Interactions between phylogenetic trees and fossils when estimating evolutionary timescales

I explore the impact of extinct lineages and limited morphological character data on the expected delay between the origin time of a clade and the age of its oldest known fossil (the clade-fossil delay). The size of the clade-fossil delay, and variation in its size between clades, fundamentally impacts the extent to which the fossil record is informative about the ages of different clades. The clade-fossil delay is thus a crucial quantity when estimating the timing of branching events in phylogenetic trees (divergence time estimation). I show that both extinct lineages and limited morphological character data increase the clade-fossil delay, especially in datasets with few fossils, which is particularly common when estimating divergence times in flowering plants. Though linked to taphonomic biases, these results are distinct in that they are underpinned by interactions between extinct lineages, limited morphological data, and the nested structure of phylogenetic trees. I discuss the likely impacts of these findings on divergence time analyses and the evolutionary studies that depend on them, and suggest that both a fundamental re-appraisal of the purpose of divergence time estimation, alongside the development of new methods, is required.