Biased Butterfly mutations challenges NeoDarwinism

-



The journal article "Base Composition, Codon Usage, and Patterns of Gene Sequence Evolution in Butterflies" by Näsvall et al. (2023) investigates the association between base composition and codon usage bias on gene sequence evolution in butterflies and moths (Lepidoptera). The authors used comparative genomics to analyze whole genome sequences from 25 Lepidoptera species, including an in-depth analysis of underlying patterns and processes in the wood white butterfly (Leptidea sinapis).

The data revealed significant G/C to A/T substitution bias (mutation bias) at the third codon position, with some variation in the strength of the bias among different butterfly lineages. However, the substitution bias was lower than expected from previously estimated mutation rate ratios, partly due to the influence of GC-biased gene conversion (gBGC). Biased gene conversion (BGC) is a process in which one allele of a gene has a higher probability of being copied than the other allele during recombination. This can lead to a change in the frequency of alleles in a population, and can be a powerful force driving change.

The authors also found that A/T-ending codons were overrepresented in most species, but there was a positive association between the magnitude of codon usage bias and GC-content in third codon positions. This suggests that codon usage bias in butterflies is partly dependent on compositional constraints.

In addition, the tRNA-gene population in L. sinapis showed higher GC-content at third codon positions compared to coding sequences in general and less overrepresentation of A/T-ending codons. This suggests that tRNA availability may play a role in shaping codon usage bias in butterflies.

Finally, the authors found an inverse relationship between synonymous substitutions and codon usage bias. This suggests that codon usage bias in butterflies may also be influenced by optimal translation efficiency.

Overall, the study by Näsvall et al. (2023) provides new insights into the complex interplay between mutation bias and codon usage bias in shaping gene sequence change in butterflies. The findings suggest that all of these factors play a role in determining the base composition and adaptive rates of genes in this group of insects.

The study has important implications for our understanding of genome change in general. It shows that even in groups of closely related species, there can be significant variation in the patterns of gene sequence change. This variation is likely due to a combination of factors, including mutation bias and codon usage bias and demographic history.

The study also highlights the importance of considering all of these factors when interpreting estimates of selection. For example, if codon usage bias is not taken into account, it can lead to overestimating the strength of selection on synonymous sites.

The article challenges neo-Darwinism in a few ways.

First, the study found that the evolutionary rate in butterflies is affected by a complex interplay between mutation bias and gBGC on codon usage. This suggests that neo-Darwinism's emphasis on natural selection as the primary driver of evolution may be oversimplified.

Second, the study found that the substitution bias in butterflies is lower than expected from previously estimated mutation rate ratios. This suggests that there are other forces, such as gBGC, that are counteracting the effects of mutation bias on gene sequence change.

Third, the study found that A/T-ending codons are overrepresented in most butterfly species. This suggests that the butterfly genome is under some kind of constraint that favors the use of A/T-ending codons. This constraint could be related to codon usage, gene expression, or some other aspect of genome function.

Overall, the findings of this study suggest that neo-Darwinism's understanding of gene sequence evolution is incomplete. The study found that other forces, such as mutation bias and gBGC are playing an important role in shaping the change of butterfly genomes.

In addition to the above, the study also found that there is an inverse relationship between synonymous substitutions and codon usage bias in butterflies. This suggests that selection is acting on synonymous sites, which is something that neo-Darwinism does not account for.

Overall, the study provides evidence that neo-Darwinism's understanding of gene sequence evolution is incomplete and that other forces are playing an important role in shaping the evolution of butterfly genomes.

The study suggests that neo-Darwinism needs to be updated to account for the other forces that are shaping gene sequence change.

gBGC (genome-wide biased gene conversion) and AT mutation bias are natural cellular mechanisms, as opposed to neo-Darwinian DNA polymerase mutations.

Neo-Darwinian DNA polymerase mutations are random errors that occur during DNA replication. They are a source of genetic variation, but they are also a major source of harmful mutations.

gBGC is a process in which DNA is preferentially converted from one sequence to another. This process can be biased towards or against particular sequences, such as AT or GC sequences. gBGC is thought to be a major source of mutations in some organisms, such as bacteria and yeast.

AT mutation bias is a process in which DNA mutations are more likely to occur in AT sequences than in GC sequences. This bias is thought to be due to the chemical structure of DNA, which makes AT sequences more susceptible to mutation.

gBGC and AT mutation bias are both natural cellular mechanisms that can lead to mutations. However, they are different from neo-Darwinian DNA polymerase mutations in several ways. First, gBGC and AT mutation bias are not random. Instead, they are biased towards or against particular sequences. Second, gBGC and AT mutation bias can occur even in the absence of DNA replication. In contrast, neo-Darwinian DNA polymerase mutations can only occur during DNA replication.

gBGC and AT mutation bias are important because they can contribute to the adaptation of organisms. For example, gBGC has been implicated in the development of antibiotic resistance in bacteria. AT mutation bias has been implicated in the development of human cancers.

Overall, gBGC and AT mutation bias are complex and important cellular mechanisms that can have a significant impact on adaptation and human health.

Comments

Post a Comment

Popular posts from this blog

No, the EES is not just a add on to Neo-Darwinism aka the Modern Synthesis

-
Image
" The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis fthe theory of evolution) are, if not outright overturned replaced by a new and incomparably more complex vision of the key aspects of evolution (EES). So, not to mince words , the Modern Synthesis is gone" -Eugene Koonin, an evolutionary biologist (Cited by over 270,000 evolutionary scientists.) The Extended Evolutionary Synthesis (EES) represents a significant departure from the traditional neo-Darwinian framework, also known as the Modern Synthesis . While both theories aim to explain evolutionary change, they differ fundamentally in their underlying mechanisms and the roles they assign to various biological processes. A crucial point of divergence lies in the interpretation and application of the term " evolutionary ," particularly concerning the incorporation of epigenetic mechanisms....
Read more

Is the random mutational model of evolution on its way out?

-
Image
While the random mutational model of evolution has long been a cornerstone of evolutionary biology, the Extended Evolutionary Synthesis (EES) and the study of epigenetics are challenging its core assumptions. The Random Mutational Model and Its Limitations The traditional view of evolution, often called the Modern Synthesis or neo-Darwinism , emphasizes random genetic mutations as the primary source of variation. Natural selection then acts upon this variation, favoring individuals with advantageous traits. This model has been successful in explaining some evolutionary phenomena, but it also has limitations: It struggles to explain complex adaptations: The idea that complex features like the eye or the immune system arose solely through random mutations seems statistically improbable. It overlooks the role of the environment: The traditional model treats the environment as a selective force, but it doesn't fully consider how organisms can actively respond to and s...
Read more

ERVs and Common Descent: A Reassessment in Light of Recent Findings

-
Image
Endogenous retroviruses (ERVs) have long been considered strong evidence for the common descent of humans and chimpanzees. These remnants of ancient viral infections, embedded in the genomes of both species, were once thought to be non-functional "junk DNA." The premise was that the shared presence of these seemingly random insertions in corresponding genomic locations could best be explained by a shared evolutionary history. However, recent research, such as the "Switching Sides" article published in May 2021, has challenged this assumption by demonstrating that ERVs play a functional role in the development of the human embryo and immune system. This discovery raises questions about the validity of using ERVs as primary evidence for common descent. The Traditional Argument for Common Descent The traditional argument for common descent based on ERVs rests on the following points: Random Insertion: Retroviral insertions are thought to occur randomly in...
Read more