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Updated: Aug 29, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

Phylogenetic Analysis That Models Compositional Heterogeneity over the Tree.

Peter G Foster¹

¹Department of Life Sciences, Natural History Museum, London, UK.

Methods in Molecular Biology (Clifton, N.J.)

|September 9, 2022

Summary

This summary is machine-generated.

Phylogenetic models can be improved to account for evolutionary changes. The new Node-Discrete Compositional Heterogeneity (NDCH2) model better fits evolutionary data and improves tree accuracy.

Keywords:

Bayesian MCMC Compositional heterogeneity Marginal likelihood Maximum likelihood Model adequacy Model fit Models of evolution Non-homogeneous Non-stationary Phylogenetics Posterior predictive simulation

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Last Updated: Aug 29, 2025

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

Evolutionary biology
Computational biology
Phylogenetics

Background:

Molecular sequence composition varies, indicating evolutionary change over time.
Standard phylogenetic models assume compositional homogeneity, leading to inaccuracies with heterogeneous data.
Existing models struggle to capture compositional variations across evolutionary trees.

Purpose of the Study:

To introduce and evaluate the Node-Discrete Compositional Heterogeneity (NDCH) model for phylogenetic analysis.
To address limitations of existing models in handling compositionally heterogeneous datasets.
To present an improved model, NDCH2, for more accurate phylogenetic inference.

Main Methods:

Development and application of the NDCH and NDCH2 models.
Phylogenetic analysis using bacterial SSU rRNA datasets.
Implementation of models within the P4 software package.

Main Results:

The NDCH model accommodates compositional differences across phylogenetic trees.
The NDCH2 model offers improvements over NDCH, addressing its limitations.
Both models significantly enhance model-to-data fit and improve tree topology accuracy.

Conclusions:

Compositional heterogeneity is crucial in phylogenetic analyses.
The NDCH and NDCH2 models provide more accurate phylogenetic reconstructions.
These models and associated software enhance the analysis of evolutionary processes.