The human brain is often described as the most complex natural structure known. While this statement may not be the view of all scientists, the brain is undoubtedly a very convoluted structure that continues to hold many mysteries. As with any structure, the brain relies greatly upon the interactions between its individual components to function properly. When these components carry out their functions, the brain can effectively control all bodily functions and facilitate speech and thought, but even minor changes can have an extreme impact on the brain’s functionality. In fact, changes within the brain are among the leading causes of neurological disorders, conditions under which the brain operates differently. Certain neurological disorders can have relatively small impacts on behavior and physical appearance, while other can cause severe changes or even be fatal. Numerous neurological disorders are congenital (appear at birth) and extensive studies have been performed to link these disorders to mutations in specific genes. Understanding how these disorders come about and their evolutionary origin can be critical to developing new therapeutic techniques. A research team headed by Dr. Alexander Lucaci and armed with diverse computational techniques, plotted the evolutionary history of a gene associated with the neurological disorders Huntington’s disease.

The Genetic Basis of Disorders

Any who have learned of diseases are likely to have heard that genetic factors can cause individuals to become predisposed to diseases - or that these factors can even cause disease themselves. Genes, as subunits of the larger genome, are what define us and make us who we are. So how can they be the root of diseases?

The answer lies in mutations and other changes that alter the expression of certain genes. The core concept of biology states that DNA, the key molecule that stores all genetic information, gives rise to messenger RNA (mRNA), a sort of copy of a segment of DNA. This mRNA undergoes a process known as translation to produce the proteins that perform key functions that support cellular metabolisms. To learn more about the process of transcription and translation, visit the Scientific Advancement of May 2023. Proteins are essential as catalysts, energy storage, structural support, and more. However, the specific structure of proteins is perfectly suited to their functions. If the protein production process is impaired or altered, the shape of the protein is changed and it is no longer able to fulfill its purpose.

The molecular structure of keratin, a protein found in the hair and nails of mammals. With its specialized shape, keratin is able to act as a resistant structural protein. Image credit: (Gaurav et al., 2018).

Altered and non-functional proteins are often the result of mutations and epigenetic factors that influence the processes of transcription and translation. Mutations (more thoroughly discussed in the Scientific Advancement of April 2023) are changes in the sequence of nitrogenous bases (adenine, guanine, cytosine, and thymine) that compose a certain segment of DNA. The particular sequence of bases in a gene codes for amino acids in a certain order. During the transcription process, the order of nitrogenous bases is preserved in the mRNA, which is used as a template to assemble amino acids in the proper order. When a mutation occurs, this order can be disrupted or one or more incorrect amino acids can be included in the protein, altering its structure and often rendering it nonfunctional.

Beyond mutations, epigenetic factors can also influence protein production. Epigenetics is the study of non-genetic factors that can influence genetic expression by either suppressing or expressing genes. Epigenetics factors can be proteins produced within an organism’s body or compounds from the outside environment. In many cases, epigenetic factors can influence gene expression by marking certain genes or changing chromosomal configuration. Marking genes can allow for the docking of proteins and other entities that suppress or facilitate gene expression. Similarly, changing chromosomal configuration (which often takes the form of chromosomes condensing or decondensing) can make certain genes accessible or inaccessible to proteins and transcription factors.

A diagram of DNA wrapped around histones transitioning from a loosely coiled mass to a highly condensed chromosome. This process, which is a natural part of cell division, can also be caused by epigenetic factors. The condensation of DNA can make certain genes inaccessible and prevent the production of associated proteins. Image credit: David O. Morgan.

While some mutations and epigenetic factors confer benefits to a person or organism, the majority create inefficient or nonfunctional proteins that can impair essential cellular functions. Dr. Lucaci and colleagues focused their research efforts on the Rem2 gene, the producer of the Rem2 protein which plays a role in the regulation of calcium channels in neurons. Calcium channels, which allow calcium ions (Ca2+) to pass through, are essential to maintaining chemical balance in neurons and for neuronal firing. Mutations in the Rem2 gene can lead to altered Rem2 proteins that impair the function of calcium channels and disrupt chemical balances of calcium ions. A mutated Rem2 gene has been linked to Huntington’s Disease, a significant neurological disorder, and Long QT Syndrome, a cardiac irregularity. Dr. Lucaci’s team utilized comparative genomics to reconstruct the evolutionary history of the Rem2 gene through the mammalian lineage. They hope that their findings might provide key insight into the gene that might aid future therapies designed to target Huntington’s Disease and other severe disorders linked to mutated Rem2.

Ion channels are typically protein complexes that span the width of the plasma membrane and allow compounds in and out of the cell. Ion channels are essential to maintaining chemical balances within the cell. Image credit: (Kabra & Pattnaik, 2020)

While it is clearly important to study the Rem2 gene when searching for gene-related therapies, it may seem strange that they decided to analyze its evolutionary history. To understand the relevance of the gene’s evolution, let’s take a look a deeper look at the primary mechanism of evolution: natural selection.

The Biology: Natural Selection

Any student of biology is familiar with the theory of evolution and the idea of ‘survival of the fittest’. While this phrase may be the bane of some evolutionary biologists, it does encapsulate the idea that organisms that are best adapted to their environment are those that tend to survive. Evolution at its core is the genetic change of populations over time as beneficial random mutations confer an advantage to those who have them. The environmental factors and other pressures that cause evolution to take place are collectively grouped under the term natural selection. The force that these pressures exert on the organisms within the environment is generally referred to as the selective pressure. Natural selection drives evolution by creating conditions that would favor an organism with a particular characteristic and disadvantage an organism with another characteristic or variant of the same characteristic. As an example, if the world were to enter another Ice Age similar to the Last Glacial Maximum, the new, colder environment would exert a selective pressure on organisms. If we were to consider a fox in this situation, a fox that had acquired a random mutation that gave it lighter colored fur may have a better chance of surviving if it can become camouflaged against the snow. This animal would survive to reproduce and the trait would spread throughout the population: a key example of evolution.

A fox with a darker coat might be less likely to survive in an environment with high rates of snowfall. Image credit: Michele Theall.

The concept of natural selection might seem relatively straightforward, but its full complexity is revealed to those who study evolution and ecology. Staying with the basics of evolution, there are different types of natural selection created by different environmental pressures. Generally, the classes of natural selection are divided based on the observed phenotypic change in the organism. Let’s take a look at a few variations of natural selection and how they impact animal populations.

Directional Selection

When one thinks of natural selection and the process of evolution, they are likely picturing directional selection in action. In essence, directional selection is when natural selection features one extreme of a particular feature. To use an example, let us revisit the foxes in a future Ice Age that we mentioned previously. Instead of fur color, let us assume that this population of foxes remains one color but that some individuals have acquired mutations that allow them to grow larger in size. The cold environment would generally favor larger foxes since they are better able to conserve heat and survive the incredibly cold winters. As such, the population experiences positive directional selection as the large extreme of size is favored in the fox population.

Positive directional selection, displayed visually by the red density curve in the graph above, favors the ‘positive’ extreme of a trait in the population. In our case, we have labeled foxes with a large size as being on the positive end of the scale. Now suppose that the Ice Age was coming to an end and global temperatures began to rise. Smaller individuals would be favored in such an environment as they would be able to lose heat to the environment more effectively. Thus, the average individual in the population would be smaller, as represented in the blue density curve above. The trend toward the negative extreme, or negative directional selection, can also occur when the proper selective pressures exist. Of course, this terminology is highly dependent on what variant of a trait is labeled as positive and negative. However, the key idea that a single extreme of a trait is favored persists in any variant of directional selection. While directional selection may be what most people envision when imagining the process of evolution, it is not the only variant of natural selection.

Diversifying Selection

Returning to our fox example, consider an Ice Age environment that contains abundant hot springs. In our hypothetical environment, the temperature is cool in certain areas due to a lower global temperature, yet it remains warm in others due to the geothermal activity driving the hot springs. As such, both warm and cool habitats exist within the range of our single fox population. The presence of a cool environment would clearly favor large foxes due to their ability to retain heat and hot pockets would favor smaller foxes since they can lose heat. So, which size category of foxes wins out? The answer: both.

In this type of natural selection, termed diversifying selection, both extremes of a trait are favored by environmental conditions while the more moderate trait is not. As such, both extremes become equally prevalent in the population. This type of selection is known as diversifying selection since it promotes greater diversity of a characteristic within the population.

Stabilizing Selection

Directional selection favors one extreme of a trait and diversifying selection favors both, but selective pressures do not always favor the extreme variants of a characteristic. Suppose that our foxes enter a period that includes winters with low temperatures and summers with very high temperatures. As the environment fluctuates to cold temperatures, small foxes would find it difficult to survive, and large foxes would struggle to survive in higher temperatures. In this case, foxes of a middling size would have the best chance of survival as they are best adapted to both temperature extremes of their environment.

The foxes are experiencing stabilizing selection, where the intermediate size category is favored and the extreme sizes are selected against. Stabilizing selection can be represented by a curve with a single peak centered right above the moderate variant of the trait in question.

Purifying Selection

While directional, diversifying, and stabilizing selection depend on which variant of a trait is selected for, purifying selection acts in a different way. In fact, many of the other types of selection work in combination with purifying selection to create the patterns seen in living populations. Purifying selection is when natural selection favors a specific trait or allele (variant of a gene), regardless of its extremity. In purifying selection other variants of the trait or allele are selected against and a rather uniform version of that characteristic is seen across the population. In the fox population, purifying selection would occur in either type of directional selection and in stabilizing selection. In each of these cases, one variant of the characteristic is selected for. Thus, all can be categorized as purifying selection. A common example of purifying selection is birth weight. Generally, if a fetus is too small it is malnourished and unlikely to survive and a large fetus may not survive birth or might cause the death of the mother. As such, a narrow range of birth weights are selected for since they confer the best chance of survival.

Each mode of selection is clearly very applicable to populations of organisms, but how would they relate to a single gene such as the Rem2 gene? Well, the traits that experience selective pressures arise due to mutations in an organism’s genome - or changes to one or more genes. As such, the Rem2 gene and other genes might experience pressures that would favor an extreme form of the gene in directional selection or a more moderate form of the gene in stabilizing selection. Clearly, the lines for extremity are not as clear cut when speaking of a protein, yet when they are defined these modes of natural selection can even be applied on the scale of a gene.

The Findings

Dr. Lucoci and colleagues analyzed the evolutionary history of the Rem2 gene and how natural selection shaped it over time. They decided to trace its history through the group Mammalia (all mammals extinct and living) by selecting examples from a variety of living mammals and reconstructing the Rem2 gene in a selection of extinct mammals from the past 250 million years. The team used sequence alignment (learn more about sequence alignment in the Course) to compare Rem2 genes across each taxon. Comparisons of the similarity of the Rem2 genes and other key genes contained among the mammalian genomes facilitated the construction of a phylogenetic tree displaying the relationships among the mammalian species.

In addition to comparing the genes themselves, Python software was used to model the proteins that would be produced from each Rem2 gene. The structures of the proteins were compared to analyze how their functions would differ across each of the mammalian taxons evaluated.

Digital models of the structure of the Rem2 protein in humans (*Homo sapiens*), the house mouse (*Mus musculus*), and the greater mouse-eared bat (*Myotis myotis*). The proteins have been superimposed in the rightmost image to reveal the similarity of the Rem2 protein in distantly related mammals. Image credit: (Lucoci et al., 2024).

Using the comparative genomic analyses and comparison of protein models, the team deduced that the Rem2 protein had changed relatively little since mammals first evolved. This could be seen in the similarity between the Rem2 sequences in each of the mammalian species evaluated and the inherent morphological similarity in the Rem2 protein structures. The Rem2 gene, which was classified as a highly conserved sequence (experienced little change over time), experienced extreme purifying selection. Natural selection consistently favored a certain form of the Rem2 gene (and consequently a specific protein shape and structure) and individuals with a mutated Rem2 gene were generally selected against. Commenting on the role of purifying selection, the researchers note that the specific shape of the Rem2 gene may be essential to its function in moderating calcium ion channels. Since other forms of the protein did not function properly and likely caused health conditions in afflicted individuals, they were less likely to survive. This caused the functional variant of the Rem2 gene to spread throughout the population of a mammal ancestor and to be largely conserved in distantly related mammalian taxa.

The investigation encompassed a vast selection of genetic sequences within Mammalia, yet the authors note that a major limitation of their study was their taxonomic diversity. They suggest that future studies might include all tetrapods and lobe-finned fish to pinpoint the origins of the variant of the Rem2 gene seen in mammals and to better understand its early evolution. The authors hope that a better understanding of the evolutionary history of Rem2 and other genes tied to largely incurable diseases might pave the way for future therapies and treatments. To learn more about Rem2 and its evolution, view the full article published in Frontiers in Bioinformatics.

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