Estimating Divergence Times and Diversification Rates with the Unresolved Fossilized Birth-Death Process

Using Fossilized Birth-Death (FBD) models for tip-dating analyses provides an advantageous alternative to traditional node-dating methods in phylogenetic studies. However, their widespread adoption has been hindered by the challenges of gathering morphological data and the computational complexity when dealing with numerous fossils.

Recent research suggests that FBD models can serve as effective priors for molecular clock analyses, even in situations where morphological data are absent, as long as temporal information and clade assignments are available. Heath et al. (2014) presented an unresolved FBD model that incorporates uncertainty in fossil placements analytically, eliminating the need for morphological data.

This study reveals a flaw in the topological enumeration approach employed by Heath et al. (2014) to account for unresolved fossil attachments, which leads to an overestimation of configurations involving multiple fossil taxa resolving into a single clade. By providing a correction to this factor, a valid marginalized unresolved likelihood can be derived.

The implementation of this corrected method is demonstrated using empirical datasets of Cetacea, Emydidae, and Palaeodictyopterida, showcasing its ability to converge and produce reasonable estimates efficiently, even when hundreds of fossils are involved.