Darwin verses Lamarck

The vast majority of natural selection calculations rely on nonsynonymous to synonymous calculations.  This is because for 60 years this axiom of NeoDarwinism thought synonymous mutations were neutral, meaning that they do not affect the fitness of an organism. Therefore, the ratio of nonsynonymous to synonymous mutations (e.g., Ka/Ks) can be used to estimate the strength of natural selection acting on a gene. Non-neutral synonymous mutations have a significant impact on natural selection calculations.  For example, if a gene is under strong purifying selection, then the Ka/Ks ratio will be low. However, if the gene is under relaxed purifying selection, or even positive selection, then the Ka/Ks ratio will be higher. Therefore, if non-neutral synonymous mutations are present in a gene, then the Ka/Ks ratio will not be an accurate estimate of the strength of natural selection. In this article "The distribution of fitness effects among synonymous mutatio...

The vast majority of natural selection calculations rely on nonsynonymous to synonymous calculations.  This is because synonymous mutations are generally thought to be neutral, meaning that they do not affect the fitness of an organism. Therefore, the ratio of nonsynonymous to synonymous mutations (Ka/Ks) can be used to estimate the strength of natural selection acting on a gene. However, recent studies have shown that synonymous mutations can also be non-neutral, meaning that they can affect the fitness of an organism. This is because synonymous mutations can affect gene expression, RNA splicing, and protein folding. For example, a synonymous mutation can change the codon usage (Codon bias) of a gene, which can affect the expression of that gene. Or, a synonymous mutation can change the splicing pattern of a gene, which can produce different proteins. Non-neutral synonymous mutations can have a significant impact on natural selection calculations. For example,...