Inferences from tip-calibrated phylogenies: a review and a practical guide

Area of Science:

• Evolutionary Biology
• Computational Biology
• Genomics

Background:

• Molecular dating estimates evolutionary event timing using sequence data.
• Traditional methods rely on fossil or biogeographical calibration points.
• Fast-evolving genomes and ancient DNA enable new calibration approaches.

Purpose of the Study:

• To review the state-of-the-art in tip-dating phylogenetic trees.
• To discuss recent applications and common pitfalls of tip-dating.
• To provide a practical guide for performing tip-dating analyses.

Main Methods:

• Tip-dating calibrates phylogenetic trees using sampling dates of sequences (terminal nodes).
• Leverages genomic data, including ancient DNA, for calibration.
• Employs statistical models to handle evolutionary heterogeneity and large datasets.

Main Results:

• Tip-dating extends molecular clock analyses to taxa with sparse fossil records.
• Enables inferences on divergence times, substitution rates, and past demography.
• Applicable across diverse taxa and spatiotemporal scales.

Conclusions:

• Tip-dating is a powerful and increasingly versatile method for molecular clock inference.
• Advances in statistical modeling and data availability enhance its utility.
• Careful application is crucial to avoid common pitfalls in phylogenetic analysis.