Tip dating with fossil sites and stratigraphic sequences

Area of Science:

• Evolutionary biology
• Paleontology
• Computational phylogenetics

Background:

• Tip dating is crucial for phylogenetic analysis, but current methods can decouple fossil ages from the same site.
• Existing uniform tip age priors lack the ability to link fossils from a single geological formation.

Purpose of the Study:

• To develop a novel MCMC proposal for tip dating that links fossil ages from the same site.
• To incorporate stratigraphic ordering and age bounds for fossil sites.
• To implement these methods in an open-source BEAST2 package called palaeo.

Main Methods:

• Developed a new MCMC proposal to link fossil ages from the same site, accounting for site age uncertainty.
• Extended the method to allow stratigraphic ordering of fossil sites with bounds on the sequence.
• Implemented the proposals in the palaeo package for BEAST2.
• Tested on early vertebrate fossils, specifically acanthodians from the MOTH and Turin Hill sites.

Main Results:

• Linked tip ages significantly increased the precision of age estimates compared to unlinked ages.
• The MOTH site was supported as being younger than the Turin Hill site.
• A minor impact on the phylogenetic tree topology of acanthodians was observed.

Conclusions:

• The new MCMC proposals enhance phylogenetic accuracy by linking fossil ages from the same site.
• This method improves age estimations in evolutionary studies, particularly for sites with multiple fossils.
• The palaeo package offers a valuable tool for researchers using tip dating with specimen-level data.