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Author Topic:   Molecular Population Genetics and Diversity through Mutation
Faith 
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Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 4 of 455 (784832)
05-24-2016 6:04 AM
Reply to: Message 1 by Genomicus
05-23-2016 7:59 PM


But I'm just as mathematically challenged as ever
Although I appreciate that you want to keep the math to a simple level, even that's probably going to be too much for me, sad to say. And I didn't have probability theory in high school either. I'd like to be able to think in terms of math about these things but it isn't happening. (I comfort myself with the thought that Darwin also admitted to being mathematically challenged.) So I may not be able to stick it out on this thread very long.
I will begin by noting that genetic drift eliminates diversity in a population. Genetic drift, of course, is basically a sampling error -- there are a number of cool images on the web that can help you visualize why genetic drift, by itself, removes genetic diversity in a population. So both genetic drift and selection eliminate diversity in a population; both of these processes weed out alleles at a given locus.
Yes, thank you, good place to start, with processes that do eliminate genetic diversity. I have to admit that the term "sampling error" has always escaped my understanding despite many efforts to make sense of it, but nevertheless I think I have a visual grasp of what drift actually does.
But if you are answering my argument it needs to be kept in mind that what I’m focused on is the phenotypic changes that are considered to be evolution, those which accumulate in a population to the point of defining a new subspecies, changes which require the loss of genetic diversity you are discussing. If this isn’t kept in mind it starts to sound like I have some interest in loss of genetic diversity as such, for no good reason. But again, the point is that it must accompany the phenotypic changes we identify as evolution. While I include selection as one of the processes that brings about these changes, I think the more powerful mechanism of change is geographic isolation / reproductive isolation of a subpopulation, which is why that is the example I usually use, and ring species are my favorite example of how the changes occur from daughter population to daughter population. I can only predict that loss of genetic diversity must accompany each new subpopulation of course, and I’m aware that hybrid zones may occur and that gene flow may not completely cease between some subpopulations, but since selection and drift lose genetic diversity, it seems to be a good general prediction for this situation too. Ring species get some dramatic new phenotypic variations. What I’d like to see set up as a lab experiment is basically a ring species, daughter population to daughter population changes monitored for gemetic diversity.
If evolution, meaning the production of a population-wide change in phenotypic presentation (black wildebeests to blue wildebeests, normal lizards to large-headed lizards, Darwin’s finches and so on, all changes normally called evolution) always requires a reduction in genetic diversity, that is obviously contrary to what evolution needs in order to do what the ToE says it does. (Yes, I’ll get to the claim that mutations counteract this). As I understand it, genetic drift may or may not involve phenotypic changes. The Wikipedia article on drift says that, and also says there is an ongoing debate about whether drift or selection is the real cause of evolution. I have in mind that wherever you have phenotypic changes that become characteristic of a population you also have loss of genetic diversity because you can’t get those changes without removing the genetic diversity.
As both of these processes remove genetic diversity in a population of organisms, I will focus on genetic drift. Note that my argument holds perfectly well for selection; however, the mathematics for selection are slightly more intricate, so I will go there only if necessary.
Now comes the math. Why does genetic drift weed out diversity? For starters, let G = the probability that 2 alleles (from the same locus) randomly chosen from the population are identical.
Thus, G = how much genetic variation there is in the population.
Well, I was going to make a big effort to follow the math but I’m already at sea. I give up on the math already. Sorry. There is probably no way I’m going to be able to participate on this thread. I’m going to continue far enough to get a sense of the logic of it at least, and comment on that, but that may mean I’m hopelessly off topic.
First observation: all your description of the math is hypothetical, if this then that so that I have no idea what actual facts, if any, are described by these calculations.
But now let’s take a look at the role of mutation in this.
Mutation puts variation into a population at the rate 2Nu, where u = the mutation rate for selectively neutral alleles. Why 2Nu? Well, there are 2N gene copies per generation, and u = mutation rate, so these are multiplied together to get the overall rate at which variation enters the population.
More precisely, u = the mutation probability for a given allele. So u = the probability that an allele in a given locus of a gamete will have a mutation. When mutation rate is taken into consideration, then, we must revise the equation for G’. Remember, G’ is the probability of 2 alleles picked at random from the population will be identical after one generation; if G = 1, all alleles are the same; if G = 0, no alleles are the same.
So the new equation, taking mutation into consideration, is this:
G’ = (1-u)^2 * [1/2N + (1-1/2N)*G]
What is 1-u? The factor 1-u is the probability that a mutation did not occur in one allele. But remember these are diploid organisms (2 allele copies), so the probability that a mutation didn’t take place in either allele is (1-u)^2 -- it is multiplied by itself (the two events are independent, so a la basic probability theory, they are multiplied instead of added). Why 1-u? Well, u = the probability that a mutation does happen; u must necessarily be less than 1, so 1-u is the probability of the allele not having a mutation.
Okay, now let’s plug in some numbers. Say the mating population size is 100 and G = 50%. Let’s say the mutation rate is 10^-5 (pretty standard mutation rate for a number of diploid organisms). That means there’s a 1 in 100,000 chance that a given allele will mutate. After one generation, G’, the probability of 2 alleles being identical (picked randomly from given loci) is: 50.248995%, which is extremely close to the 50.25% reported above, where mutation was NOT taken into consideration. However, what happens when the population size is increased?
When the population size is 100,000 (instead of a mere 100), the probability of randomly picking 2 identical alleles begins decreasing. After one generation, it’s 49.99925%. Each generation, the probability inches closer to 0. In other words, because of mutation, the probability of randomly picking out 2 identical alleles increasingly becomes 0. This, in turn, means that there’s an enormous amount of genetic diversity in the population. In short, mutation has an effect that can and does counter both genetic drift and the forces of selection.
I don’t see anything in all of that to tell me about the actual rate of mutations, but isn’t that what we need to know?
The challenge is for Faith to show that:
(1) The mathematics undergirding these processes become irrelevant in isolated founding populations, which represent a sampling of the allele frequency of the ancestor population. Clearly, if founding populations are quite small and geographically isolated, then genetic drift and selection will work to eliminate genetic diversity. Often, the result will be extinction. But if the founding population is sufficiently large, then mutation will be enough to continue adding diversity to the gene pool, generation after generation -- despite selection and genetic drift.
Well, now I see that you are saying the same thing I’ve answered many times in this argument already: it doesn’t matter how much new genetic variability you can put into, or put back into, a population, when it is evolving a new population of new phenotypes, a new look, the trend is going to be to loss of genetic diversity, no matter how much new diversity may have been added. As I put it above, you can't get the phenotypic changes without removing the genetic diversity. So if you are adding genetic diversity, you are obviously not removing genetic diversity.
The processes that bring about the new phenotypes, that is, that are actively evolving the population, have to get rid of whatever genetic diversity doesn’t support the new phenotypes, and the end is going to be the same no matter how much diversity is added: a subspecies with reduced genetic diversity, and if many daughter populations succeed one another eventually the loss of genetic diversity should be quite dramatic. And if during all these evolutionary changes new genetic diversity is added, all that can do is interfere with the formation of the phenotypes that is underway. It can happen, of course, but then it isn’t evolution.
(2) Most mutations are too detrimental for any of this to be of real meaning in biology, or beneficial mutations too rare for positive selection to have something to work on.
Well, that’s information I get from evolutionists, I don’t make it up. Of course I draw conclusions from it they don’t draw.
(3) While mutation can overcome the reduced diversity wrought by genetic drift, selection is necessarily always strong enough that mutation cannot overcome its reductive effects.
But I think you are making the common mistake of thinking of this as a simple process of addition and subtraction, but it’s not. The selective or subtractive processes that bring about the new phenotypes toward a new subspecies HAVE to get rid of the genetic diversity that doesn’t support them. It isn’t just a matter of more or less, it’s a matter of REQUIRING loss of genetic diversity in order to get the phenotypic changes which are normally identified with evolution. True, as I’m often reminded, nature couldn’t care less about preserving emerging phenotypes, but the point I’m making is that the ToE DOES care and is always describing the production of new phenotypes a la microevolution as an open-ended process that just keeps on going making endless new variations. But if selection eliminates genetic diversity you’d think that would be a caution right there. Additions CAN’T overcome this effect because subtraction is REQUIRED if evolution is occurring. Breeding by artificial selection should get this across, and Darwin was right to apply that method to nature. He just didn’t recognize the necessity of the loss of genetic diversity, and that lack of recognition continues today.
So I’m probably way off topic since I can’t deal with the math. And as so often happens when I spell out all this I've probably left out necessary information or garbled something important. Oh well.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 1 by Genomicus, posted 05-23-2016 7:59 PM Genomicus has replied

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 Message 7 by Modulous, posted 05-24-2016 11:59 AM Faith has replied
 Message 18 by Genomicus, posted 05-24-2016 7:51 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 8 of 455 (784847)
05-24-2016 4:29 PM
Reply to: Message 7 by Modulous
05-24-2016 11:59 AM


Fitness graphic
HBD posted that graphic quite a while ago and it's just as mystifying to me now as it was then, as mystifying as math.
Of course reality is messy, a lot messier than the descriptions I'm giving which are an attempt to streamline things down to essentials. There are conditions in which populations are stable, that is, NOT EVOLVING, which is what Hardy-Weinberg is describing. It is actually described AS not evolving. Gene flow of any sort also reverses the evolution I'm talking about, any addition of genetic diversity reverses it, but I've already said that.
Again, what I am focusing on is what happens when you are getting the active production of new phenotypes in reproductive isolation, because that is the clearest expression of evolution, usually believed to be THE way all life evolved from former life. But the fact is that this leads ultimately to genetic depletion, yes even with all the additions you can throw at it -- as long as new phenotypes are being produced you are getting a loss of genetic diversity.
What that graphic is designed to show I really have no idea, however.
I can agree that natural selection is one way genetic diversity is reduced as new phenotypes are expressed, making it one version of what I'm arguing. I just think it's clearer to emphasize the factor of reproductive isolation of a subpopulation, which is also brought about by natural selection but can be seen a lot more clearly in the example of geographic isolation.

This message is a reply to:
 Message 7 by Modulous, posted 05-24-2016 11:59 AM Modulous has replied

Replies to this message:
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 10 of 455 (784849)
05-24-2016 4:52 PM
Reply to: Message 6 by PaulK
05-24-2016 7:55 AM


The endless dance of the wishful refutation
As Modulous has pointed out this is a bad argument for reasons that have been pointed out before - and which are implicit in the post you are answering. The times when a new species is forming is just a fraction of the lifetime of a successful species - and the rest of that time is when we expect the increases to occur.
And I've answered that I don't know how many times. You can get all the increases you want, taking all the time you want, it makes no difference to the point I'm making. There are certainly periods when active evolution is not occurring, most of the time no doubt.
But when evolution does occur, when new phenotypes are being formed out of all that increase, selected out of it, isolated out of it, then you are also getting the loss of genetic diversity I'm talking about, in the population that is evolving. The parent population may remain stable, not evolving, accumulating increase. I'm only talking about where evolution is occurring. The increases contribute only to a static condition of a population, you are only getting evolution when particular phenotypes are selected out to become the new characteristic of a new subpopulation, which can form in many ways, sometimes even within the parent population, but is most clearly seen when geographically isolated from the parent population.
(For good reason. Losses should slow when a species is increasing in population, and the number of mutations appearing is proportional to population size.)
Leaving aside the crucial question of just what sort of mutations are appearing in just what proportions to just what purpose, losses will slow when a population is genetically STABLE, increasing in numbers or not. If it's an evolving subpopulation, with new gene frequencies that have yet to be reproductively worked through the whole population, then the population will be increasing while the losses may be increasing at the same time by drift.
And, of course, this is one of the points that you haven't been able to refute.
You keep saying that and I keep saying you're wrong. I guess we can do this little dance endlessly. The last time I said it was in post 903 on the Science in Creationism thread.
ABE: I see you repeated your point in messager 9:
You have yet to offer any valid reason why diversity cannot be restored between speciation events.
I never said it couldn't be restored. What I'm saying is that it makes no difference because when the population is actively evolving all that increase gets pared down to favor a few phenotypes with the concomitant loss of genetic diversity. Even if you have a new trait all it can do is contribute to a new subspecies with reduced genetic diversity. The hopeful belief of the ToE that further variation is endless is brought to a halt at that point no matter what traits are involved.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 6 by PaulK, posted 05-24-2016 7:55 AM PaulK has replied

Replies to this message:
 Message 12 by PaulK, posted 05-24-2016 5:13 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 14 of 455 (784853)
05-24-2016 5:23 PM
Reply to: Message 13 by Modulous
05-24-2016 5:14 PM


Re: Fitness graphic
I'm telling you that people that know the maths say you are wrong, you can't understand the maths.
Actually, what I've seen of Dr. A's and Genomicus' math shows me that math is only as good as the person's conceptualization of the actual situation. If it's not conceptualized correctly then the best mathematical expression is nothing but garbage in garbage out. That's how increases in genetic diversity are proved by math, by simply assuming it's possible when it's not. The graphic in your post is no doubt a case of the same error.
It is actually described AS not evolving.
Maybe, but its still part of evolution whether the phenotypes are changing or not.
Oh yeah yeab yeah, EVERYTHING is evolution, yeah yeah, but that's why I keep saying ACTIVE evolution, because I'm describing the specific process where you are getting new characteristic phenotypes and ultimately a new subspecies based on those phenotypes. That is NOT happening in your stable population. And Hardy-Weinberg DOES describe a stable population that is NOT EVOLVING, showing that I'm using the term correctly and you are not.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 15 of 455 (784854)
05-24-2016 5:34 PM
Reply to: Message 12 by PaulK
05-24-2016 5:13 PM


Re: The endless dance of the wishful refutation
And there is a failure to think things through. In an increasing population a larger proportion of the offspring survive. That will reduce losses from drift and selection
But it can't reduce the original loss of genetic diversity from the new gene frequencies caused by the formation of the new subpopulation in the first place.

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 Message 12 by PaulK, posted 05-24-2016 5:13 PM PaulK has replied

Replies to this message:
 Message 28 by PaulK, posted 05-25-2016 12:55 AM Faith has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 26 of 455 (784878)
05-25-2016 12:16 AM
Reply to: Message 18 by Genomicus
05-24-2016 7:51 PM


Re: But I'm just as mathematically challenged as ever
dup
Edited by Faith, : No reason given.

This message is a reply to:
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 27 of 455 (784879)
05-25-2016 12:18 AM
Reply to: Message 18 by Genomicus
05-24-2016 7:51 PM


Re: But I'm just as mathematically challenged as ever
If necessary, I'll endeavor to walk you through the math.
Not necessary but thanks.
For now, though, I'll stick with word-based reasoning. Here's what I'm going to respond to:
Well, now I see that you are saying the same thing I’ve answered many times in this argument already: it doesn’t matter how much new genetic variability you can put into, or put back into, a population, when it is evolving a new population of new phenotypes, a new look, the trend is going to be to loss of genetic diversity, no matter how much new diversity may have been added. As I put it above, you can't get the phenotypic changes without removing the genetic diversity. So if you are adding genetic diversity, you are obviously not removing genetic diversity.
The processes that bring about the new phenotypes, that is, that are actively evolving the population, have to get rid of whatever genetic diversity doesn’t support the new phenotypes, and the end is going to be the same no matter how much diversity is added: a subspecies with reduced genetic diversity, and if many daughter populations succeed one another eventually the loss of genetic diversity should be quite dramatic. And if during all these evolutionary changes new genetic diversity is added, all that can do is interfere with the formation of the phenotypes that is underway. It can happen, of course, but then it isn’t evolution.
You state that the process giving rise to novel phenotypes "have to get rid of whatever genetic diversity doesn’t support the new phenotypes." I'm not sure if this is a typo on your part or a genuine misunderstanding of terminology. The only process that gives rise to new phenotypes (barring epigenetic mechanisms) is mutation; natural selection and genetic drift only determines the distribution of that new phenotype in the population.
I sometimes don't get the whole thought expressed. 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. And the same thing should be happening with other traits, some now being more frequent and coming to contribute to the new population while others that were frequent in the original population are now less frequent and may even disappear. Thus you get a new set or new mix of phenotypes in your new population, eventually amounting to a new subspecies. Of course it's an oversimplification but the logic should be correct enough. And the smaller the subpopulation the more dramatic the new appearance will be, and the greater the loss of genetic diversity.
That being said, your argument is fatally flawed, and here's why.
It is indeed true that while a new trait is increasing in frequency throughout the population, there is a loss in heterozygosity among the relevant alleles (that is, the alleles which encode the specific proteins that constitute the novel trait on a molecular level). There are some exceptions, as caffeine noted, but these aren't relevant here and the exceptions would further refute your argument anyway.
So, from that perspective, you're right: as a new trait is evolving, there is a decay in heterozygosity among the relevant alleles.
Good, your specificity is welcome.
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.
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? My first take, I could be wrong, is that neither should be the case. Some genes should remain heterozygous, perhaps some become heterozygous, though I’m not sure about how that happens.
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.
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.
The experimental facts of life, however, demonstrate that as one beneficial phenotype gains in frequency in the population, plenty of other selectively neutral phenotypes will emerge in the population -- phenotypes which are not related to the function of the beneficial phenotype.
I agree and I do take that into account. I don’t think it affects my basic argument so I don’t normally discuss it.
Also, more as a side issue perhaps, I don't think in terms of the emerging phenotypes as {beneficial, I guess because because I don't think much in terms of natural selection or of mutations, I'm thinking in terms of random changes in frequency of a species' built in genes/alleles as the driving element in evolution.
They are most likely neutral with respect to adaptation, at least adaptation that would come about from environmental pressure. I've come to see most adaptations as produced by these random genetic changes rather than by the environment, genetic changes which then lead the organism to gravitate to whatever in the environment suits it.
So: the lizards on Pod Mrcaru that developed the large heads and jaws and tougher digestive system didn't develop all that because of a loss of their usual food in their new environment or a greater abundance of food that required the heavier jaws and tougher digestive system, they simply evolved the new physical abilities by random genetic combinations from new gene frequencies and then gravitated to the food best suited to their new abilities.
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. It's not a crucial point I guess, that is it doesn't particularly further my argument, it's just something I think is true, and it has the virtue of saving what could be an enormous cost to the organism from natural selection.
So I'd reword your statement: "plenty of other selectively neutral phenotypes will emerge in the population -- phenotypes which are not related to the function of the beneficial new dominating or high-frequency phenotype."
And that I agree with. I think some of the other selectively neutral phenotypes will also contribute something to the overall phenotypic presentation of the new population after it has thoroughly worked through all its new frequencies over some number of generations.
And these selectively neutral phenotypes, too, will -- fueled by mutation -- spread through the population according to the statistics of population genetics.
Even if the high-frequency phenotypes among them do spread, they would merely become part of the overall phenotypic presentation of the population after enough generations for the new presentation to emerge as more or less homogeneous, and they aren’t selectively neutral if they are that high frequency that they do in fact spread as you describe, they are in fact among the selected, and genetic diversity will be lost for them as for the more obvious phenotypes such as the gray fur that replaces the brown over some generations.
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. If I draw it I get accused of bias but the conclusion seems to me to be so inevitable I keep being amazed that mutations are so consistently invoked as the source of genetic variation. Not only is a beneficial mutation rare, it’s even rarer in the sex cells where it might have an impact on offspring, and the unlikelihood of its being selected makes it even rarer still, 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 --you might as well dismiss mutations as of no use at all. But no, they are constantly invoked as the fuel for evolution.
Mutations are needed if the ToE is correct about evolution beyond the Kind or evolution from a dog to something that is not a dog, but for microevolution built-in alleles are all that is needed, their combinations are just about endless in themselves, can produce an enormous variety of dogs or whatever organism is evolving. 1) There is no need for mutations, and 2) if they arose while a population was evolving they'd only interfere with the new phenotypes that are forming, and 3) 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.
These phenotypes, then, provide the "raw genetic material" -- or the genetic diversity -- for further evolution to continue. In short, while one particular beneficial trait will gain in frequency at the expense of other alleles, selection will only "weed out" the alleles which are selectively relevant to the function of the beneficial trait.
This last statement is correct according to my thinking too, but despite the presence of other traits in the population it depends on the size of the population whether they will come to affect the phenotype or not. The low frequency ones won’t. 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. What would cause evolution to resume would be the selection, random or otherwise, of another small population to become reproductively isolated with a new set of gene frequencies that may allow expression to those that have been dormant, genetic diversity will be lost with respect to those other traits in the new population and the beat goes on.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 30 of 455 (784884)
05-25-2016 4:33 AM
Reply to: Message 28 by PaulK
05-25-2016 12:55 AM


Re: The endless dance of the wishful refutation
It will not bring back the lost alleles, it may well not add diversity at the loci of those alleles. But your argument is not concerned with those details, only with overall diversity, which can be increased by adding new alleles at other loci. And we still await a sound argument that overall diversity must decrease despite the evidence.
There is no such evidence.
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, more low frequency alleles may begin to drop out. Drift has the same effect.
Nothing is going to "add new alleles at other loci" in a population split. All loci are subject to new gene frequencies. Some alleles will be higher frequency than before and may contribute a new phenotype to the population but it won't involve an increase in genetic diversity, and since any remaining competing allele may eventually drop out that will add to the decrease in genetic diversity.
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. But if it did it would also have to be selected and that means some other allele will probably have to drop out, so after many generations of mixing of the alleles you may have a new subspecies including one mutated allele in the mix, and an overall loss of genetic diversity.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


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 replied

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

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


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.

This message is a reply to:
 Message 38 by Genomicus, posted 05-26-2016 12:22 AM Genomicus has replied

Replies to this message:
 Message 47 by caffeine, posted 05-26-2016 2:54 PM Faith has replied
 Message 74 by Genomicus, posted 05-28-2016 2:01 AM Faith has not replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


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.

This message is a reply to:
 Message 40 by PaulK, posted 05-26-2016 8:07 AM PaulK has replied

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


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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 Message 41 by herebedragons, posted 05-26-2016 10:33 AM herebedragons has not replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


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.

This message is a reply to:
 Message 33 by PaulK, posted 05-25-2016 6:39 AM PaulK has replied

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 46 of 455 (784960)
05-26-2016 2:38 PM
Reply to: Message 23 by herebedragons
05-24-2016 11:08 PM


You are looking at the wrong part of the system
When you have a population of over a million individuals, say of black wildebeests, you are probably getting something like Hardy-Weinberg equilibrium in reality.
Geographic isolation prevents or limits gene flow, but by itself, isolation does not bring about genetic change. All combinations of alleles present in the daughter population are also present in the parent population.
A change in gene frequencies does indeed bring about genetic change, it's even given as a definition of evolution. Put "Evolution as a change in gene frequency" into Google. The first line of the Berkeley page on the subject says "Microevolution is a change in gene frequency in a population." (Windows 10 doesn't let me copy links or I haven't figure out how to yet)
And even Genomicus agrees, which is why I prefer to debate her rather than anyone else here:
Genomicus in message 22 writes:
... I should also add that new phenotypes can arise through novel allele combinations in a diploid organism, so this wouldn't technically be a mutation.
HBD writes:
Orchids - 80,000 +/- species... no sign of genetic depletion
Dogs - 100s of breeds... no sign of genetic depletion
Fruit flies (Drosophilidae) - 4,000 species... no signs of genetic depletion
Cats (Felidae) - 41 species... cheetahs have severe genetic depletion, but not domestic cats
So how have these species maintained genetic diversity according to your hypothesis?
You insist on talking about the ENTIRE population of a species, which I'm NEVER talking about. Sure you can have lots of genetic diversity in the whole population, and dogs as a whole species certainly have lots of genetic diversity. AS I'VE SAID MANY TIMES.
What you are failing to get is that I'm only talking about EVOLVING populations, that is, populations where you are getting new phenotypes due to new gene frequencies, which requires losing alleles for competing phenotypes. The point is to illustrate what EVOLUTION does, and what it does is reduce genetic diversity in the service of producing a new subspecies. It's from this sort of observed evolution (microevolution of course), that is, the observed production of new variations, that the ToE takes its idea that there is nothing to stop variation from continuing indefinitely, but if in fact there is a trend to decreased genetic diversity, that must NECESSARILY occur with the production of new variations, the ToE has been refuted. Doesn't matter how much genetic variation remains in stable populations, or gets added wherever you want to add it, the processes of EVOLUTION, meaning the production of new species or subspecies from whatever genetic diversity is present, MUST reduce genetic diversity. Evolution itself must bring evolution to a stop.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 23 by herebedragons, posted 05-24-2016 11:08 PM herebedragons has replied

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 48 of 455 (784965)
05-26-2016 3:05 PM
Reply to: Message 47 by caffeine
05-26-2016 2:54 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.

This message is a reply to:
 Message 47 by caffeine, posted 05-26-2016 2:54 PM caffeine has replied

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