Tree shape-based approaches for the comparative study of cophylogeny.

Area of Science:

• Evolutionary Biology
• Phylogenetics
• Coevolutionary Studies

Background:

• Cophylogeny describes congruent evolutionary relationships between interacting species.
• Quantifying the degree of cophylogeny is crucial for understanding coevolutionary dynamics.

Purpose of the Study:

• To investigate and evaluate tree shape distance measures for quantifying cophylogeny.
• To develop novel kernel distance measures for labeled and unlabeled trees.

Main Methods:

• Implemented a reverse-time simulation model of pathogen phylogenies within a host tree.
• Evaluated 18 distance measures, including two newly developed kernel distances, using simulated and real datasets.
• Assessed measures based on cospeciation probability, host switching, and pathogen speciation rates.

Main Results:

• Certain distance measures proved more informative for specific coevolutionary parameters, particularly non-extreme values.
• Analysis of real datasets showed clustering of studies with high concordance, indicating consistent interpretation.
• The developed kernel distances accommodate branch lengths and varying tree sizes.

Conclusions:

• Tree shape distance measures are valuable tools for quantifying cophylogeny.
• Findings support the use of these measures in coevolution research.
• Results encourage the development of simulation-based methods for estimating coevolutionary parameters.