Evolution of the Genome: Videos & Practice Problems

Genome evolution occurs through mechanisms such as mutations, gene duplication, and alternative splicing. Mutations, including point mutations, can alter gene function and regulatory sequences, impacting gene expression. Gene duplication leads to gene families with specialized functions, exemplified by hemoglobin. Alternative splicing allows for different protein isoforms from the same gene, while exon shuffling combines exons from different genes, enhancing genetic diversity. Repetitive DNA sequences and mobile genetic elements also contribute to genomic changes, influencing gene structure and regulation, ultimately driving evolutionary processes.

Mutations

Hi, in this video we're going to be talking about genome evolution. The next few videos on this topic are all going to be associated with ways the genome evolves. The first topic we're going to discuss is mutations, which are known to drive evolution. Mutations cause gene evolution in a particular gene, but they also promote genome evolution for the entire organism's genome. This can happen in many different ways. One way we are familiar with are point mutations, which result in a single nucleotide pair change. We know these can be beneficial as they can help the organism, or they can be detrimental, but generally, they all arise through some type of error in DNA replication.

When we consider genes or mutations within genes, we think of them as just affecting gene function. However, when thinking about mutations in the genome, we realize that mutations can occur both in the gene and in regulatory DNA sequences that control processes like transcription or replication. These regulatory sequences are just as important, if not more important, than mutations in the genes themselves. Thus, if the mutation is in the gene, it's going to affect the activity of the gene, the interactions the gene can have, and the stability of the gene. These are generally easy to spot because there is an immediate effect that we can observe. However, if the mutation is in the regulatory DNA, it's not as easy to see because the regulatory mutations will affect how genes are expressed. This could result in a complete on or off switch, which is quite clear, but it doesn't have to be just on or off. It could be a little less or a little more expression. These tiny changes can accumulate over time to create significant genomic evolution changes that affect gene expression as a whole.

As an example of how this happens, consider two amino acids starting from a given nucleotide sequence. Most of these sequences are exactly the same, but a single point mutation can change an amino acid from arginine to threonine, which can have huge effects on the protein. This change is not just altering the amino acid but also transforming it from a basic to a polar amino acid, which can have substantial impacts on protein structure and function. Now, let's move on.

Gene Duplication

Okay, so this video is going to focus on another mechanism of whole genome evolution, and that is gene duplication. Gene duplication is a main driver of genomic evolution. One of the things that gene duplication creates are things called gene families, which are groups of genes with similar sequences but specialized functions. If you were to look at the sequences, they are going to look really similar but have very unique and specific functions in the sound. How does this relate to gene duplication? Well, gene families arise from gene duplication because you have one gene, and it duplicates. Now each copy is free and is going to accumulate mutations that are different from the other copy. And so those mutations are going to result in different functions despite the fact that they have similar overall sequences. Like I said, they are the result of gene duplication. One major example of a gene family arising from gene duplication is actually hemoglobin. You can see here that there are four subunits, two alpha subunits and two beta subunits. Originally, each one of these four came from an original gene, which we'll just call the hemoglobin precursor. I don't actually know what the name is. I just made that up. So we have this hemoglobin precursor, and it duplicated into two, which then duplicated into four. These four subunits are what we currently have as humans. Let me back out. So you can see that I think you can see most of it. But these four subunits are what we currently have as humans, and they all have arisen from this hemoglobin precursor. How does gene duplication happen? It's not something that the cell intends to do, but it does it fairly often. Gene duplication actually arises from improper crossing over during mitosis. We haven't gone over mitosis yet, and it's probably been a while since you heard that term in your intro biology class. But if you remember, crossing over leads to more genetic diversity because it's switching gene segments between nearby chromosomes or between its chromosome pair. This happens through a process called homologous recombination. You don't necessarily need to know what that means right now. We'll go over it in the future. But when you have two chromosomes, and they're aligned properly, then the genes on this chromosome are going to equally move over to the genes on this chromosome, and they're just going to switch genes and it's not going to cause a problem. But if the chromosomes are misaligned, then you're going to have genes that are here on my palm moving to genes that are here on my fingers, and that's going to just result in chaos and gene duplication. The result of improper crossing over is you get one chromosome with an extra gene copy and one with no copy. Let's scroll down to the example and just look at that for a second, and then we'll go back up and do some of the more terms. But here you have two chromosomes with the same genes on them. What you can see are the three genes, A, B, and C. Now, when they're lined up like this, it makes sense. And if they were just to switch this way, this A and A, it would be fine. It wouldn't cause any sort of duplication. But if they're lined up here and here, what happens is you get one chromosome that actually just completely deletes this B gene; it's gone, it's deleted. And you get the second chromosome, which has two copies, and that results in a duplicated gene. With duplicated genes, we can have these unique functions, but we can also have some just sort of side effects. One of these things is called a pseudogene. These are duplicated genes but have really lost their functional ability. They are still present in the genome, but they have no function. They've either just accumulated so many mutations that they can't do anything anymore, or they've been moved to a place that no longer is transcribing, such as heterochromatin areas. But it happens. One of the ways this happens is through this term called processed pseudogenes. So what happens is that you have this gene; it's duplicated and gets transcribed normally like any other gene. It gets transcribed into RNA. But then it happens where it actually goes back to DNA and integrates itself into a chromosome potentially in a location where it's never going to be transcribed again. That's what we call processed pseudogenes. Now, we've been talking about genome or talking about gene duplication in terms of genes. But actually, there's this process of whole genome duplication, which is exactly what it sounds like, where the entire genome of an organism is duplicated. And you can imagine this can cause just kind of chaos in the cell; doesn't always, but it can. And so the whole genome is copied but remains inside the cell. When you started, you had a cell with one genome, and now you have a cell with two nearly identical genomes. And you would think that most things would die if this happened to them. And they do. But some organisms have really evolved to live with these extra copies of the genome. And so we classify these organisms based on their polyploidization, which is sort of the number of whole genome duplications. This can be common in fungi and plants. It also happens in some frog species a lot, and you can see that a duplicated genome makes the frog nearly twice the size of its single genome counterpart. It's a really interesting process. But the purpose of this talk is to discuss whole genome genomic evolution in terms of gene duplication, which can happen as single genes or as whole genes, mainly the result of improper crossing over. So, let's move on.

Splicing

Okay, so now we're going to talk about another way that the genome evolves and that's through entrance and splicing events. So, do we remember what introns are, first from either previous videos you've seen or your intro class? Right, so introns are the non-coding regions of a gene and they are not used and cut out during processing, whereas exons are the coding regions of the gene. And so, most organisms contain introns and exons in most of their genes but it's not completely universal. Actually, histone proteins don't seem to have introns, or at least not a lot of them. And so, yeah, it's mostly universal but not entirely process. Now, there are two concepts that I want to really mention that can play a big role in evolution, and that's alternative splicing and exon shuffling. So first, alternative splicing, this is the combining of exons from one gene in new orders. So, this occurs in about 50 to 90% of human genes. And so, what happens is, we'll just go down to the example here we look. And so we have these four genes 1234. And here are the introns, these sort of line sections here with no genes in them, and no exons—These are exons and these are introns. Sorry, from this spoke. And what happens is that through alternative splicing you get you get 13 and 2. So these are obviously in a different order than what they were before. And so, this creates what is known as an isoform. So these are different forms of the same protein produced through alternative slicing. So we have this one form that's 1-3-2, we could have another one that's 1-4-2. We could have another one, that's 1-3-4 or 2-1-4. Any of these different combinations here of exon combinations, and each one of these would be an isoform. So this is considered the same protein, just sort of different forms of it. Now, exon shuffling is different because this is actually combining the exons from two different genes. And so, you can imagine that's a huge process of gene evolution because you're actually combining these different regions from these different genes into the same protein. So, this can happen mainly through exon duplication. So, there's be an extra copy and that extra copy is free to do whatever it wants to an evolution. And that could involve exon shuffling Or the exon can be moved to some type of different genomic location. I'm going to talk a lot about gene jumping in future topics. You don't need to know about it now. Just sort of know that exon shuffling is the combining of exons from two different genes. So now let's move on.

Repetitive DNA Sequences

Okay. So in this video, we're going to talk about another way that the genome evolves. And that's through actually repetitive DNA sequences which are exactly what they sound like. But surprisingly, even though you may not have heard of them or at least not talked about them very much in previous classes, they're actually extremely common in the human genome and in other organisms' genomes as well. So one of these repetitive DNA sequences are actually just simple sequence repeats. There can be thousands - I mean thousands - of copies of these very short sequences, 1 to 500 nucleotides long, just dispersed throughout the genome. So in fruit flies, the sequence, one of these sequences is ACA_CT. You don't need to know, you don't need to memorize that specific sequence. I'm just using this as an example. But if you were to look at the fruit fly genome, what you would see is this sequence repeated a ton of times just throughout. And it's so unusual because they really have no genetic information. They're not transcribed. So what's their function? What are they doing? Scientists have ideas, but there's no kind of really big consensus on what these simple short repeats are doing other than sort of taking up space in the genome.

So that's one way you can imagine that the genome evolves because it has to work its way around all of these short sequence repeats that are just found throughout the genome. Now, another way is through mobile genetic elements. And so these are DNA sequences that can move through the genome. So what do I mean by moving? Well, I actually mean moving; they actually can sort of jump through the genome and change locations and insert themselves into a gene or remove themselves from a gene and insert themselves into another one or regulatory sequences. So they can just sort of move throughout the genome, and by themselves, these aren't necessarily repetitive DNA sequences. But one common feature of these elements is that they contain repetitive DNA flanking regions. And so these are really important in allowing the gene to move, but also for gene evolution because they have all of these repetitive sequences that are just interspersed throughout the genome. So one form of mobile genetic element that we're going to talk about more in the future are transposons, and they can actually move as RNA or DNA. And how they affect evolution is what I've already said: they can just insert in a gene. They can affect gene structure or regulation; they can insert in regulatory regions. All of these sorts of insertions you can imagine have drastic effects on the evolution of the genome. So now let's move on.

Which of the following is not a driver of genome evolution?

• A. Mutations
• B. Gene duplication
• C. Alternative Splicing
• D. Histone modifications

Answer: (D)

Which of the following genomic changes are most likely to cause pseudogenes?

• A. Point Mutations
• B. Gene Duplications
• C. Exon Shuffling
• D. Transposons

Answer: (B)

Protein isoforms are created through which process?

• A. Point Mutations
• B. Alternative Splicing
• C. Exon Shuffling
• D. Simple Sequence Repeats

Answer: (B)

Here’s what students ask on this topic:

What are the main mechanisms of genome evolution?

The main mechanisms of genome evolution include mutations, gene duplication, alternative splicing, exon shuffling, repetitive DNA sequences, and mobile genetic elements. Mutations, such as point mutations, can alter gene function and regulatory sequences, impacting gene expression. Gene duplication leads to gene families with specialized functions, exemplified by hemoglobin. Alternative splicing allows for different protein isoforms from the same gene, while exon shuffling combines exons from different genes, enhancing genetic diversity. Repetitive DNA sequences and mobile genetic elements contribute to genomic changes by influencing gene structure and regulation, ultimately driving evolutionary processes.

How do point mutations affect genome evolution?

Point mutations affect genome evolution by altering a single nucleotide pair in the DNA sequence. These mutations can occur in both coding and regulatory regions of the genome. In coding regions, point mutations can change the amino acid sequence of proteins, potentially altering their structure and function. In regulatory regions, point mutations can affect gene expression by modifying transcription factor binding sites or other regulatory elements. These changes can be beneficial, neutral, or detrimental to the organism, and over time, they contribute to the genetic diversity and evolution of the genome.

What is gene duplication and how does it contribute to genome evolution?

Gene duplication is a process where a gene is copied within the genome, resulting in two or more copies of the same gene. This can occur due to errors in DNA replication or improper crossing over during meiosis. Gene duplication contributes to genome evolution by providing additional genetic material that can accumulate mutations independently. Over time, these mutations can lead to the development of new functions for the duplicated genes, forming gene families with specialized roles. An example is the hemoglobin gene family, which evolved from a single ancestral gene through multiple duplication events.

What role do repetitive DNA sequences play in genome evolution?

Repetitive DNA sequences, which are short sequences repeated many times throughout the genome, play a significant role in genome evolution. Although they do not encode proteins, they can influence genome structure and function. These sequences can affect the regulation of nearby genes, contribute to chromosomal rearrangements, and provide sites for homologous recombination. Additionally, repetitive DNA sequences can serve as substrates for the insertion of mobile genetic elements, further driving genomic changes. Their presence and variability contribute to genetic diversity and the evolutionary adaptability of organisms.

How does alternative splicing contribute to genetic diversity?

Alternative splicing contributes to genetic diversity by allowing a single gene to produce multiple protein isoforms. During RNA processing, different combinations of exons from the same gene are spliced together, resulting in various mRNA transcripts. This process can generate proteins with different functions or properties from the same genetic sequence. In humans, alternative splicing occurs in 50-90% of genes, significantly expanding the proteome and enabling organisms to adapt to different environmental conditions and developmental stages. This mechanism enhances the complexity and versatility of gene expression, contributing to evolutionary processes.