GC bias apart from neodarwinism


The article "Genomic Legacies of Ancient Adaptation Illuminate GC-Content Evolution in Bacteria" by Zhang et al. (2022) challenges the neo-Darwinian view of genomic GC content evolution in bacteria. Neo-Darwinism is the prevailing theory of evolution, which states that evolution is driven by natural selection acting on genetic variation. However, the authors of this study argue that the variation in genomic GC content cannot be explained by natural selection alone. They propose that the variation is instead due to the legacies of ancient adaptation, which are the genetic changes that occurred in bacteria in response to past environmental challenges.

The authors of the study analyzed the base composition and functional inventory of 11,083 representative bacterial genomes. They found that the genomic GC content is bimodally distributed, with most bacteria having either high or low GC content. This bimodal distribution is not random, but is instead constrained by the phylogeny of the bacteria. This suggests that the variation in genomic GC content is not due to recent changes in natural selection, but is instead a legacy of ancient adaptation.

The authors also found that the variation in genomic GC content is correlated with the DNA replication and repair (DRR) system. This is a fine tuned system for sequence change, not a NeoDarwinian random mutation feature. The DRR system is responsible for copying and repairing DNA, and it is essential for bacterial survival. The authors found that bacteria with high GC content tend to have a more efficient DRR system, while bacteria with low GC content tend to have a less efficient DRR system. This suggests that the variation in genomic GC content is a trade-off between DNA stability and replication efficiency.

The authors of the study argue that their findings support a new model for bacterial evolution. In this model legacies of ancient adaptation occur which in turn affect the mutational biases that occur in the genome. These mutational biases can then lead to further changes in genomic GC content. This model is in contrast to the neo-Darwinian model, which states that natural selection acts directly on genetic variation.

The findings of this study have important implications for our understanding of bacterial evolution. They suggest that the variation in genomic GC content is not random, but is instead a product of ancient adaptation. This has implications for our understanding of how bacteria respond to environmental change, and how they evolve to resist antibiotics.

The study by Zhang et al. does not rule out other models of evolution. However, their findings do suggest that the legacies of ancient adaptation play an important role in the evolution of genomic GC content in bacteria. This is a new and exciting finding that could lead to a better understanding of how bacteria evolve.

In addition to the scientific implications, the findings of this study also have philosophical implications. The neo-Darwinian model is based on the assumption that natural selection is the only driving force of evolution. However, the findings of this study suggest that other factors, such as the legacies of ancient adaptation, can also play a role. This challenges the neo-Darwinian view of evolution and opens up the possibility of other, non-Darwinian models of evolution.

The study by Zhang et al. is a significant contribution to our understanding of bacterial evolution. Their findings suggest that the variation in genomic GC content is not random, but is instead a product of ancient adaptation. This has implications for our understanding of how bacteria respond to environmental change, and how they evolve to resist antibiotics. The findings of this study also have philosophical implications, challenging the neo-Darwinian view of evolution and opening up the possibility of other, non-Darwinian models of evolution.

Article Snippets

the genomic GC content (genomic GC) varies greatly but presents some level of phylogenetic stability, making it challenging to explain based on current hypotheses

the biased conservation of various stress-related genes, especially the DRR-related ones, implies distinct adaptive processes in the ancestral lineages of high- or low-GC clades which are likely induced by major environmental changes

mutational biases resulting from these legacies of ancient adaptation have changed the course of adaptive evolution and generated great variation in the genomic GC

GC content has been shown to be an important factor in microbial ecology and evolution, and the genomic GC of bacteria can be characterized by great intergenomic heterogeneity, high intragenomic homogeneity, and strong phylogenetic inertia, as well as being associated with the environment

Current hypotheses concerning direct selection or mutational biases cannot well explain these features simultaneously.

Our findings of the genomic GC showing that ancient adaptations have transformed the DRR system and that the resulting mutational biases further contributed to a bimodal distribution of it offer a more reasonable scenario for the mechanism

when thinking about the evolution of life, diverse processes of adaptation exist,

Bacteria are usually supposed to be subject to a high level of purifying selection in light of huge effective population sizes (1). The situation hence can become confusing when it comes to how bacteria have generated great variation in their genomic base composition (i.e., genomic GC content [GC content]) during their adaptive evolution

The genomic GC content of bacteria, which can vary enormously from below 20% to nearly 75%, is not normally distributed at odds with the expectation from an entirely stochastic model

The correlations detected between the genomic GC and a few selective agents favor an environmental constraint on the base composition to some extent

In conventional views, bacteria evolve rapidly in response to environmental changes, leaving most genetic variations nonpersistent

However, previous studies have revealed remarkable phylogenetic inertia in the genomic GC, hinting at a certain level of stability of the base composition despite ever-changing environments over long timescales

Thus, some attention has shifted from direct selection toward the effect of genetically conserved components, the DNA replication and repair (DRR) proteins, which potentially cause mutational biases and introduce intricate effects on the genomic GC

To date, several DRR-related proteins have been considered responsible for the variation in genomic GC

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