Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites

Area of Science:

• Computational Biology
• Molecular Evolution
• Phylogenetics

Background:

• Felsenstein's maximum-likelihood method is a standard for DNA phylogeny inference.
• This method assumes constant nucleotide substitution rates across sites, which is often biologically unrealistic.
• Real sequence data analysis reveals significant variation in substitution rates among sites.

Purpose of the Study:

• To extend Felsenstein's maximum-likelihood phylogeny inference method.
• To incorporate variation in nucleotide substitution rates across sites.
• To improve the accuracy of phylogenetic reconstruction from DNA sequences.

Main Methods:

• The study extends Felsenstein's maximum-likelihood approach.
• It incorporates the gamma distribution to model rate variation across nucleotide sites.
• Numerical examples are used for demonstration and comparison.

Main Results:

• The extended method explicitly models rate heterogeneity across sites.
• A numerical example demonstrates the improved fit of the gamma distribution model.
• The proposed method shows better data fit compared to models with constant rates.

Conclusions:

• The gamma distribution effectively models rate variation across sites in DNA sequence evolution.
• The extended maximum-likelihood method provides a more realistic and accurate approach to phylogeny inference.
• This work offers an improved tool for analyzing molecular evolution and constructing phylogenetic trees.