Trends in substitution models of molecular evolution.

Miguel Arenas

doi:10.3389/fgene.2015.00319

Abstract

Substitution models of evolution describe the process of genetic variation through fixed mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost 40 years after the development of first substitution models, highly sophisticated, and data-specific substitution models continue emerging with the aim of better mimicking real evolutionary processes. Here I describe current trends in substitution models of DNA, codon and amino acid sequence evolution, including advantages and pitfalls of the most popular models. The perspective concludes that despite the large number of currently available substitution models, further research is required for more realistic modeling, especially for DNA coding and amino acid data. Additionally, the development of more accurate complex models should be coupled with new implementations and improvements of methods and frameworks for substitution model selection and downstream evolutionary analysis.

Highlights

Substitution models of evolution describe the rates of change of fixed mutations among sequences and constitute the basis of the evolutionary analysis of genetic data at the molecular level
The first substitution models that corrected the effects of multiple replacements were documented a long time ago (Jukes and Cantor, 1969; Dayhoff et al, 1978; Kimura, 1980), they were not applied in evolutionary analysis until much later when they were implemented in phylogenetic software packages based on maximum-likelihood (ML) methods (Felsenstein, 1991; Swofford, 1993)
It was noted that substitution model misspecification might bias phylogenetic inferences (Posada and Crandall, 2001; Minin et al, 2003; Lemmon and Moriarty, 2004)

Summary

Introduction

Substitution models of evolution describe the rates of change of fixed mutations among sequences and constitute the basis of the evolutionary analysis of genetic data at the molecular level.

Results

Conclusion