*2.4. Synonymous (KS) and Nonsynonymous (KA) Substitution Rate Analysis*

Nucleotide mutations that do not cause amino acid changes are known as synonymous mutations, whereas nonsynonymous mutations do cause changes to the amino acid sequence. The Ka/Ks ratio (or dN/ds) of nonsynonymous substitution (Ka) and synonymous substitution (Ks) is the selection pressure of an encoded protein, which can be used to determine whether the gene encoded by the protein is under selection pressure. If Ka/Ks > 1, the protein is considered to be positively selected; if Ka/Ks = l, the protein is neutral; and if Ka/Ks < 1, the protein is considered to have undergone purifying selection. It is generally believed that synonymous mutations are not subject to natural selection, whereas nonsynonymous mutations are.



**Table 4.** Genes from the chloroplast genomes of *Pyrus*.
