Evolutionary Change of Amino Acid Sequences

Abstract Before the invention of rapid methods of DNA sequencing in 1977 (Maxam and Gilbert 1977; Sanger et al. 1977), most studies of molecular evolution were conducted by using amino acid sequence data. Although amino acid sequencing was time consuming and error prone, some important principles of molecular evolution, such as evolution by gene duplication (Ingram 1963; Ohno 1970) and the molecular clock (Zuckerkandl and Pauling 1962; Margoliash 1963), were discovered by the study of amino acid sequence data. At the present time, DNA sequencing is much simpler than amino acid sequencing, and amino acid sequences are usually deduced from nucleotide sequences by using the genetic code. However, amino acid sequences are still useful for evolutionary studies; they are more conserved than DNA sequences and thus provide useful information on long-term evolution of genes or species. They are also almost indispensable for aligning DNA sequences of protein-coding genes. Furthermore, the mathematical model for the evolutionary change of amino acid sequences is much simpler than that of DNA sequences. For these reasons, we first consider the evolutionary change of amino acid sequences.