BIOL1400 4th Exam

Evolution=

central theme of Biology

Explains unity(shared DNA, metabolism) and diversity (species variety)

Darwin’s key ideas

decent with modification, natural selection

evidence for evolution

fossils, direct observation of natural selection, experiments, DNA comparisons

Basis of evolution

Darwin: natural selection drives evolution

Mendell: discovered inheritance patterns → explained how traits are passed from parents to offspring.

Genetic differences provide the raw material of evolution

Genetic variation

Phenotypic, genotypic, Polygenetic, single gene traits

mutations

creates new alleles, source of genetic variation, only mutations in gametes impact evolution

sexual reproduction

creates most genetic variation, crossing over, independent orientation, random fertilization

gene pool

all copies of every allele in a population

Darwin’s observations

variation among individuals in populations, heritability, populations produce more offspring than can survive and resources allow

natural selection

differential survival and reproduction based on heritable traits (non-random)

evidence of natural selection

Galapagos finches: Dry years → large seeds → bigger beaks survive → average beak depth increases

Pesticide resistance

Head lice resistance

microevolution

change in allele frequencies in a population over generations

Natural selection, genetic drift, gene flow

Genetic drift

random changes in allele frequencies stronger in smaller populations

bottleneck effect

founder effect

bottleneck effect

drastic reduction in population

founder effect

new population started by few individuals

gene flow

movement of alleles between populations through migration/gametes, reduces differences between populations

adaptive evolution

better fit between organisms and their environment

relative fittness

number of fertile offspring an individual produces relative to others. Fittest individuals are those that contribute most genes to the next generation

Natural selection alters variations

natural selection acts on phenotypes

Directional

Stabilizing

Disruptive

Directional selection

favors one extreme phenotype

Stabilizing selections

favors intermediate phenotypes

Disruptive selection

favors both extreme phenotypes

Sexual selection

form of natural selection where certain traits increase mating success

Intrasexual

Intersexual/mate choice

Intrasexual selection

competition for mates

Intersexual/mate choice selection

females pick based on best looks → good genes

sexual dimorphism

noticeable difference in appearance/size between sexes: males are showier

Evolution of Drug-resistant microorganisms

antibiotic resistance develops if misused

if you miss a dose, it gives the microorganisms a chance to adapt and become resistant to the drug

natural selection in microbes

random mutations generate variants, nonrandom selection favors survival of resistant strains, evolution is continuous and dynamic, making it challenging to eradicate disease

Why organisms are imperfect

selection can only act on existing variation, historical constraints, adaptations are compromises, interaction of chance(storms), natural selection(small population) and environment(unpredictable)

Why HIV evolves quickley

high mutation rate during replication (reverse transcriptase lacks proof reading) viral variants some resistance to drugs due to mutations

Due to rapid evolution, making an HIV vaccine is very difficult

Viral replication cycles

Lytic cycle- destroys host cell

Lysogenic cycle- doesn’t immediately destroy host

membranous envelopes with glycoprotein spikes

animal viruses, help entry/exit from host cells, DNA/RNA

Plant viruses

most RNA viruses, spread through plasmodesmata and vectors (insects)

Emerging viruses

new/rapidly spreading viruses

How viruses emerge

mutations, cross-species transmission, isolated populations

Retrovirus

HIV, RNA virus that makes DNA via reverse transcription

Explain why heritable differences in organisms’ phenotypes must be due to genetic differences. Why aren’t all phenotypic differences heritable? Give an example of a phenotypic difference that is heritable and one that is not heritable

Heritable traits come from genes passed to offspring. Some traits come from the environment only. Examples: Heritable- Eye color; Not heritable- muscle size from exercise.

If all the individuals in a population had identical genotypes, could the population evolve? If not, why not? If so, how?

If all genotypes are identical -> no evolution by selection (no variation)

Population could evolve later if new mutations or gene flow occur

Explain why an individual (e.g. you) CANNOT evolve.

Evolution = change in allele frequencies in a population over generations

An individual's genes don’t change - only populations evolve

Your friend tells you that polar bears evolved to have thick fur because it was necessary for them to survive in cold temperatures. Correct your friend’s misunderstanding.

Polar bears didn’t evolve thick fur because they needed it

Bears with naturally thicker fur survived better, passed on genes

Evolution acts on existing variation, not need or effort

Give at least two reasons that evolution cannot lead to organisms that are perfectly suited for their environment. Use hypothetical (or real) examples to illustrate your reasons

Trade offs- a trait helping one function can harm another

Changing environments- perfect today may fail tomorrow

Evolution = good enough, not perfect

Explain why mutations are important in the context of evolution even though they rarely cause significant changes in allele frequencies.

Mutations= sources of new alleles

Most have little effect, but without them, no new variation -> no evolution

Which mechanism(s) of microevolution, if any, would be likely to increase genetic diversity (variation) in a population? Decrease genetic diversity? Explain your reasoning

Mechanism	Effect on Diversity	Why
Mutation	↑ Increases	Creates new alleles
Gene flow	↑ Increases	Adds alleles from other populations
Genetic drift	↓ Decreases	Random allele loss
Natural selection	↑ or ↓	Depends on type of selection
Nonrandom mating	↓	Reduces heterozygosity

Which of the following statements about evolution is true?

Evolutionary change can increase the frequency of a harmful trait in a population.

Evolutionary change CANNOT lead to organisms that are perfectly suited for their environment. Which of the following correctly explain(s) why?

A trait that is beneficial in some ways can decrease an organism’s ability to survive and reproduce in other ways.

Environmental conditions can change.

Genetic variation arises randomly in a population.

ALL OF THE ABOVE!!!!

Which of the following, if any, correctly describes evolution?

A. Both individuals and populations can undergo evolutionary change.

B. Natural selection leads to organisms with the ideal set of traits to survive and reproduce in their current environment.

C. Some mechanisms of evolutionary change can introduce new alleles into a population in order to generate specific traits.

D. A population’s allele frequencies can only be altered by one mechanism of microevolutionary change at any given time.

E. NONE OF THE ABOVE!!!

The goal of the analysis was to test the hypothesis that genetic drift leads to decreased genetic variation in small populations (16 flies). What would be an appropriate control group ?

Populations of flies that start with 50% of each allele and are kept at 100 individuals each generation.

Explain why/how genetic drift influences the allele frequencies of all populations at all times

Random fluctuations in the frequency of alleles from one generation to the next. This process is driven by chance and can lead to the loss of genetic variation, the fixation of certain alleles, or the emergence of new traits. Key words/phrases: Random sampling, founder effect, bottleneck effect, inheritance, and small population size.

Explain why the allele frequencies of smaller populations are more likely to be significantly altered by genetic drift vs. the allele frequencies of larger populations.

The limited gene pool of small populations makes random fluctuations more likely to occur and persist. Over time, certain gene variants may become fixed in the population, meaning they are present in every individual, while others may be lost. Key words/phrases: loss of genetic diversity, vulnerable, reduced adaptive potential, susceptible. 

Which of the following correctly describes the relationship between genetic drift and population size?

Small populations are more likely to be affected by genetic drift than large populations.

Gene flow is defined as change in the allele frequencies of a population due to movement between populations. Which of the following is/are examples of gene flow?

Pollen (sperm) from one population of trees is carried by strong winds and fertilizes the eggs of trees in another population.

Use hypothetical (or real) examples to explain the difference between a population bottleneck and the founder effect that are different from the ones we mentioned.  Why are they examples of genetic drift?

Bottleneck- A volcanic eruption kills most of a lizard population, leaving only 5 survivors. 

Founder effect- a few birds blown off course land on an island and start a new colony with different allele frequencies than the mainland.

In both cases, allele frequencies change due to random sampling not selection

Explain why population bottlenecks and the founder effect usually change the allele frequencies in populations.  Why do they lead to situations in which there is an increased chance for genetic drift via random fertilization to lead to additional changes in allele frequencies?

They shrink population size, so the few individuals left carry only a small, random sample of the original alleles

Small populations experience strong effects of chance, including random fertilization which causes further shifts in allele frequencies across generations

If two populations have virtually identical allele frequencies, can gene flow between them lead to evolutionary change?  Why or why not?

No. If allele frequencies are the same, movement of individuals doesn’t change the genetic makeup of either population.

Describe a scenario in which gene flow would be likely to significantly alter the allele frequencies of a population.  Now describe a situation in which gene flow would most likely have little to no effect on allele frequencies

Big effect: a small island population of rabbits receives many migrants from the mainland that carry different coat-color alleles. The small populations allele frequencies shift quickly.

Little effect: a few migrants enter a very large population, and their alleles are diluted with no meaningful  frequency change.

Do you think that gene flow typically increases genetic variation, typically decreases genetic variation, or is equally likely to increase or decrease genetic variation in populations?  Explain your reasoning.

It usually increases variation within populations, because it introduces new alleles.

It can reduce variation between populations by making them more genetically similar.

A group of bears moves from one side of a mountain to join a different population of bears that lives on the other side of the mountain.  Is this an example of gene flow?  If so, why?  If not, why not?

Yes, if they interbreed with the bears on the other side, because alleles move between populations. 

If they do not interbreed, then no gene flow occurs.

Why are small populations sizes such a big concern for scientists working to preserve endangered species?

Small populations are vulnerable to genetic drift, inbreeding, loss of genetic diversity, and random events, which can reduce fitness and increase extinction risk.

Which of the following correctly describes the relationship between genetic drift and population size?

Small populations are more likely to be affected by genetic drift than large populations

Gene flow is defined as change in the allele frequencies of a population due to movement between populations. Which of the following is/are examples of gene flow?

Pollen (sperm) from one population of trees is carried by strong winds and fertilizes the eggs of trees in another population.

Which of these mechanisms of microevolution, if any, also favor(s) traits (i.e. specifically lead to increased frequency of traits) that can increase an individual’s fitness?

A. mutations

B. gene flow

C. genetic drift

D. All of the above

E. NONE OF THE ABOVE!!!

Reminder: These mechanisms are equally likely to increase OR decrease the frequency of traits that improve an organism’s fitness

Based on your understanding of evolution, which of the following statements provides a reasonable explanation for the increase in vancomycin-resistant bacteria after vancomycin was introduced as a treatment?

A random mutation occurred that allowed bacteria to resist vancomycin, and bacteria with the mutation were able to survive and reproduce better in the presence of vancomycin.

A population of lizards varies in leg length, which is a heritable trait. Their main predators are snakes. Lizards with long legs are able to run more quickly to escape. Lizards with short legs are able to climb trees better to escape. In this situation, natural selection is most likely to have a ________ effect on lizard leg length.

disruptive

Which of the following statements correctly describes natural and/or sexual selection?

Sexual selection could favor a trait that increased an individual’s ability to reproduce, but decreased their ability to survive.

Which of the following statements correctly compare(s) artificial selection and natural selection?

Artificial selection has an end goal; natural selection does not progress towards a particular goal.

Use hypothetical (or real) examples to explain the difference between a population bottleneck and the founder effect that are different from the ones we mentioned.  Why are they examples of genetic drift?

Bottleneck- A volcanic eruption kills most of a lizard population, leaving only 5 survivors. 

Founder effect- a few birds blown off course land on an island and start a new colony with different allele frequencies than the mainland.

In both cases, allele frequencies change due to random sampling not selection

Explain why population bottlenecks and the founder effect usually change the allele frequencies in populations.  Why do they lead to situations in which there is an increased chance for genetic drift via random fertilization to lead to additional changes in allele frequencies

They shrink population size, so the few individuals left carry only a small, random sample of the original alleles

Small populations experience strong effects of chance, including random fertilization which causes further shifts in allele frequencies across generations

If two populations have virtually identical allele frequencies, can gene flow between them lead to evolutionary change?  Why or why not?

No. If allele frequencies are the same, movement of individuals doesn’t change the genetic makeup of either population

Describe a scenario in which gene flow would be likely to significantly alter the allele frequencies of a population.  Now describe a situation in which gene flow would most likely have little to no effect on allele frequencies

Big effect: a small island population of rabbits receives many migrants from the mainland that carry different coat-color alleles. The small populations allele frequencies shift quickly.

Little effect: a few migrants enter a very large population, and their alleles are diluted with no meaningful  frequency change

Do you think that gene flow typically increases genetic variation, typically decreases genetic variation, or is equally likely to increase or decrease genetic variation in populations?  Explain your reasoning

It usually increases variation within populations, because it introduces new alleles.

It can reduce variation between populations by making them more genetically similar

A group of bears moves from one side of a mountain to join a different population of bears that lives on the other side of the mountain.  Is this an example of gene flow?  If so, why?  If not, why not?

Yes, if they interbreed with the bears on the other side, because alleles move between populations. 

If they do not interbreed, then no gene flow occurs.

Why are small populations sizes such a big concern for scientists working to preserve endangered species?

Small populations are vulnerable to genetic drift, inbreeding, loss of genetic diversity, and random events, which can reduce fitness and increase extinction risk.

What factors determine the relative evolutionary fitness of an individual?  Do only the most evolutionarily fit individuals in a population pass their genes on to the next generation

Fitness = how many viable offspring an individual leaves relative to others. Many individuals contribute genes; not only the “most fit,” just those that successfully reproduce

Explain why “survival of the fittest” is NOT an appropriate way to define natural selection.  Write a definition for natural selection using your own words

 It overemphasizes survival and implies perfection; selection acts on reproduction, not just survival. Natural selection: individuals with heritable traits that improve reproductive success leave more offspring, changing population traits over time.

Explain how natural selection changes allele frequencies in populations.  What determines which alleles are beneficial?

Alleles that improve survival/reproduction become more common. “Beneficial” depends on the current environment.

What evidence would you need to support the hypothesis that a trait is an adaptation in a particular species?

You must show the trait is heritable, increases fitness, and evolved in response to specific environmental pressures

Some insects look very similar to the flowers of a particular species of plant that’s in the area where they live.  The insects’ shape and coloration is considered an adaptation because it improves their ability to hide from predators.  If that species of plant suddenly disappeared, would the shape and coloration of the insects still be considered an adaptation?  Why or why not?

Only if the trait still increases fitness. If it no longer helps them avoid predators, it is no longer adaptive in that environment

In dry years, short grass in a field has a higher relative fitness than tall grass.  In wet years, tall grass survives and reproduces better than short grass.  Is this an example of stabilizing, disruptive, or directional selection?  Explain your answer

Directional selection—the favored extreme switches depending on wet vs dry years.

A population of lizards varies in heritable characteristics such as color, tree climbing ability, and ability to run on the ground.  The primary predators of the lizards are birds and foxes.  Use this scenario to describe a situation in which stabilizing selection would be observed.  Under what conditions might directional selection be observed?  Disruptive selection?  (Feel free to introduce more heritable traits that vary in the population and/or other environmental factors.)

Stabilizing: Medium climbing ability avoids both foxes (ground) and birds (high branches).

Directional: If fox predation increases, better climbers are favored.

Disruptive: Birds attack high branches and foxes attack the ground, so only very high or very low perchers survive.

Explain why traits favored in sexual selection may decrease an individual’s ability to survive

They can be costly—bright colors, calls, or large structures attract mates and predators.

Do you think artificial selection typically increases or decreases genetic variation?  Explain your reasoning.

 Usually decreases it because humans repeatedly breed a small set of desired traits.

Propose a hypothesis to explain why, when grown in the wild, many species of artificially selected plants have a lower relative fitness than wild varieties.

Selected traits suit human care, not natural environments, so they compete poorly, resist stress less, or reproduce less effectively

For each mechanism of microevolution, describe a hypothetical (or real) scenario other than the ones from class to illustrate how the mechanism acts to change the distribution of heritable phenotypes (allele frequencies) in a population.

• Mutation: A random DNA change creates a new coloration allele in beetles.

• Gene flow: Migrating wolves bring new coat-color alleles into a pack.

• Genetic drift: A storm kills most island birds randomly, changing allele frequencies.

• Natural selection: Pesticide-resistant insects survive and leave more offspring.

• Sexual selection: Peahens prefer brighter males, increasing those alleles.

Describe two different scenarios in which a population could undergo rapid evolutionary change (i.e. within one generation)

• A disease kills only individuals lacking a resistance allele.

• A flood isolates a tiny surviving subset of a population (strong drift).

Describe two different scenarios in which evolution could introduce new alleles into a population.

• Mutation creates a novel enzyme.

• Immigration brings new alleles into a previously isolated population

Explain why viruses must enter cells to replicate (reproduce).

They lack ribosomes, enzymes, and energy systems; they need host cell machinery to make proteins and copy genomes

What are the three main ways viruses differ from one another?

Genome type (DNA/RNA; single/double-stranded), capsid/envelope structure, and host range

In what ways do viruses differ from cells? What similarities do they share?

Viruses are acellular, cannot reproduce alone, and lack metabolism. Both have genetic material and can evolve

Describe the structure of the HIV virion (make a sketch if it helps) and explain how HIV’s genome is different from the genome of a cell

Spherical enveloped virus with glycoprotein spikes, capsid, enzymes (reverse transcriptase, integrase, protease). Genome = two copies of single-stranded RNA, not double-stranded DNA like cells

Identify the steps involved in the life cycle of HIV.

 Bind → enter → reverse-transcribe RNA → integrate DNA → transcribe/translate → assemble → bud → mature

The influenza virus, which causes the flu, has a virion structure similar to HIV and also has a single stranded RNA genome. Influenza viruses can infect epithelial (skin cells), but not T cells. Propose a hypothesis to explain why. Use the experiment we discussed in class to design an analysis to test your hypothesis. Identify your experimental condition and all of the essential control conditions.

Hypothesis: Epithelial cells—but not T cells—express the receptor influenza binds.

Test: Expose both cell types to identical influenza doses. Controls:

• Positive control: cells known to be infectable by influenza.

• Negative control: cells lacking the receptor or inactivated virus.

Measure viral entry/replication via fluorescence or PCR.

Which of the following statements, if any, correctly describes the mechanisms of microevolution?

Gene flow can increase the frequency of an allele that decreases an individual’s relative fitness.

What control group must be included to be able to interpret the results of this experiment?

Samples of T cells not treated with any antibodies and infected with HIV.

Describe the process by which HIV enters cells including the names of the cellular receptor proteins HIV uses to attach to cells

HIV binds CD4 plus a coreceptor(CCR5) on the host cell. Binding triggers fusion of the viral envelope with the cell membrane.

Describe the basic steps of HIV’s life cycle after the virus enters a cell. Include the functions of the two HIV enzymes we discussed

1. Entry/fusion

2. Reverse transcriptase makes DNA from viral RNA

3. DNA enters nucleus; integrase inserts it into host genome

4. Host machinery transcribes and translates viral genes

5. Assembly and budding

6. Maturation by protease

Think about functions of HIV reverse transcriptase, cellular DNA polymerase, and cellular RNA polymerase. In what ways are the three enzymes similar? How are they different?

Similar: All copy nucleic acids

Different: RT copies RNA -> DNA and is error-prone, DNA polymerase copies DNA -> DNA high fidelity, RNA polymerase copies DNA -> RNA also more accurate than RT

Why is it necessary for certain HIV enzymes (e.g. reverse transcriptase) to be present in HIV virions?

Host cells cannot convert RNA -> DNA or integrate viral DNA, so HIV must bring reverse transcriptase ( and other essential enzymes) with it

Once HIV enters a cell, the cell is permanently infected with HIV (i.e. it can’t get rid of the virus), and when the cell divides, the daughter cells produced are also infected. What step in HIV’s life cycle explains this?

The integration of viral DNA into the host chromosome means every cell division copies the protovirus into daughter cells

Explain why integration of the HIV genome into a cell’s chromosome is required for production of new virions

Once integrated, the viral DNA is treated as host DNA, so the cell’s machinery transcribes and translates viral genes needed for new virions

HIV can undergo rapid evolutionary change. Based on what you know about the role of mutations in evolution, explain why the high error rate of reverse transcriptase plays an important role in the rapid evolution of HIV populations

More replication errors = more mutations, creating genetic diversity that speeds evolution and adaptation.