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Updated: Oct 2, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference.

Remco R Bouckaert¹

¹School of Computer Science, University of Auckland, Thomas Building, Room 407 3 Symonds St Auckland 1010 New Zealand.

Systematic Biology

|February 25, 2022

Summary

This summary is machine-generated.

We introduce Bayesian Integrated Coalescent Epoch PlotS (BICEPS), a novel method for coalescent model inference. BICEPS enables accurate demographic reconstruction and analysis of population size changes, outperforming traditional models.

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Area of Science:

Evolutionary biology
Computational phylogenetics
Population genetics

Background:

Coalescent models are fundamental for inferring population histories from genetic data.
Existing methods like the Bayesian skyline model have limitations in efficiently inferring demographic parameters.
Accurate demographic reconstruction is crucial for understanding population dynamics, bottlenecks, and evolutionary trajectories.

Purpose of the Study:

To develop an efficient inference method for coalescent epoch models.
To improve the accuracy and convergence of demographic inference, especially for complex population histories.
To provide a more powerful alternative to existing Bayesian phylogenetic models.

Main Methods:

Integration of population size parameters to simplify model inference.
Development of advanced Markov chain Monte Carlo (MCMC) proposals for enhanced tree sampling.
Application of the Bayesian Integrated Coalescent Epoch PlotS (BICEPS) framework within the BEAST 2 software.

Main Results:

BICEPS successfully integrates out population size parameters while still enabling posterior sampling.
The method allows for detailed demographic reconstruction, including bottlenecks and full population histories.
Simulations confirm the power and correctness of BICEPS, showing improved performance over standard methods.
Application to SARS-CoV-2 genomic data demonstrates BICEPS's ability to handle analyses that challenge traditional approaches.

Conclusions:

BICEPS offers a more robust and efficient approach to Bayesian phylogenetic inference of demographic history.
The method enhances the analysis of population dynamics and evolutionary processes.
BICEPS is available as an open-source package for BEAST 2, featuring a user-friendly interface.