Models of Protein Evolution

1. Models of Protein Evolution Amino acid sequences (20 amino acids) Protein-coding DNA sequences

2. Models for Amino Acid Sequences DNA (4 x 4 rate matrix) vs amino acid (20 x 20) resulting in many more parameters and thus, computation time Consequently, amino acid models have concentrated on empirical approaches EMPIRICAL (several implemented in MrBayes; model = fixed ) NON-EMPIRICAL (model = “variable” in MrBayes)

3. Models for Amino Acid Sequences EMPIRICAL (several implemented in MrBayes; model = fixed ) 20 x 20 matrices Dayhoff et al. (1978) matrix based on the observation of 1572 accepted mutations between 34 superfamilies of closely related sequences JTT matrix (Jones et al. 1992; Gonnett et al. 1992): same methodology as Dayhoff, but with modern databases (other later modifications for transmembrane Jones et al. 1994) mtREV (Adachi and Hasegawa 1995, 1996) matrix derived from maximum likelihood-inferred replacements in mitochondrial proteins of 20 vertebrate species WAG (Whelan and Goldman 2001) matrix derived from maximum likelihood improvement of JTT Poisson assumes equal stationary state frequencies and equal substitution rates (equivalent to JC model for DNA). Not really empirical, but it is fixed

4. Dayhoff Evolutionary Mutation Matrix