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Author Topic:   Molecular Population Genetics and Diversity through Mutation
caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 11 of 455 (784850)
05-24-2016 4:56 PM
Reply to: Message 1 by Genomicus
05-23-2016 7:59 PM


Nitpick alert
So both genetic drift and selection eliminate diversity in a population; both of these processes weed out alleles at a given locus.
Certain types of selection can work to maintain diversity, such as in cases of heterozygote advantage.
Not that this affects any of your argument, but I can't resist a good nitpick.

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caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


(1)
Message 47 of 455 (784963)
05-26-2016 2:54 PM
Reply to: Message 39 by Faith
05-26-2016 3:03 AM


Some very simple maths.
I'm having difficulty understanding exactly where your misunderstanding stems from here, but maybe some very simple maths can help.
No, because NO source of additional genetic diversity can overcome the processes that of necessity must reduce it in order to produce new phenotypes. The rarity of mutations is a separate topic.
But this is of course nonsense. Of course the rate of mutations matter. If an average of ten alleles are vanishing each generation due to drift or selection, while an average of 5 alleles are added by mutations, then of course the genetic diversity of the population will decline.
To say that nothing can overcome this decline however is fairly obviously wrong. If instead of 5 new alleles appearing each generation through mutation, there were 15, then diversity would be increasing. 15 is larger than 10. What's difficult about this?
On the subject of the real world:
OK, I see, and this is so as a TREND and with respect to the salient characteristics of the subspecies that is developing. There could still be great diversity for other characteristics of the creature that don’t show up in the new phenotype. The estimate of heterozygosity for human beings now is something like 7% IIRC, but taking a wild guess back a few thousand years it could have been as much as 50% or 70% or higher, and some loci could have retained a higher percentage than others even now.
I don't think the idea of an estimate of heterozygosity in humans is coherent. You can't be homozygous in the abstract; you are homozygous or hetrerozygous at a specific locus. Everyone will be homozygous at certain loci and heterozygous at others. A quick Google search to figure out where you might have got this statistic from led me to an estimate that the average protein coding gene is heterzygous about 9% of the time in humans (cited to this 1999 article from Nature Genetics for anyone interested who has access), so maybe this is what you heard.
The idea that humans were much more genetically diverse a few thousand years ago, however, is almost certainly wrong, and for a very simple reason. The human population has expanded exponentially over the last few thousand years, which implies a few things.
1. An expanding population is generally under less selection pressure. When a population starts expanding rapidly (as ours is) then it means that factors which used to kill people before they could reproduce or which reduced fertility through other means are apparently less of a problem. These pressures which might otherwise be driving fitter alleles to fixation are not as pressing (there is clearly a much better way to express than I'm managing!)
2. Genetic drift is less powerful in larger populations. This is fairly obvious. If an allele is present in 10% of a population of ten individuals, it can go extinct by a rock falling on someone's head. If it's present at 10% in the modern human population then it's present in double the population of the US. It would take a much longer time for it to dwindle by chance.
3. Adding more people to the population means adding more mutations. More babies are born every week than would be annually in the Palaeolithic, and every one of them carries new mutations. Regardless of the probability of any mutation arising, it's obviously going to happen more if there are more opportunities for it to happen.
I'm sure Gemonicus is able to demonstrate these concepts more rigorously if necessary, but I know you hate maths and this all seems intuitive without even glancing at algebra (though maybe not the ham-fisted way I describe it...).

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caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 50 of 455 (784970)
05-26-2016 4:00 PM
Reply to: Message 48 by Faith
05-26-2016 3:05 PM


Re: Some very simple maths.
You are missing the whole point of why adding genetic diversity makes no difference to what I'm saying.
I just explained it to HBD again. Please read the last paragraph of that Message 46 to him.
I did read that, and your view of evolution is confused - it doesn't only happen in small, isolated populations.
But the important point is that this does not matter! Even on your confused version of evolution there's no required, long term decline in diversity. Think about your small isolated population which experiences a loss of genetic diversity because some alleles spread to fixation quickly, in the process making a specific phenotype characteristic of the population. What happens afterwards? If this is a successful phenotype, and the population is able to expand, new alleles can appear and spread, restorng genetic diversity to the population.
Why would this not be able to happen?

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caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 66 of 455 (785068)
05-27-2016 2:06 PM
Reply to: Message 53 by 14174dm
05-26-2016 4:46 PM


Re: Some very simple maths.
Instead of arguing math and semantics, could we find examples?
Otzi the Iceman and King Tutankhamun & family have had dna analyses. I've tried but haven't found what I'm looking for.
Good thinking, but better than looking at individuals like Oetzi would be to look a samples from multiple members of ancient populations. And if we stick to historical periods even better since the dating cannot be as easily dismissed, as a YEC would be bound to do for anything claimed to be Palaeolithic in age.
Thankfully we have many such samples, so it should be simple to check whether they have much higher allelic diversity than modern populations. Frustratingly, though, I can't find anything that addresses the question directly, since studies of historical DNA samples are usually addressing questions other than creationist fantasies. I'll let you know if I have any luck.

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caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 69 of 455 (785076)
05-27-2016 2:46 PM
Reply to: Message 67 by Faith
05-27-2016 2:16 PM


Re: Some very simple maths.
What you would look for is a higher percentage of heterozygosity throughout the genome. Perhaps significantly less junk DNA.
But I don't believe Oetzi is that old. He ate "highly processed" grains for one thing. Not that I think he bought his cereal at the supermarket, but it suggests something a little more modern than is usually imputed to him. Give up on the radiometric dating and it's all guesswork.
Knowing that your response would be along these lines is precisely why I suggested looking to historical populations rather than to someone like Oetzi. Thankfully we have plenty of DNA from historical contexts, from individuals who lived during the Roman Empire, for example, which I think we can all agree about about 2,000 years old.
Looking at heterozygosity in a single individual doesn't tell us a great deal. If we can look at allelic diversity across a large sample and see if it differs from today.

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caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


(1)
Message 178 of 455 (785534)
06-06-2016 2:13 PM
Reply to: Message 162 by Faith
06-06-2016 7:37 AM


Re: Mt DNA vs microsatellites vs chromosomal DNA as measures of genetic diversity
This discussion has gone weird and I'm not up to trying to correct it. The REAL point, which I probably contributed to garbling as much or more than anyone else, is whether after you get a breed, or in nature a subspecies, the lost genetic diversity will be made up by mutations. I say isn't going to happen and if it did you wouldn't want it to if you were a breeder, from which I conclude it hardly ever happens anyway. But if it did it would never make up for what has been lost in arriving at the breed or species, which is the alleles for ALL the other breeds or subspecies of the Dog Kind or Cat Kind or cattle Kind or whatever it is. And if it did you could never hold on to a breed at all and Nature wouldn't have recognizable species at all.
Let's try and keep this in simple terms.
We have a population with four alleles, A. B. C and D. The proportion doesn't matter for the sake of our example.
Part of the population is separated, for whatever reason. This subpopulation only has alleles A, B and C. Over a few generations C is lost to drift. Now it only has A and B. B has a selective advantage over A in this environment, and over time B becomes fixed and all the As die out.
The original population is much bigger, and B offers no special benefit in the original environment. So now we have two populations:
Population 1 has alleles A, B, C and D.
Population 2 only has allele B.
This is the picture you're describing, if I understand it right. Here's the reductive processes of evolution making populations distinct from one another.
Now, you claim that mutation would muddle the distinctness of these gene pools and then we would no longer have distinct species, but I cannot see why.
Let's imagine mutations occur in Population 1 that introduce the new alleles E and F. Meanwhile, a mutation occurs in Population 2 that introduces allele G.
Now we have:
Population 1, containing A, B, C, D, E and F
Population 2, containing B and G.
Did these mutations muddy the distinctions between the two populations? Clearly not. They made them more distinct.

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caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


(2)
Message 187 of 455 (785593)
06-07-2016 3:13 PM
Reply to: Message 183 by Faith
06-07-2016 11:40 AM


Re: Mt DNA and microsatellites as measures of genetic diversity
Sure, but it's a reasonable wild guess from where I sit that there's something weirdly wrong about using MtDNA, microsatellites and nucleotides to measure genetic diversity. I've gone from total inability to understand any of it to suspicions born of a bit of knowledge. Now I'm suspecting too much trust in the ToE as the cause of such a weirdness. But yes, this is just my own ponderings, you can ignore me for now, carry on.
Whilst something completely different I stumbled across something relevant to this thread. The article was talking about testing the hypothesis of population bottlenecks by comparing heterozygosity and total allele diversity - the idea being that if the former was higher in proportion to the latter it implied a bottleneck. A reduction in population would eliminate rare alleles but not common ones; so heterozygosity may not be affected if there was more than one common allele, but total diversity would.
Ignoring whether this is a good test for a moment, the logic does make a good point that heterozygosity is not necessarily a good test of genetic diversity. Consider the two very small populations of five individuals below, with each pair of letters representing on diploid individual, and each different letter being a different allele:
Population 1:
AB AB AB AB AB
Population 2:
AC DB AE FG FH
Both populations are equally heterzygous at this locus, but population 2 is clearly much more genetically diverse.

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caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 206 of 455 (785636)
06-08-2016 12:20 PM
Reply to: Message 196 by Faith
06-08-2016 4:35 AM


Re: Mt DNA and microsatellites as measures of genetic diversity
So are you saying that MtDNA and microsatellites are measuring nucleotide diversity?
You can measure nucleotide diversity in any type of DNA. DNA is constructed of nucleotides.

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caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


(3)
Message 214 of 455 (785652)
06-08-2016 2:15 PM
Reply to: Message 211 by Faith
06-08-2016 1:17 PM


Re: You are looking at the wrong part of the system
It really does help conversation if the context is taken into account. I was talking about the formation of domestic breeds and how once you have the breed you've been developing you don't want mutations coming along because they would mess up the traits you've so carefully established. And the reason I make this argument is that I keep hearing how mutations can just increase genetic diversity after you have a breed or subspecies as if that would be a good thing. First it doesn't happen, you aren't going to get new traits from mutations, but if you did it would only prevent the formation of a breed or a recognizable species in the wild.
I already tried to explain in very simple terms why this is wrong back in Message 178, which you didn't react to. Adding new mutations will obviously make two populations more distinct from one another. It wouldn't muddy the boundaries between them.
Now, if all you're claiming is that mutations would be intentionally selected against by a breeder maintaining a specific characteristic, then fine. Mutations which remove desired traits from a population of domestic animals are, indeed, purposely eliminated. And in the wild, the breeder's role is played by natural selection - some parts of our DNA are highly conserved, meaning they vary little or not at all amongst different people (and in some cases even amongst different species). These stretches of DNA clearly do important things that are easy to mess up, so all changes are selected against.
But there is nothing to stop the rest varying. Why would there be?

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caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


(1)
Message 252 of 455 (785724)
06-09-2016 1:16 PM
Reply to: Message 242 by Faith
06-09-2016 6:32 AM


Re: Still await the rationalization for MtDNA & MicSat gen div measures
The topic that still needs explanation is the idea that you can measure genetic diversity by mutations in mitochondrial DNA and microsatellite DNA -- both areas that seem to have nothing to do with the actual losses under discussion, such as the loss of genetic diversity that is necessary to forming breeds and species, and the loss that at the extreme endangers creatures such as the cheetah and the elephant seal.
mtDNA and microsattelite DNA are both subject to exactly the same pressures as the rest of the genome - selection and drift. Processes which we've agreed tend to reduce. I'm not sure where you're coming from exactly, but if you're thinking these are different because they do not have phenotypic effects, then that's not correct. With relevance to our discussion of dog breeds, changes in a microsatellite region of RUNX2 in dogs seem to be involved in the different facial length of different breeds, for example.
Oddly you still haven't explained what nucleotide diversity is in relation to the loss of diversity that brought about the endangered species. It appears to be something else, something separate, something irrelevant.
Because nucleotide diversity is genetic diversity. DNA is made of nucleotides. Saying that a population has high nucleotide diversity means that there are lots of differences in the DNA of different members of the population. It's the same thing we're talking about.
----------------------
On a more general note, I think some clarity might be introduced by pointing what we actually mean by mutation, since from reading your posts I'm not sure you mean the same thing.
Mutation means a change in DNA. When we say we have observed a mutation, what we usually mean is that we can see differences in the DNA of an organism from its parent(s). If Mum and Dad both have a C at locus x, while their daughter has a G, this is a mutation. We cannot claim that the ancestral genome had all these capabilites within it; since we have the ancestral genomes. For whatever reason, the daughter's genome has changed, and this is what we call a mutation.

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caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


(1)
Message 289 of 455 (785812)
06-11-2016 2:38 PM
Reply to: Message 281 by Faith
06-11-2016 1:04 PM


An allele by any other name
You complained before about the use of too much jargon, and it's true that scientists do sometimes use unnessecary jargon, as with any specialists. Some degree of jargon is useful though, as it allows people to express a clear and well-defined concept, whereas common everyday words may be interpreted slightly differently by different people.
And I think that's part of what's causing this discussion to move nowhere, in that you're using slightly different definitions for certain bits of jargon that are causing us all to talk past you. As a case in point:
But mutations are predominantly accidents that are of no use to the organism so I can't think of that as the solution, it has to be some other kind of "mutation." Of course now that I think of it I don't know how many of those extra alleles are really alleles either, do I? Do you? I mean as opposed to "neutral" or "deleterious" mutations.
'Allele' just means different form of a gene. If a mutation occurs in a gene, then we have a new allele. If the new allele creates a less fit organism, then it's a deleterious allele. If it functions the same way as the old despite its different gene sequence, or if the differences have no effect on fitness, then the mutation was neutral. It's a new allele regardless, though, since it's a different form of a gene.
---------------------------
The 'tandem', in 'tandem repeat', just means 'in a row', which is the original meaning of tandem. The more common meaning of 'cooperating' I think comes from tandem bicycles, since the riders cooperate. But a tandem bicycle is called a tandem in the first place because the cyclists are sat in a row.

This message is a reply to:
 Message 281 by Faith, posted 06-11-2016 1:04 PM Faith has replied

Replies to this message:
 Message 290 by Faith, posted 06-11-2016 2:43 PM caffeine has replied

  
caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 294 of 455 (785817)
06-11-2016 3:03 PM
Reply to: Message 290 by Faith
06-11-2016 2:43 PM


Re: An allele by any other name
"Allele" implies USEFUL CODING FUNCTIONAL form of a gene
No, it doesn't, which is why I said we need to introduce some definitions Otherwise we're just going to misunderstand each other and get nowhere. Which is standard for most arguments on the internet but probably not what we should aim for.

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caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 314 of 455 (785849)
06-12-2016 7:44 AM
Reply to: Message 312 by Faith
06-12-2016 6:57 AM


Re: Mutations are not alleles
Then there was that Wikipedia article that pretty much defined polymorphic genes as disease-causers.
You seem to have overlooked a key word in the paragraph you posted:
quote:
A gene is said to be polymorphic if more than one allele occupies that gene’s locus within a population.[1] A polymorphic variant of a gene may lead to the abnormal expression or to the production of an abnormal form of the gene; this may cause or be associated with disease.
I would write more, but I'm off out to watch the football, which Turkey may win. They may, but Croatia are the favourites.

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caffeine
Member (Idle past 1025 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


(2)
Message 449 of 455 (786704)
06-25-2016 9:47 AM
Reply to: Message 431 by Faith
06-23-2016 10:18 PM


Re: Once again now, evolution of new phenotypes REQUIRES loss of genetic diversity
No, I say mutations themselves stop the processes of evolution that form new species, I certainly haven't said that mutations mean evolution will never stop, because evolution requires selection which always reduces genetic diversity. If you add diversity after you have a new species as a result of evolution/selection/reduction of genetic diversity, you simply lose your species. It's no longer the same species. You may get something else, even another species eventually, but you'll have lost the species originally selected. This isn't evolution(...)
I think you need to reread this. You're saying that mutations changing a species so that it eventually ends up as a different species is not evolution. This is exactly what everyone else means by evolution.

This message is a reply to:
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