lecture 9 The evolution of populations and origins of genetic variation

Question 1

The evolution of populations

Answer 1

What is a population?
A population is a group of interacting potentially interbreeding individuals of a species.

Each individual of a population carry alleles, and the alleles of each individual vary from another.

Are all organisms diploid?

Some populations have a large allelic diversity; and others are made of individuals that are almost identical so low allelic diversity.

Population genetics: the study of patterns of allelic diversity and their change in frequency over time

Question 2

evolution of mosquito populations

Answer 2

Use of organophosphates insecticides started in 1969, France.

But the mosquitoes started to coming back in 1972!

Ester gene encodes esterase.

Esterase degrades toxins including organophosphates insecticides.

Ester1 allele: present at frequency of 60% in costal populations in 1973! And present at less than 20% in populations 11km from the ocean!

By 1975, Ester1allele was present at frequency of 100%.

Question 3

Genetic drift –‘Random mating

Answer 3

The population is made up of sexually reproducing organisms that mate at random… not really the case!

Species evolve to strong preferences about their choice of mate… while random is more around pollen in peas.

Genetic drift describes how allele frequencies fluctuate unpredictably from one generation to the next..

Genetic drift tends to reduce genetic variation through losses of alleles..

Question 4

Genetic drift and hardy-weinberg theorem

Answer 4

The Hardy-Weinberg theorem-the genotype and allele frequencies:

Assumptions:

1.Absence of environmental factors /outside forces →same allele frequency of a population … environmental factors do have a role!

2.A population is infinitely large →variation due to chance is not significant from a generation to generation … not the case in real populations and genetic drifts!

3.All genotypes at a locus are equally likely to survive and reproduce→there is no selection … however, selection of a particular genotype changes allelic frequency →evolution!

4.No alleles enter or leave a population through migration and no mutation in the population …comment?

Question 5

Mechanisms of evolution

Answer 5

1.Alteration of allelic frequency
2.Genetic drifts
3.Natural selection
4.Migration
5.Mutation

Question 7

How do we calculate allele frequency?

Answer 7

The frequency of an allele in a population can be calculated
*For diploid organisms, the total number of alleles at a locus = 2

*The total number of dominant alleles at a locus is 2 alleles for each homozygous dominant individual

*or 1 allele for each heterozygous individual; the same logic applies for recessive alleles

By convention, if there are 2 alleles at a locus, p and q are used to represent their frequencies

The frequency of all alleles in a population will add up to 1

For example, p+ q= 1

Question 8

complete the formative assessment questions

Question 9

what is genetic drift

Answer 9

Genetic drift is the random, nonrepresentative sampling of alleles from a population during breeding.

Drift is a mechanism of evolution because it causes the allelic composition of a population to change from generation to generation.

Alleles are lost due to genetic drift much more rapidly in small populations than in large populations.

Genetic bottlenecks and Founder effects

Question 10

Bottleneck effect

Answer 10

A genetic bottleneck is an event in which the number of individuals in a population is reduced drastically.

*Even if this dip in numbers is temporary, it can have lasting effects on the genetic variation of a population

Genetic variation makes evolution possible

Question 11

Founder effect

Answer 11

When asmall number of founding individuals leave a larger population and colonise a new habitat this results in a genetic bottleneck.

But only a small subset of the genetic diversity of the source population is likely to be included in the new population, and the relative frequencies of these alleles may be very different from what they had been before.

This is called a founder effect

Question 12

. Genetic variation..

Answer 12

Even brief bottleneck events can lead to drastic reductions in the amount of genetic variation within a population,

and this loss of allelic diversity can persist for many generations after the event.

The founder effect is a loss of allelic variation that accompanies the founding of a new population from a very small number of individuals.

Founder effects can cause the new population to differ considerably from the source population

Question 13

. Natural selection

Answer 13

The selection occurs when individuals in a population vary in their fitness.

Natural selection is the only mechanism that consistently causes adaptive evolution..

Evolution by natural selection involves both chance and “sorting”

–New genetic variations arise by chance
–Beneficial alleles are “sorted” and favored by natural selection

Question 14

what is fitness in relation to natural selection

Answer 14

Fitness: the reproductive success of a particular phenotype.

Relative fitness is the contribution an individual makes to the gene pool of the next generation, relative to the contributions of other individuals

Selection favors certain genotypes by acting on the phenotypes of certain organisms

Studying the actual fitness of organisms is rather complicated..

For example: measuring the number of offsprings and their relative phenotypes and variations and the relationship between genotype and phenotype…

Question 15

what is adaptive evolution in relation to natural selection

Answer 15

Natural selection increases the frequencies of alleles that enhance survival and reproduction

Adaptive evolution occurs as the match between an organism and its environment increases
-Because the environment can change, adaptive evolution is a continuous process

Diploidy maintains genetic variation in the form of hidden recessive alleles

Heterozygotes can carry recessive alleles that are hidden from the effects of selection

The sickle-cell allele causes mutations in haemoglobin but also confers malaria resistance

Question 16

Antagonistic pleiotropy

Answer 16

Antagonistic pleiotropy is a concept in genetics and evolutionary biology where a single gene has multiple effects (pleiotropy), and these effects have opposing fitness consequences. Specifically, a gene may have a beneficial effect in one context (such as early in life or under certain environmental conditions) but a detrimental effect in another context (such as later in life or under different environmental conditions).

Here are some key points about antagonistic pleiotropy:

Pleiotropy: This occurs when one gene influences multiple phenotypic traits. In the case of antagonistic pleiotropy, these influences have both positive and negative effects on an organism’s fitness.

Opposing Effects on Fitness: The beneficial and detrimental effects of a gene with antagonistic pleiotropy can occur at different times or in different environments. For example, a gene might enhance reproductive success early in life but contribute to aging-related diseases later in life.

Evolutionary Implications: Antagonistic pleiotropy is an important concept in evolutionary biology because it helps explain why certain traits that are harmful in some contexts persist in populations. If the beneficial effects of a gene increase an organism’s reproductive success, that gene may be favored by natural selection, even if it has negative effects later in life.

Aging and Lifespan: One well-known application of antagonistic pleiotropy is in the study of aging. Genes that promote early-life fertility and survival may also contribute to the deterioration of physiological functions and increased susceptibility to diseases in old age. This trade-off can help explain why aging occurs from an evolutionary perspective.

Examples:

p53 Gene: This gene plays a crucial role in tumor suppression by regulating cell division and apoptosis. However, its activity can also lead to the depletion of stem cells and contribute to aging-related tissue degeneration.
Sickle Cell Trait: The sickle cell allele provides resistance to malaria in heterozygous individuals but causes sickle cell disease in homozygous individuals.
Overall, antagonistic pleiotropy highlights the complex trade-offs that can arise in the evolution of genes and traits, illustrating that the effects of genetic variation are context-dependent and can have both positive and negative impacts on an organism’s fitness across its lifespan.

Question 17

Negative and positive selection

Answer 17

Negative and positive selection are two fundamental concepts in evolutionary biology that describe how natural selection acts on genetic variation within populations. These processes influence which alleles (gene variants) increase or decrease in frequency over time.

Negative Selection (Purifying Selection)
Definition: Negative selection, also known as purifying selection, occurs when deleterious alleles are removed from the population. This type of selection acts to eliminate harmful genetic variations that decrease an organism’s fitness.

Mechanism: When a mutation occurs that negatively affects the organism’s survival or reproductive success, individuals carrying this mutation are less likely to survive and reproduce. As a result, the frequency of the deleterious allele decreases in the population over time.

Outcome: Negative selection helps maintain the stability of an organism’s genome by conserving beneficial or neutral alleles and removing harmful ones. This leads to the preservation of functional genetic sequences and the prevention of the accumulation of detrimental mutations.

Examples:

Mutations that cause lethal or severe genetic disorders, such as cystic fibrosis or Tay-Sachs disease, are typically subject to strong negative selection.
Alleles that lead to metabolic inefficiencies or structural defects in proteins are also likely to be eliminated by negative selection.
Positive Selection (Darwinian Selection)
Definition: Positive selection, also known as Darwinian selection, occurs when beneficial alleles increase in frequency within a population because they confer a selective advantage to individuals carrying them.

Mechanism: When a mutation occurs that improves an organism’s survival or reproductive success, individuals carrying this mutation are more likely to survive and reproduce. This results in the beneficial allele becoming more common in the population over successive generations.

Outcome: Positive selection drives evolutionary change by promoting advantageous traits that enhance an organism’s fitness. This can lead to adaptation to changing environments, new ecological niches, or improved physiological functions.

Examples:

The CCR5-Δ32 allele, which provides resistance to HIV infection, has increased in frequency in certain human populations due to positive selection.
The evolution of lactase persistence in some human populations, allowing adults to digest lactose, is another example of positive selection driven by the dietary benefits of milk consumption.
The development of antibiotic resistance in bacteria is a classic case of positive selection, where mutations that confer resistance to antibiotics become prevalent due to the selective pressure exerted by antibiotic use.

Summary
Negative Selection removes harmful alleles from the population, maintaining the integrity of essential functions and reducing the frequency of deleterious mutations.
Positive Selection promotes beneficial alleles, leading to the adaptation and evolution of new traits that enhance survival and reproduction.
Both types of selection are essential for shaping the genetic landscape of populations and driving the evolutionary process.

Question 18

6. Micro and Macroevolution

Answer 18

Why are there many more species per square mile in the tropics than near the poles?

Why are there 1.5 million species of beetles and just one species of gingko tree?

Microevolutionis evolution occurring within populations, including adaptive and neutral changes in allele frequencies from one generation to the next.

Macroevolutionis evolution occurring above the species level, including the origination, diversification, and extinction of species over long periods of evolutionary time

Question 19

Microevolution?

Answer 19

Microevolutionis a change in allele frequencies in a population over generations

Three mechanisms cause allele frequency change:
*Natural selection
*Genetic drift
*Gene flow

Only natural selection causes adaptive evolution

Question 20

Drivers of macroevolution

Answer 20

Drivers of macroevolution:

*Changing environments
*Speciation and Extinction

Question 21

Techniques in studying evolution..

Answer 21

.Radioactive dating and carbon dating →age of fossil

2.Electron microscopy, histology & imaging →structure of tissues, organs, shells

Question 22

Molecular technologies

Answer 22

Protein electrophoresis

Sanger sequencing (1977)

PCR (1983)

Human Genome Project (1990 –2003)

Next-generation sequencing (2000s onwards) –454, Illumina

New systems: Pac Bio, Nanopore

Bioinformatics –lagging behind

Question 23

What a phage is and how is subjected to evolution?

Answer 23

A phage, short for bacteriophage, is a type of virus that specifically infects and replicates within bacteria. Phages are among the most abundant and diverse entities in the biosphere and play a significant role in regulating bacterial populations and driving bacterial evolution. Here’s an overview of what phages are and how they are subject to evolution:

What is a Phage?
Structure: A typical bacteriophage consists of a protein coat (capsid) that encases its genetic material, which can be either DNA or RNA. Many phages also have a tail structure that helps them attach to and penetrate bacterial cell walls.

Life Cycles:

Lytic Cycle: In this cycle, a phage infects a bacterium, takes over the bacterial machinery to replicate its genetic material, produces new phage particles, and ultimately lyses (breaks open) the bacterial cell to release new phages.
Lysogenic Cycle: Some phages can integrate their genetic material into the host bacterial genome, becoming a prophage. The phage genome is replicated along with the bacterial DNA without killing the host. Under certain conditions, the prophage can reactivate and enter the lytic cycle.
How Phages are Subject to Evolution
Phages evolve through several mechanisms, influenced by genetic variation, selective pressures, and interactions with their bacterial hosts:

Mutation: Phages, like all organisms, can acquire mutations in their genetic material. These mutations occur spontaneously during replication and can result in changes to phage proteins, such as those involved in host recognition, replication, and escape from host defenses. Some mutations can be beneficial, enhancing phage fitness in a particular environment.

Genetic Recombination: Phages can exchange genetic material through recombination processes, especially during co-infection of a bacterium by multiple phages. Recombination can create new genetic variants by mixing different segments of phage genomes, potentially leading to new traits such as expanded host range or resistance to bacterial defenses.

Horizontal Gene Transfer (HGT): Phages can acquire genes from their bacterial hosts or other phages through horizontal gene transfer. This can include genes that confer advantages in host infection, evasion of bacterial defenses, or replication efficiency. For example, phages can carry toxin genes or antibiotic resistance genes, which can be transferred to bacteria, influencing bacterial evolution.

Selective Pressures: Phages are subject to various selective pressures in their environments, such as the presence of specific bacterial hosts, bacterial immune defenses (e.g., CRISPR-Cas systems), and environmental conditions. Phages that are better adapted to these pressures are more likely to replicate and persist. For instance, phages that evolve mechanisms to evade bacterial CRISPR defenses will have a selective advantage.

Host Interaction: The co-evolutionary arms race between phages and their bacterial hosts drives the evolution of both parties. Bacteria evolve defense mechanisms such as restriction-modification systems, CRISPR-Cas systems, and surface receptor mutations to resist phage infection. In response, phages evolve countermeasures to overcome these defenses, such as anti-CRISPR proteins and mutations that alter their attachment proteins.

Environmental Factors: Environmental changes, such as shifts in bacterial community composition, temperature, pH, and nutrient availability, can influence phage evolution. Phages that can adapt to changing conditions will have a higher likelihood of survival and replication.

Summary
Phages are viruses that infect bacteria and are subject to evolution through mutation, genetic recombination, horizontal gene transfer, selective pressures, and interactions with their bacterial hosts. This evolutionary process leads to a dynamic and ongoing co-evolutionary relationship between phages and bacteria, significantly impacting microbial ecology and evolution.