GC-biased gene conversion changes ultraconserved elements without Natural Selection

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Ultraconserved elements (UCEs) are regions of DNA that are highly similar across a wide range of species, even those that have been separated by hundreds of millions of years of evolution. This high degree of conservation suggests that UCEs play essential roles in biology, but their exact functions are still not fully understood.

Some scientists have argued that the lack of evolution in UCEs over billions of years is evidence that they are not the product of natural selection.

The article "GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes" is a research paper published in the journal Genome Research in October 2023. The paper investigates the role of GC-biased gene conversion (gBGC) in the change of ultraconserved elements (UCEs), which are highly conserved regions of the genome that are thought to play critical biological functions. 

GC-biased gene conversion (gBGC) is a natural mechanism apart from random mutations. It is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. gBGC is thought to be caused by the preferential repair of mismatches in heteroduplex DNA in favor of G/C bases.

The existence of UCEs is a challenge to the theory of Neo-Darwinism. It suggests that there are other factors, besides gradual mutations, that play a role in evolution.

The authors of the paper identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird genomes, respectively. They found that these UCEs are functionally constrained and that their adjacent genes are prone to widespread expression with low expression diversity across tissues.

The authors also found that a proportion of UCEs in specific lineages have evolved rapidly. Notably, up to 62.1% of fast-changing UCEs in test lineages were found to have resulted from gBGC. 

The authors conclude that gBGC plays an important role in facilitating lineage-specific accelerated change of UCEs. 

This research is significant because it provides new insights into the mechanisms of DNA change in mammals and birds. It also suggests that gBGC may play a more important role in NonDarwinian adaptation   than previously thought.

Here are some additional points from the article:

  • UCEs are typically defined as regions that are at least 100 base pairs long and are at least 95% conserved between two distantly related species.

  • gBGC is a process that results in the preferential conversion of AT base pairs to GC base pairs.

  • The authors found that gBGC is more likely to occur in UCEs that are located near genes that are highly expressed and have low expression diversity across tissues.

  • The authors also found that gBGC is more likely to occur in UCEs that have undergone recent changes in their regulatory activity.

Overall, this study provides new insights into the role of gBGC in the change of UCEs and suggests that gBGC may play a more important role than NeoDarwinian ones.


The article challenges neo darwinism in two main ways:

  • It suggests that a non-adaptive process, GC-biased gene conversion, may be responsible for the change of ultraconserved elements (UCEs). UCEs are highly conserved sequences that are essentially identical across many different species, and they are thought to play important roles in essential biological functions. Neo Darwinism predicts that such important sequences would be highly resistant to change, as any changes are likely to be harmful and therefore eliminated by natural selection. However, the article shows that UCEs in mammalian and avian genomes are actually changing at an accelerated NonDarwinian rate, and that this change is being driven by GC-biased gene conversion. GC-biased gene conversion is a process that favors the fixation of guanine and cytosine alleles over adenine and thymine alleles. It is not thought to be adaptive, as it can result in both beneficial and harmful changes to DNA.

  • It suggests that GC-biased gene conversion may be a major driver of genomic change in general. The article shows that GC-biased gene conversion is not limited to UCEs, but is also active in other parts of the genome. This suggests that GC-biased gene conversion may be playing a major role in shaping the change of genomes as a whole. This is a challenge to neo darwinism, as it suggests that non-adaptive processes may be more important in driving evolution than previously thought.

The article shows that GC-biased gene conversion is a powerful non-adaptive force that is driving significant NonDarwinian  changes in genomes.

Here is a more specific example of how GC-biased gene conversion could challenge neodarwinism:

Imagine a UCE that contains a regulatory sequence that is essential for the expression of an important gene. Neodarwinism predicts that this UCE would be highly resistant to change, as any changes to the regulatory sequence are likely to be harmful and therefore eliminated by natural selection.

However, GC-biased gene conversion could potentially change the regulatory sequence without any negative consequences. This is because GC-biased gene conversion does not favor any particular sequence, but simply favors GC alleles over AT alleles. Therefore, GC-biased gene conversion could change the regulatory sequence to a different sequence that is still functional.

If GC-biased gene conversion changes the regulatory sequence in a way that is beneficial to the organism, then natural selection will favor the change. However, it is also possible that GC-biased gene conversion changes the regulatory sequence in a way that is neutral or even harmful. In these cases, the change is likely to persist in the population, even though it is not favored by natural selection.

This example shows how GC-biased gene conversion could lead to the evolution of UCEs, even though natural selection is expected to resist such changes. This is a challenge to neodarwinism, as it suggests that non-adaptive processes may be more important in driving evolution than previously thought.

Article snippets

Ultraconserved elements (UCEs) are the most conserved regions among the genomes of evolutionarily distant species and are thought to play critical biological functions.

UCEs rapidly evolved in specific lineages, and whether they contributed to adaptive evolution is still controversial.

we identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird genomes,

up to 62.1% of fast-evolving UCEs in test lineages are much more likely to result from GC-biased gene conversion (gBGC).

our results show that gBGC played an important role in facilitating lineage-specific accelerated evolution of UCEs.

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