From "Exons" to "Junk DNA" - Common Ancestry just got harder

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The move from exonic DNA (2%) to epigenetic phenotypic bias

For years scientists claimed common ancestry based on exonic DNA. The figure above includes such a claim. However they only used 2% of the DNA so if they claimed humans and chimps were 98% the same it was in fact 98% of the 2%. 

These early studies used exonic DNA for common ancestry. Exons are the coding regions of genes, and they are relatively conserved across species, meaning that they change less over time than non-coding regions.


With the discovery that NeoDarwinian "Junk DNA" is not "junk" this has changed.

Exonic DNA no longer useful for common ancestry as non-exonic DNA. This makes it difficult to use exonic DNA to infer evolutionary relationships between species.

Non-exonic DNA (Junk DNA) on the other hand, is more useful for inferring evolutionary relationships between species.

Some specific reasons why exonic DNA is not as useful for common ancestry include:

  • Exons are typically shorter (2%) than non-exonic DNA (98%), which makes them less informative for phylogenetic analysis.

  • Exons are more likely to be conserved between species than non-exonic DNA, which makes it difficult to distinguish between shared ancestry and convergent evolution.

  • Exons are more likely to be subject to selection bias, which can skew the results of phylogenetic analysis.

For these reasons, scientists now use non-exonic DNA, such as introns and intergenic regions, when inferring evolutionary relationships between species.

Epigenetic phylogenetics is the study of how epigenetic inheritance patterns can be used to reconstruct evolutionary relationships between organisms. Phenotypic bias is the tendency of certain phenotypes to be more likely to arise than others, even in the absence of natural selection. These two concepts challenge neo darwinism in a number of ways.


Epigenetic methyl tags changes the phenotype 

First, epigenetic inheritance can lead to rapid phenotypic change without any changes to the underlying DNA sequence. Therefore comparing "pounds" of DNA is a non-sequitur. This is because epigenetic marks can be passed down from parents to offspring, and these marks can influence gene expression and phenotype. This means that populations can evolve new phenotypes without having to wait for new mutations to arise and be fixed by natural selection.

Second, epigenetic bias can constrain the range of possible phenotypes that can evolve. This is because epigenetic marks can make certain genes more or less likely to be expressed, which can limit the number of different developmental pathways that are available. This can lead to the evolution of convergent phenotypes in unrelated groups of organisms, as they independently evolve similar epigenetic modifications.


Ants with the same genotype but differing phenotypes 

Third, epigenetic inheritance can allow for the transmission of acquired traits. This is because epigenetic marks can be influenced by environmental factors, such as diet, stress, and exposure to toxins. This means that organisms can pass on the effects of their environment to their offspring, even though these effects are not encoded in the DNA sequence.

Overall, epigenetic phylogenetics and phenotypic bias challenge neo darwinism by suggesting that evolution is more complex and dynamic than previously thought, and that epigenetic inheritance plays a significant role in shaping the diversity of life on Earth.

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