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Population Genetics

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Biology

Most individuals in a population do not look exactly the same. Think of a group of plants- even if they belong to the same species and look similar in general, some might be taller, others may have more leaves, or their flowers might be a little different in coloration. These traits in an individual (such as height, number of leaves, and flower coloration in plants) are dictated by the genetic information that this individual carries. To assess genetic similarities or differences among individuals, we need to study this at the population level.

Population genetics refers to the study of the genetic variation among the individuals within and between populations and the evolutionary mechanisms that influence this variation.

A simple definition of a population is a group of organisms from the same species that live in a specific area and naturally interact and breed. When we talk about the genotype, we refer to an organism's genetic makeup. If we want to refer to the total set of genes and alleles for all organisms in a population, we call it a gene pool.

We mainly assess genetic variation in population genetics by determining the frequency of genes and alleles within populations and if these change over time and/or space. The proportion of a specific genotype within a population is called its genotype frequency. However, the proportion of a specific phenotype within a population is called its phenotype frequency. An allele frequency is the proportion of a specific allele within a population.

The field of population genetics represents an extension of Gregor Mendel's heredity principles, integrated with Darwin's theory of evolution by natural selection. Let's first have a quick review of the main terms from mendelian genetics that we will use in population genetics:

  • The trait color of the eyes in humans is determined by the genes inherited from our parents. A gene has a specific location on a chromosome, called the locus (plural loci). The gene for eye color has different variants or alleles, which determine the different colors like brown, blue, green, etc. The brown color in eyes is dominant over the other colors. When a person has one allele for the brown color and the other for the blue color, their eyes will be brown because it is the dominant allele (the blue allele would be recessive). Thus their genotype will be constituted by two different alleles (heterozygous genotype), but their phenotype will be brown eyes.

When there is complete dominance of an allele over the other, the homozygous dominant (AA) and the heterozygous (Aa) genotypes have the same dominant phenotype (brown eyes). Only the recessive homozygotes (aa) expresses the recessive phenotype (blue eyes).

Population Genetics Example

Let's see an example to understand how these definitions and concepts relate to population genetics. Think of a hypothetical plant population of 1000 individuals. These plants are now in the flowering season, and there are some individuals with purple flowers and others with white flowers. Researchers found that this population has two alleles for this locus: one dominant and one recessive allele. They also studied the genetic composition of all individuals in this population, so we know the genotype and phenotype for each individual: AA (purple flower) = 460, Aa (purple) = 430, aa (white) = 110.

Alleles are usually represented by letters in population genetics. A dominant allele is represented by a capital letter (A) and the recessive one by the corresponding lower-case letter (a). You can use any letter you want, but we usually start with A/a and follow the alphabetical order if we add other genes for other traits.

The allele for the purple color is dominant over the white one. We know that because, as we saw above, two genotypes have the same phenotype. Can you identify these genotypes? (you can check the table below). Now let's fill this table with the information we have:

We can find any frequency by counting the number of individuals (n) with a certain phenotype and dividing this by the total number of individuals (N) in the population:

Frequency of phenotype X = n (number of individuals with phenotype X)

N (total number of individuals in the population)

And you would do the same for any genotype or allele.

PhenotypeGenotypeNumber of individuals (n)Calculating genotype frequencyGenotype frequency
Dominant (purple)AA460460/10000.46
Aa430430/10000.43
Recessive (white)aa110110/10000.11
Total (N)10001000/10001

The total frequency for any trait we study is always 1, which means that the frequencies of all genotypes in a population add up to 1 (AA + Aa + aa = 1), the same for alleles (A + a = 1). Frequencies always go from 0 to 1 (as percentages always go from 0 to 100%). In population genetics, a frequency of 0 would mean that an allele is not present in the population, while a frequency of 1 means the allele is the only one present in the population; in this case, the allele is fixed in the population.

Factors Affecting Population Genetics

The allele and genotype frequencies we calculated in the previous example are like a snapshot of that population at a certain point in time or space. Do you think these frequencies will remain the same over time? It is common for allele frequencies in a population to change over time, which means a population has evolved. It is important to remember that while natural selection acts on individuals, the population evolves. When allele frequencies change in a relatively short time or a few generations, it is called microevolution (which usually refers to changes at the population level).

If a population's allele and genotype frequencies do not change across generations, it means it is not evolving. Such a population is in Hardy Weinberg equilibrium. You can learn more about this here.

In addition to natural selection, other evolutionary processes that affect allele frequency are:

  • mutation
  • nonrandom mating
  • genetic drift
  • genetic flow.

These mechanisms can affect a population at any time, and several can act upon an allele or gene simultaneously. Each mechanism's effect on a population varies and can increase or decrease genetic variation, allele frequency, or adaptation.

Population Genetics Factors affecting population genetics StudySmarter Factors affecting population genetics,

Mutations

Mutations are unpredictable changes in the nucleotides that form a DNA sequence. These are the base for genetic variation since mutations can produce new alleles. A mutation occurs in individual organisms, and for a mutation to have a long-term effect on the population, it must be heritable to be transmitted to the subsequent generations. When a mutation happens in somatic cells (body cells), it affects the organism, but it is not transmitted to the next generation (offspring). For a mutation to be heritable, it must occur in a reproductive cell (gametes = sperm or egg). Although mutations are important for creating genetic variation, they do not happen often enough to affect allele frequency. However, the effect can be significant when natural selection or other evolutionary mechanisms act on these mutations.

Nonrandom Mating

In wild populations, individuals usually choose another individual for breeding based on the phenotype (indirectly choosing the corresponding genotype). For example, female birds might prefer to mate with male birds that are similar in coloration. In other words, not all individuals will have the same probability to breed, so it is not random. Nonrandom mating can change the genotype frequencies, but not the allele frequencies, within a population (thus, its effect on evolution is debatable).

Genetic Drift

Genetic drift is a random change in the allele frequencies within a population.

Genetic drift causes a reduction in the genetic variability in the population, and the changes caused by genetic drift are usually not adaptive (because they are random, caused by chance). Random natural disasters such as hurricanes, flooding, or landslides can affect animal and plant populations. Many individuals may die due to these random events, even if they are well adapted to their environment. The key factor here is that these drift effects are stronger in small populations because a dramatic reduction in an adaptive allele or genotype can decrease the overall fitness of that population. It is less likely that a large population will lose a significant percentage of these adaptive alleles or genotypes. A sudden reduction in population size (and its genetic variability) caused by adverse environmental conditions is a bottleneck. When a small part of a population colonizes a new area, it is called the founder effect.

You can learn more about genetic drift here.

Gene Flow

Many animals move from their birth population to a different one during the breeding season; this is a type of migration. Migrants can introduce a new allele to a population, or if it carries the same alleles already present in the population, they can change the frequency of the allele. Gene flow is a movement of alleles between populations and can cause changes in allele frequency. Interchanging alleles between two populations tend to counteract the effects of natural selection and genetic drift; hence, genetic flow usually decreases the differences or variations between these populations.

You can learn more about genetic flow here.

Natural Selection

The genotypes (and corresponding phenotypes) with greater survival and reproduction probabilities for a specific environment will contribute more offspring to the next generation through natural selection. Natural selection causes a change in adaptive allele frequency (higher survival and reproduction probabilities). Natural selection acts on the phenotype of an individual, but it is the population that adapts to a particular environment.

You can learn more about natural selection here.

Population Genetics - Key takeaways

  • Population genetics assess the genetic variation within populations. This occurs mainly by determining the frequency of alleles and genotypes and if these change over time and/or space.
  • In population genetics, a frequency of 0 means that an allele is not present in the population, while a frequency of 1 means the allele is the only one present. In this case, the allele is fixed in the population.
  • It is common for allele frequencies in a population to change over time, which means a population has evolved.
  • Natural selection is not the only way evolution occurs; other evolutionary processes are mutation, nonrandom mating, genetic drift, and genetic flow.
  • Mutations are the basis for genetic variability on which natural selection acts since mutations can produce new alleles. For a mutation to have a long-term effect on the population, it must be heritable and transmitted to subsequent generations. In other words, it must occur in reproductive cells (gametes = sperm or eggs).
  • Nonrandom mating usually changes the genotype frequencies within a population, but not the allele frequencies.
  • Natural selection causes a change in adaptive allele frequency, resulting in higher survival and reproduction probabilities.
  • Genetic drift causes a reduction in the genetic variability of the population. Usually, these changes are non-adaptive (because they are random, caused by chance). These effects are stronger in smaller populations than in larger populations.
  • Genetic flow usually makes populations more similar (decreases the difference or variation between populations).

Population Genetics

Population genetics is the study of the genetic variability among the individuals within and between populations, and the evolutionary mechanisms that influence this variability.

The biological significance of genetic diversity between populations is that each population is more fit to local conditions, according to the combination of traits that gave them an advantage in that environment. Moreover, maintaining genetic diversity allows a population to adapt to future changes in the environment.

There are three main sources of genetic variation in a population: mutations (create new genes/alleles), gene flow/migration (introduce new genes/alleles), and sexual reproduction (create new combinations of genes/alleles). 

Genetic diversity increases a population´s chances of survival by providing a more diverse array of traits that increases the probability of some individuals in the population to adapt to changing environmental conditions and pass on these traits to the next generations.

Genetic variation can be maintained in most populations through the same mechanisms that can increase it: mutations, gene flow/migration, and sexual reproduction. Another important factor would be shifting environmental or external conditions, as selection would favor different genotypes adapted to specific conditions at a different time or space.

Final Population Genetics Quiz

Question

The genetic composition for an organism constitutes its genotype, while the genetic information for a population is: 

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Answer

gene pool 

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Question

If all the copies of a certain locus have the same allele through a population, then the allele frequency for that allele is:

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Answer

1.0 

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Question

What does population genetics study? 


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Answer

The genetic variation among the individuals within and between populations and, the evolutionary mechanisms that influence this variability

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Question

How can we assess the genetic variation in a population? 


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Answer

By determining the frequency of genes and alleles within populations and, if these change over time and/or space 

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Question

When an allele has complete dominance over the other, which genotypes will express the dominant phenotype? 


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Answer

The homozygous dominant (AA) and the heterozygous (Aa) genotypes 

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Question

What does it mean when an allele is fixed in a population? What would its frequency be? 


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Answer

It means that is the only allele present in that population, and it would have a frequency of 1

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Question

Mention the five evolutionary processes that can influence the allele frequency in a population: 


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Answer

mutation, nonrandom mating, genetic drift, genetic flow and, natural selection 

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Question

What does it mean that the allele frequencies within a population have changed over time? 


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Answer

It means that the population has evolved for that trait

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Question

Which evolutionary mechanism(s) can increase the genetic variation in a population?

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Answer

mutation 

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Question

Which evolutionary mechanism(s) can decrease the genetic variation in a population?

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Answer

genetic drift

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Question

When does nonrandom mating happen? 


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Answer

When individuals choose a mating partner based on some phenotypic trait. Thus, not all individuals in a population have the same probability to breed. 

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Question

Why are genetic drift effects more important in small populations? 


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Answer

Because a dramatic reduction in an adaptive allele or genotype can decrease the overall fitness of that population. It is less likely that a large population will lose a significant percentage of these adaptive alleles or genotypes. 

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Question

Which of the five evolutionary mechanisms that drive evolution, is nonrandom and causes mainly adaptive changes in a population? 


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Answer

Natural selection 

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Question

Why does gene flow usually make populations more similar to each other? 

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Answer

it decreases the difference or variation between populations

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Question

Only small populations are subject to genetic drift.

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Answer

False

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Question

The main effects that genetic drift might have within populations, especially small populations, are (select all that apply): 

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Answer

reduction in genetic variation and 

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Question

How do natural selection and genetic drift differ in their effects on a population?

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Answer

Natural selection tends to lead to adaptive changes (that increase the survival and reproductive probabilities) while changes caused by genetic drift are usually nonadaptive

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Question

How do natural selection and genetic drift differ in their causes?

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Answer

Natural selection occurs because there are differential reproductive and survival probabilities among individuals in a population, and beneficial alleles will be passed on to the next generation, while harmful ones will be reduced in frequency or eliminated. Genetic drift is caused by random events, not related to an allele being beneficial or harmful.

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Question

How can genetic drift lead to speciation?

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Answer

The random shifts in alleles frequencies in each population can increase the differences among populations of the same species. If one population continues to diverge and isolate from the other ones, it can eventually lead to speciation.

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Question

When a large part of a population is suddenly wiped out due to a dramatic environmental event, this is called: 

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Answer

bottleneck 

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Question

When a small part of a population colonizes a new area, this is called: 

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Answer

founder effect

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Question

Which ones of the following can be considered random events that can cause genetic drift?

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Answer

wildfire

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Question

Gene flow refers to the movement of only adult individuals between populations

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Answer

False, gene flow also refers to the movement of gametes between populations (like with wind-pollinated plants) 

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Question

Would you expect more gene flow between populations of frogs or between populations of birds? 

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Answer

Between populations of birds, as they can move greater distances (they have more mobility) 

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Question

Gene flow _____ the genetic variation in a population, and ____ genetic differences between populations? 



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Answer

increases, decreases 

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Question

A gene or allele introduced in a population will always be beneficial and therefore its frequency will increase with next generations. 


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Answer

False

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Question

When gene flow is reduced or stops between two populations: 


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Answer

each population continues to adapt to their local conditions and their genetic pool keeps diverging 

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Question

Gene flow, genetic drift, and natural selection are similar because they: 


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Answer

can produce changes in allele frequencies in a population 

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Question

Contrarily to natural selection, both gene flow and genetic drift:  


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Answer

are random and usually lead to nonadaptive evolution 

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Question

Contrarily to gene flow, both genetic drift and natural selection (select all that apply): 

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Answer

reduce genetic variation within a population

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Question

Imagine a population of birds subdivided into two populations A and B.  Each population lives at the top of a mountain and are separated by a valley. Initially, there were blue birds in both subpopulations and green individuals were only found in population A. Twenty years later, green individuals are also present in population B. What is the most probable scenario?

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Answer

an increase in gene flow between the two populations

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Question

In a population of 1000 plants, purple flower color (A) is dominant over white (a). If p = 0.8 and q = 0.2, how many individuals would you expect to be homozygous dominant, heterozygous, and homozygous recessive? How many plants would you expect to have purple flowers, and how many would have white flowers?

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Answer

AA: 640, Aa: 320, aa: 40; purple: 960, white: 40

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Question

A population is in Hardy Weinberg equilibrium if:

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Answer

there is no natural selection 

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Question

Which of the following would violate the conditions of Hardy-Weinberg equilibrium?

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Answer

a population undergoing natural selection

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Question

A geneticist is studying a population of plants. She examines samples of the population’s DNA over several years, and finds the following data:

Generation

Allele A frequency

Allele a frequency

1

0.85

0.15

2

0.76

0.24

3

0.64

0.36

4

0.51

0.49

5

0.42

0.58

Does this provide evidence of natural selection in this population? 

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Answer

Yes, because it shows that the previously favorable or neutral allele A is now being selected against in favor of allele B.

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Question

You are studying a gene with only two alleles: dominant C and recessive c. In a population of 500 organisms, the proportion expressing the homozygous recessive phenotype is 0.42. The calculated allele frequencies p and q, respectively, have values that are closest to:

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Answer

0.35 and 0.65

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Question

A population in genetic equilibrium has a frequency of the recessive homozygous genotype (tt) of 0.16. Calculate the allele frequencies for T and t, and the expected frequencies for genotypes TT and Tt.


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Answer

t = 0.4, T = 0.6; TT = 0.36, Tt = 0.48

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Question

The dominant phenotype has a frequency of 0.96 in a population in Hardy Weinberg equilibrium. Calculate the allele frequency for A and a, and the expected frequencies for AA, Aa and aa.

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Answer

A = 0.8, a = 0.2; AA = 0.64, Aa = 0.32, aa = 0.04

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Question

The genotype frequencies for a population were estimated in BB = 0.6 and bb = 0.4. Does this population satisfy the Hardy Weinberg principle of equilibrium?

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Answer

No, this population does not satisfy the Hardy Weinberg equilibrium. There are 2 alleles in the population, but 0 heterozygotes, thus it does not meet the mathematical requirement of   (furthermore, if you try to get the alleles frequencies from BB and bb, they do not add up to 1)

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Question

If all the copies of a certain locus have the same allele through a population, then the allele frequency for that allele is:

Show answer

Answer

1.0 

Show question

Question

The Hardy Weinberg principle states that:

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Answer

it does not matter if an allele is dominant or recessive, its frequency stays stable from one generation to the next

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Question

How does reducing gene flow cause speciation?

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Answer

When gene flow is reduced or stops between two populations, each population continues to adapt to local conditions and their genetic pool keeps diverging, eventually leading to speciation.

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Question

Which one of the following mechanisms can alter a population’s allele frequencies? 

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Answer

genetic drift 

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Question

When individuals choose their mates based on some trait, the mixing of gametes will not be random. Which of the conditions for Hardy-Weinberg equilibrium is being violated?

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Answer

random mating

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Question

A hurricane hit a small frog population on an island, a large portion of the population dies. Which of the conditions for Hardy-Weinberg equilibrium is being violated?

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Answer

no genetic drift 

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Question

A study estimated that each year, about 10% of new individuals in a bird population come from other populations. Which of the conditions for Hardy-Weinberg equilibrium is being violated?

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Answer

no gene flow 

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Question

Due to the introduction of an invasive butterfly, plants with red flowers are more frequently eaten by the caterpillars than plants with pink or white flowers in the same population. Therefore, red flower plants now produce less offspring than the other two phenotypes. Which of the conditions for Hardy-Weinberg equilibrium is being violated?

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Answer

no natural selection 

Show question

Question

Which of the following are usual consequences of genetic drift in small populations? 

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Answer

nonadaptive changes in allele frequency 

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Question

In the water snake example from the article, snakes with a band pattern coloration are maintained in the islands’ populations because: 

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Answer

The band pattern allele is reintroduced constantly by migrant snakes 

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Question

How is the introduction of new variants through gene flow similar to a mutation?

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Answer

Both are random. The effect of natural selection to increase or decrease the frequency of an introduced allele will depend on the allele’s impact (beneficial, neutral, or disadvantageous).

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