The Evolutionary Trends in Substitution Models: A Review

Substitution models have become a fundamental tool in evolutionary biology, particularly in phylogenetics. These models describe the rates of change of fixed mutations among sequences and provide the basis for the analysis of genetic data at the molecular level. Over the years, numerous substitution models have been developed to mimic the evolution of complex real datasets. In this article, we will review the current trends in substitution models of DNA, codon, and amino acid sequence evolution, including their advantages and pitfalls.

The early days of substitution models saw the development of simple models that corrected for multiple replacements. However, these models were not widely applied until much later when they were implemented in phylogenetic software packages based on maximum-likelihood (ML) methods. Today, a large number of substitution models exist, and new ones are emerging to better mimic real evolutionary processes.

One of the most well-established substitution models is the General Time Reversible (GTR) model. This model assumes that the rates of substitution are constant across all sites in a sequence. The GTR model has been widely used in phylogenetic inference due to its ability to accurately reconstruct evolutionary relationships among organisms. However, recent studies have suggested that there may be room for improving this model, particularly for DNA coding and amino acid data.

The development of more accurate complex models is essential for evolutionary analysis. This requires coupling new implementations with improvements in methods and frameworks for substitution model selection and downstream evolutionary analysis. Despite the large number of currently available substitution models, further research is required to achieve more realistic modeling, especially for DNA coding and amino acid data.

In conclusion, substitution models have come a long way since their inception. From simple models that corrected for multiple replacements to complex models that mimic real evolutionary processes, these models have become an essential tool in evolutionary biology. As new models emerge, it is crucial to evaluate their performance and identify areas where improvement is needed. Ultimately, the goal of substitution modeling is to provide a more accurate representation of evolutionary processes, enabling us to better understand the history of life on Earth.

Gtr model of evolution