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Allele frequency

Allele frequency describes how often an allele (a variant of a gene) appears in a population. In this video, eye color is used as an example, with brown (B) eyes being dominant and blue (b) eyes being recessive. Allele frequency (or genotype frequency) can also differ from phenotype frequency. Created by Sal Khan.

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  • leaf green style avatar for user Lori H
    Is autism a genetic disorder? If so, which chromosome determines the mutation? What about autism spectrum disorders such as Asperger's syndrome?
    (5 votes)
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    • leafers tree style avatar for user AutoTurtle
      Autism spectrum includes a wide range of Autistic-like disorders that present with similar traits. Significantly, many of these disorders are caused by Copy Number Variants (CNV), or duplications or deletions of chromosome regions. Recent research in this area has focused on SNP's (Single Nucleotide Permutations) in genes whose dysfunction have correlations with ASD (Autism Spectrum Disorder).

      Affected genes include MECP2, FOXP1, Neuroligins and Neurexins - often only one of these is the cause.

      The reason that Autism has such a complex etiology (origin) is due to two factors: 1) The source of dysfunction can arise from a single change among many genes, and 2) the nature of the disorder (or where the patient falls on the "spectrum") relies on when the affected gene is expressed.

      Simply put, Autism results from the brain requesting a gene during development, and getting a result that is too big or too small. A good (advanced) reference is an article by Ebert and Greenberg, published in Nature, 2013.
      (18 votes)
  • leaf blue style avatar for user Lucy Salinas
    I don't know the difference of Allele Frequency (ex. of Bb and bb) and the possibility of the offspring having the dominant gene.
    (6 votes)
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  • mr pants teal style avatar for user colinjamieson96
    Isn't a gene essentially a strand of DNA that has a specific number of base pairs, and that strand "codes" for a specific trait (such as eye colour, hair colour, and teeth size)?

    And just going a bit further, are alleles just variations of a gene (or strand of DNA), that code for the same trait but with physical differences (for ex. the gene is eye colour, but one allele codes for blue eyes, and another brown)?
    (4 votes)
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    • piceratops ultimate style avatar for user Just Keith
      Yes and no.
      Genes are found on strands of DNA, they are not themselves a strand of DNA.
      A gene is a sequence of base pairs that code for a specific protein, not a specific phenotypic trait as such. The various proteins interact in very complex ways to form traits. So, genes do not, strictly speaking, code for phenotypic traits. However, a specific trait might be reliant on the protein produced by one gene for some key aspect of its nature. So while we might often say the gene for this or that trait, what is more accurate is saying the gene for the protein is involved in this or that trait.

      Genes, in fact, tend to be involved in multiple phenotypic traits because the protein they code for can be used in a variety of ways.

      Alleles are variations of genes, yes. But they may or may not produce observable differences in some phenotypic trait. The reason is that proteins tend to be very large molecules and so a few minor changes here or there in their structure may or may not have much of an effect on their functions. So, some alleles produce proteins that produce pretty much identical phenotypic traits. Also, remember that some amino acids can be coded for by more than one codon, so some alleles merely contain different ways of coding for the same protein.

      But, obviously, some alleles, even with minor changes, can produce proteins that lead to significantly different traits. Eye color is not a good example because there are many genes involved in that (perhaps as many as 16 genes).
      (12 votes)
  • blobby green style avatar for user Al V.
    Is brown dominant to other eye color alleles in the real world?
    (4 votes)
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  • starky ultimate style avatar for user Sojourn Soulman
    What causes some people to be born albino?
    (4 votes)
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  • duskpin tree style avatar for user Elizabeth
    so to be clear punnet squares so the percentage of phenotype for brown, and allele frequency is just focusing on one allele?
    (4 votes)
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    • piceratops tree style avatar for user riyaxgupta
      The percentages for the phenotypes are based the offspring's appearance/expressed trait, which results from the genotype (the combination of different alleles). Punnet squares allow you to find the the possible combinations of alleles of that offspring can have, and the probability that a combination will occur. In Sal's example, 50% of the population will have brown eyes (Bb, which is the genotype). You are correct in that allele frequency is the percentage of specific allele in a population :) So even though the dominant trait is expressed in 50% of the population, only 25% of the possible alleles are B.
      (3 votes)
  • blobby green style avatar for user Sarah Roo
    At the end of the video when he says p+q = 1, isn't the problem giving you p^2 and q^2 so to find the allele frequency you would have to find p and q by itself and to do so you would have to square root?
    (3 votes)
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    • orange juice squid orange style avatar for user Ryan Hoyle
      No, you don't need to square anything. It's more simple than that. One in four alleles is the dominant one therefore p=25% or 0.25. Three in four alleles is the recessive one so q=75% or 0.75. The total is 100% or 1, therefore for a gene with two alleles, p+q=1 always.
      (3 votes)
  • starky tree style avatar for user Amyntas
    What makes certain alleles dominant, and others recessive?
    (3 votes)
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  • male robot donald style avatar for user O'Shea Gresham
    How can it be three that code for blue eyes when there is only one pair of alleles that codes for blue eyes so wouldn't that be 25%?
    (3 votes)
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  • leafers ultimate style avatar for user Andrew
    Are hazel eyes special ?
    (2 votes)
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Video transcript

Voiceover: What I want to do with this video is explore the idea of allele frequency. Allele frequency. Just as a reminder, an allele is a variant of a gene. You get a variant of a gene from your mother, and you get another variant of the gene from the father. So, when we're talking about the allele, we're talking about that specific variant that you got from your mother or your father. We've seen this before, but now let's dig a little bit deeper. To help us get our heads around this, we'll start with a fairly common model for this. We're going to think about eye color. Obviously, this is a very large simplification, but let's just assume that we have a population where there's only two variants of an eye color gene. Let's first assume there is an eye color gene. Let's assume there's two variants. One variant, one allele for eye color, we'll use the shorthand, capital B. Let's say that's the allele for brown. Brown eye color. We're going to assume that this one is dominant. It's dominant over the other allele. Now the other allele, we're going to assume is for blue eye color, and we'll represent that with a lower case B. So that is blue eye color, and we're going to assume that this is recessive. Once again, this is review. Someone who has one of the big B alleles, the brown alleles, it doesn't matter what their other allele is going to be, because it's either going to be another brown or it's going to be a blue, they're going to show brown eyes. This is going to be brown eyes, and this is going to be brown eyes, because the capital B is dominant. The only way to get blue eyes is to be a homozygote for the recessive allele. All of that, of course, is review. We've seen that before. Now let's think about allele frequency. To think about that, I'll set up a very artificially small population. Let's say our population has exactly two people in it. Population has exactly two people in it, Person 1 and Person 2, and let's say we're able to look into their DNA and figure out their genotypes. Person 1, say, has a capital B allele, has a brown allele and a blue allele, while Person 2 has two blue, two blue alleles. Given that we know the genotypes in this artificially small population, we could start thinking about the allele frequencies. Or the frequencies of the different alleles. What do you think is going to be the frequency the frequency of the brown allele in this population? I encourage you to pause this video and think about this on your own. I'm assuming you've had a go at it, so you might be tempted to say, "Looks like one out of two people "have it, maybe it's 50%." But that wouldn't be the right way to think about allele frequencies. In allele frequencies, you want to dig a little bit deeper and look at the individual alleles. When you look at that, you say, "Okay, there's "four individual alleles in this population, or there's "four variants, or there's literally four chromosomes "that are carrying that gene in this population." Out of them, one of them carry, one of them is the capital B allele, so we could say that that is going to be zero point two five, or 25%. Once again, 25% of the genes for eye color have the capital B allele, have the brown allele. Now we can do the same, ask ourselves the same question for the lower case B allele. What fraction of the genes in this population are code for or represent the lower case B, the blue allele? Once again, I encourage you to pause the video and think about it. Well, very similar idea. There's four genes in the population that are coding for eye color. Of them, one, two, three code for or are the lower case blue allele. So that's zero point seven five or 75%. 75% of the genes code for the lower case blue allele, while 25 are the brown allele. I really want to hit this point home, how this is different than, say, the phenotype frequency. If I asked you, in the population, if I asked you the percent of brown-eyed people, so now I'm talking about phenotype, what would that be? Well, there's two people in the population. One of them is exhibiting brown eyes, so that's going to be one-half. Similarly, if I were to ask you what is the percentage of people who are blue-eyed that, too, would be one-half. This person is one of the two people, they're exhibiting blue eyes. But allele frequency, we're digging deeper, we're looking at the genotypes. We're saying out of the four genes here, one of them is the big B allele, so that's 25% of the gene population codes for the brown allele and 75% is the blue allele. This is really important to internalize. Because once we internalize this, then as we'll see, that the ideas in the Hardy-Weinberg principle start to make a lot of sense. I'll do a little bit of foreshadowing. We can denote this, this is just a convention that's often used, by the lower case letter P, and we can use lower case Q to denote the frequency. So lower case P is the frequency of the dominant allele, lower case Q the frequency of the recessive allele. What's true here? What's true of P, what's going to be true of P plus Q, what's P plus Q going to be equal to? I encourage you to pause the video again and think about that. What is this going to be equal to? Well, when we started off, we said that there's only two potential, that's one of the assumptions we assumed, we assumed there's only two alleles in this population, in kind of the allele population for this gene population for this trait. The frequency of the dominant ones plus the frequency of recessive ones, well everyone's going to have one of those two, so if you add those two frequencies, it's going to have to add to 100%. We see that there. One-fourth plus three-fourths is one, or 100%. And 25% plus 75% is also 100%. So we could say P plus Q is equal to 100%, or we could say that P plus Q is equal to one. Is equal to one. So, in the next video, we're going to start from the seemingly fairly simple idea, to get to a more richer and fairly neat idea that's expressed in the Hardy-Weinberg equation.