Individual Codon Approach
Additional information can be gleaned by determining the dN/dS ratio at specific codons within a gene sequence. For instance, the frequency-tuning region of an opsin may be under enhanced selective pressure when a species colonises and adapts to new environment, whereas the region responsible for initializing a nerve signal may be under purifying selection. In order to detect such effects, one would ideally calculate the dN/dS ratio at each site. However this is computationally expensive and in practise, a number of dN/dS classes are established, and each site is shoehorned into the best-fitting class.
The first step in identifying whether positive selection acts on sites is to compare a test where the dN/dS ratio is constrained to be < 1 in all sites to one where it may take any value, and see if permitting dN/dS to exceed 1 in some sites improves the fit of the model. If this is the case, then sites fitting into the class where dN/dS > 1 are candidates to be experiencing positive selection. This form of test can either identify sites that further laboratory research can examine to determine possible selective pressure; or, sites believed to have functional significance can be assigned into different dN/dS classes before the model is run.
Read more about this topic: Ka/Ks Ratio
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