Amino acid dating ppt
Following the seminal works of Muse and Gaut (1) and Goldman and Yang (2), most early applications of codon-based evolutionary models were focused on evaluations of selective effects operating at different positions along a gene or at different time points along the phylogeny (see refs. Many of these approaches have modeled selective effects using a parameter representing the nonsynonymous/synonymous rate ratio.However, this may not be ideal, in particular because it amounts to ignoring differences between different pairs of possible amino acid replacements resulting from nonsynonymous point mutations.Although the Halpern and Bruno framework has attractive features, their model has hardly been used since (but see ref. Reasons for this hiatus include the fact that a large number of sequences are required to reliably infer site-specific amino acid fitness parameters and that such site-specific codon substitution models are computationally highly demanding.Meanwhile, working with models that operate at the amino acid level, several studies have shown that maximally heterogeneous parameterizations may be unreliable, and that a more reasonable balance between this and homogeneous parameterizations is required (e.g., refs. In particular, using mixture models to capture across-site heterogeneities in amino acid propensities in the context of profile HMMs (15), or of protein phylogenomics (11, 16, 17), has generally been found to give an improved model fit over either of these extremes (e.g., refs. Furthermore, algorithmic developments for performing the needed probability calculations [relying on data-augmentation-based Markov chain Monte Carlo (MCMC) sampling] have recently allowed for richer substitution models to become tractable (e.g., refs. Here, we integrate recent developments from previous works to explore a nonparametric approach previously used for amino acid level modeling (11, 16) within the mutation-selection codon substitution modeling framework.Using a posterior predictive simulation diagnostic, we further show that the modeling approaches capture global features of selection, and, using Bayes factors, that they lead to a significant improvement in statistical fit.We propose the framework as a reference mutation-selection model, and discuss further developments and applications that it could enable, contributing to a merger of phylogenetics and population genetics. The GTR model is given by two sets of parameters: six parameters (five effective degrees of freedom) governing the exchangeability of each (unordered) pair of nucleotides, as well as four global nucleotide propensity parameters (three effective degrees of freedom, for a total of 5 3 = 8 parameters).
We combine MCMC methods for the Dirichlet process with MCMC update operators on mutational parameters, branch lengths, hyperparameters (although using a fixed tree topology), embedded within a data-augmentation-based system (20, 24), giving us the means to sample from the overall joint posterior distribution.In recent years, questions regarding selective effects have diversified, such as in the work of Yang and Nielsen (5), who propose a test for selection on codon usage.This test is based on models that invoke a multidimensional specification of scaled selection coefficients, based on either 20 or 61 (under the universal genetic code) scaled fitness parameters—adding 19 or 60 degrees of freedom to the underlying codon substitution model—in contrast with the more conventional use of the single nonsynonymous/synonymous rate ratio parameter, viewing all nonsynonymous events as equivalent (e.g., see ref. By assigning scaled fitness parameters to each of the 20 amino acids, or to the 61 sense codons, Yang and Nielsen obtained scaled selection coefficients associated with each type of possible event from the difference in scaled fitness between the states before and after the event.In the mutation-selection framework in particular, this calls for a more elaborate reference model for protein-coding sequence evolution.Interestingly, the original motivations of Halpern and Bruno (9), over a decade ago, were in fact to account for site specificities of amino acids within the mutation-selection modeling framework.However, these approaches have not yet consolidated results from amino acid level phylogenetic studies showing that selection acting on proteins displays strong site-specific effects, which translate into heterogeneous amino acid propensities across the columns of alignments; related codon-level studies have instead focused on either modeling a single selective context for all codon columns, or a separate selective context for each codon column, with the former strategy deemed too simplistic and the latter deemed overparameterized.