How Epigenetics and HGT relate to Gene Duplication


How Epigenetics and HGT relate to Gene Duplication 

Gene duplication, the creation of extra copies of genes within a genome, is a crucial driving force. It provides raw material for the emergence of new traits and the diversification of species. But how genes get duplicated is only part of the story. Epigenetics, the study of heritable changes in gene expression that don't involve alterations in DNA sequence, plays a vital role in shaping the fate of these duplicated genes.

Here's how epigenetics comes into play after gene duplication:

1. Silencing redundant copies: Imagine having two identical copies of a gene. Keeping both might seem unnecessary, and indeed, one copy often gets silenced through epigenetic mechanisms like DNA methylation (adding methyl groups to DNA) or histone modifications (chemical changes to proteins spooling DNA). This prevents expression of the redundant gene, potentially saving resources and avoiding harmful interactions.


2. Divergence and specialization: Epigenetic modifications can also lead to the divergence of duplicated genes over time. Different epigenetic patterns on each copy can influence their expression levels and tissue specificity. This can eventually lead to one copy taking on a new function, while the other retains the original function, a process called subfunctionalization.


3. Evolutionary tinkering: Silencing one copy through epigenetics allows the other copy to change without harming the organism. If beneficial, they can be preserved leading to the development of a new gene with a novel function, a process called neofunctionalization.


Overall, epigenetics acts as a sculptor, shaping the landscape of duplicated genes. It can silence unnecessary copies, promote divergence and specialization, and even pave the way for the birth of entirely new genes. This intricate interplay between genes and their epigenetic decorations has played a crucial role in shaping the vast diversity of life on Earth.

Here are some additional points to consider:

  • The relationship between epigenetics and gene duplication is still being actively researched, and there's much we still don't know.

  • Epigenetic modifications can be reversible, unlike neo darwinism, allowing for dynamic changes in gene expression over time and in response to environmental cues.

  • Studying epigenetics in the context of gene duplication can help us understand the origins of genetic diversity and the emergence of new traits.

In addition there is a relationship between horizontal gene transfer (HGT) and gene duplication, though they represent distinct evolutionary processes.

Horizontal gene transfer involves the transfer of genetic material between organisms that are not parent and offspring. This can happen through different mechanisms, such as plasmids, viruses, or even direct cell-to-cell contact. HGT can introduce entirely new genes into an organism's genome, providing it with novel capabilities or adaptations.


While they are distinct processes, HGT and gene duplication can sometimes interact with each other. For example:

  • HGT can lead to subsequent gene duplication: In some cases, a gene acquired through HGT may be advantageous enough to warrant duplication within the recipient's genome. This can allow for increased expression of the gene or the evolution of new functions from the duplicated copies.

  • Gene duplication can facilitate HGT: Having multiple copies of a gene can make it more likely that one of the copies will be involved in HGT. This is because a duplicated gene is less essential for survival, making it more expendable if it were to be transferred to another organism.

Overall, both HGT and gene duplication are important evolutionary mechanisms that have played a major role in the diversification of life on Earth. While they are distinct processes, they can sometimes interact with each other, further contributing to the complexity and adaptability of living organisms.

Here are some additional details about the relationship between HGT and gene duplication:

  • HGT is more common in prokaryotes (bacteria and archaea) than in eukaryotes (plants, animals, fungi, etc.). This is likely because prokaryotes have simpler genomes and fewer regulatory mechanisms to prevent the integration of foreign DNA.

  • The rate of HGT can vary greatly among different lineages of organisms. Some organisms, such as certain bacteria, are known to be "promiscuous" HGT recipients, while others rarely acquire genes through this mechanism.

  • Gene duplication is also more common in some lineages than in others. For example, the yeast genome has undergone several rounds of whole-genome duplication, resulting in a large number of paralogous genes.


Gene Duplication by Epigenetics and HGT Challenging Neo-Darwinism

Neo-Darwinism emphasizes the role of random mutations and natural selection in driving organismal change. However, recent discoveries in gene duplication, particularly those involving epigenetics and horizontal gene transfer (HGT), have challenged some of the core tenets of Neo-Darwinism. Here's how:

1. Challenging the Randomness of Mutations:

  • Epigenetic gene duplication: This process involves the creation of gene copies through modifications in DNA methylation or histone acetylation, without altering the underlying DNA sequence as per neo darwinism. These copies can then develop  independently, potentially leading to novel functions. Critics argue that epigenetic duplication, guided by environmental cues, is not random, introducing a Lamarckian-like element (inheritance of acquired characteristics) into evolution.

  • HGT: This phenomenon involves the transfer of genetic material between organisms, often across species boundaries. HGT can provide organisms with readily adapted genes, bypassing the slow and potentially disadvantageous process of random mutation and selection. This challenges the idea of gradual, incremental evolution favored by Neo-Darwinism.

2. Questioning the Dominance of Natural Selection:

  • Gene redundancy and subfunctionalization: Duplicated genes can initially be redundant, providing a buffer against deleterious mutations in one copy. This redundancy can create a "safe space" for development of novel functions without the immediate pressure of natural selection.

  • Adaptive HGT: The acquisition of genes through HGT can be highly advantageous, providing organisms with instant access to adaptations honed in other lineages. This challenges the notion that all adaptations arise through the gradual accumulation of beneficial mutations within a single lineage.

3. Emphasizing the Role of Environmental and Developmental Cues:

  • Epigenetic regulation: The expression of duplicated genes can be influenced by epigenetic modifications, which themselves can be responsive to environmental cues. This suggests that the environment can play a more active role in shaping evolutionary trajectories than previously thought under neo darwinism.

  • Developmental HGT: HGT can occur during crucial developmental stages, influencing the formation of body plans and the expression of other genes. This highlights the importance of developmental processes in shaping evolutionary outcomes.

Overall, gene duplication by epigenetics and HGT add complexity beyond the picture of evolution painted by Neo-Darwinism. They suggest that evolution might be less random, more rapid, and more responsive to environmental and developmental cues than previously thought. This has led to calls for a broader synthesis of evolutionary theories like the Extended Evolutionary Synthesis, incorporating these new insights.

The challenges posed by gene duplication and HGT highlight the need for a more nuanced understanding of evolutionary processes, one that acknowledges the diverse mechanisms and influences that shape the living world.

Ref:

Epigenetic silencing may aid evolution by gene duplication

Horizontal gene transfers as metagenomic gene duplications

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