Integrating Fossil Preservation Biases in the Selection of Calibrations for Molecular Divergence Time Estimation

Abstract

The selection of fossil data to use as calibration age priors in molecular divergence time estimates inherently links neontological methods with paleontological theory. However, few neontological studies have taken into account the possibility of a taphonomic bias in the fossil record when developing approaches to fossil calibration selection. The Sppil-Rongis effect may bias the first appearance of a lineage toward the recent causing most objective calibration selection approaches to erroneously exclude appropriate calibrations or to incorporate multiple calibrations that are too young to accurately represent the divergence times of target lineages. Using turtles as a case study, we develop a Bayesian extension to the fossil selection approach developed by Marshall (2008. A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibrations points. Am. Nat. 171:726-742) that takes into account this taphonomic bias. Our method has the advantage of identifying calibrations that may bias age estimates to be too recent while incorporating uncertainty in phylogenetic parameter estimates such as tree topology and branch lengths. Additionally, this method is easily adapted to assess the consistency of potential calibrations to any one calibration in the candidate pool.

Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts

“…Statistical rate analyses identified two increasing shifts in the moss and liverwort phylogenies. The average timing of those shifts was highly congruent across the three increasingly conservative prior calibrations employed to model fossil age uncertainty, confirming that increasing the width of the prior used for fossil age calibration has very little effect on the median or average age estimates but increases the confidence intervals surrounding each age estimate 27,28 . Liverworts exhibited an earlier shift than mosses, with an average dating back to the mid-Jurassic.…”

Hemisphere-scale differences in conifer evolutionary dynamics

“…The discrepancy in age estimates most likely results from differences in the implementation of prior age distributions, because both studies used a similar set of fossils as minimum age constraints. Mao et al (24) generally used extremely wide uniform priors on age distributions associated with each fossil, potentially biasing posterior densities toward older divergence ages (25). Our conservative use of fossils as stem taxa with narrower lognormal prior age distributions potentially may bias estimates toward younger ages, but the marked relative differences between Northern and Southern Hemisphere clades that are the primary focus of this study remain unaffected.…”

A timeline for terrestrialization: consequences for the carbon cycle in the Palaeozoic

“…In conclusion, the application of these new methods addresses some of the known limitations of the molecular clock-based approach. Better estimates are likely to be achieved through a comprehensive synthesis of genomic evidence and data from the fossil record, but this integration will need to address issues such as conflicting information between different fossils and alternative assignments of fossil material depending on whether taxonomic interpretations or character evolution are considered [100,101].…”