dn ds ratio

In molecular phylogenetic studies, the ratio of the number of non-synonymous nucleotide substitutions to the number of synonymous nucleotide substitutions. In the case of functionally important (or otherwise constrained) genes, ds is expected to exceed dn (dn/ds <1). Because most amino acid changes will disrupt protein structure and those non-synonymous substitutions (dn) causing them will not be maintained. In a non-functional pseudogene, there will be no discrimination between them and equal numbers of dn and ds are expected (dn/ds=1). When natural selection is acting to favor changes at the amino acid level, it is predicted that dn will exceed ds, hence a high dn/ds ratio. In classical MHC loci, in the peptide binding regions (allele-specific sequences) because of heterozygote advantage/frequency-dependent selection, there is always a high dn/ds ratio (>1) whereas in the remainder of the gene dn/ds <1 (due to functional constrains). This suggests balancing selection is acting on peptide binding regions.