Name: why some gene regions evolve faster
Uploaded: 2020-11-23T11:47:33.000Z
Duration: 2 min 5 s
Channel: JoVE

K12 Standards

north-carolina-k-12-science-standard-course-of-study

North Carolina K-12 Science Standard Course of Study

9-12

Biology

Biological Evolution- Unity and Diversity

LS.Bio.9.2

Gene Evolution - Fast or Slow?

The way that mutations affect the survival of a cell depends greatly on the location of the genetic change. In regions of the genome that do not code for genes or regulatory regions, mutations may have little effect, such that the cell can often continue as usual.
The overall effect is that non-coding sequences are free to change fairly rapidly in evolutionary terms, meaning these regions of a genome may be almost unrecognizable even in two closely related species.
However, in coding sequences, mutations are not so freely adopted. While in very rare cases they may be beneficial, such as a mutation in a gene for an enzyme creating a better binding affinity for the substrate; the majority will be detrimental.
Let&#8217;s look at the 16s rRNA gene, for example. It encodes a structural RNA forming part of the ribosome. Some of the regions of this RNA are critical to ribosome function, and changes in these segments are exceptionally rare. These highly conserved regions change so slowly that they can be used to examine sequence homology across phyla, kingdoms, and even all living species - making them a valuable tool for studying relationships between even distantly related organisms.
However, there are still sections of the 16s rRNA sequence less critical to function, which may evolve slightly faster. These &#8220;variable regions&#8221; can be useful for elucidating relationships between more closely related species &#8211; such as genera or even strains of bacteria.
Overall, this leads to the phenomenon that different genome regions may evolve at vastly different rates, even within regions encoding a single gene.

gene evolution - fast or slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code for a protein might experience high selection pressure, because any changes in their sequence are likely to result in a protein which is less capable of performing its function optimally. However, occasionally a mutation in one of these regions will result in a beneficial outcome that contributes to the overall fitness of the organism, and such mutations often persist and may even become fixed in populations. When comparing the frequency of these mutation events to the relatively regular changes seen in non-coding sequences, this is exceedingly rare, and so in general coding regions are considered as evolving slowly.
It is also true that there is a measurable amount of variation in the levels of sequence conservation within coding sequences, and this is seen across all organisms. For instance, take the example of a receptor protein. Such proteins typically have different regions that may perform functions such as ligand binding, or intracellular signaling, or membrane integration. In this case, a mutation in the region that is involved in ligand binding may produce a protein that is less efficient at binding the ligand. Therefore, selection pressure would likely be high on the particular nucleotides coding for this part of the protein. However, in the section of the protein which spans the membrane, there may be less effect seen if an amino acid substitution occurs, and therefore lower levels of selection pressure. Under these conditions, we might see that two regions of the same protein-coding gene might have different rates of evolution.
Sequencing Genes or Genomic Regions to Build Phylogenies
This variation in the speed of genome evolution over different regions can be studied to answer questions about evolutionary relationships. Genes and gene regions can be selected and sequenced over groups of individuals to answer questions as narrow as &#8220;are these populations potentially different species?&#8221; or as broad as &#8220;how do these phyla place into the tree of life?&#8221;. For the former, selecting a gene that has a relatively lightly conserved region would help to identify population-level differences. Conversely, to answer questions over groups as diverse as phyla, a highly conserved gene region may provide enough homology to produce a phylogeny of such groups. Commonly used regions for molecular phylogenetic analyses such as these include ribosomal rRNA genes (such as 16s rRNA, 18s rRNA, or 28s rRNA), or genomic regions known as ITS (Internal Transcribed Spacers, I or II) which sit between the ribosomal rRNA subunit genes.

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain ...

Education

JoVE Core

Molecular Biology

Unit 1

DNA, Cells, and Evolution

KEY TERMS AND CONCEPTS

why some gene regions evolve faster

Gene regions do not all change at the same rate. In eukaryotes, long stretches of DNA do not code for proteins or RNAs. Some of these non-coding regions include important regulatory sequences, but most have no known function. Because little or no selection pressure acts on them, they often change the fastest over evolutionary time.

Protein-coding regions usually evolve more slowly. A change in a coding sequence can alter a protein and make it less effective at doing its job. That creates strong selection pressure to keep the sequence unchanged. Still, a rare mutation can improve fitness, and those helpful changes may spread through a population and even become fixed.

Rates of change can also differ within the same gene. A receptor protein, for example, may have one part for ligand binding, another for intracellular signaling, and another for membrane integration. A mutation in the ligand-binding region may reduce how well the protein binds its target, so selection pressure there can be high. In the membrane-spanning region, an amino acid change may have less effect, so that part may evolve more slowly or more freely.

These differences in sequence conservation help scientists study evolutionary relationships. Researchers can choose and sequence genes or genomic regions to ask narrow questions, such as whether two populations may be different species, or broad questions, such as how phyla fit into the tree of life. Lightly conserved regions can reveal small differences, while highly conserved regions can still show homology across very distant groups. Common choices for molecular phylogeny include ribosomal rRNA genes such as 16s rRNA, 18s rRNA, and 28s rRNA, as well as ITS regions, or internal transcribed spacers, between the ribosomal subunit genes.

Why Some Gene Regions Evolve Faster

the dna helix

DNA Structure and Base Pairing

DNA has a helical structure that helps store genetic information. The double helix is the shape formed by two strands that twist around each other. This structure is a key feature of DNA in cells. The two strands are held together by base pairing. Bases on one strand match with bases on the other strand in a regular way. This pairing helps keep the DNA molecule stable and organized. The helix shape also helps explain how DNA fits into chromosomes and carries instructions for living things. By...

the central dogma

DNA to Protein: Central Dogma Steps

The central dogma explains how genetic information moves from DNA to RNA to protein. This flow is a key idea in molecular biology. It helps show how cells use genes to make the molecules that carry out work. DNA stores the instructions for making proteins. During transcription, a gene in DNA is copied into RNA. The RNA then carries that message to the next stage. In translation, the RNA message is used to build a protein. Proteins do much of the cell’s work, so this process connects genes to...

prokaryotic cells

Inside Prokaryotic Cell Structure

Prokaryotic cells have a simple internal structure compared with many other cells. They are usually divided into two groups: bacteria and archaea. These cells have no nucleus, so their DNA is not enclosed in a membrane-bound compartment. Instead, the genetic material is found in the nucleoid, a region where the DNA is located in the cell. Some prokaryotic cells also contain plasmids, which are small extra DNA molecules. A capsule may surround the cell and provide an additional outer layer. <br...

eukaryotic compartmentalization

Cell Compartments in Eukaryotes

Eukaryotic cells use compartments to organize many different jobs inside one cell. These compartments help separate processes so they can happen in the right place. The compartment called the cytosol is the fluid part of the cell. It surrounds the other internal structures and helps support many cell processes. Inside the cell, membrane-bound organelles create distinct microenvironments. A microenvironment is a small internal space with conditions that fit a specific task. This separation...

the tree of life - bacteria, archaea, eukaryotes

the-tree-of-life-bacteria-archaea-eukaryotes

How Life Is Classified Into Three Domains

The tree of life shows how organisms are related through evolution. Its root represents the common ancestor of all life on Earth. From that point, branches spread out like a tree. The tips of the branches represent living, or extant, species. Species that no longer exist, called extinct species, appear closer to the center of the tree. Today, these organisms are grouped into three domains: bacteria, archaea, and eukaryotes. Scientists still debate these divisions, so the tree of life keeps...

mutations

How Mutations Change DNA

Mutations are changes in DNA. They can alter the genetic code and affect how genes work. In high school biology, students often study mutations to understand how DNA changes can influence traits. The transcript focuses on two common mutation types: point mutations and frameshift mutations. A point mutation changes one nucleotide, which is one DNA building block. A frameshift mutation happens when nucleotides are added or removed and the reading frame shifts. These changes matter because they...

Gene regions do not all change at the same rate. In eukaryotes, long stretches of DNA do not code for proteins or RNAs. Some of these non-coding regions include important regulatory sequences, but most have no known function. Because little or no selection pressure acts on them, they often change the fastest over evolutionary time. Protein-coding regions usually evolve more slowly. A change in a coding sequence can alter a protein and make it less effective at doing its job. That creates...

genome size and the evolution of new genes

genome-size-and-the-evolution-of-new-genes

How Genome Size Shapes New Genes

Genome size can vary widely, and it also helps show how new genes form. Every living organism has a genome, whether it uses RNA or DNA. Yet the size of that genome can be very different from one organism to another. One major difference is whether the organism is prokaryotic or eukaryotic. Prokaryotic genomes usually have little to no non-coding sequence, which means genes are packed closely together in operons along the chromosome. Eukaryotic genomes contain long stretches of non-coding DNA...

gene families

How Gene Families Evolve and Diversify

Gene families are groups of genes that are thought to come from a shared ancestor. They usually form when a gene is copied by mistake during cell division. The original gene stays under selection pressure to keep its job, while the extra copy can change more quickly over time. Some copied genes gain a new role in the organism. When that happens, they are called paralogs, which are two genes in the same species that evolved from one common ancestral gene. Gene families also include orthologs,...

types of genetic transfer between organisms

types-of-genetic-transfer-between-organisms

How Genes Move Within and Across Generations

Genetic transfer is the movement of genetic information from one organism to another. It happens in two main ways: vertical gene transfer and horizontal gene transfer. Vertical gene transfer moves genes from one generation to the next. It is much more common than horizontal gene transfer. Vertical gene transfer happens during both sexual reproduction and asexual reproduction. In both cases, one or more organisms pass some or all of their genome to their offspring. This kind of transfer occurs...

key terms and concepts

Explore why non-coding DNA often changes quickly, why coding genes are more conserved, and how scientists use gene sequences to build phylogenies.

Why Some Gene Regions Evolve Faster | JoVE K12

molecular biology

JoVE Core Molecular Biology showcases the molecular processes of the cell through clear and concise animated video lessons. Additionally, in scientist-in-action videos, these concepts' application is demonstrated through real experiments in modern laboratories.

Next Generation Science Standards

High School

Life Science

heredity-inheritance-and-variation-of-traits

Heredity: Inheritance and Variation of Traits

HS-LS4-1

Florida Department of Education

SC.912.L.15

SC.912.L.15.2

new-york-state-science-learning-standards

New York State Science Learning Standards

Natural Selection and Evolution

HS-LS4-1.

Development of Antibiotic Resistance

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Fitness
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Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major ...

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes ...

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Ribozymes

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Use models to illustrate the conditions required for natural selection, including the overproduction of offspring, inherited variation, and the struggle to survive.

LS.Bio.9.3

Construct an explanation to explain how natural selection leads to adaptations within populations.

LS.Bio.9.4

Extinction

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LS.Bio.10.1

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Multi-species Conserved Sequences

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Taxonomy

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Phylogeny

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Use models (including dichotomous keys, scientific nomenclature, cladograms, phylogenetic trees) to identify organisms and exemplify relationships.

LS.Bio.10.2

Understand natural selection as a mechanism for biological evolution.

Why Some Gene Regions Evolve Faster

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