporating uncertainty in the age of the fossil site itself. We also include an extension, allowing fossil sites to be ordered in a stratigraphic column with age bounds applied only to the top and bottom of the sequence. These MCMC proposals are implemented in a new open-source BEAST2 package, palaeo. We test these new proposals on a dataset of early vertebrate fossils, concentrating on the effects on two sites with multiple acanthodian fossil taxa but wide age uncertainty, the Man On The Hill (MOTH) site from northern Canada, and the Turin Hill site from Scotland, both of Lochkovian (Early Devonian) age. The results show an increased precision of age estimates when fossils have linked tip ages compared to when ages are unlinked, and in this example leads to support for a younger age for the MOTH site compared with the Turin Hill site. There is also a minor effect on the tree topology of acanthodians. These new MCMC proposals should be widely applicable to studies that employ tip dating, particularly when the terminals are coded as individual specimens.

Highlights

Tip dating is increasingly used as a method to calibrate molecular phylogenies and to analyse phylogenies with fossil taxa (Gavryushkina et al, 2017; Lee et al, 2014; Ronquist et al, 2012)
We demonstrate the effect of the RelativeFossilSiteDateRandomWalker on taxa from the Devonian Red Bay Group from Spitzbergen, taxa from the older Fraenkelryggen and younger Ben Nevis formations (Fig. 1C)
The effective prior on age of the Fraenkelryggen Formation taxa was concentrated in the older part of the age uncertainty range, while the converse was true for the Ben Nevis Formation taxa

Summary

Introduction

Tip dating is increasingly used as a method to calibrate molecular phylogenies and to analyse phylogenies with fossil taxa (Gavryushkina et al, 2017; Lee et al, 2014; Ronquist et al, 2012). Central to tip dating are the ages given to the individual fossil taxa (or tips). Current implementations of tip dating only allow tip ages to vary independently from each other This has the undesired effect of separating the ages of fossil taxa from the same site. A striking example, from the empirical dataset used in this study, is the so-called ‘‘wonder block’’ from the Man On The Hill (MOTH) site from the Lochkovian (419.2–410.8 million years) of northern Canada (Hanke & Wilson, 2006) This single block contains the acanthodians Obtusacanthus, Brochoadmones and Lupopsyrus (Hanke & Wilson, 2006), but these fossils can be separated by millions of years in a tip-dated analysis in which age uncertainty is dealt with in the typical manner (King et al, 2017)

Methods

Results

Discussion

Conclusion