# The origins of recessive genes

1. Jan 17, 2012

### James_Frogan

Hi everyone,

I'm studying physics and not biological sciences, but I've been wondering about recessive genes recently. Given my background, do be kind on the explanations. My question is: if a recessive gene tends to be overcome by the dominant gene, how do recessive traits still display today?

What I understand of genes: if there is a dominant gene in a pair, then the dominant gene trait will show (eg black hair in black-blonde combination). If 2 people with black hair have a child, it's possible to have a blond baby if they both have black-blonde genes.

From a mathematical viewpoint, the probability of black-black and blonde-blonde producing a black-blonde is 100%. The probability of a black-blonde and a black-black producing a black-blonde is 25% (and black-black 75%). And 2 black-blondes have 50% chance of black-blonde and 25% chance pure black or blonde.

If the early human population were mostly black haired, how did blonde haired people defy the probabilities and become numerous? They would mathematically start off and die shortly after, if I see my probabilities correctly. Obviously this is not the case, so what am I misunderstanding about genes?

2. Jan 17, 2012

### atyy

Last edited: Jan 17, 2012
3. Jan 17, 2012

### Ygggdrasil

Two points:

1) Recessive traits will not die off on their own. Although the proportion of individuals with the recessive trait is small, there will still be some carriers of the trait (individuals who show the dominant trait but carry one copy of the recessive gene, in the example above the black-blonde individuals). If you do the math, you can find the proportion of people with the recessive trait will reach an equilibrium value, known as the Hardy-Weinberg Equilibrium.

2) Deriving the Hardy-Weinberg equilibrium requires assuming that every individual has an equal opportunity of reproducing and that reproduction is a random process. This is not true for many traits. Traits can be under natural selection such that individuals with a certain trait have a much higher probability of reproducing than individuals without that trait. Sometimes this can be due to a fitness advantage (individuals with a certain trait are able to outcompete others for resources) or due to sexual selection (individuals with a certain trait, due to biological or cultural reasons, are able to outcompete others for mates). If blonde hair were an adaptation that promoted survival as humans moved to more Northern climates, for example, then this could explain how the number of blonde individuals become more numerous over time.

Blonde individuals could also become more numerous for other reasons, such as luck or chance. For example, consider if only a small number of prehistoric humans migrated from Africa to Europe. These humans in Europe would have a large area with many resources, so their population could expand greatly. If this small group by chance had an unusually large proportion of individuals with blonde hair (or carriers of the blonde hair gene), this could have contributed to the increase in the proportion of the blonde hair trait. This effect is known as the bottleneck effect or the founder effect.

4. Jan 17, 2012

### bobze

To add to the excellent post that Yggg has put up;

Its actually a lot more complicated than just "dominant or recessive". Most genes aren't really an easy binary system like that and there is some degree of expression from both genes that contribute to the phenotype.

For the sake of learning genetics "pure" dominant/recessive traits are used, but that is only a very tiny fraction of the picture.

5. Jan 18, 2012

### James_Frogan

Thanks atyy, Ygggdrasil and bobze.

I omitted the mutation that occurs to adapt to environments and the various other factors mentioned.

About the Hardy-Weinberg problem, doesn't the recessive trait population q^2 require a large enough sample size? For the first person that received a blonde-blonde or albino-albino gene, that would make his q^2 value a very very small number?

Cheers ;) learning so much from this

6. Jan 19, 2012

### epenguin

This is the explanation (incomplete IMO but OK enough now) usually given to the blonde and light-skinned trait. That light skin allowed better vitamin D synthesis in the northern places which not much sun. But in Africa and Australia you have enough sun not to need it plus you need to wear less clothes - white then becomes a disadvantage. E.g. white farmers in Australia get a high frequency of skin cancers.

The largest lot of populations in Africa that you would call definitely 'black' may owe their predominance to this blackness. That is they are a successful offshoot which though predominant part of the population is minority part of the continent's genetic variation, they are relatively recent, originating around 60,000 years ago I heard. The closer-to-original trait is the colour of Bushmen and Pygmies - more of a reddish-brown. Considerations always subject to evolving evidence and I am not up to date. Put it past your teacher.

Remember a selection factor does not need to be very strong to predominate over time.

7. Jan 19, 2012

### thorium1010

According to wikipedia first modern humans diverged from their common ancestor 200000 years ago.

http://en.wikipedia.org/wiki/Human

Skin color is older than modern human divergence. Again from wikipedia -

http://en.wikipedia.org/wiki/Human_skin_color

Last edited: Jan 19, 2012
8. Jan 28, 2012

### Murdstone

The details of dominant/recessive genes is missing from everything I have read. Sure - blue eye dominance or something is mentioned but the mechanics are not Is it that you have slightly different base sequence for a gene attributable to a particular trait - flavors if you like.

Then there is the whole thing of what makes a gene dominant?

9. Jan 28, 2012

### thorium1010

http://en.wikipedia.org/wiki/Dominance_%28genetics%29

Blue eye is not dominant, its a recessive trait.

10. Jan 28, 2012

### Moonbear

Staff Emeritus
Hair color isn't a good example. It isn't controlled by a single gene and you get a lot of ranges of color, and not even every hair of one individual is the same color. (Also a bad example because of the prevalence of hair dyes.)

I do want to refine the terminology being used a bit. When talking about dominant and recessive, we're referring to alleles for a gene, not the gene. The gene would be for something like hair pigments, but then there are different alleles that are specifying which pigment or if it's expressed.

The other thing to remember is that recessive doesn't mean bad. Sometimes, a dominant allele is the bad one, and you get a high prevalence of a recessive trait because both homozygotes and heterozygotes for the dominant allele die off faster than the homozygotes for the recessive trait.

11. Jan 28, 2012

### bobze

Moon-- two great points.

I want to iterate again for others, the importance of the idea that simple "dominant and recessive" alleles tend to be the exception, rather than the rule for most genes we study. Not to mention complicating the fact that environment impact expression and degree of expression as well. Mendel was, quite possibly the luckiest biologist to have ever lived.

12. Feb 3, 2012

### Murdstone

Is there a biochemical difference in the gene for a trait depending upon which allele of the trait it codes for?

I know you have emphasised that phenotype is not straight forward, however, I am trying to establish if whether the concept of biochemical dominance has merit.

13. Feb 4, 2012

### Ygggdrasil

The biochemistry of the different alleles definitely affects whether the allele is dominant or recessive, but the connection is not always so straightforward. Many times a "broken" version of a gene is recessive. For example, cystic fibrosis is caused by a mutation in an ion channel called the cystic fibrosis transmembrane conductance regulator (CFTR) that prevents the ion channel for working properly. The disease allele is recessive because one functioning allele is sufficient to make enough CFTR for the body to behave normally. Only when both copies of the gene are non-functional does the disease occur.

Some "broken" version of genes, however, will inactivate the functioning copies of the genes and thus behave as dominant alleles (these are referred to as dominant negative alleles as they are dominant alleles that cause a loss of function). This is especially common when the proteins encoded by the genes function in a complex and one broken subunit in the complex is enough to render the entire complex non-functional. Another way for an allele to be dominant is though a gain-of-function mutation, in which the allele confers its trait by performing some new function (for example, an enzyme that cannot be turned off properly).

Here's a particularly good explanation of the topic with more examples:

Last edited by a moderator: May 5, 2017
14. Feb 4, 2012

### Murdstone

Thanks g - The article was very informative. Your willingness to help with focused information is appreciated.

15. Feb 5, 2012

### Murdstone

In reflecting upon the information in the excellent article on the biochemical differences in gene type (dominant) (recessive), the distinction between a mutant gene and a recessive gene seem blurred to me.

Both mutant and recessive deviate from established. They can either code for a slightly different protein or no protein.

I would consider a recessive gene a subset of mutant gene.

16. Feb 5, 2012

### epenguin

Just continue your reading and study without over-worrying to completely define words that you may find are sometimes used loosely without causing real misunderstanding. A recessive gene generally (with the exceptions mentioned by Ygggdrasil) is an unfunctional one as you say, and most often I guess because it codes for an unfunctional protein. A mutant gene means really an altered one, that is it is mutant with respect to its ancestor (Latin mutare - to change.) A mutation may result in either a functional or an unfunctional gene. All the genes you have are mutant though, with respect to some more or less distant ancestor.

If it's not confusing a mutation can sometimes restore functionality to an unfuctional gene. This can either be a 'back mutation' that restores the original gene sequence, or a mutation that restores not the polynucleotide sequence but the primary protein structure with a difference polynucleotide sequence, given the degeneracy of the genetic code, or some mutations can produce a new protein which have two mutations, two differences in protein primary structure compared with ancestor, but which compensate each other so as to give a functional protein.

Last edited: Feb 5, 2012
17. Feb 6, 2012

### Ygggdrasil

Mutations to a gene can also create dominant alleles, however. One good example here is the allele for lactase persistence (https://en.wikipedia.org/wiki/Lactose_intolerance#Lactase_persistence).

The ancestral state of this allele (in humans prior to their migration from Africa) encodes the enzyme responsible for breaking down lactose. This gene is regulated such that it gets produced in infancy and early childhood, but later gets turned off in adulthood, resulting in lactose intolerance as adults. In European populations, mutations arose in this gene that disabled the ability of the gene to be turned off in adulthood, creating alleles for lactase persistence. These alleles are dominant alleles associated with the trait of lactose tolerance in adulthood. Thus, in this case, the dominant allele is actually the mutant form of the gene.

18. Feb 23, 2012

### MrRagnarok

It's not that a recessive allele is an undesired gene and causes a nonfunctional protein. A recessive allele will simply not be expressed in the presence of a dominant allele. It recedes expression to the dominant allele. Eye color is a good example.

To keep things overly simple, lets pretend everyone has a single gene that codes for the color of their eyes. Recall that each human has two copies of every gene, so you would have two copies of this eye color gene. Each copy is called an allele. Since we have two copies they can compete with each other for expression. Lets call the brown colored eye protein B and the blue colored eye protein b. With two possible proteins and two copies of the DNA we can have three different combinations. BB, Bb or bb.

When we have BB both instructions for eye color produce a brown colored eye.
When we have bb both instructions for eye color produce a blue colored eye.

What happens when we have Bb? One copy for brown and one for blue? Turns out the brown color wins out over the blue color. Because of this it is called 'dominant'. The blue pigment coded by b is not inferior to the brown pigment in B. But simply because the brown B will [STRIKE]silence[/STRIKE] overpower the expression of the blue b, brown (B) is dominant and blue (b) is recessive.

Changing gears here a little bit here is good because, like Ygggdrasil pointed out, dominant/recessive is not the only way genes influence protein production. In fact, if dominant/recessive was the only way genes were expressed, organisms would not change much after the original genetic programming during fertilization. Cells live in an always changing environment and must be able to dynamically change as well.

For example: Gene A (which is dormant until a stressful environment) inactivates Gene B. Normally, Gene B is highly expressed, but when the cell senses stress it rapidly produces Gene A, which in turn inactivates Gene B. Shown below:

Environmental stress off: [gene A] inactive GENE B active
Environmental stress on: GENE A active product inhibits [gene B]

When the environmental stressor is relieved Gene A is down-regulated and releases inhibition from Gene B which is expressed again. Thus the organism returns to normal baseline behavior. This is an alternative way of regulating genes that is responsive to the environment and can temporarily silence Gene B 'as if' it were recessive. It is through these 'epigenetic' mechanisms that cells can control their gene levels without mutation. I.e. The genetic code in Gene B was at no time altered during its silencing. So once Gene A is removed Gene B functions as usual. A mutation would alter the code of Gene B in a way that could permanently disable or alter the protein product.

There are also ways to permanently turn genes on and off, but I think I've already gone beyond the scope of this thread!

Last edited: Feb 23, 2012
19. Feb 23, 2012

### Murdstone

My understanding now is that alleles are slightly different coded genes for the same trait.

Most understand the BB, bb, Bb model. Where things become unclear is in explaining why B is dominant over b? There is a biochemical difference between B and b, what is it about this biochemical difference that makes B dominant over b?

While not objecting, I am of the understanding that Biological Evolution downplays the role of environment, stress, in initially determining which genetic combinations are offered for selection. The standard dogma is that these initial offerings are "random". Effects of environment - ex ante - no, ex post - yes.

20. Feb 23, 2012

### Ygggdrasil

This is incorrect. Dominant alleles are not silencing recessive alleles. In most cases, whether a particular allele is dominant or negative depends on the biochemistry of the gene and the effect of the mutation on the biochemistry. For a good example, see the explanation for why the gene for red hair is recessive in the link I posted earlier (http://www.thetech.org/genetics/ask.php?id=227 [Broken]).

Last edited by a moderator: May 5, 2017
21. Feb 23, 2012

### MrRagnarok

Exactly

There are many ways that a dominant allele overpowers a recessive allele. The eye color gene encodes for melanin and B is a darker colored melanin while b is lighter. The darker color pigments in B reflects more than just blue wavelengths of light so it gives a darker appearance to the observer. Thus, in eye color both B and b are being expressed intracellularly but only B is being observed. Thus the dark brown phenotype. Link.

There is also an albino allele (a) for the eye-color gene. a is the absence of color (often due to impairments in melanin processing) and is recessive to b, so B>b>a. If our genotype was ba the we would have blue eyes even with one b simply because the blue pigment expressed by b would be more robust visually than the a pigment (which is actually a lack of pigmentation).

So there is not really a direct biochemical mechanism for eye color but rather the property of the B protein behaves differently (in terms of appearance) than b. Simply B is easier to see than b. But other dominant genes do exert competitive pressures on recessive genes. For example, lets say we have the Z dominant and z recessive protein. DNA for Z is written in an easier way to transcribe than z and this transcription efficiency makes it 20x easier to transcribe Z compared to z. This ease of transcription will result in baseline concentrations of the Z protein being 20x higher than z protein. If there are normally 1000 copies of this protein in the cell, Zz genotype will have 950 Zs and 50 zs. Even though they have the same number of alleles. In this way the Z is out-producing the protein levels vs z causing a Z trait to be expressed.

Another biochemical mechanism dominant alleles can use is RNA interference. Recall that the DNA codes for RNA and this RNA contains introns in the gene that are removed and do not directly influence the protein. These intronic pieces of RNA are usually degraded but some are designed to be complementary to the recessive allele's DNA and when this strand of RNA finds the recessive allele it attaches to the DNA in a way that inhibits this allele's transcription rendering it recessive.

This is not the end of the story and not all genes work this way, but simply some examples of what can happen.

I am unfamiliar with the field of bio evo but am familiar in epigenetics. You cannot directly change (without mutation which occurs so randomly it can be ignored) the sequence of the DNA you inherit from your mother and father. So in this regard, these initial genetic offerings are random in a sense that you get 50% mom 50% dads DNA.

But the cellular environment, even in the womb, greatly influences levels of genes that are expressed or silenced. For example a mother who is stressed while carrying a child can affect the levels of stress receptors (called glucocorticoid receptors) expressed by the fetus because the stress hormones (such as cortisol) present in the mother influence the levels of expression in the developing fetus. Outside of the womb during development, stressful times to the children (such as abandonment or reduced nurture) cause these stress receptors to be overly expressed in a way that low levels of stress cause a higher level of stress response, this is often observed as anxiety.

Other factors, such as cocaine intake by the mother, will also play a role in the expression levels of fetal (and eventually adult) proteins and anxiety levels, but science is still determining exactly what is happening there!

Last edited: Feb 23, 2012
22. Feb 23, 2012

### MrRagnarok

Well, the bulk of my post was correct. Just the usage of the word 'silence' in the last sentence was wrong so I fixed it. I agree with you in the case of eye color that b is not being silenced and have explained it more accurately in a more recent post.

But some alleles can silence other alleles. Just typically not alleles for the same gene. I posted a bit about this before I saw this post, but also in the case of genomic imprinting, maternal alleles can silence paternal alleles (or vice versa). But my understanding is that the imprinting field is still uncertain exactly how this is occurring (for instance how the cell differentiates between maternal and paternal autosomes) Link 1 Link 2

Last edited by a moderator: May 5, 2017
23. Feb 24, 2012

### Ygggdrasil

It's imporant to distinguish between the interactions between alleles at the same location on the chromosome (locus) and interactions between alleles at different loci.

Because we have two copies of each chromosome, we have two alleles of every locus in our genome. In the case where we have two different alleles at a particular locus, one allele can be dominant over the other. This dominance generally does not result from silencing or altering the protein produced by the recessive allele. Rather, how the dominance occurs is a result of the properties of the different alleles (e.g. whether the alleles are loss-of-function or gain-of-function).

As you mention, particular allele at one location on the chromosome can alter the expression another allele at a different locus. These interactions between different genes are often very important for determining the phenotype of an organism. However, having one gene alter or mask the effect of a gene at a different location is not an example of dominance, as dominance relates only to the relationship between alleles that reside at the same locus. Rather, the interactions between alleles that reside at different locations in the genome is referred to as epistasis.

I'm sorry if this is a bit pedantic and nitpicky, but students often get confused by the differences between genes and alleles, so I often find myself having to clarify this issue. Most of your posts here are correct, informative, and bring up important points, but the difference between dominance relationships vs epistasis is subtle and requires careful explanation. I'm sure all of this information is already clear to you, but I just want to make sure others reading the thread have a clear idea of what's going on.

Last edited: Feb 24, 2012
24. Feb 24, 2012

### MrRagnarok

Thanks for the precise clarification Ygggdrasil, it is important to not use terminology loosely. I thought that it was more common for the dominant allele to exert dominance over the recessive allele through some sort of direct or indirect inactivation mechanism (like Xist-mediated X chromosome inactivation). I learned this in school as the classic example, but further research now suggests, as you mention, that this appears to be an extreme example.

What happens in the case of less extreme mutations? For example, in the red hair example a mutated MC1R product impairs the natural degradation of red pigmentation. This mutation is pretty extreme since it causes a loss-of-function mutation for the MC1R protein. How is dominance exerted when two heterozygous alleles differ only in an exonic SNP (for others reading: one single base pair)? Let the SNP cause a missense (protein changing) and not nonsense (protein stopping) mutation. But the individual will still have two different proteins caused from two different (albeit slightly) alleles. Is dominance exerted here? Or does it just depend on how the missense mutation ultimately affects the final protein product?

25. Feb 24, 2012

### bobze

I pointed this out a few pages back, the answer to your question. Most protein coding genes (structural genes) aren't so simple as dominant or recessive. Most structural genes have some varying levels of codominance.

Lots of times we classify things as "dominant and recessive" based on the "big picture" (like clinical picture).

Think about sickle cell anemia. I'm sure you've learned ad nauseum that SCA is autosomal recessive in your classes. But when we call it this we are talking about how it looks clinically, not how it really works out at the molecular level.

Heterozygotes for SCA still produce the B-globin chains of sickle cell disease. If you run a western blot of a SCA carrier you can clearly see this. However, because of how hemoglobin loads oxygen (positive cooperativity) you normally don't get any SCA phenotype in the amounts the sickle cell B-globin are produced. But, under hypoxemic conditions (read; low Hb O2 saturation) this can expose the amino acids responsible for polymerization of Hb and cause cell sickling. You see this clinically when an unknown carrier of SCA spends prolonged periods at high altitude and suddenly becomes symptomatic.