Diversity, disparity, and evolutionary rate estimation for unresolved Yule trees

Area of Science:

• Evolutionary Biology
• Macroevolutionary Studies
• Phylogenetics

Background:

• Biological evolution's branching structure creates statistical dependencies in phenotypic traits among related organisms.
• Comparative macroevolutionary studies typically rely on inferred phylogenetic trees, but these trees introduce statistical uncertainty.
• Phylogenetic trees are often treated as nuisance parameters, complicating rate estimations.

Purpose of the Study:

• To develop a framework for analytically integrating over unknown phylogenetic trees in comparative evolutionary studies.
• To address the statistical uncertainty introduced by phylogenetic trees in macroevolutionary analyses.
• To enable rate estimation without requiring a fixed phylogenetic tree.

Main Methods:

• Developed a framework assuming phylogenetic trees arise from a Yule process (a continuous-time Markov branching model).
• Derived a closed-form expression for the distribution of phylogenetic diversity (PD).
• Generalized PD to represent expected trait disparity under a Yule process with Brownian motion trait evolution.

Main Results:

• Derived expressions for the distribution of expected trait disparity under a Yule tree.
• Enabled fast, likelihood-based estimation of Brownian variance for unresolved clades using trait disparity observations.
• Demonstrated a method that bypasses the need for simulation or a fixed phylogenetic tree.

Conclusions:

• The presented framework analytically integrates over unknown phylogenetic trees, simplifying comparative evolutionary studies.
• The method allows for efficient estimation of evolutionary rates even with unresolved phylogenetic relationships.
• This approach offers a significant advancement for macroevolutionary research, reducing reliance on fixed phylogenetic trees.