1. Allele Frequency

In the previous tutorial, we introduced some basic population genetics concepts, including gene pool, allele, and fixed alleles.

Allele frequency is another key concept in population genetics. An allele is an alternative version of a gene. Allele frequency is how common an allele is in a gene pool. It’s usually stated as a decimal or a percentage.

1.a. Counting Alleles

Here’s an example. The table below represents the alleles for one gene in a population of 20 mice. In this population, we’re going to look at two phenotypes: albino (white, with no pigmentation), and normal (pigmented). Two alleles control this phenotype: “A” codes for normal color, and “a” codes for albino coloration.

Normal (pigmented)

Albino

Coloration Alleles of 20 Mice
aa Aa AA AA aa
AA aa Aa Aa AA
AA aa AA AA aa
Aa Aa aa Aa aa

To find the frequency of the “a” allele, start by counting each “a” allele within this gene pool. If an individual’s genotype is “aa” then count two “a” alleles. If the individual is “Aa,” then count one “a” allele. In other words, in the first row, you’d count a total of five “a” alleles.

Go ahead and count up all the “a” alleles in each row of the gene pool. Drag the correct number into the column on the right. Then drag the total into the lower right .

[qwiz style = “border: 2px solid black;” qrecord_id=”sciencemusicvideosMeister1961-Pop-gen: Counting Alleles Exercise 1″]

[h]Counting alleles

[q labels = “top”]

Count up the number of “a” alleles in each row
aa Aa AA AA aa ___
AA aa Aa Aa AA ___
AA aa AA AA aa ___
Aa Aa aa Aa aa ___
Total of “a” alleles in this population ___

[l]1

[fx] No, that’s not correct. Please try again.

[f*] Correct!

[l]2

[fx] No. Please try again.

[f*] Excellent!

[l]3

[fx] No, that’s not correct. Please try again.

[f*] Great!

[l]4

[fx] No, that’s not correct. Please try again.

[f*] Good!

[l]5

[fx] No, that’s not correct. Please try again.

[f*] Excellent!

[l]6

[fx] No, that’s not correct. Please try again.

[f*] Great!

[l]7

[fx] No. Please try again.

[f*] Excellent!

[l]8

[fx] No. Please try again.

[f*] Great!

[l]9

[fx] No, that’s not correct. Please try again.

[f*] Good!

[l]10

[fx] No. Please try again.

[f*] Good!

[l]11

[fx] No. Please try again.

[f*] Good!

[l]12

[fx] No. Please try again.

[f*] Correct!

[l]15

[fx] No, that’s not correct. Please try again.

[f*] Good!

[l]20

[fx] No, that’s not correct. Please try again.

[f*] Great!

[/qwiz]

1.b. Figuring out allele frequencies

To figure out the frequency of “a”, take the number of “a” alleles, and divide by the total number of alleles for this gene. Since there are 20 individuals, there are a total of 40 alleles. 20/40 = ½ or 0.5 or 50%.

Here’s a few questions to check to see if you’re getting this.

[qwiz random = “true”;style = “border: 3px solid black;” qrecord_id=”sciencemusicvideosMeister1961-Pop-gen: Allele Frequency”]

[h]Allele frequency

[i]

Normal (pigmented)
Albino

[!!!]Question 1[/!]

[q]In this gene pool, the frequency of “a”, expressed as a fraction, is

Coloration Alleles for 10 Mice
aa aa AA Aa aa
AA aa aa Aa aa

[c]10/20

[c*]14/20

[c]6/20

[f]No. You have to count all the “a” alleles, and then divide by the total number of alleles. From your answer, I’m guessing that you just counted individuals who are “aa.” You have to count the alleles in the heterozygotes, too.

[f]Nice job. There are 14 “a” alleles, so the frequency of “a” is 14/20. Of course, that’s best reduced to 7/10, but that wasn’t an option…

[f]No. You have to count all the “a” alleles, and then divide by the total number of alleles. From your answer, I’m guessing that you counted the “A” allele instead.

[!!!]Question 2[/!]

[q]In this gene pool, the frequency of “a”, expressed as a percentage is

aa aa AA Aa aa
AA aa aa Aa aa

[c]30%

[c]50%

[c*]70%

[c]80%

[c]90%

[f]No. You have to count all the “a” alleles, and then divide by the total number of alleles. Convert to a %. Make sure you count the “a” alleles in the heterozygotes.

[f]No. You have to count all the “a” alleles, and then divide by the total number of alleles. Convert to a %. Make sure you count the “a” alleles in the heterozygotes.

[f]Excellent. There are 14 “a” alleles, out of a total of 20 alleles. 14/20 = 70%

[f]No. You have to count all the “a” alleles, and then divide by the total number of alleles. Convert to a %. Make sure you count the “a” alleles in the heterozygotes.

[f]No. You have to count all the “a” alleles, and then divide by the total number of alleles. Convert to a %. Make sure you count the “a” alleles in the heterozygotes.

[!!!]Question 3[/!]

[q]In this gene pool, the frequency of “A”, expressed as a percentage is

aa aa AA Aa aa
AA aa aa Aa aa

[c*]30%

[c]50%

[c]70%

[c]80%

[c]90%

[f]Excellent. There are 6 “A” alleles, out of a total of 20 alleles. 6/20 = 30%

[f]No. You have to count all the “A” alleles, and then divide by the total number of alleles. Convert to a %. Make sure you count the “A” alleles in the heterozygotes.

[f]No. You have to count all the “A” alleles, and then divide by the total number of alleles. Convert to a %. Make sure you count the “A” alleles in the heterozygotes.

[f]No. You have to count all the “A” alleles, and then divide by the total number of alleles. Convert to a %. Make sure you count the “A” alleles in the heterozygotes.

[f]No. You have to count all the “A” alleles, and then divide by the total number of alleles. Convert to a %. Make sure you count the “A” alleles in the heterozygotes.

[!!!]Question 4[/!]

[q]In this gene pool, the frequency of “A”, expressed as a decimal is

aa aa AA Aa aa
AA aa aa Aa aa

[c]0.2

[c*]0.3

[c]0.5

[c]0.7

[c]0.9

[f]No. You have to count all the “A” alleles, and then divide by the total number of alleles. Convert to a decimal. Make sure you count the “A” alleles in the heterozygotes.

[f]Yes.There are 6 “A” alleles, out of a total of 20 alleles. 6/20 = 0.3

[f]No. You have to count all the “A” alleles, and then divide by the total number of alleles. Convert to a decimal. Make sure you count the “A” alleles in the heterozygotes.

[f]No. You have to count all the “A” alleles, and then divide by the total number of alleles. Convert to a decimal. Make sure you count the “A” alleles in the heterozygotes.

[f]No. You have to count all the “A” alleles, and then divide by the total number of alleles. Convert to a decimal. Make sure you count the “A” alleles in the heterozygotes.

[/qwiz]

2. Allele frequency case study: The Peppered Moth

Let’s apply the idea of allele frequency to a famous case study of evolutionary biology: the peppered moth. This moth has two forms: mostly light colored, with specks of black (which is where the “peppered” part of the name comes from) and a much darker form. The allele for dark coloration is dominant.

Light (left) and dark (right) forms of the peppered moth. Wikimedia commons

The allele frequency for this coloration gene varies in different populations, and has also changed over time. In the mid-1800s, in moth populations that lived in forests where tree trunks were covered with white colored lichens, dark moths were rare (2% of the population), with 98% of the moths having the typical peppered form.

Once you know the frequency of each phenotype, you can use a formula to calculate the allele frequencies (we’ll learn about this formula in the next tutorial in this series). Using that formula, you can determine that the frequency of the recessive allele (for light coloration) was about 99%, while the frequency of the dominant allele was about 1%.

peppered moth(Lichte_en_zwarte_versie_berkenspanner)
Peppered moths, dark (dominant) and light (recessive) phenotypes on a light colored tree. Credit: “Lichte en zwarte versie berkenspanner” by Martinowksy via Wikimedia Commons.

The frequency of the dominant allele was so rare because it produced a phenotype which, in certain forests, was deadly. It’s not that the allele made the moths unhealthy. Rather, it was all about camouflage. The peppered moth, when it’s not flying, rests on the trunks of trees. Here’s what a light and dark colored moth looks like on a light colored tree. If you were a bird, which color moth would be easier for you to find?

Over time, mostly as a result of industrial pollution that killed the lichens and covered the tree trunks with dark soot, the population (and its gene pool) changed. By 1895, 95% of the moths were dark colored. That means that the frequency of the alleles had shifted: the recessive allele had fallen to just over 2% frequency, while the dominant allele was now at 98% frequency.

3. Misconception Alert! “Dominant Allele” does not mean “Most Common Allele”

The case of the Peppered moth allows us to demolish a misconception about genes and populations: the false idea that dominant alleles, because they’re dominant, must be common. Intuitively, it makes sense: if these alleles are dominant, why don’t they come to dominate? However, this intuition is wrong. What we’ll see is that the frequency of an allele has nothing to do with whether it is dominant or recessive.

Read below, dragging in the correct term as needed

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[h]Misconception Alert: Dominant Alleles

[i]

[q labels = “top”]

The actor Kyle Pacek is an achondroplasiac. His condition is caused by a dominant allele. Source: Wikipedia

Let’s start by looking at some data about diseases caused by dominant alleles. One such disease is Achondroplasia: it’s a form of dwarfism. If you inherit the gene for this condition, you’ll be born with extremely _______ limbs. The condition is rare: According to the US national library of medicine, (http://ghr.nlm.nih.gov/condition/achondroplasia) the condition occurs in between 1/15,000 and 1/40,000 newborns. So, it’s caused by a dominant allele, and it’s _____.

The same is true of Huntington’s disease, a disease of the nervous system, also caused by a dominant allele. Huntington’s is extremely ______: it shows up in 3 to 7 of every 100,000 births in people of European ancestry. It’s even less common in some other populations, including people of Japanese, Chinese, and African descent.

[l]short

[fx] No. Please try again.

[f*] Great!

[l]rare

[fx] No. Please try again.

[f*] Great!

 

[q labels= “top”]

Similarly, think of other phenotypes which in a genetic sense, are recessive. If you went up to Norway or Sweden, you’d see a lot of people with blond ______ and blue eyes. While both of these phenotypes are caused by multiple genes, the dominant alleles for darker hair and brown eyes are both somewhat rare in these populations, while the __________ alleles (for blond hair and blue eyes) are much more common.

Blond hair, blue eyes: two recessive traits in very high frequencies in Norway and Sweden.
Blond hair, blue eyes: two recessive traits in very high frequencies in Norway and Sweden. Source: Wikipedia

The confusion might come from the word “dominant.” When we think of something that’s dominant, we think that it should be able to overcome something less dominant. But while that works in the genotype and phenotype of a single person, with dominant alleles __________ recessive alleles, it simply doesn’t work in populations.

We can extend this idea a little further. Dominant alleles, as we’ve seen, won’t increase in __________. And unless certain processes are at work in a gene pool, any allele’s frequency will stay about the same. If allele frequencies are changing, then some evolutionary process is at work in that population. In upcoming tutorial in this series, we’ll start looking at what those processes are.

 

 

 

[l]frequency

[fx] No. Please try again.

[f*] Correct!

[l]hair

[fx] No. Please try again.

[f*] Good!

[l]masking

[fx] No, that’s not correct. Please try again.

[f*] Correct!

[l]recessive

[fx] No, that’s not correct. Please try again.

[f*] Great!

[/qwiz]

4. Allele frequencies and fixed alleles in dogs

Rhodesian Ridgeback: Dogs with pedigrees are homozygous for many genes. Source: Wikipedia
German Shepherd Golden Retriever Mutt: Mixed breed dogs are heterozygous for many genes. Source, Wikipedia

For a final example, let’s think about allele frequencies in dogs. If you buy a dog with a pedigree (a dog of known breed), then you’re buying a certain look and disposition. You can count on this because dog breeds are controlled populations where the gene pool is closely guarded by dog owners who care about the breed. In other words, if you buy a Rhodesian Ridgeback, you can be assured that your new puppy had two parents who were both Rhodesian Ridgebacks. For all the traits that define the breed, these dogs are completely homozygous. Most of the defining alleles, in other words, are fixed, and would have an allele frequency of 1.0 (or 100%) in these very artificial gene pools.

If your preference is for mutts, then your dog is probably heterozygous for many genes. As a result, when you breed two mutts, the offspring’s appearance is much less predictable.

5. Checking Understanding

Got it? In this module, we’ve examined the concept of allele frequency.

If you feel that you understand this concept well, take this brief quiz. If not, carefully re-read the material above, and then take the quiz.

[qwiz style=”width: 600px; min-height: 0px; border: 3px solid black;” qrecord_id=”sciencemusicvideosMeister1961-Pop-gen: Allele Frequencies, Checking Understanding”]

[h]Quiz: Allele frequencies in populations

[!!!!!!] question 1 +++++++++[/!!!!!!]

[q topic= “determining_allele_frequency”]Allele frequency is

[c] the total number of homozygous individuals found in a population’s gene pool.

[c] The number of dominant alleles found in a gene pool.

[c*] the percentage or fraction of all alleles for a specific gene represented by one specific allele.

[f] No. Measuring the number of homozygotes will move you toward figuring out the allele frequency, but that’s not the best answer. Allele frequency is simply how common an allele is in a gene pool.

[f] No. Measuring the number of dominant will move you very close toward  figuring out the allele frequency, but that’s not the best answer. Allele frequency is simply how common an allele is in a gene pool.

[f] Yes. Allele frequency is simply how common an allele is in a gene pool, represented by a percentage or a fraction.

[!!!!!!] question 2 +++++++++[/!!!!!!]

[q topic= “determining_allele_frequency”]The letters below represent the alleles for a single gene that controls fur color in a population of mice. In this population, the frequency of the ‘a’ allele is

aa Aa aa Aa
Aa aa aa aa
aa Aa aa Aa

[c] 50%

[c*] 19/24, or 79.16%

[c] 7/12 or 58.33%

[f] No. I’t looks like you counted only the ‘a’ allele in homozygous recessives (’aa’). To get the proper frequency, you have to count the ‘a’ allele in the heterozygotes, too. Recount all the ‘a’ alleles, and divide by the total number of alleles in this population (24).

[f] Exactly. There are 19 ‘a’ alleles out of a total of 24 alleles in this population. That means the frequency is 19/24, or 79,16%

[f] No. 7/12 is the frequency of homozygous recessives  (‘aa,’ ) in this population of 12. The frequency of ‘a’ is found by counting every ‘a’ allele, and dividing by the total number of alleles in the population (24).

[!!!!!!] question 3 +++++++++[/!!!!!!]

[q topic= “determining_allele_frequency”]The letters below represent the alleles for a single gene that controls fur color in a population of mice. In this population, the frequency of the dominant allele is

aa Aa aa Aa
Aa aa aa aa
aa Aa aa Aa

[c] 5/12, or 41%

[c] 20/24, or 83.33%

[c*] 5/24, or about 21%

[f] No. 5/12 is the frequency of individuals who have the dominant phenotype. To find the frequency of the dominant allele (’A’), you have to count every ‘A’ allele, and then divide by the total number of alleles in the population (24).

[f] No. I think that you confused which allele is the dominant allele, and which one is recessive. ‘A’ is the dominant allele. Count all the ‘A’s, and divide by the total number of alleles to get the answer.

[f] Perfect. There are 5 ‘A’ alleles, out of a total of 24 alleles in this population. That makes the frequency of  ‘A’ 5/24, or about 21%

[!!!!!!] question 4 +++++++++[/!!!!!!]

[q topic= “determining_allele_frequency”]The letters below represent the alleles for a single gene that controls fur color in a population of mice. In this population, the frequency of the recessive allele is

Aa aa aa Aa aa aa Aa aa
Aa aa AA Aa Aa aa Aa aa

[c] 23

[c*] 23/32, or 71.9%.

[c] 16/32 or 50%

[f] No. It looks like you counted the number of ‘a’ alleles correctly, which is a good start. But ‘frequency’ is about the proportion of a specific allele in a gene pool.  Now, divide the number of recessive alleles by the total number of alleles to get the frequency of ‘a.’

[f] Correct. There are 23 ‘a’ alleles, and 32 alleles in total. The frequency of ‘a’ in this gene pool is 23/32, or 71.9%

[f] No. It looks like you forgot to count the ‘a’ alleles in the heterozygotes. Count ALL of the ‘a’ alleles, then divide by the total number of alleles (24)

[!!!!!!] question 5 +++++++++[/!!!!!!]

[q topic= “determining_allele_frequency”]The letters below represent the alleles for a single gene that controls fur color in a population of mice. In this population, the frequency of the dominant allele is

Aa aa aa Aa aa aa Aa aa
Aa aa AA Aa Aa aa Aa aa

[c] 50%

[c] 23/32, or 71.9%.

[c*] 9/32 or 28.1%

[f] No. It looks like you counted the frequency of individuals with a dominant phenotype. What you need to do is count every instance of the ‘A’ allele, and divide by the total number of alleles in the population.

[f] No. You figured out the frequency of the recessive allele, ‘a.’ Now use the same method to figure out the frequency of the dominant allele.

[f] Yes. There are 9 ‘A’ alleles, and 32 alleles in total, for a frequency of 28.1%

[!!!!!!] question 6 +++++++++[/!!!!!!]

[q topic= “determining_allele_frequency”]If an allele is fixed in a population, then its frequency would be

[c] 0, or 0%

[c] 0.5, or 50%

[c*] 1.0, or 100%

[f] No. If an allele is fixed, then it’s the only allele for that gene in the population. An allele whose frequency is 0 doesn’t exist in the population. Next time, choose another answer.

[f] No. If an allele is fixed, then it’s the only allele for that gene in the population. An allele whose frequency is 0.5 would make up half of the alleles in a population for a specific gene. Next time, choose another answer.

[f] Exactly. If an allele is fixed, then it’s the only allele for that gene in the gene pool.  its frequency would be 1.0, or 100%.

[!!!!!!] question 7 +++++++++[/!!!!!!]

[q topic= “determining_allele_frequency”]Which of the following is true about purebred dogs?

[c] For most of the genes in the dog genome, purebred dogs are more heterozygous than mutts.

[c*] They have many more fixed alleles than mutts.

[f] No. Purebred dogs have been bred for the predictable traits of their breed. For these traits, members of a purebred breed are mostly homozygous.

[f] Yes. Purebred dogs have, through the process of selective breeding, become extremely homozygous at many alleles, leading to many fixed alleles within their populations.

[!!!!!!] question 8 +++++++++[/!!!!!!]

[q topic= “determining_allele_frequency”]A group of breeders is trying to create a new breed of dog. As they do, which of the following would you expect to be true?

[c*] For each trait that the breeders are trying to define, the frequency of the alleles for that trait should be steadily rising.

[c] For each trait that the breeders are trying to define, the frequency of the alleles for that trait should be steadily falling.

[f] Yes. Breeders will be selecting for the new phenotype they’re trying to create. As they do, the frequency of the alleles for those phenotypes will steadily rise.

[f] No. It’s the opposite. Breeders will be selecting for the new phenotype they’re trying to create. As they do, what will happen to the frequency of the alleles for those traits?

[!!!!!!] question 9 +++++++++[/!!!!!!]

[q topic= “natural_selection_in_gene_pools”]True or false? In any population, the most common allele is the dominant allele.

[c]True

[c*]False

[f] No. The frequency of an allele has nothing to do with whether it’s dominant or recessive.  Just think about the fact that some disease-related alleles are dominant, yet rare (like the allele for achondroplasiac dwarfism). Or the fact that in the Scandinavian countries, some phenotypes controlled by recessive alleles (blue eyes, for example) are the most common.

[f] Correct. The frequency of an allele has nothing to do with whether it’s dominant or recessive. Recessive alleles can be more common that dominant alleles. It all depends on the allele, the evolutionary history of the population, and selective pressures from the environment.

[x]

[restart]

[/qwiz]

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