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Author Topic:   Molecular Population Genetics and Diversity through Mutation
PaulK
Member
Posts: 16049
Joined: 01-10-2003
Member Rating: 2.2


Message 31 of 455 (784886)
05-25-2016 5:16 AM
Reply to: Message 30 by Faith
05-25-2016 4:33 AM


Re: The endless dance of the wishful refutation
quote:

There is no such evidence.

Your refusal to accept the evidence does not make it go away. It is still a fact that genetic diversity is greater than you can easily account for even given your own views, never mind the history of life that the evidence really shows to us.

quote:

Mutation is the only thing that could increase the genetic diversity and I dispute that you could get a single beneficial mutation in the short time frame for all the above to occur.

Which is a complete irrelevance since we do not need beneficial mutations, nor do we need to restrict the timescale to the short periods of time that you are prepared to look at.

It's past time you stopped dancing and tried to engage in honest discussion


This message is a reply to:
 Message 30 by Faith, posted 05-25-2016 4:33 AM Faith has responded

Replies to this message:
 Message 32 by Faith, posted 05-25-2016 5:20 AM PaulK has responded

  
Faith
Member
Posts: 35107
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 32 of 455 (784887)
05-25-2016 5:20 AM
Reply to: Message 31 by PaulK
05-25-2016 5:16 AM


Re: The endless dance of the wishful refutation
Your refusal to accept the evidence does not make it go away. It is still a fact that genetic diversity is greater than you can easily account for even given your own views, never mind the history of life that the evidence really shows to us.

Evidence of what genetic diversity where? You don't know what you are talking about.


This message is a reply to:
 Message 31 by PaulK, posted 05-25-2016 5:16 AM PaulK has responded

Replies to this message:
 Message 33 by PaulK, posted 05-25-2016 6:39 AM Faith has responded

  
PaulK
Member
Posts: 16049
Joined: 01-10-2003
Member Rating: 2.2


(3)
Message 33 of 455 (784889)
05-25-2016 6:39 AM
Reply to: Message 32 by Faith
05-25-2016 5:20 AM


Re: The endless dance of the wishful refutation
quote:

Evidence of what genetic diversity where? You don't know what you are talking about.

You mean that YOU don't know what I'm talking about despite all the discussion here.

Odd how you can't even remember how you have difficulty finding any examples of your "genetic depletion" - and how one of the examples you tried to give us is due to a bottleneck in historical times - and you can't even show that it produced the phenotypic changes you expect (elephant seals because you probably won't remember that unless I remind you)

And, you propose that there was a major bottleneck in the recent past such that some populations were reduced to single pairs - and that the descendants of these pairs became multiple modern species. The cytochrome-C argument given recently shows that genetic diversity at the level of sequences can't be easily explained without allowing for mutations to appear and become fixed since your bottleneck. And let us not forget that there are human genes with large numbers of alleles (hundreds IIRC - but certainly many more than the maximum of 10 we'd expect from an effective population of 5 people)

Edited by PaulK, : One clarification


This message is a reply to:
 Message 32 by Faith, posted 05-25-2016 5:20 AM Faith has responded

Replies to this message:
 Message 44 by Faith, posted 05-26-2016 2:17 PM PaulK has responded

  
Modulous
Member (Idle past 554 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 34 of 455 (784892)
05-25-2016 8:03 AM
Reply to: Message 27 by Faith
05-25-2016 12:18 AM


Re: But I'm just as mathematically challenged as ever
You will get new phenotypes simply from a new set of gene frequencies. Not new in the sense of novel but new to the population. If the parent population was characterized by brown fur the new subpopulation may have more alleles for gray fur and after some period of mixing of the new gene frequencies over some number of generations the new population will now look gray or mostly gray, differing from the original population by that particular trait.

Which is what would happen if mutations did not happen.

Let's look at a simple example population with 2 members (sexually reproducing). In this population there can be NO MORE than 4 alleles in the entire population for any gene. Without mutation there can never be any more alleles in this population. There could be less, but there cannot be more.

However an error occurs when copying the DNA during reproduction, and it mutates the gene we are looking at. Now there are 5 alleles.

In a Hardy-Weinberg equilibrium (no selections, no drift etc) with only mutations happening the number of alleles very very probably goes up each generation. Agreed?

In an analogy, this would be like photocopying something. Each photocopy is going to be slightly different than the last as noise in the machine and the optics results in speckly dots starting to appear in the copies. There's no selection, and once a dot is in place it stays (no drift), so each copy is different, there is much variety. Right?

But to the general point, the whole genome should have new gene frequencies as a result of the population split...all the alleles throughout the genome should have undergone the same changes: some higher frequency than they were in the original population, some lower, including many also not changed or much changed in frequency.

It may be a terminology confusion of your own, or it might be indicative of something more. A genome does not have gene frequencies.

A population split does not imply new gene frequencies NECESSARILY although, due to the number of genes and the law of large numbers they are PROBABLY going to vary slightly, depending on actual numbers. If the subpopulation is a perfectly representative sample, there will be, by definition, no change in allele frequencies, this is not likely - but the subpopulation will be a sampling of the main population so the frequencies are likely to be similar - especially for the main alleles. In order to not die off it needs to be large enough to be sustainable, and so we can discount small populations from consideration.

So a subpopulation of a predominantly brown fur allele population is likely to mostly have brown fur alleles too.

Think of it in a different context. Let's say I were to pick 1,000 Americans at random. If I were to ask you, "How many of them will answer, "Yes", to the question, "Are you a Christian?"", what would you say? Well the real number isn't important here, let's say 70% Why? Because just about every random sample we take gives us approximately a 70% "Yes" response. We know the sample is a reasonable approximation to the whole.

Obviously geography plays a role in both cases, and this can lead to some differences - but the heavily represented alleles are likely to make it across and still be one of the most significant alleles in the subpopulation. The sampling error we get through just picking a population from a geographic area is more likely to affect alleles that aren't common to begin with rather than ones that are.

But as to mutations: in every discussion I've ever read, mutations are treated as sort of an article of faith, their actuality not being demonstrated, or the mere presence of a newly expressed phenotype gets it called a mutation without warrant. It’s science that describes them as so predominantly either deleterious or neutral and so extremely rarely of any value to the organism, but the obvious conclusion isn’t drawn from those facts.

Actually the obvious conclusion IS drawn from these facts. Equilibrium is the norm.

Not only is a beneficial mutation rare

The problem is that the rate of beneficial mutation is not fixed. At times of ACTIVE evolution the number of mutations that would be beneficial goes up. Some mutations that were harmful before ACTIVE evolution began are now considered beneficial because of whatever started ACTIVE evolution (eg., a new location with different challenges). This allows the populations to 'crawl' towards a new local and optimal set of phenotypes with the same variety.

This is shown visually on the video I posted earlier. I again urging taking a look at it to get a grasp on the principles. Once you get those, then we can look at the evidence to see if that's how it works in nature. When the populations are sitting on the peaks of the mountains, any mutation that would knock their kids of their peak is considered harmful. The steeper the sides, the more harmful mutations exist compared to neutral mutations. By definition, there are few beneficial mutations, and for an organism right at a peak fitness - there are zero beneficial mutations. All mutations are necessarily worse that the best possible.

ACTIVE evolution occurs when the definition of 'best possible' changes by a significant degree for enough generations. During ACTIVE evolution some organisms have traits that are closer to the 'best possible' than others, so these do better and reproduce more. The population then 'clusters' around the 'close enough' group in the next generation as the close enoughs have a naturally imposed bias towards reproducing offspring more so there will be necessarily more of them 'close enough' in the next generation.

The next group also is clustered around here, they may hover around here, but the tendency for a while is to weed out all the old optimal alleles and we have a population that is a little phenotypically different, but growing in diversity. New combinations of existing alleles will account for some of the variety, of course, but some alleles are getting lost and whenever an offspring has a mutation in the regions in question it pushes it closer to 'best possible', and that biases the next generation towards being a bit closer on the whole to 'best possible', and this intrinsic bias means there could be a 'mutational pathway' (a chain of one mutation to the next) of beneficial or neutral mutations that exist between the old optimal and the new optimal and if there is, by randomly trying all the possibilities - life will either find that pathway or get as close as it can.

the fact, that I didn't make up, that most are by far deleterious or neutral and anything at all beneficial is rare to the point of vanishing, means to me that mutations contribute nothing to the evolution of new varieties.

This is true only in equilibrium. Not during ACTIVE evolution. That's the key takeaway from my post.

But evolution doesn't continue once a population is established from its particular set of gene frequencies after some number of generations of inbreeding. It could even settle down to a Hardy-Weinberg stability for some great period of time.

Again, Hardy-Weinberg isn't and cannot be real. It would imply the laws of thermodynamics are false. It means the genome never gets a harmful mutation, a neutral mutation or a beneficial one. It means that the death of an animal is never related to its genetics. It's just not going to happen.

What you mean is an Evolutionarily Stable State

quote:
"A population is said to be in an evolutionarily stable state if its genetic composition is restored by selection after a disturbance, provided the disturbance is not too large. Such a population can be genetically monomorphic or polymorphic." --Maynard Smith (1982).

Again, just a minor quibble, but the possibility for misunderstandings for technical terms can result in unnecessary bickering, I find. I'll try to remember if you are referring to Hardy Weinberg you probably mean ESS instead. During ESS, most mutations are harmful (hence 'restored by selection after a disturbance') or neutral. This is what we see most of the time for most traits.

Watch the video Faith, seriously. It's the best explanation it's only 3 minutes long. I've watched hour long documentaries when you entered them into discussion as sources, if you are unable to watch youtube videos such as https://www.youtube.com/watch?v=4pdiAneMMhU are you able to watch videos in any format. I'm very keen because even if you disagree with evolution, understanding what's happening in this video will allow us to have mathematical discussions using English so much easier.

If the video is still nonsense to you, here is another one that takes more time to explain the concept, and it doesn't use biological evolution as its only example.


https://www.youtube.com/watch?v=JPTIZbGGYmk

Edited by Modulous, : No reason given.


This message is a reply to:
 Message 27 by Faith, posted 05-25-2016 12:18 AM Faith has not yet responded

  
herebedragons
Member (Idle past 182 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 35 of 455 (784896)
05-25-2016 9:38 AM
Reply to: Message 30 by Faith
05-25-2016 4:33 AM


Allele frequency alone is insufficient
If all the alleles in a parent population except one come over to a reproductively isolated daughter population, that will be a reduction in genetic diversity. If the daughter population is significantly smaller than the parent there should be a decrease of more than one allele. Then as higher frequency alleles bring out new phenotypes in the population over some number of generations,

Allele frequency alone is not sufficient to explain evolution (or even microevolution if you wish).

Parent: {90% a1, 10% a2, 60% b1, 40% b2, 40% c1, 60% c2, 10% d1, 90% d2}

Subpopulation: {60% a1, 40% a2, 100% b2, 60% c1, 40% c2, 100% d1}

What genotypes exist in the subpopulation that don't exist in the parental population?

How is this sufficient to explain observed genotypes of species or subspecies?

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 30 by Faith, posted 05-25-2016 4:33 AM Faith has not yet responded

  
NoNukes
Inactive Member


Message 36 of 455 (784898)
05-25-2016 12:00 PM
Reply to: Message 27 by Faith
05-25-2016 12:18 AM


Re: But I'm just as mathematically challenged as ever
Duplicate. produced in part by glitch when submitting response.

Edited by NoNukes, : No reason given.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King

If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams


This message is a reply to:
 Message 27 by Faith, posted 05-25-2016 12:18 AM Faith has not yet responded

  
NoNukes
Inactive Member


(1)
Message 37 of 455 (784900)
05-25-2016 12:09 PM
Reply to: Message 27 by Faith
05-25-2016 12:18 AM


Re: But I'm just as mathematically challenged as ever
Same with Darwin's finches. There was no lack of a range of foods available in the environments they inhabited, but some finches developed beaks suitable to berries, and some to nuts and some to insects and so on, simply from becoming geographically isolated from other populations and developing the new beaks from new gene frequencies.

Your statements about what must have happened ignore the effect of selection. That is a strange thing for you to ignore. It is not just the geographic isolation from other populations that is available to favor beak development. In fact it is not clear that such things play a roll at all. It is primarily, and more importantly, observably, the competition for food or other necessity that weeds out birds who cannot cope as well as other birds with the situation in a new environment. According to your theory it would be mere accident, and completely inexplicable that the new allele frequencies just happen to correspond to advantages in the environment. One might anticipate that in the new situation beaks might get smaller or remain the same if sampling was random. On the other hand, natural selection driving which birds prosper explains the situation extremely well.

In my opinion, and in any objective view as well, that is an example of reality supporting one proposition and not supporting the other. Such support is not proof, but it is evidence and it cannot be claimed that the evidence supports both your proposition and the theory of evolution equally well.

Whether or not you personally believe in natural selection, you are not going to be able to assume it away without evidence if you want to be convincing.

I believe you are at least partially right about variation. Mutation rarely plays a role during the selection process. Darwin neither recognized, nor observed mutation in action. It would be just as coincidental and unbelievable that mutation showed up 'just in time' to be useful in a new environment as it would be that mere resampling produced anything useful in nature. On the other hand, the theory of evolution is in total agreement with that. The real story according to the TOE is that essentially all of the genetic variation that lies behind the phenotypes that are screened for in a selection process is produced randomly by mutation.

Darwin did in fact observe variation in phenotype within the parent population, something which completely disabuses the idea that variation prevents forming a subspecies. The idea is silly anyway. One only need look at the cosmetic and genetic variations among people of one race to observe that there is plenty of room for both genetic and phenotypic variability without having individuals being kicked out of their race.

While we are focusing now on the founders effect, let's recall that evolution and changes of gene frequency are observed in situations where there is no isolation at all, but there are environmental changes and it is quite clear that the reasons for the change in population is driven by some animals simply not surviving to produce offspring due to competition.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King

If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams


This message is a reply to:
 Message 27 by Faith, posted 05-25-2016 12:18 AM Faith has not yet responded

  
Genomicus
Member (Idle past 391 days)
Posts: 852
Joined: 02-15-2012


Message 38 of 455 (784923)
05-26-2016 12:22 AM
Reply to: Message 27 by Faith
05-25-2016 12:18 AM


Re: But I'm just as mathematically challenged as ever
However, what you apparently fail to take into consideration is the entire diversity of the population's gene pool. In other words, while one set of alleles might become increasingly homozygous in the population by virtue of so-called "active evolution" of a trait, there are literally thousands of other chromosomal loci which are witnessing an increase in allelic heterozygosity (that is, an increase in diversity). What you have failed to demonstrate is that while a given trait is evolving, ALL alleles must necessarily tend towards homozygosity (even if these alleles have little to do with the trait under consideration).

Well, no, I haven't failed to take into account that there are plenty of other genes that are being affected at the same time although it’s true I don’t spend time focusing on them. You stymied me for a while with your statement that an increase in allelic heterozygosity is an increase in diversity. It took a while for me to see that you made a mistake there: you are confusing gene frequency with genetic diversity. The former is just an increase in the quantity of an allele, the latter would be an increase in kinds of alleles, which isn’t going to happen in a reproductively isolated population, except by mutations of course.

No, an increase in allelic heterozygosity is an increase in genetic diversity. Heterozygosity at a locus under consideration is a pretty standard way to measure genetic diversity in a population. See here (warning: it's a PDF; it's a "primer" on population genetics which you might find easier to understand than standard pop gen textbooks).

If a given locus exhibits a high degree of heterozygosity within a population, it means that there's whole range of different, diverse allelic combinations at that locus. Ipso facto, there's an increase in genetic diversity when there's an increase in heterozygosity (and here, when I say "increase," I do not mean an increase in frequency of a particular allelic combination; I mean an increase in diverse allelic combinations throughout the population).

What you have failed to demonstrate is that while a given trait is evolving, ALL alleles must necessarily tend towards homozygosity (even if these alleles have little to do with the trait under consideration).

Not sure what you are saying. Do you mean my argument requires ALL alleles to tend towards homozygosity or do you mean that this is to be expected in reality?

Your argument appears to require that the allelic sites become increasingly homozygous. For if allelic sites, or chromosomal loci, do not become increasingly homozygous while a novel trait is evolving, then the population has plenty of genetic diversity -- even if novel traits are evolving. And if the population has this genetic diversity, your argument falls apart.

But to the general point, the whole genome should have new gene frequencies as a result of the population split, except for any that are always fixed, which you would know more about than I do, and just like the ones that are making the major changes in the look of the population by working through the population from generation to generation, all the alleles throughout the genome should have undergone the same changes: some higher frequency than they were in the original population, some lower, including many also not changed or much changed in frequency. Most of them probably wouldn’t affect the phenotype, but there should be some differences that do contribute to the change in appearance of the new population in relation to the original population.

So what's the problem here? You're basically just saying that there's going to be a change in allele frequency when the population splits, but that's not any kind of "limit" to continued evolution of the species.

In any case the decrease I have in mind is specifically due to the high frequency traits that will dominate the appearance of the new population.

As a novel, beneficial trait gains in frequency throughout the population, than the alternative allelic combinations for that trait will decrease in frequency. That is correct, yes, but the problem here is what exactly?

But as to mutations: in every discussion I've ever read, mutations are treated as sort of an article of faith, their actuality not being demonstrated...

Umm, we know mutations actually happen. Do you deny that mutations occur?

...or the mere presence of a newly expressed phenotype gets it called a mutation without warrant.

Umm, maybe among lay people, but if you actually read the scientific literature and biology papers, we don't assume any new phenotype is the result of a mutation. New phenotypes can arise through epigenetic mechanisms, so usually molecular genetic techniques are employed to determine the actual cause of a new phenotype in a population. It's very, very often mutation, by the way -- and this can be verified with nucleotide sequence data.

It’s science that describes them as so predominantly either deleterious or neutral and so extremely rarely of any value to the organism, but the obvious conclusion isn’t drawn from those facts.

Most mutations in Metazoan genomes are selectively neutral; this is the present consensus among geneticists, evolutionary biologists, and others in the field given the preponderance of evidence which points to that conclusion.

And as I suspected, your argument does really end up boiling down to the notion that beneficial mutations are too rare to fuel Metazoan evolution.

Not only is a beneficial mutation rare, it’s even rarer in the sex cells where it might have an impact on offspring...

Actually, beneficial mutations happen all the time. While the ratio of beneficial mutations to selectively neutral ones may make it seem like beneficial mutations are rare, this is no way means that beneficial mutations are so rare as to not be a driver of the emergence of novel morphological, physiological, or biochemical systems. You have yet to demonstrate otherwise.

...and the time frame required can be so enormous – as I keep noting, the cheetah has been waiting around forever for a mutation to get it out of its genetic purgatory...

Wut? A single mutation won't add significant genetic diversity to the cheetah population. What's needed is an elevated rate of mutation in the cheetah population if they are ever to get out of their "genetic purgatory." The equations in the OP demonstrate very nicely why there's extremely low genetic diversity among cheetahs; the small population size, coupled with a not-very-high mutation rate, means that genetic drift and inbreeding (which is basically just an extension of the sampling error that genetic drift is) will continue to decrease the diversity of the cheetah gene pool. So I have no idea where this "waiting around for a mutation to get them out of their 'genetic purgatory'" comes from, since it's not like a single mutation will do that.

that I didn't make up, that most are by far deleterious or neutral and anything at all beneficial is rare to the point of vanishing, means to me that mutations contribute nothing to the evolution of new varieties.

See above. Beneficial mutations aren't so incredibly rare that they are unable to contribute to the evolution of new species and higher taxa. This is something that you have made up without any empirical basis.


This message is a reply to:
 Message 27 by Faith, posted 05-25-2016 12:18 AM Faith has responded

Replies to this message:
 Message 39 by Faith, posted 05-26-2016 3:03 AM Genomicus has responded

  
Faith
Member
Posts: 35107
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 39 of 455 (784927)
05-26-2016 3:03 AM
Reply to: Message 38 by Genomicus
05-26-2016 12:22 AM


Re: But I'm just as mathematically challenged as ever
However, what you apparently fail to take into consideration is the entire diversity of the population's gene pool. In other words, while one set of alleles might become increasingly homozygous in the population by virtue of so-called "active evolution" of a trait, there are literally thousands of other chromosomal loci which are witnessing an increase in allelic heterozygosity (that is, an increase in diversity). What you have failed to demonstrate is that while a given trait is evolving, ALL alleles must necessarily tend towards homozygosity (even if these alleles have little to do with the trait under consideration).

Well, no, I haven't failed to take into account that there are plenty of other genes that are being affected at the same time although it’s true I don’t spend time focusing on them. You stymied me for a while with your statement that an increase in allelic heterozygosity is an increase in diversity. It took a while for me to see that you made a mistake there: you are confusing gene frequency with genetic diversity. The former is just an increase in the quantity of an allele, the latter would be an increase in kinds of alleles, which isn’t going to happen in a reproductively isolated population, except by mutations of course.

No, an increase in allelic heterozygosity is an increase in genetic diversity. Heterozygosity at a locus under consideration is a pretty standard way to measure genetic diversity in a population. See here (warning: it's a PDF; it's a "primer" on population genetics which you might find easier to understand than standard pop gen textbooks).

Funny, I've known that and yet forgot it in this exchange: I've even said that the way to measure genetic diversity to test my argument is by looking for increases in homozygosity. I’ve saved the link and skimmed through it. There may be too much math there for me, however.

You said heterozygosity can increase from parent to daughter and I accepted that possibility but I would still expect that the overall trend would be to increasing homozygosity, which would show up more clearly after a series of population splits such as in ring species. I figured it would probably happen where high frequency homozygous genes in the parent population that become low frequency in the daughter population could pair with an allele that was low frequency and now is high frequency, Which would be something like:

Parent population has lots of homozygous blue eyes, 90% bb’s, a scattering 8% of brown heterozygous Bb’s and a few 2% brown homozygous BB’s. The population split happens to take a slice of the parent population that has most of the B’s (leaving the parent population almost totally homozygous blue which will soon become totally so because the few remaining B’s will drop out). So what in the parent population was very high frequency b’s, in the daughter population are low frequency, say 20%, while the B’s have become high frequency, say 60% Bb and 20% BB. Barring selective pressure for one or the other, besides the high frequency heterozygous Bb’s, this would also make for more heterozygous pairings in the new population than in the parent, which could increase over the generations. So more heterozygosity at that locus in the new population.

But yes, increased homozygosity is THE sign of reduced genetic diversity. The question now is whether the fact that heterozygosity can increase in some cases is enough to overcome the predicted trend to increased homozygosity.

If a given locus exhibits a high degree of heterozygosity within a population, it means that there's whole range of different, diverse allelic combinations at that locus. Ipso facto, there's an increase in genetic diversity when there's an increase in heterozygosity (and here, when I say "increase," I do not mean an increase in frequency of a particular allelic combination; I mean an increase in diverse allelic combinations throughout the population).

The question, again, is whether this increase in heterozygosity could occur in a geographically / reproductively isolated daughter population to any extent to offset the trend to homozygosity or reduction of alleles. You are describing a situation that starts out with high genetic diversity in general, which I suppose to generally increase the farther back you go along any evolving line, and where that is the case there should still be a trend to increased homozygosity all down the evolving chain of daughter populations, but it wouldn’t be particularly dramatic until you have less genetically diverse populations splitting into daughter populations, especially into significantly smaller populations.

In any case I think you’d be very hard-pressed to demonstrate that I’m wrong about the TREND to decreased genetic diversity, or to make a case for an actual increase. Population splits do very much what natural selection does as far as changing gene frequencies goes, and you’ve agreed that natural selection reduces genetic diversity. A daughter population is a sort of selected population, randomly selected in this case, and even if some increase can occur over that of the parent at some loci there’s no way that could be the trend of change, because of the principle you have also already agreed with, that developing new phenotypes requires the loss of competing alleles. (Even in the case of our new high frequency B’s there is a reduction of the b’s after all.)

What you have failed to demonstrate is that while a given trait is evolving, ALL alleles must necessarily tend towards homozygosity (even if these alleles have little to do with the trait under consideration).

Not sure what you are saying. Do you mean my argument requires ALL alleles to tend towards homozygosity or do you mean that this is to be expected in reality?

Your argument appears to require that the allelic sites become increasingly homozygous.

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. (At least some percentage of “junk DNA” could be formerly fixed loci where mutation killed the allele).

For if allelic sites, or chromosomal loci, do not become increasingly homozygous while a novel trait is evolving, then the population has plenty of genetic diversity -- even if novel traits are evolving. And if the population has this genetic diversity, your argument falls apart.

No it doesn’t, it just means, as I say above, that the loss is a trend over time. There was a lot more genetic diversity in the past, that has been decreasing over time, more in some evolving lines than others no doubt. More and more homozygosity has been accumulating over the last few thousand years. When it was very high you could even have populations developing from very few individuals, even only two, that would have high enough genetic diversity to produce many new subpopulations after it. It’s only in recent times that we are seeing enough decrease in genetic diversity to be threat to some species. Even so there are still populations with plenty of diversity. None of this changes my argument that homozygosity will be the trend down any line of evolving subpopulations, slow or fast, dramatic or hardly discernible, but always the trend.

But to the general point, the whole genome should have new gene frequencies as a result of the population split, except for any that are always fixed, which you would know more about than I do, and just like the ones that are making the major changes in the look of the population by working through the population from generation to generation, all the alleles throughout the genome should have undergone the same changes: some higher frequency than they were in the original population, some lower, including many also not changed or much changed in frequency. Most of them probably wouldn’t affect the phenotype, but there should be some differences that do contribute to the change in appearance of the new population in relation to the original population.

So what's the problem here? You're basically just saying that there's going to be a change in allele frequency when the population splits, but that's not any kind of "limit" to continued evolution of the species.

If the trend is to reduced genetic diversity / increased homozygosity, it depends on how much gen diversity you start with how soon you’ll reach that point, but the trend itself is contrary to the ToE, which needs, and in fact assumes, abundant genetic diversity from subpopulation to subpopulation. If the trend is in the other direction, the ToE fails. Even adding mutations can’t help it if the actual processes of evolution that produce new phenotypes, which is supposed to be the evidence of evolution after all, must reduce genetic diversity which would include that added by mutations.

In any case the decrease I have in mind is specifically due to the high frequency traits that will dominate the appearance of the new population.

As a novel, beneficial trait gains in frequency throughout the population, than the alternative allelic combinations for that trait will decrease in frequency. That is correct, yes, but the problem here is what exactly?

The problem is that the trend contradicts the expectation of the ToE that you can always get new variations, there will be an endless supply of new variations, all based on seeing species vary greatly over generations. The idea that a mammal evolved from a reptile assumes enormous continuing or growing genetic diversity (over hundreds of millions of years yet), or that eventually a dog will evolve into something that isn’t a dog is the expectation we get from the ToE. If the trend is to reduced genetic diversity that can’t happen. There are plenty of “new species” out there, so named because they can no longer interbreed with the parent organism, that are thought of as a step to further evolution, whereas my bet is that the majority of them are suffering from severe genetic depletion which is hardly any kind of foundation for further evolution, but in fact evidence that evolution has come to the point where no further variations are possible.

But as to mutations: in every discussion I've ever read, mutations are treated as sort of an article of faith, their actuality not being demonstrated...

Umm, we know mutations actually happen. Do you deny that mutations occur?

Oh bazillions of them occur, only most of them are of no use to the organism. I think their supposed utility is simply assumed, imposed on any genetic change as its supposed source merely because the ToE says it must be, when there really is no actual evidence that mutation could produce useful changes.

...or the mere presence of a newly expressed phenotype gets it called a mutation without warrant.

Umm, maybe among lay people, but if you actually read the scientific literature and biology papers, we don't assume any new phenotype is the result of a mutation. New phenotypes can arise through epigenetic mechanisms, so usually molecular genetic techniques are employed to determine the actual cause of a new phenotype in a population. It's very, very often mutation, by the way -- and this can be verified with nucleotide sequence data.

Very very often is how often? How reliable is the test? Are there any other ways it could be explained? While I can imagine a normal healthy form of mutation, that could possibly have produced the many alleles for a given locus for instance, most information about mutations suggests anything but something normal and healthy. “Mistake in replication,” long long list of genetic diseases, thousands IIRC, very very short list of mutations known to do anything beneficial.

It’s science that describes them as so predominantly either deleterious or neutral and so extremely rarely of any value to the organism, but the obvious conclusion isn’t drawn from those facts.

Most mutations in Metazoan genomes are selectively neutral; this is the present consensus among geneticists, evolutionary biologists, and others in the field given the preponderance of evidence which points to that conclusion.

And as I suspected, your argument does really end up boiling down to the notion that beneficial mutations are too rare to fuel Metazoan evolution.

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.

Not only is a beneficial mutation rare, it’s even rarer in the sex cells where it might have an impact on offspring...

Actually, beneficial mutations happen all the time. While the ratio of beneficial mutations to selectively neutral ones may make it seem like beneficial mutations are rare, this is no way means that beneficial mutations are so rare as to not be a driver of the emergence of novel morphological, physiological, or biochemical systems. You have yet to demonstrate otherwise.

But if selection reduces genetic diversity then it’s going to treat any source of genetic diversity the same way, selecting some, reducing or eliminating others, and if the inevitable trend is to reduced genetic diversity, it doesn’t matter what the source of the additional diversity might be it’s going to end up at best as a phenotype in a new subspecies that lacks the genetic diversity to vary further.

...and the time frame required can be so enormous – as I keep noting, the cheetah has been waiting around forever for a mutation to get it out of its genetic purgatory...

Wut? A single mutation won't add significant genetic diversity to the cheetah population. What's needed is an elevated rate of mutation in the cheetah population if they are ever to get out of their "genetic purgatory." The equations in the OP demonstrate very nicely why there's extremely low genetic diversity among cheetahs; the small population size, coupled with a not-very-high mutation rate, means that genetic drift and inbreeding (which is basically just an extension of the sampling error that genetic drift is) will continue to decrease the diversity of the cheetah gene pool. So I have no idea where this "waiting around for a mutation to get them out of their 'genetic purgatory'" comes from, since it's not like a single mutation will do that.

OK, so any genetically compromised species will face the same kind of problem, and if that’s what “speciation” amounts to, we’ve got a deteriorating system that isn’t going to be able to reverse itself.

that I didn't make up, that most are by far deleterious or neutral and anything at all beneficial is rare to the point of vanishing, means to me that mutations contribute nothing to the evolution of new varieties.

See above. Beneficial mutations aren't so incredibly rare that they are unable to contribute to the evolution of new species and higher taxa. This is something that you have made up without any empirical basis.

Funny, I thought it was standard evo information.

But basically I have to doubt what you are saying, that beneficial mutations occur in any appreciable numbers. However, again, it wouldn’t make any difference in the scenario I’m describing, since the selective processes HAVE to reduce it to get new phenotypes.

Edited by Faith, : No reason given.


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PaulK
Member
Posts: 16049
Joined: 01-10-2003
Member Rating: 2.2


Message 40 of 455 (784933)
05-26-2016 8:07 AM


Why neutral and deleterious mutations count
It should be obvious.

The heterozygosity measure in no way depends on fitness measures. The only question is whether the two alleles at the locus in question are the same or different. If they are the same, the individual is homozygous, if not heterozygous.

If we measure diversity by counting the range of alleles again, fitness does not matter.

Or again diversity is about the current state of the population. We should not count an allele differently if it was the product of a mutation or not (and what counts as "not" and how do we tell ?)

Or again, if the loss of an allele counts as a loss of diversity the gain of that allele should count as an increase. Alleles lost through selection are necessarily less fit - equivalent to a deleterious mutation. (Granted there are complications but they don't really impact the point)

So, I think that it is quite obvious to anyone who considers the matter that simply for considering their contribution to diversity all mutations count. Or rather that all alleles in the population count, whether they are considered mutant or not.

To forestall the obvious objection, what happens in future generations matters but that is a different question from the diversity of the current generation and it can only be prejudged in the case of the more severe deleterious mutations - even mildly deleterious mutations may be retained and spread by drift. And so long as the mutant allele is present it should be counted.


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herebedragons
Member (Idle past 182 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 41 of 455 (784942)
05-26-2016 10:33 AM
Reply to: Message 40 by PaulK
05-26-2016 8:07 AM


Re: Why neutral and deleterious mutations count
Another thing to point out as to why neutral (and slightly deleterious) mutations count...

When we refer to a mutation being neutral, we are specifically referring to the effect of selection. In reality all mutations have an effect on the dynamics of the genome, even if the effect is imperceptible. I got into a discussion several years ago about how stream energy changes when restrictions are introduced (starting here Message 1411). Even a small stone thrown into a river changes the dynamics of the river even though the change may be imperceptible. Keep adding stones and eventually the change will be noticeable. Throw in a large barrier and the change may be immediately noticeable.

Mutations work the same way on a molecular level. Even a single base pair mutation causes a different dynamic - even if that change is imperceptible - and that effect may be independent of its effect on fitness. For example, a G-C pair has 3 hydrogen bonds while an A-T pair has only 2 hydrogen bonds. So a point mutation from an A to a G would increase genomic stability slightly even though it may have no effect on fitness. But add up enough of these neutral point mutations and you can have a noticeably different genome.

Now consider a large mutation such as a duplication. The duplication may be completely invisible to selection, and therefore neutral, but it significantly changes the dynamics of the genome. For one thing, there are more bases to duplicate, so more energy and resources are consumed in replication. This may seem insignificant at first but consider the amount of repetitive regions in genomes and it can really add up. In addition, since the duplication is invisible to selection, it can freely accumulate mutations until it does have some type of fitness effect.

So, while mutations may be neutral in regard to fitness, there are not neutral in regard to the genome. Mutations count whether they are neutral or not.

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


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Faith
Member
Posts: 35107
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 42 of 455 (784955)
05-26-2016 1:59 PM
Reply to: Message 40 by PaulK
05-26-2016 8:07 AM


Re: Why neutral and deleterious mutations count
I agree with this post in general. But I still take the position that mutations aren't going to make a difference in the outcome of reduced genetic diversity in an evolving population. You could double the genetic diversity in a stable population and still, when selection or the random selection of the splitting off of a subpopulation occurs, new phenotypes are going to emerge simply from the new higher gene frequencies, and former phenotypes that are now low frequency will fade away, while alleles competing with the new phenotypes will necessarily also be reduced and perhaps disappear. You may (hypothetically) have lots of mutated alleles to begin with, but when you are getting evolution there's no more genetic increase, just reduction. And evolution IS the point, isn't it?

Edited by Faith, : No reason given.


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Faith
Member
Posts: 35107
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 43 of 455 (784957)
05-26-2016 2:04 PM
Reply to: Message 41 by herebedragons
05-26-2016 10:33 AM


Re: Why neutral and deleterious mutations count
I've thought all along there can't really be such a thing as a truly neutral mutation, it's got to affect things somehow, but I'm cynical enough to think even neutral mutations are destructive and do no good thing to an organism no matter what.

But anyway, granting whatever needs to be granted about mutations adding to diversity and all that, when a population is evolving and bringing out new phenotypes your mutations are going to be treated like any other alleles and the end result has to be reduced genetic diversity. Because that's what evolution does. You don't get new subspecies without losing alleles.


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Faith
Member
Posts: 35107
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 44 of 455 (784958)
05-26-2016 2:17 PM
Reply to: Message 33 by PaulK
05-25-2016 6:39 AM


Re: The endless dance of the wishful refutation
Odd how you can't even remember how you have difficulty finding any examples of your "genetic depletion" - and how one of the examples you tried to give us is due to a bottleneck in historical times - and you can't even show that it produced the phenotypic changes you expect (elephant seals because you probably won't remember that unless I remind you)

Oh I remember elephant seals as an example of depleted genetic diversity, but how am I know what you are referring to with your general statements? I also remember Dr. A's American Curl but when he says he's refuted me with some example or other I don't think of that as the example because it doesn't refute anything, it's a whole nother process from what I'm talking about.

And I don't really know what you are saying about elephant seals here either.

And, you propose that there was a major bottleneck in the recent past such that some populations were reduced to single pairs - and that the descendants of these pairs became multiple modern species.

Yes I certainly recall that, the idea being that there was sufficiently great genetic diversity at that time so that such a bottleneck wouldn't have the disastrous effects it would have today. Increasing homozygosity continues with the formation of every new species/subspecies, but it doesn't make such a huge difference when the genetic diversity starts out extremely high as it would have back then, such as for instance there likely having been many more genes for a given trait than there are now (most of that genetic diversity now in the Junk DNA cemetery)

The cytochrome-C argument given recently shows that genetic diversity at the level of sequences can't be easily explained without allowing for mutations to appear and become fixed since your bottleneck.

Sorry, that particular example means absolutely nothing to me.

And let us not forget that there are human genes with large numbers of alleles (hundreds IIRC - but certainly many more than the maximum of 10 we'd expect from an effective population of 5 people)

It was six, so twelve. And I've many times allowed that there had to have been some kind of "mutation" to bring about the increase in alleles per locus. Something more orderly than random accidents I would suppose.


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PaulK
Member
Posts: 16049
Joined: 01-10-2003
Member Rating: 2.2


Message 45 of 455 (784959)
05-26-2016 2:17 PM
Reply to: Message 42 by Faith
05-26-2016 1:59 PM


Re: Why neutral and deleterious mutations count
quote:

I agree with this post in general. But I still take the position that mutations aren't going to make a difference in the outcome of reduced genetic diversity in an evolving population.

We're all pretty much agreed that diversity will decrease during speciation events. The question is to what degree it can recover afterwards. I take the position that it can recover sufficiently that evolution will not cease for lack of diversity. At least not as a consequence of evolution rather than. say, human interference or the sun becoming a Red Giant star, as it will eventually.


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 Message 42 by Faith, posted 05-26-2016 1:59 PM Faith has not yet responded

  
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