Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit

Area of Science:

• Paleontology and Evolutionary Biology
• Computational Phylogenetics

Background:

• Stratigraphic data integration into phylogenetic analysis is debated and not standard paleontological practice.
• Bayesian tip-dated (morphological clock) methods have reignited discussions on incorporating time-calibrated phylogenetics.

Purpose of the Study:

• To explore how tip-dating affects the recovery of evolutionary relationships compared to other phylogenetic methods.
• To investigate the influence of diversification dynamics on the tree model's preference for stratigraphic fit.

Main Methods:

• Analysis of multiple datasets using various phylogenetic methods, including parsimony, undated Bayesian, and Bayesian tip-dating.
• Evaluation of phylogenetic tree topologies using stratigraphic fit metrics: Gap Excess Ratio (GER) and Stratigraphic Completeness Index (SCI).
• Assessment of character signal strength by successive deletion of incomplete taxa.

Main Results:

• Tip-dated phylogenies show outlier topologies compared to parsimony and undated Bayesian methods.
• Tip-dating consistently yields trees with better stratigraphic fit (higher GER and SCI) due to the fossilized birth-death model.
• The model's preference for stratigraphic fit is modulated by diversification rates; low rates favor higher GER.
• Topological differences between methods are more pronounced in areas with weaker character data.

Conclusions:

• Tip-dating intuitively incorporates stratigraphic data, but strong character evidence can override stratigraphic fit preferences.
• The study highlights the complex interplay between stratigraphic data, character signal, and diversification dynamics in phylogenetic reconstruction.