What time is it? Interactions between trees and fossils

Molecular sequence data is not in itself informative about absolute evolutionary timescales. Fossils are therefore often analysed alongside molecular data in order to generate time-scaled reconstructions of the tree-of-life. Here, I analyse interactions between fossils and molecular based reconstructions of the tree-of-life, and explore the implications of these interactions for time-scaling the tree of life. I use simulations to explore two types of interaction: the extinct lineage effect and the character evolution effect. The extinct lineage effect describes the effect of extinct lineages on the expected delay between the origin of a clade and the age of its oldest known fossil. Meanwhile, the character evolution effect explores the impact of limited morphological character data on the lengths of this delay. Both of these effects can significantly distort the relationship between the age of clades and the origin of their oldest fossils, especially in datasets with many species. These impacts are entirely distinct from taphonomic biases often discussed in the context of the fossil record. I discuss the implications of these effects for divergence time estimation, highlighting that they are likely to impact methods that rely on both node and tip-calibration. This further suggests that both a fundamental re-appraisal of the purpose of divergence time estimation, alongside the development of new methods, is required.