Temporal scales for phenotypic traits

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In summary, the conversation discusses the concept of temporal stability of traits and whether there is a known structure-function relationship between genes and the duration for which traits are expressed. There is also a mention of epigenetics and its role in controlling gene expression. It is noted that while DNA may determine certain traits, it cannot predict how long those traits will last over generations. Overall, the molecular mechanisms behind temporal stability and inheritance patterns are still not fully understood.
  • #1
Pythagorean
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I'm not sure how far the word phenotype extends into particular traits of species (for instance, is a genetic tendency towards a particular disease a phenotypic trait?), so please let me know if I violate the definition.

I'm curious if there's a known structure-function relationship between genes (and or the transcribing proteins) and the temporal stability of traits.

For instance, skin color would have a long temporal scale. If people get separated geographically, they develop different skin colors (by and large) just as animals develop different patterns.

Eye color, on the other hand (a medium temporal scale) is much more diverse even across different human races. So is genetic disease. So the temporal scale is on the order of human lifetimes (i.e. a new eye color can come with each birth)

What about changes in genetic expression within a lifetime due to environmental effects? For instance, if I expose myself to the cold and suppress my appetite, I'll upregulate mitochondrial sirt3 expression, which is associated with longevity (so, a short temporal scale, within the lifetime of the organism).

What is it that makes some traits much more stable than others? And how is this stability coded temporally?
 
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  • #2
Sorry but I didn't quite get what you meant. How do you define "temporal stability of traits"? I am sorry but English is not one of my strong points.
 
  • #3
you probably see more variation in eye color because it's less detrimental to have the wrong eye color in the wrong environment.

melanin content of skin, though, has a profound effect. from burning in the tropics to vitamin D production up north. inuit aren't as pale as nordics, but they've had so much reliance on the sea for food that they don't have to adapt to that level.

i would expect eye color to be on a longer time scale than skin color, with most eye variation showing up in places like trade routes.
 
  • #4
Sorry but I didn't quite get what you meant. How do you define "temporal stability of traits"? I am sorry but English is not one of my strong points.

I just mean the length of time over which the traits hold. There may be a proper word for it, but I don't know what it is.

@ Proton Soup

I can see the reasonable evolutionary explanations. I'm more curious about the molecular mechanisms. For instance, are traits with a longer 'temporal stability' 'further down' in the genetic code (less accessible) or is there no known correlation between genetic structure and temporal stability.
 
  • #5
Pythagorean said:
I'm not sure how far the word phenotype extends into particular traits of species (for instance, is a genetic tendency towards a particular disease a phenotypic trait?), so please let me know if I violate the definition.

Yes that can be considered a phenotypic trait.
Pythagorean said:
I just mean the length of time over which the traits hold. There may be a proper word for it, but I don't know what it is.

I am also not aware of the word if such a term exists.
Pythagorean;3291084I said:
I'm more curious about the molecular mechanisms. For instance, are traits with a longer 'temporal stability' 'further down' in the genetic code (less accessible) or is there no known correlation between genetic structure and temporal stability.

I think I understood what you are asking for; the degree of gene expression on a temporal scale, as opposed to magnitude of expression, as a function of its accessibility. You may have a look at this.
http://en.wikipedia.org/wiki/Spatiotemporal_gene_expression (not a very well written article)
http://en.wikipedia.org/wiki/Gene_expression#Transcriptional_regulation

The period of time for which a trait is expressed depends upon when it starts and ends. That is one mechanism which I think is not very well known. I could not find any significant scholarly resources regarding this except perhaps http://www.google.co.in/url?sa=t&so...dm-DQ&usg=AFQjCNGB3zmaKLGn5J1LkGGkKXyfIvYyfw".

However the inheritance patterns for things like skin colour and eye colour are not coded in DNA. Check http://en.wikipedia.org/wiki/Epigenetics
 
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  • #6
mishrashubham said:
However the inheritance patterns for things like skin colour and eye colour are not coded in DNA. Check http://en.wikipedia.org/wiki/Epigenetics

Are you sure ? inheritance pattern(most not all) or genotype almost all coded in DNA (esp skin color and eye color) Epigenetics is method of control of gene expression.
 
  • #7
thorium1010 said:
Are you sure ? inheritance pattern(most not all) or genotype almost all coded in DNA (esp skin color and eye color) Epigenetics is method of control of gene expression.

I am talking about the inheritance patterns, not the traits themselves. Existence of a trait over many generations is a result of selection. DNA does not code for how many generations the trait will last. Yes DNA may say that X should have a pale skin colour but it does not say, or more precisely cannot say, that X's great great great great great great great great great great great great grandchild will also have a pale skin colour.
 
  • #8
mishrashubham said:
I am talking about the inheritance patterns, not the traits themselves. Existence of a trait over many generations is a result of selection. DNA does not code for how many generations the trait will last. Yes DNA may say that X should have a pale skin colour but it does not say, or more precisely cannot say, that X's great great great great great great great great great great great great grandchild will also have a pale skin colour.

Well yes of course not as the great great great great great great great great great great great great grandchild of anyone only has ~1 part in 16,000 of their genome identical to yours.

Epigenetics is different to inheritance patterns over time. Do you have any citations for epigenetics governing colouring? I'd be quite interested in any
 
  • #9
Pythagorean said:
I just mean the length of time over which the traits hold. There may be a proper word for it, but I don't know what it is.

@ Proton Soup

I can see the reasonable evolutionary explanations. I'm more curious about the molecular mechanisms. For instance, are traits with a longer 'temporal stability' 'further down' in the genetic code (less accessible) or is there no known correlation between genetic structure and temporal stability.

Epigenetics plays a part, probably, of protecting some traits from being wrecked by mutations.

What determines how "stable" a trait is over evolutionary time though, is selection. If selection is strong, variants from the "norm" are quickly weeded out of the population which stabilizes and fixes the trait in question. So its not that variants don't arise to those traits, rather that those variants are unsuccessful, evolutionary speaking.

Traits which are "very stable" or ultraconserved, generally serve essential cellular functions--So variance within them isn't tolerated well by selection.

Gene duplication provides a mechanism for those "essential" traits the opportunity to be changed without the loss of essential function and selection penalty against changing them.
 
  • #10
ryan_m_b said:
Well yes of course not as the great great great great great great great great great great great great grandchild of anyone only has ~1 part in 16,000 of their genome identical to yours.

Epigenetics is different to inheritance patterns over time. Do you have any citations for epigenetics governing colouring? I'd be quite interested in any

What I am trying to say is that DNA inherently cannot guarantee the existence of a trait in future generations. DNA has control as long as the organism is alive. After that it is things like selection and epigenetics that decide whether the trait will stay or not.

Regarding citations, no I don't have any as of now. I'll post later if I find anything since rigorous searching on the net is a bit difficult on a mobile phone.
 
  • #11
mishrashubham said:
What I am trying to say is that DNA inherently cannot guarantee the existence of a trait in future generations. DNA has control as long as the organism is alive. After that it is things like selection and epigenetics that decide whether the trait will stay or not.

Regarding citations, no I don't have any as of now. I'll post later if I find anything since rigorous searching on the net is a bit difficult on a mobile phone.

Lol tell me about it, last year I had to do a presentation on the future of nanomedicine but at the time only had internet access through my iphone...

Though regarding inheritance the genes passed down will be the ones expressed by the progeny. Selection acts on the gene frequency within a population with regards to the fitness that gene expression (which is affected epigenetically) grants.
 
  • #12
OK so I have access to my laptop now.

ryan_m_b said:
Though regarding inheritance the genes passed down will be the ones expressed by the progeny. Selection acts on the gene frequency within a population with regards to the fitness that gene expression (which is affected epigenetically) grants.

Epigenetic changes can be passed on to progeny although they usually fade away over many generations.

When I added the link to epigenetics after my sentence about skin colour, I did not imply a direct connection between the two but as a method to reinforce the idea of DNA not operating at a multigenerational level.
 
  • #13
mishrashubham said:
Epigenetic changes can be passed on to progeny although they usually fade away over many generations.

When I added the link to epigenetics after my sentence about skin colour, I did not imply a direct connection between the two but as a method to reinforce the idea of DNA not operating at a multigenerational level.

Again probably not using the right word, DNA is essential to carry information from generation to generation. Probably where you should distinguish is that not all genes express in progeny or they are controlled by factors (eg epigenetics) in reducing or controls gene expression
 
  • #14
thorium1010 said:
Again probably not using the right word, DNA is essential to carry information from generation to generation.

I don't think I am denying that.
 
  • #15
mishrashubham said:
I don't think I am denying that.

Better would be gene or gene expression. All genes are inherited, but some of them maybe modified or controlled in their expression
One example is lactose intolerance , all humans have the capacity to produce lactase enzyme (in this case i mean infants) and soon after the enzyme production reduces due to down regulation of gene, but the gene does not disappear. All of us inherit it from our parents.
Only in certain populations, the gene continue to produce the enzyme through adulthood esp those that rear cattle, hence do not suffer from lactose intolerance.
 
  • #16
thorium1010 said:
Better would be gene or gene expression. All genes are inherited, but some of them maybe modified or controlled in their expression
One example is lactose intolerance , all humans have the capacity to produce lactase enzyme (in this case i mean infants) and soon after the enzyme production reduces due to down regulation of gene, but the gene does not disappear. All of us inherit it from our parents.
Only in certain populations, the gene continue to produce the enzyme through adulthood esp those that rear cattle, hence do not suffer from lactose intolerance.

That is all very right. But could you please tell me where exactly I went wrong in my previous posts? I would be happy correct myself.
 
  • #17
@ bobze & mushra

I recognize that we're talking about epigenetics (though I thought 'epigenetics' was more of a catch all for "non DNA inheritance"). I guess I'm curious about the difference between genes expressed throughout your life and genes that can turn on and off throughout your life and how they're driven. To what extent is expression inherited vs. driven by the environment?

I guess what I mean (in not so many words) is how are introns coupled to the environment? Are introns less stable than exons?
 
  • #18
Pythagorean said:
I recognize that we're talking about epigenetics (though I thought 'epigenetics' was more of a catch all for "non DNA inheritance"). I guess I'm curious about the difference between genes expressed throughout your life and genes that can turn on and off throughout your life and how they're driven.

Wikipedia has a good article on this. http://en.wikipedia.org/wiki/Regulation_of_gene_expression


Pythagorean said:
I guess what I mean (in not so many words) is how are introns coupled to the environment? Are introns less stable than exons?

Again what exactly do you mean by "stable"?
 
  • #19
Well, let's start with the single question, does expression always entail transcription?

Then, what the difference, molecularly, between life-long expressions (eye and hair color) and more immediate expression (I previously was using the sirt3 example, but that already has the difference of being mitochondrial).
 
  • #20
Pythagorean said:
Well, let's start with the single question, does expression always entail transcription?

Yes in order to be expressed a gene must be first transcripted and then translated.

Pythagorean said:
Then, what the difference, molecularly, between life-long expressions (eye and hair color) and more immediate expression...

Like in the above posts, gene expression is regulated. There are many ways of doing this. Quoting from the wiki
Any step of gene expression may be modulated, from the DNA-RNA transcription step to post-translational modification of a protein.

That page basically tells you most of the ways in which gene expression can be regulated.
 
  • #21
I understand that there's a sea of mechanisms out there.

What I'm asking is if there's a general distinction (using this mechanistic classification scheme if you like) between different temporal scales of regulation it is it all mixed up?

I would think, naively, that something like allosteric modulation would have a short temporal scale associated with it, for instance. But maybe not, maybe a constant supply of effector is maintained for a particular expression throughout an organisms life so that the alosteric modulation perpetuates.
 
  • #22
Looks like someone may have half-answered my question:

http://www.sciencedaily.com/releases/2010/10/101014144312.htm

Chromosomes hold thousands of genes, with some situated in the middle of their linear structure and others at either end. In their analysis, the NYU and Princeton researchers found that genes located in the middle of a chromosome were less likely to contribute to genetic variation of traits than were genes found at the ends. In other words, a gene's location on a chromosome influenced the range of physical differences among different traits.
The biologists also considered why location was a factor in the variation of physical traits.

Using a mathematical model, they were able to show that genes located near lots of other genes are evolutionarily tied to their genomic neighbors. Specifically, natural selection, in which variation among vital genes is eliminated, also removes the differences in neighboring genes, regardless of their significance. In C. elegans, genes in the centers of chromosomes are tied to more neighbors than are genes near the ends of the chromosomes. As a result, the genes in the center are less able to harbor genetic variation.
 
  • #24
mishrashubham said:
If that is the answer then I definitely understood your question wrong.

It only really focuses on the much longer time scales, but it definitely declares a relationship between structure and "stability".
 
  • #25
To reapproach your question

Pythagorean said:
Then, what the difference, molecularly, between life-long expressions (eye and hair color) and more immediate expression (I previously was using the sirt3 example, but that already has the difference of being mitochondrial).

The only difference is that there are factors that regulate gene expression of temporary traits depending upon external stimulus while genes for hair colour do not suffer from such regulation.
 
  • #26
mishrashubham said:
To reapproach your question
The only difference is that there are factors that regulate gene expression of temporary traits depending upon external stimulus while genes for hair colour do not suffer from such regulation.

Ok, that's a good start. As far as I know, transcription factors have a strong influence on expression. Are you saying, for instance, that there are no transcription factors for not-temporary traits?

Orr... is there a chromosomal location difference between temporary traits and not-temporary traits that doesn't allow TF access to conserved traits?
 
  • #27
Pythagorean said:
Ok, that's a good start. As far as I know, transcription factors have a strong influence on expression. Are you saying, for instance, that there are no transcription factors for not-temporary traits?

When I said "factors" I didn't specifically refer to transcription factors (that was my mistake). I meant that while temporary traits are regulated so as to be active only for a certain period of time (with the help of any or all of the mechanisms mentioned in previous posts), non-temporary traits are regulated so that they may be expressed for long periods of time (either by upregulating or not downregulating).

Pythagorean said:
Orr... is there a chromosomal location difference between temporary traits and not-temporary traits that doesn't allow TF access to conserved traits?

About three quarters of the genome is wrapped around nucleosomes so it takes some special transcription factors in order to access to these regions. The only other way is by unwrapping the DNA. So there might be a connection there. A study that I found links gene conservation and nucleosome density
brendelgroup.org/WikiVB/data/media/home/cms/teaching/tigs26-476.pdf

The most striking feature revealed by global
mapping is the contrast between nucleosome density in
regulatory regions and that in transcribed sequences. In
budding yeast, >90% of the promoters contain stretches of
DNA with very low nucleosome occupancy [3,4,6,8,11,12].
These nucleosome-depleted regions (NDRs) are on average
~150 bp in length, roughly enough to accommodate a
single nucleosome. The NDRs play a crucial role in transcription
regulation (see below). The rest of the promoter
sequence is assembled into nucleosomes. Some of these
nucleosomes have unusual properties, including enrichment
in certain histone variants and high turnover rates
[15–18], which might also contribute to the regulation of
gene expression.
 
  • #28
mishrashubham said:
About three quarters of the genome is wrapped around nucleosomes so it takes some special transcription factors in order to access to these regions. The only other way is by unwrapping the DNA. So there might be a connection there. A study that I found links gene conservation and nucleosome density
brendelgroup.org/WikiVB/data/media/home/cms/teaching/tigs26-476.pdf

Very interesting! This exactly the kind of study that interests me. I might venture that this is one of the structural differences that sets eukaryote phylogenetic tree structure apart from bacteria tree structure and allows for more stable, long-lived phyla in eukaryote lineages.

Thanks for your input so far mish!
 
  • #29
Pythagorean said:
Thanks for your input so far mish!

You are welcome. You had a very interesting question which I never thought of myself. So thanks for sharing.
 

1. What is a temporal scale for phenotypic traits?

A temporal scale for phenotypic traits refers to the timeframe over which changes in a particular physical or behavioral characteristic, or phenotype, occur. This could range from short-term changes, such as daily fluctuations, to long-term changes, such as those that occur over multiple generations.

2. How are temporal scales determined for phenotypic traits?

The temporal scale for a phenotypic trait is typically determined by the lifespan and reproductive cycle of the organism. For example, if studying a short-lived insect species, the temporal scale may be measured in days or weeks, whereas for a long-lived mammal, it may be measured in years or decades.

3. Why is understanding temporal scales important in studying phenotypic traits?

Understanding temporal scales is critical in studying phenotypic traits because it allows scientists to accurately measure and track changes in these traits over time. This can provide valuable insights into how traits evolve and adapt in response to environmental changes, as well as how they are influenced by genetic and epigenetic factors.

4. Can temporal scales vary for different phenotypic traits within the same organism?

Yes, it is possible for temporal scales to vary for different phenotypic traits within the same organism. For instance, a plant may have a short-term temporal scale for traits related to leaf growth, but a longer-term temporal scale for traits related to flowering and seed production.

5. How can understanding temporal scales for phenotypic traits inform conservation efforts?

Understanding temporal scales for phenotypic traits can provide important information for conservation efforts, as it can help identify which traits are most vulnerable to environmental changes and which species may be most at risk. By tracking changes in these traits over time, scientists can also assess the success of conservation strategies and make informed decisions about how to protect and preserve vulnerable species.

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