Natural Selections last stand the Selection--Mutation-Drift model


The selection-drift mutation model was the prevailing theory of codon bias for many years. It proposed that codon bias was primarily driven by selection for optimal translation efficiency. The SDM model is not without its limitations. One limitation is that it assumes that all populations are large and have constant mutation rates. In reality, populations can be small and have variable mutation rates. This can lead to different evolutionary outcomes than what is predicted by the SDM model. Another limitation of the SDM model is that it does not take into account the effects of gene flow, which is the movement of genes between populations. Gene flow can can introduce new alleles into a population, and it can also reduce the effects of drift.

Recent studies have shown that GC bias also plays a significant role in codon bias.

GC bias is the tendency for certain nucleotides, guanine (G) and cytosine (C), to be more abundant in DNA than others, such as adenine (A) and thymine (T). This bias can affect the frequency of synonymous codons, as some codons contain more Gs and Cs than others. For example, the codon CTG for leucine is more frequently used than the codon TTA, even though they both encode the same amino acid.

The relationship between GC bias and codon bias is complex, but it is thought that GC bias can influence codon usage in several ways. First, it can affect the fidelity of DNA replication. Gs and Cs are more stable than As and Ts, so they are less likely to be misread during replication. This means that genes with a high GC content are more likely to be accurately replicated, which can help to preserve optimal codon usage.

Second, GC bias can affect the rate of transcription. Genes with a high GC content are more likely to be transcribed efficiently, which can lead to increased protein production. This can be beneficial for genes that are involved in essential cellular processes, as it ensures that they are expressed at a high level.

Third, GC bias can affect the stability of mRNA. mRNA with a high GC content is more resistant to degradation, which can help to ensure that it is translated efficiently. This is important for genes that are expressed in a transient manner, as it allows them to produce a burst of protein before the mRNA is degraded.

In addition to this there has also been a growing body of research on the role of epigenetics in evolution. Epigenetics is the study of how environmental factors can change gene expression without changing the DNA sequence. Epigenetic changes can be inherited from parents to offspring, and they can have a significant impact on evolution.

The combination of new models of evolution and research on epigenetics is providing a more complete understanding of how evolution works. This new understanding is helping us to better understand the evolution of complex traits, such as intelligence and disease resistance. It is also helping us to develop new strategies for adapting to a changing environment.

Overall, GC bias is a complex phenomenon that has a significant impact on codon usage. The selection-drift mutation model has been replaced by a model that takes into account  GC bias, codon bias and epigenetics. This new model provides a more complete understanding of codon bias and its implications for gene expression without SDMs natural selection.


Comments

Post a Comment

Popular posts from this blog

Beyond the Sequence: The Epigenetic "Fingers" That Play the DNA Keyboard

Image
Imagine the keyboard itself is not a standard piano keyboard, but a modular synthesizer, capable of producing an almost infinite array of sounds. The DNA sequence, then, represents the fundamental building blocks of this synthesizer, the raw materials from which all sounds are generated. Epigenetics, our "fingers," manipulates these building blocks, adjusting parameters like volume, timbre, and rhythm, transforming the raw potential of the DNA sequence into a symphony of cellular functions. We can further refine the "fingers" analogy. Consider that each finger represents a distinct epigenetic mechanism: DNA methylation, histone modifications, and non-coding RNA.  DNA methylation, for instance, might be the "index finger," capable of precisely silencing specific genes, like muting individual keys on the synthesizer. Histone modifications, the "middle finger," could represent the ability to adjust the accessibility of the DN...
Read more

Why are Christian philosophers running towards Darwin while biologists are "running" away?

Image
As nature reveals the strength of epigenetics and the weakness of Neo-Darwinism, biologists are “running” away from the long-standing accepted theory. In The Federalist , April 2019, Benjamin Dierker reviews “Why one-third of biologists now question Darwinism”: "Current estimates are that approximately one-third of professional academic biologists who do not believe in intelligent design find Darwin’s Theory inadequate to describe all of the complexity in biology.” Dierker continues, “The important note is that these are not ideologues or religious zealots, nor do they propose a god or biblical solution.  Rather, they find problems in the lack of explanatory power of Darwin’s theory in light of modern understanding of mutation, variation, DNA sequencing and more. These expressions of doubt do not reject naturalism or evolution per se, but the rigor of the Neo-Darwinian model for explaining the development of life.” For 40 years, scientists calculated natural se...
Read more

Rewriting the Rules: Epigenomic Mutation Bias Challenges Randomness in Evolution

Image
This research challenges the long-held dogma that mutations occur randomly, irrespective of their consequences, by demonstrating a clear, epigenome-mediated mutation bias in Arabidopsis thaliana . The study meticulously unveils how mutation rates are not uniform across the genome but are significantly reduced in functionally constrained regions, particularly within gene bodies and essential genes. This discovery fundamentally alters our understanding of evolutionary processes, suggesting that mutation is not a purely directionless force. "Mutation bias reflects natural selection in Arabidopsis thaliana" This opening statement encapsulates the core finding: mutation rates are not random but reflect epigenetic pressures. The authors demonstrate that mutations are less frequent in crucial genomic regions, directly contradicting the prevailing theory of random mutation. This observation suggests an active mechanism that minimizes deleterious mutations in essentia...
Read more