gBGC - more parsimonious than Natural Selection

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The paper "GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands" by Neiman and Gophna (2015) presents new evidence that GC-biased gene conversion (gBGC) is a widespread phenomenon in bacteria. There have been many add on confirmatory articles.

gBGC is a recombination-mediated process that tends to increase the GC content of DNA over time. It was previously thought to be restricted to sexual eukaryotes since meiosis (recombination) occurs then, but Neiman and Gophna show that it is also likely to operate in bacteria. This is because DNA repair in bacteria and eukaryotes  have similar recombination features (above).

The authors present two main lines of evidence in support of their hypothesis. First, they show that there is a positive correlation between GC content and evidence of recombination in a wide range of bacterial species. Second, they show that this bias towards G/C nucleotides in recombining genes cannot be explained by selection on codon usage.

If gBGC is indeed widespread in bacteria, it has a number of important implications for our understanding of bacterial genome change. First it occurs outside of Darwin's natural selection. For example, it can explain a number of previously unexplained observations, such as the apparent non-equilibrium of base substitution patterns and the heterogeneity of gene composition within bacterial genomes. Additionally, it suggests that gBGC may play a role in driving the change of GC content in bacteria, which is known to be higher than what would be predicted by Darwin alone.

This is a significant finding, as it has the potential to change our understanding of bacterial genome change in a number of ways.

Here are some of the potential implications of gBGC for bacterial genome change:

  • gBGC may be a major driver of the change of GC content in bacteria.

  • gBGC may influence the rate and pattern of gene change in bacteria.

  • gBGC may "mimic" selection on codon usage and other gene features; in other words, change is due to a natural mechanism not natural selection. 

  • gBGC may plays a role in the fast change of important traits. NeoDarwinism acts very slowly. 

The authors first discuss the evidence that bacterial genomes are generally above the GC-content predicted from their mutational bias towards AT. Mutational bias towards AT refers to the observation that mutations that result in a change from a guanine (G) or cytosine (C) to an adenine (A) or thymine (T) occur more frequently than mutations in the opposite direction.

This is due to epigenetic methylation of cytosine that spontaneously deaminates to tyrosine. This is also a biased change apart from Darwin's random mutations.

This suggests that some other force is driving the genomic GC-content towards higher values in virtually all bacterial species.

The authors then consider the possibility that selection is acting on synonymous sites to favor GC-rich alleles. However, they reject this hypothesis because the difference of GC% between recombinant and non-recombining genes is higher at the third position of codons, where synonymous substitutions are most common.

The authors then propose that gBGC is the most likely explanation for the high GC-content of bacterial genomes. This process has already been observed in a variety of eukaryotes, and the authors argue that it is likely also present in bacteria.

They point out that the intensity of the relationship between GC-content and recombination is comparable to that observed in humans where the impact of gBGC on base composition is known to be strong.

They argue it is important to consider gBGC when studying the forces that shape bacterial genomes ergo don't automatically assume natural selection lest your study will be biased.

The authors specifically answer the question about how gBGC might account for the strong variations of GC-content observed across bacterial species, the authors argue that the intensity of gBGC could vary between species. This could be due to differences in the biased repair mechanisms, or to differences in the efficiency of the gBGC process itself. As GC pairs have more hydrogen bonds (3) than AT pairs (2) they are more stable and likely to be maintained during DNA repair which is similar to combination (meiosis). This asexual bacteria and humans can share GC bias despite human meiosis (sex).

The authors also point out that gBGC is a stochastic process, so there will be some variation in the GC-content of different genomes, even if the intensity of gBGC is the same. 

The article discusses the evidence for and against two possible explanations for the observed increase in GC content in bacterial genomes over time: natural selection and GC-biased gene conversion (gBGC).

Natural selection: The authors argue that it is difficult to explain the observed patterns of GC content evolution under a natural selection model. For example, selection on amino acid content would not be able to explain the higher GC content at synonymous sites compared to non-synonymous sites. Additionally, selection on codon usage would not be able to explain the higher GC content in recombining genes even in species that favor A/U-ending codons. Finally, the article notes that the relationship between GC content and recombination is also observed in intergenic regions, which are unlikely to be under selection for any particular GC content.

They  argues that gBGC is a more parsimonious explanation for the observed patterns of GC content evolution in bacteria than selection. gBGC is known to occur in eukaryotes, and the passage suggests that it may also be widespread in bacteria. Additionally, gBGC can have a significant impact on bacterial genome change, and it can interfere with the efficiency of selection.

Conclusion: The passage concludes that gBGC is the more likely explanation for the observed increase in GC content in bacterial genomes over time. The passage also argues that gBGC is an important natural mechanism to consider when studying bacterial genomes.

The evidence against natural selection is quite strong, and gBGC is a known process that can have a significant impact on GC content.

gBGC can interfere with the efficiency of selection, and it can lead to false positives in the search for regions under positive selection in a genome. This means that it is important to consider gBGC when interpreting the results of studies on based on natural selection as bBGC "mimics" natural selection. 

It's the situation of having  "a bird in hand" where gBGC explains change without Darwin.

More research is needed to fully understand the role of gBGC in bacterial genome evolution, but Neiman and Gophna's paper provides a strong foundation for future studies in this area.

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