How to date a molecular phylogeny: Comparison of effective priors between node calibration and FBD

Time-calibrating a phylogenetic tree is a fundamental step in phylogenetic inference, as it allows the study of macroevolutionary processes such as lineage diversification, trait evolution, and historical biogeography. To this end, the fossilized-birth-death (FBD) process, a stochastic process that coherently integrates fossils into phylogenies, is increasingly used as an alternative to traditional ad hoc node-calibration densities. However, the effective prior distribution on node ages induced by the FBD has never been investigated before, hindering an informed choice between the two approaches. Here, we analyze two empirical datasets (crocodylians and fireflies) by applying several models of time-calibration, including traditional node calibrations and FBD. We show that the effective node age priors induced by the FBD process in the absence of morphological data are comparable to those induced by uniform node calibrations with minimum equal to the age of the calibrating foss..., , # Data from: How to date a molecular phylogeny: Comparison of effective priors between node calibration and FBD

Dataset DOI: [10.5061/dryad.0rxwdbsfj](https://doi.org/10.5061/dryad.0rxwdbsfj)

## Description of the data and file structure

This compressed file archive contains all data and scripts used in the study, as well as scripts to plot figures and tables with results (effective priors and posterior node ages for the Crocodylia and Lampyridae analyses).

### Files and variables

#### File: SupplementaryMaterial.zip

**Description:** 

`data` folder: contains data files used for the study

* `crocs` subfolder: Contains all aligned molecular sequences used for the phylogenetic analysis of Crocodylia, in fasta format.
* `crocs_extant.tre`: Tree topology of extant Crocodylia in nexus format, used as constraint for the node calibration analyses.
* `crocs_fossil.tre`: Tree topology of extant + calibrating fossil Crocodylia in nexus format, used as constraint for the FBD analyses.
* `cr..., ,