Distance measures in terms of substitution processes

Area of Science:

• Computational Biology
• Evolutionary Biology
• Bioinformatics

Background:

• Phylogenetic reconstruction requires accurate distance measures.
• New methods like asynchronous, LogDet, and paralinear distances offer tree additivity.
• Mechanistic understanding of these evolutionary distances is limited.

Purpose of the Study:

• To review new phylogenetic distance measures within a unifying framework.
• To clarify the relationships among asynchronous, LogDet, and paralinear distances.
• To investigate the impact of rate variation on tree additivity.

Main Methods:

• Review of existing literature on phylogenetic distance measures.
• Analysis within the framework of continuous-time substitution processes.
• Examination of site-to-site rate variation in sequence evolution models.

Main Results:

• A unifying framework based on continuous-time substitution processes clarifies new distance measures.
• Site-to-site rate variation can be corrected for homogeneous, stationary, and time-reversible models if rate distribution is known.
• Non-stationary models with rate variation preclude tree-additive pairwise distance measures due to identical sequence pair distributions across different tree topologies.

Conclusions:

• The continuous-time substitution process provides a mechanistic interpretation for new phylogenetic distance measures.
• Correcting for rate variation is possible in some models but not in non-stationary ones.
• The limitations of existing distance measures under non-stationary models are highlighted, impacting phylogenetic tree accuracy.