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Related Experiment Video

Updated: May 10, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model.

Ian Roberts¹, Richard G Everitt^1,2, Jere Koskela^1,3

¹Department of Statistics, University of Warwick, Coventry, United Kingdom.

Plos Computational Biology

|April 21, 2025

Summary

This summary is machine-generated.

This study introduces StructCoalescent, an R package for analyzing pathogen migration history using the structured coalescent model. It efficiently infers population sizes and migration rates from genomic data, improving infectious disease epidemiology.

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Last Updated: May 10, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

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Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

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Published on: December 27, 2010

Area of Science:

Genomics
Epidemiology
Computational Biology

Background:

Pathogen genome sequencing is crucial for infectious disease epidemiology.
Phylogeographic analysis using the structured coalescent model is informative but computationally intensive for large datasets.

Purpose of the Study:

To develop an efficient method for Bayesian inference of pathogen migration history, population sizes, and migration rates.
To address the computational limitations of the exact structured coalescent model for large-scale genomic data.

Main Methods:

Utilized the exact structured coalescent model on precomputed dated phylogenies.
Developed an efficient reversible jump Markov Chain Monte Carlo (MCMC) scheme.
Implemented the method in a new R package called StructCoalescent.

Main Results:

Demonstrated the scalability and correctness of the StructCoalescent method using simulations.
Compared the performance of the new method with existing software.
Successfully applied the method to real pathogen genomic datasets.

Conclusions:

The StructCoalescent package provides an efficient and scalable solution for phylogeographic analysis of pathogen genomes.
The method is relevant for current data scales and research questions in infectious disease epidemiology.
Enables robust inference of migration history, population dynamics, and rates between geographical locations.