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A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution.

Mandev S Gill¹, Lam Si Tung Ho², Guy Baele³

¹Department of Statistics, Columbia University, New York, NY 10027, USA.

Systematic Biology

|November 1, 2016

Summary

This summary is machine-generated.

We introduce a new model for trait evolution on phylogenetic trees, improving upon standard Brownian diffusion. This relaxed directional random walk (RDRW) model offers more detailed insights into viral evolution and phylogeography.

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Published on: August 14, 2018

Area of Science:

Statistical Phylogenetics
Computational Biology
Evolutionary Biology

Background:

Understanding quantitative measurements in molecular sequence data is crucial for phylogenetics.
Brownian diffusion is a common but restrictive model for trait evolution on phylogenetic trees.
Existing models may not accurately capture complex evolutionary processes.

Purpose of the Study:

To develop a more flexible model for multivariate continuous trait evolution on phylogenetic trees.
To relax the restrictions of standard Brownian diffusion by incorporating estimable means and branch-specific trends.
To enable scalable analysis of large datasets in phylogenetics and comparative studies.

Main Methods:

Introduction of the relaxed directional random walk (RDRW) model.
Development of a computationally efficient dynamic programming approach for likelihood computation.
Implementation within a Bayesian inference framework for simultaneous reconstruction of molecular and trait data.
Visualization tools for evolutionary reconstructions.

Main Results:

The RDRW model accommodates branch-specific directional trends while maintaining identifiability.
The method scales efficiently to large datasets.
Application to HIV-1 spatiotemporal spread revealed clearer viral dispersal dynamics.
Analysis of HIV-1 antigenic evolution showed a drift towards increased resistance to VRC01 broadly neutralizing antibody.

Conclusions:

The RDRW model provides a more accurate and detailed understanding of trait evolution compared to standard Brownian diffusion.
This new model enhances the study of phylodynamics, phylogeography, and comparative genomics.
The RDRW model has significant utility in analyzing viral evolution and disease dynamics.