4/12/2024 0 Comments Gtr model of dna evolutionĪ variety of nucleotide substitution models have been devised, most of which are special cases of the general time-reversible (GTR) model in which each of the six pairwise nucleotide changes can have a distinct rate, and the frequencies of the four nucleotides are allowed to take different values. This is an increasingly important concern in the modern genomic era, with the growing use of multiple loci that have probably been subject to different substitution processes. The assumed model of nucleotide substitution can exert a significant influence on phylogenetic estimation. Although the models are simplifications of the "true" evolutionary processes and are clearly wrong, they are approximations that have been widely accepted. For DNA sequences, the models are the evolutionary characterisation of one nucleotide being replaced by another one. Both methods are based on the likelihood function, which needs explicit models of evolution to capture the underlying evolutionary processes in sequence data. Together with model-adequacy tests, accurate model selection will serve to improve the reliability of phylogenetic inference and related analyses.Īmong the rigorous methods of tree reconstruction that are available, maximum likelihood (ML) and Bayesian inference (BI) have dominated phylogenetic studies in recent years. Our results indicate that the Bayesian information criterion and decision theory should be preferred for model selection. The hierarchical likelihood-ratio test performed poorly when the true model included a proportion of invariable sites, while the Bayesian information criterion and decision theory generally exhibited similar performance to each other. Such dissimilarity was the highest between the hierarchical likelihood-ratio test and Akaike information criterion, and lowest between the Bayesian information criterion and decision theory. Our results also indicate that in some situations different models are selected by different criteria for the same dataset. We demonstrate that the Bayesian information criterion and decision theory are the most appropriate model-selection criteria because of their high accuracy and precision. To better understand the performance of different model-selection criteria, we used 33,600 simulated data sets to analyse the accuracy, precision, dissimilarity, and biases of the hierarchical likelihood-ratio test, Akaike information criterion, Bayesian information criterion, and decision theory. Appropriate selection of nucleotide substitution models is important because the use of incorrect models can mislead phylogenetic inference. Explicit evolutionary models are required in maximum-likelihood and Bayesian inference, the two methods that are overwhelmingly used in phylogenetic studies of DNA sequence data.
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