dNdS

dNdS, often written as dN/dS or Ka/Ks, is a ratio used in molecular evolution to quantify selective pressures on protein-coding genes. dN denotes the rate of nonsynonymous substitutions (those that change the amino acid) per nonsynonymous site, while dS denotes the rate of synonymous substitutions (silent changes) per synonymous site. Because synonymous changes are typically neutral with respect to protein function, dN/dS serves as an indicator of the balance between new amino-acid changes and the removal or retention of such changes by selection.

Interpreting the ratio, a dN/dS value below 1 indicates purifying (negative) selection, which removes deleterious amino-acid changes. A value above 1 suggests positive (diversifying) selection, favoring new amino-acid variants. A value around 1 is consistent with neutral evolution or relaxed constraint. The ratio can be assessed for entire genes, specific sites, or across phylogenetic lineages, using pairwise comparisons or codon-based models along a tree.

Common analytical approaches rely on codon-based maximum likelihood methods implemented in software such as PAML, HyPhy, or related tools. These include site models (variation of dN/dS among codons), branch models (variation among lineages), and branch-site models (episodic selection affecting particular sites on lineages).

Limitations include statistical uncertainty at low divergence, saturation of synonymous sites at long evolutionary distances, and potential biases from recombination or codon usage. Consequently, dN/dS is most informative when interpreted alongside functional and evolutionary context, rather than as a definitive measure of selection in isolation.