Calculations of Natural Selection have finally failed


The Ka/Ks ratio was developed by several scientists, including:

  • John M. Cameron (1995)

  • Neil Goldman and Zhiwu Yang (1994)

  • Laurence D. Hurst (2002)

  • Yoshihiro Ina (1995)

According to a search on PubMed, there are over 20,000 journal articles that mention the Ka/Ks ratio. The first article to mention the ratio was published in 1994, and the number of articles has been increasing steadily ever since.

The Ka/Ks ratio is a measure of the relative rates of synonymous and nonsynonymous substitutions between two DNA sequences. Synonymous substitutions are those that do not change the amino acid sequence of the protein encoded by the DNA. Nonsynonymous substitutions are those that do change the amino acid sequence. Per NeoDarwinism a beneficial nonsynonymous mutation is fixed by natural selection. 


The Ka/Ks ratio is used to estimate the strength of (Darwinian) selection on a particular gene or region of DNA. A Ka/Ks ratio of 1 indicates that the gene is evolving neutrally, meaning that there is no selective pressure on the gene. A Ka/Ks ratio greater than 1 indicates that the gene is under positive (Darwinian) selection, meaning that there is a selective advantage for certain amino acid changes. A Ka/Ks ratio less than 1 indicates that the gene is under purifying (negative) selection, meaning that there is a selective disadvantage for certain amino acid changes.

The Ka/Ks ratio has been used to study a wide variety of organisms, including bacteria, viruses, plants, and animals. 

The Ka/Ks ratio is a measure of the relative rates of nonsynonymous and synonymous substitutions in a gene. It is used to infer the direction and magnitude of natural selection acting on the gene. Epigenetic changes, on the other hand, are heritable changes in gene expression that do not involve changes in the DNA sequence. Therefore, Ka/Ks ratios are not reflected with epigenetics.

Epigenetic changes can be caused by a variety of factors, including DNA methylation, histone modification, and RNA interference. These changes can affect the way genes are expressed, but they do not change the underlying DNA sequence. As a result, Ka/Ks ratios will not be able to detect epigenetic changes.

However, epigenetic changes have a significant impact on gene expression and can lead to phenotypic changes.

The study of epigenetics is a relatively new field but it is clear that epigenetic changes play an important role in gene regulation and human health.

Non-fit synonymous mutations negate the Ka/Ks ratio.

The Ka/Ks ratio is a measure of the relative rates of nonsynonymous (Ka) and synonymous (Ks) substitutions in a gene or genome. A high Ka/Ks ratio indicates that nonsynonymous substitutions are more common than synonymous substitutions, which is often interpreted as evidence of positive selection, where beneficial mutations are favored by natural selection.

However, non-fit synonymous mutations can also lead to a high Ka/Ks ratio. Non-fit synonymous mutations are mutations that do not change the amino acid sequence of the protein, but they may still disrupt the gene's expression or function. These mutations occur at a relatively high rate.

As a result, a high Ka/Ks ratio does not indicate positive selection. It is important to consider other factors, such as the functional impact of the mutations, in order to interpret the Ka/Ks ratio correctly.

Here are some other factors that can affect the Ka/Ks ratio:

  • The gene's function. Genes that are essential for survival can lead to a lower Ka/Ks ratio.

  • The gene's location. Genes that are located in regions of the genome such as the protein-coding regions, are more likely to have a high Ka/Ks ratio.

  • The evolutionary history of the gene. Genes that have recently undergone rapid evolution, such as genes that are involved in adaptation to a new environment, are more likely to have a high Ka/Ks ratio.

Overall, with Ka/Ks it is important to be aware of its limitations. By considering other factors, such as the functional impact of the mutations and the gene's function and location, we can get a more accurate picture of the evolutionary forces that have shaped the gene.

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