In instances in the eukaryotic genome, DNA sequences represent evolutionary vestiges of duplicated copies of genes. What are such regions called and what are their characteristics?

The eukaryotic genome is a repository of an organism's evolutionary history, with its complexity underpinned by various genetic alterations and environmental adaptations.

One of the fascinating aspects of the eukaryotic genome is the presence of pseudogenes, which are essentially 'fossil' genes that no longer function due to mutations. These genetic elements are remnants of active genes that once played a role in the organism's physiology. Over time, as species evolve and adapt to new environments, certain genes may become redundant or less optimal. Subsequently, these genes can accumulate mutations leading to their inactivation, which converts them from functional genes to pseudogenes.

Pseudogenes act as a window into the past, revealing historical gene functions and providing insight into how genomes have expanded and diversified through duplication and mutation events. This helps scientists understand the mechanisms of genome evolution and the factors influencing genomic complexity in eukaryotes.

DNA sequence duplication is a key driver in the expansion and evolution of the eukaryotic genome. Duplication events can lead to the creation of an extra copy of a gene, known as a paralog, which can then evolve new functions or become a pseudogene.

Duplication Mechanisms

There are several mechanisms through which DNA duplication occurs, including error-prone DNA replication during cell division, unequal crossing-over during meiosis, and the activity of mobile genetic elements. These duplicated sequences can become integral parts of the genome, providing raw material for evolution. The presence of duplicates allows one gene copy to maintain its original function while the other undergoes mutation and selection, potentially leading to new gene functions. However, some duplicates accumulate deleterious mutations that result in loss of function, labeling them as pseudogenes.

Gene inactivation mutations are alterations in the DNA sequence that render a gene non-functional. Such mutations can affect various components of a gene, from its coding sequences to regulatory elements.

Types of Inactivating Mutations

These mutations include insertions, deletions, nonsense mutations introducing premature stop codons, and mutations in promoters or enhancers that prevent gene expression. Gene inactivation is a common fate for duplicated gene copies, leading to pseudogenization. Once a gene becomes redundant or less favorable for an organism's survival, selective pressures on maintaining its functionality are reduced, allowing inactivating mutations to accumulate over generational time scales. This process is a testament to the dynamic and mutable nature of the genome, reflecting an ongoing balance between the emergence of new functions and the decay of old ones.

The retrotransposition process is an intriguing mode of genome evolution, wherein a gene is copied from RNA back into DNA and then inserted into a new location in the genome. This process can result in the formation of pseudogenes known as retrotransposed or processed pseudogenes.

Retrotransposition Steps

During retrotransposition, an mRNA transcript of a gene is reverse-transcribed by an enzyme into DNA, which is then re-integrated into the genome. This can occur through the action of retrotransposons, which are mobile genetic elements. The retrotransposed copies often lack introns and regulatory regions necessary for proper gene expression and can quickly accumulate mutations that inactivate them. While these 'copy-and-paste' duplicates do not initially provide a novel function, they increase genetic variability within the population, serving as raw material for potential future evolution.