3/12/2023 0 Comments Gtr evolution modelThis perspective provides an overview on the trends of substitution models of DNA, codon and amino acid evolution, including goals, and pitfalls of well-established substitution models. Nevertheless, recent studies suggest that there is still room for improving the commonly used substitution models (e.g., Keane et al., 2006). A large number of substitution models exist and new models are emerging to mimic the evolution of particularly complex real datasets. Nowadays, substitution models are routinely used in diverse areas of evolutionary biology. As a consequence, the selection of the best-fit substitution model became an essential stage in the pipeline of phylogenetic inference ( Posada and Crandall, 1998, 2001), which also increased the popularity of substitution models in phylogenetics. Then, it was noted that substitution model misspecification might bias phylogenetic inferences ( Posada and Crandall, 2001 Minin et al., 2003 Lemmon and Moriarty, 2004). Although, 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). 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. 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. 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. 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. 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. 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. Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.
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