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Author | Topic: No genetic bottleneck proves no global flood | |||||||||||||||||||||||||||||||||||||||||||
Tangle Member Posts: 9514 From: UK Joined: Member Rating: 4.8
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However, this discussion about rabbits has been interesting because it shows what could happen when instead of inbreeding working the new frequencies through the whole new population, rabbits go off and start small new populations. Their rapid reproductive rate would keep the worst effects of genetic drift from reducing their genetic diversity while their going off into smaller groups would prevent new phenotypes from becoming characteristic. With herd animals like the wildebeest the new gene frequencies would eventually get worked through the whole herd through some number of generations, but rabbits wouldn't allow that to happen. Nevertheless, barring some other habit or feature that further affects this, we should expect new phenotypes in the population at large. Biologists do not expect new phenotypes to pop into existence after a bottleneck and the two extreme examples of the rabbits and the deer demonstrate that. Similarly cheetahs, seals and bison are still cheetahs, seals and bison. This is a factual thing, Faith; if you have examples of new phenotype following a bottleneck, please produce them.
However, this discussion about rabbits has been interesting because it shows what could happen when instead of inbreeding working the new frequencies through the whole new population, rabbits go off and start small new populations. Their rapid reproductive rate would keep the worst effects of genetic drift from reducing their genetic diversity while their going off into smaller groups would prevent new phenotypes from becoming characteristic. With herd animals like the wildebeest the new gene frequencies would eventually get worked through the whole herd through some number of generations, but rabbits wouldn't allow that to happen. Yes, reproductive rate is identified by both papers as likely being the reason that both the deer and the rabbits recovered gentic diversity. Note that Faith, recovered genetic diversity - not developed new phenotypes.
Nevertheless, barring some other habit or feature that further affects this, we should expect new phenotypes in the population at large. Nope. Not unless there is selection pressure or long term drift which happen in populations that have not undergone a bottleneck just as much as those that have.
AND both the articles you posted do make it clear that reduced genetic diversity is certainly expected from a bottleneck Well of course, that's a mathematical certainty!
although the point they are making is that there are circumstances that mitigate this effect. They can't reverse it though. In the case of the rabbit, genetic diversity recovered to the extent that there was no difference between the host European population and the new Australian population. In the deer, genetic diversity recovered to almost the same level as the Oklahoma population within 70 years - although still different enough to show a bottleneck. (H=.692 vs H=.742). btw, in your earlier post you described the rabbit's H of .5 as 'enormous'.Life, don't talk to me about life - Marvin the Paranoid Android "Science adjusts it's views based on what's observed. Faith is the denial of observation so that Belief can be preserved."- Tim Minchin, in his beat poem, Storm.
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RAZD Member (Idle past 1434 days) Posts: 20714 From: the other end of the sidewalk Joined:
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Biologists do not expect new phenotypes to pop into existence after a bottleneck and the two extreme examples of the rabbits and the deer demonstrate that. Similarly cheetahs, seals and bison are still cheetahs, seals and bison. A little overstated imho. Small phenotypic change - fur color, length, curliness, some increase or decrease in size, for example - can occur and would not be unexpected.
Yes, reproductive rate is identified by both papers as likely being the reason that both the deer and the rabbits recovered gentic diversity. Note that Faith, recovered genetic diversity - not developed new phenotypes. Significant new phenotypes, such as new subspecies, which is what Faith is thinking, are not expected, they could occur but don't have to occur without selection pressure for such changes. by our ability to understand Rebel American Zen Deist ... to learn ... to think ... to live ... to laugh ... to share. Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)
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Faith  Suspended Member (Idle past 1473 days) Posts: 35298 From: Nevada, USA Joined: |
I'm thinking small phenotypic changes, and as you agree, those should be expected from new gene frequencies -- or, as you say, "would not be unexpected" though I think they should actually be expected.
The idea that I'm expecting some large "significant" change, no, I'm just expecting typical microevolution of external traits. But I'm thinking of subspecies as simply a new population that has been worked through by the new gene frequencies over enough generations to get a characteristic appearance to the group. I don't consider that a "large" change. Nothing new is added, it's just the gene frequencies doing their thing. Apparently there are some species where this doesn't happen, such as rabbits, due to their rapid reproductive cycle and their habit of forming small groups instead of mixing their genes by breeding through the main population as, say, herd animals would do. The numbers Tangle gave for percentage of heterozygosity I'm going to have to spend some time on, because they are very large compared to my understanding that the human percentage is only around 7%. Edited by Faith, : No reason given. Edited by Faith, : No reason given. Edited by Faith, : No reason given. Edited by Faith, : No reason given.
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Faith  Suspended Member (Idle past 1473 days) Posts: 35298 From: Nevada, USA Joined: |
Yes, .5 IS enormous since I've been thinking the typical percentage must be in the neighborhood of the human percentage of 7%.
Selection pressure is not needed when you have such a significant bottleneck which would produce dramatically new gene frequencies. To which genetic drift would also contribute, but apparently not in the case of the rabbits according to that article as their habits mitigate that effect.
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RAZD Member (Idle past 1434 days) Posts: 20714 From: the other end of the sidewalk Joined:
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I'm thinking small phenotypic changes, and as you agree, those should be expected from new gene frequencies -- or, as you say, "would not be unexpected" though I think they should actually be expected. Within a stable ecology selection would be towards the population average, both by survival and by reproduction. This is why stasis occurs. Thus any changes would necessarily be relegated to fairly minor aspects that would not decrease survival or reproduction, such as the types of variations I mentioned.
The idea that I'm expecting some large "significant" change, no, I'm just expecting typical microevolution of external traits. But I'm thinking of subspecies as simply a new population that has been worked through by the new gene frequencies over enough generations to get a characteristic appearance to the group. I don't consider that a "large" change. Nothing new is added, it's just the gene frequencies doing their thing. A new subpopulation is a larger change in phenotype than I would expect, as it means that some selection is occurring to isolate variations into a breeding group. That you don't consider it "large" is inconsequential to me, seeing as it is just your opinion, based on a fantasy that you have concocted which is not only unsupported, but the actual evidence points the other way: that such changes are due to mutations not pre-existing hidden never before seen alleles. Let's take another example: the Galapagos\Darwin finches as studied by the Grants: Evolution: Library: Finch Beak Data Sheet
quote: Note that only beak size changed, and this is a fairly minor phenotypical change. These are larger changes to the phenotypes than we should expect for the Australian rabbits, because (a) the populations were smaller and (b) the ecology changed to the point that small beaked finches could not survive, and it was only when the ecology changed back that small beaks reappeared. This is also similar to the Peppered Moths -- shifting populations in response to ecological stress.
Apparently there are some species where this doesn't happen, such as rabbits, due to their rapid reproductive cycle and their habit of forming small groups instead of mixing their genes by breeding through the main population as, say, herd animals would do. And a lack of selection pressure. There is still gene flow between family groups as mates are usually taken from outside families, and this leads to gene flow throughout the breeding population and prevents in-breeding.
The numbers Tangle gave for percentage of heterozygosity I'm going to have to spend some time on, because they are very large compared to my understanding that the human percentage is only around 7%. I'll let you and Tangle sort this out. Edited by RAZD, : ..by our ability to understand Rebel American Zen Deist ... to learn ... to think ... to live ... to laugh ... to share. Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)
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RAZD Member (Idle past 1434 days) Posts: 20714 From: the other end of the sidewalk Joined:
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Selection pressure is not needed when you have such a significant bottleneck ... Selection pressure may be reduced but it would still likely be prevalent. The major pressure would be for survival, as reproductive selection would be reduced.
... To which genetic drift would also contribute, ... Which normally reduces available genotypes. particularly the rarer alleles.
... a significant bottleneck which would produce dramatically new gene frequencies. ... The gene frequencies would match the original population if the selection pressure is reduced, especially for sexual selection: alleles that do not exist cannot be selected, and normally would most likely not include rare alleles from before the bottleneck -- hence the expected reduction. My feeling is that if the rabbits came from a domesticated stock (highly likely imho) that then selection for domestic use has already reduced variability before going to Australia, and thus would not be much affected compared to the original domestic stock. by our ability to understand Rebel American Zen Deist ... to learn ... to think ... to live ... to laugh ... to share. Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)
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Tangle Member Posts: 9514 From: UK Joined: Member Rating: 4.8 |
RAZD writes: A little overstated imho. Small phenotypic change - fur color, length, curliness, some increase or decrease in size, for example - can occur and would not be unexpected. I wouldn't expect anything new from a sub-population would you? Take two mice out of a population and I'd expect them to produce mice with the characteristics of some of the mice within the population. These differences may become more fixed with time if they're not deleterious - like we expect more red headed Scots than English redheads (caution, maybe apocryphal!). But, as you say, these irrelevant differences in average phenotypes is not what Faith is looking for, she thinks that species level changes come from isolation and bottlenecks almost instantly and biology knows that it doesn't. Plus, the examples we have of even severe bottlenecks - rabbits, deer, cheetah, bison, seal haven't produced materially different phenotypes. I wonder if it's possible to tell the difference between an Austarlian rabbit and a French rabbit - even with a DNA sample? Edited by Tangle, : No reason given.Life, don't talk to me about life - Marvin the Paranoid Android "Science adjusts it's views based on what's observed. Faith is the denial of observation so that Belief can be preserved."- Tim Minchin, in his beat poem, Storm.
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Faith  Suspended Member (Idle past 1473 days) Posts: 35298 From: Nevada, USA Joined: |
A little overstated imho. Small phenotypic change - fur color, length, curliness, some increase or decrease in size, for example - can occur and would not be unexpected.
I wouldn't expect anything new from a sub-population would you? You aren't thinking of the effect of changed gene frequencies, nor, apparently, of the fact that a sub-population would certainly HAVE changed gene frequencies.
Take two mice out of a population and I'd expect them to produce mice with the characteristics of some of the mice within the population. Recognizable changes from the pattern of the population aren't going to show up in the first generation, possibly not until after a few generations, and then it might only be that one phenotype that showed up from time to time in the larger population becomes characteristic of the new population, but along with other traits as well so that a new "look" is created. Even raccoon subpopulations develop slightly different recognizable traits from others although they are still certainly raccoons. In a sense there is nothing more common than this phenomenon I'm talking about.
These differences may become more fixed with time if they're not deleterious - like we expect more red headed Scots than English redheads (caution, maybe apocryphal!). Yes, that's the basic idea. But it shouldn't just be a change in a single trait. Hair type, eye color, skin color etc., even bodily structure, may also become characteristic as the population inbreeds.
But, as you say, these irrelevant differences in average phenotypes is not what Faith is looking for, she thinks that species level changes come from isolation and bottlenecks almost instantly and biology knows that it doesn't. But these "irrelevant" differences are EXACTLY what I'm looking for. What YOU think "species level changes" would be is NOT what I think they would be, which is one reason I keep objecting to the usual definition of "species" and "speciation." I think what are called by those names are nothing but such small changes brought about by the usual microevolutionary processes that have proceeded to the point where there is enough of a genetic mismatch to prevent continued breeding with the former population. I don't think that takes much, just a series of phenotypic changes of what you call the "irrelevant" sort, from the new gene frequencies, that accumulate in the population over a number of generations until there is that genetic mismatch with former populations. I'm suggesting this can happen when the new population's genetic diversity is appreciably reduced from that of the former populations.
Plus, the examples we have of even severe bottlenecks - rabbits, deer, cheetah, bison, seal haven't produced materially different phenotypes. I wonder if it's possible to tell the difference between an Austarlian rabbit and a French rabbit - even with a DNA sample? "Materially different" means what? I'm not looking for big changes, remember, just a new "look," like the difference between the black wildebeests and the blue. The different herds are recognizably different herds with superficlally different characteristics, but they are still clearly wildebeests. And again, from this discussion it seems that rabbits might not develop a subpopulation characteristic because of their habit of forming small colonies rather than inbreeding within the larger population.
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Tangle Member Posts: 9514 From: UK Joined: Member Rating: 4.8
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Faith writes: I think what are called by those names are nothing but such small changes brought about by the usual microevolutionary processes that have proceeded to the point where there is enough of a genetic mismatch to prevent continued breeding with the former population. I don't think that takes much, just a series of phenotypic changes of what you call the "irrelevant" sort, from the new gene frequencies, that accumulate in the population over a number of generations until there is that genetic mismatch with former populations. Er, yes. This is what biologists call the theory of evolution: this is how new species are formed.
I'm suggesting this can happen when the new population's genetic diversity is appreciably reduced from that of the former populations. It doesn't happen because the critters genetic diversity is reduced - if it did we would see it every time we buy a couple of hamsters. It happens because of mutation and/or by genetic drift. And for complex beasts, it happens over a long period of time. What's more, the evidence we've seen so far shows that for some, even catastrophic losses of diversity can be recovered from very quickly - all that seems to be necessary is that the animals can breed freely. Edited by Tangle, : No reason given.Life, don't talk to me about life - Marvin the Paranoid Android "Science adjusts it's views based on what's observed. Faith is the denial of observation so that Belief can be preserved."- Tim Minchin, in his beat poem, Storm.
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RAZD Member (Idle past 1434 days) Posts: 20714 From: the other end of the sidewalk Joined:
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I wouldn't expect anything new from a sub-population would you? What is "new" ? I would expect some variation/s outside an "average" phenotype, but minor (does eye color affect reproduction? survival?) but most mutations would be neutral. And as I've noted before, in a stable ecology I expect selection to favor the "average" phenotype as preferred sexual selection.
Take two mice out of a population and I'd expect them to produce mice with the characteristics of some of the mice within the population. These differences may become more fixed with time if they're not deleterious - like we expect more red headed Scots than English redheads (caution, maybe apocryphal!). Curiously, I was doing some reading last night on heterozygosity, and one article said that the predicted\expected heterozygosity from two individuals was 0.75. It seems that the way this is measured does not really quantify what we think it does from a first look, because of the way it deals with population size. And it doesn't seem to count the degree of genetic variation in the parent population. With two mice you would have somewhere between 2 and 4 possible alleles at each loci, depending on whether the two copies of DNA strings in each individual are the same or different (one maternal the other paternal). If we take an off the cuff "average" value for all alleles at 3, then 3 out of a potential 4 would be 0.75.
But, as you say, these irrelevant differences in average phenotypes is not what Faith is looking for, she thinks that species level changes come from isolation and bottlenecks almost instantly and biology knows that it doesn't. Exactly, as you can see from her reply. Part of this is her belief that there are hidden alleles tucked away that are somehow suppressed in normal population reproduction but become freed to act in small populations. It's her alternative explanation to mutations creating new alleles.
Plus, the examples we have of even severe bottlenecks - rabbits, deer, cheetah, bison, seal haven't produced materially different phenotypes. I wonder if it's possible to tell the difference between an Austarlian rabbit and a French rabbit - even with a DNA sample? And the starling population in the US compared to the UK -- introduced in NY and spread to the whole US is by our ability to understand Rebel American Zen Deist ... to learn ... to think ... to live ... to laugh ... to share. Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)
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Faith  Suspended Member (Idle past 1473 days) Posts: 35298 From: Nevada, USA Joined: |
But nobody denies that evolution occurs, and I'm glad that you agree that I've described it correctly.
Reduced genetic diversity does NOT show up in a random pair of hamsters. In fact they seem to have pretty good genetic diversity, enough to produce quite a variety of fur colors and patterns at least, They'd have to be like the cheetah with fixed loci, that is, homozygosity at all the crucial gene loci, to exhibit reduced genetic diversity. Genetic drift operates the same as selection, or the migration of individuals like the rabbits, which results in a new subpopulation, only genetic drift changes the population from within rather than by migration away from it or by the active selection of individuals. All these processes lose alleles over time, which is how reduced genetic diversity comes about. As for the long time required, even for complex beasts it shouldn't take more than a couple or three hundred years to completely blend the gene pool of the isolated population. That's about how long it has taken to establish certain cattle breeds to the point of "breeding true" throughout the whole population, which requires fixed loci for the peculiar characteristics of the breed. Yes, they are specifically bred for their characteristics but over two hundred years the methods would have changed and at first they were probably left to themselves, and with herds that go back hundreds of years even more likely left to themselves. Which is how it happens in the wild, herd animals that continue to herd together developing a characteristic "look." Although I've been ready to grant that rabbits may have habits that at least protect their genetic diversity, there is no way genetic diversity can be recovered under the circumstances of a bottleneck, and that study of deer has raised the question in my mind what on earth they are measuring when they give such high estimates of heterozygosity. I asked way back there how heterozygosity at microsatellite loci has anything to do with the heterozygosity that is needed at specific genes so that they can continue to vary, and I guess nobody knew the answer, but when deer are now discussed as recovering their genetic diversity I'm extremely skeptical about the method employed. I'd like to know: How do human beings stack up for percentage of heterozygosity as measured at microsatellite loci, and cheetahs too. As I've understood it humans have about 7% and cheetahs with their high percentage of fixed loci must have much less. Edited by Faith, : No reason given. Edited by Faith, : No reason given. Edited by Faith, : No reason given.
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Faith  Suspended Member (Idle past 1473 days) Posts: 35298 From: Nevada, USA Joined: |
What is "new" ? I would expect some variation/s outside an "average" phenotype, but minor (does eye color affect reproduction? survival?) but most mutations would be neutral. Yes, the new look of the new population isn't new in the sense that nothing like it has ever appeared before, but it's a new combination of alleles that may affect a number of traits so that where the original population was brown and long haired and green eyes with short noses and ears and tails, the new population after a number of generations of blending may be mottled short haired with blue eyes and long noses, ears and tails and a larger body and so on. It's going to be recognizably different. A new race, "species" or subspecies. I'm thinking standard Mendelian combinations of course, not mutations. Since most mutations ARE neutral there's no reason to expect them to produce new combinations, but there are plenty of built in alleles that can do just that. Some traits are governed by more than one gene so that simple dominant/recessive isn't the whole picture, but a more complicated interaction.
And as I've noted before, in a stable ecology I expect selection to favor the "average" phenotype as preferred sexual selection. Perhaps you are right about that, but there have to be traits to be selected, and that's what normal sexual recombination of existing alleles does, and after the selection individuals with the favorable genetic combinations will pair up more frequently and so on..
Take two mice out of a population and I'd expect them to produce mice with the characteristics of some of the mice within the population. These differences may become more fixed with time if they're not deleterious - like we expect more red headed Scots than English redheads (caution, maybe apocryphal!).
Curiously, I was doing some reading last night on heterozygosity, and one article said that the predicted\expected heterozygosity from two individuals was 0.75. It seems that the way this is measured does not really quantify what we think it does from a first look, because of the way it deals with population size. And it doesn't seem to count the degree of genetic variation in the parent population. This could use some more information and discussion and I've been doing some searches. I'm not sure what you are saying here, but the heterozygosity that COUNTS is at the EVOLVING LOCI, and I can't tell from any of the discussion about these things so far if that's even taken into account. The cheetah's heterozygosity must be near zero because of all their fixed (homozygous) genes for instance.
With two mice you would have somewhere between 2 and 4 possible alleles at each loci, depending on whether the two copies of DNA strings in each individual are the same or different (one maternal the other paternal). If we take an off the cuff "average" value for all alleles at 3, then 3 out of a potential 4 would be 0.75. Again the question is WHERE is this seen, at what gene loci, how many gene loci and so on. Four alleles per gene for two individuals is the highest you can get. Three is good, yes, but then you have to note how many genes can be described as being that high. If five genes govern a trait and the same two individuals also have four between them that's enormous heterozygosity for that trait. The question remains WHERE is this heterozygosity happening in the genome and how many gene comparisons are involved and so on? The original articles posted by Tangle on rabbits and deer said the heterozygosity is measured at "microsatellite loci" but there has been no explanation of why this is the focus and what it actually shows.
But, as you say, these irrelevant differences in average phenotypes is not what Faith is looking for, she thinks that species level changes come from isolation and bottlenecks almost instantly and biology knows that it doesn't. He has obviously misread something but he doesn't quote me and all I can say is that he's wrong about what I've been saying. I do think these changes come from isolation alone, but not "instantly" although the new gene frequencies are of course there from the founding of the new population, but they have to be subjected to sexual recombination through some number of generations to produce a new look to the population. And I've only used bottleneck as an example to demonstrate the extreme, otherwise the trend is the same but slower. I never said it happens "almost instantly" because I know that the new population has to inbreed for a few generations at least to bring out new traits, and if the population started out with a relatively large number of individuals, as many as a hundred, say, then I know it's going to take longer for that to happen.
Exactly, as you can see from her reply. I have NO idea how you are getting such an idea out of my reply.
Part of this is her belief that there are hidden alleles tucked away that are somehow suppressed in normal population reproduction but become freed to act in small populations. It's her alternative explanation to mutations creating new alleles. I don't think I'm describing anything hidden or strange at all, just that new gene frequencies is likely to mean that recessives that weren't expressed in the former population may occur more frequently and therefore pair up more frequently in the new, but the same could be said of dominants if recessives characterized some traits in the other population and so on, all this being normal results of normal sexual recombination. And where a number of genes govern one trait you COULD get something that had only showed up very occasionally in the first population, but new combinations of many different traits should eventually produce something that looks appreciably different from the former population. By standard methods of genetic combination, nothing unusual.
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RAZD Member (Idle past 1434 days) Posts: 20714 From: the other end of the sidewalk Joined:
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I don't think I'm describing anything hidden or strange at all, just that new gene frequencies is likely to mean that recessives that weren't expressed in the former population may occur more frequently and therefore pair up more frequently in the new ... Yes, the new look of the new population isn't new in the sense that nothing like it has ever appeared before, but it's a new combination of alleles that may affect a number of traits so that where the original population was brown and long haired and green eyes with short noses and ears and tails, the new population after a number of generations of blending may be mottled short haired with blue eyes and long noses, ears and tails and a larger body and so on. It's going to be recognizably different. A new race, "species" or subspecies. Curiously, I am reminded of Monty Python's Flying Circus "and now for something completely new" ...
I'm thinking standard Mendelian combinations of course, not mutations. Since most mutations ARE neutral there's no reason to expect them to produce new combinations, but there are plenty of built in alleles that can do just that. In "standard Mendelian combinations" each of these traits would have appeared in the general population, not just rarely but rather commonly for the alleles to be so well distributed in the population that any small contingent would have them. And this also means that there would likely be combinations of blue eyes and mottled short haired, etc. Furthermore, in "standard Mendelian combinations" there is no mathematical reason for these to suddenly all become sorted into certain individuals that would then become reproductively isolated within the rest of the population sufficiently to form such a sub-population. Nor would there be an evolutionary cause for this - there would be no positive selection for such combinations in an ecology with static selection pressure, and sexual selection would much more likely act to reduce the numbers of such random occurrences of such mathematically rare combinations. by our ability to understand Rebel American Zen Deist ... to learn ... to think ... to live ... to laugh ... to share. Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)
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RAZD Member (Idle past 1434 days) Posts: 20714 From: the other end of the sidewalk Joined: |
Take two mice out of a population and I'd expect them to produce mice with the characteristics of some of the mice within the population. These differences may become more fixed with time if they're not deleterious - like we expect more red headed Scots than English redheads (caution, maybe apocryphal!).
Curiously, I was doing some reading last night on heterozygosity, and one article said that the predicted\expected heterozygosity from two individuals was 0.75. It seems that the way this is measured does not really quantify what we think it does from a first look, because of the way it deals with population size. And it doesn't seem to count the degree of genetic variation in the parent population. This could use some more information and discussion and I've been doing some searches. I'm not sure what you are saying here, but the heterozygosity that COUNTS is at the EVOLVING LOCI, and I can't tell from any of the discussion about these things so far if that's even taken into account. The cheetah's heterozygosity must be near zero because of all their fixed (homozygous) genes for instance. The article I was reading was:
Population Bottlenecks: Heterozygosity vs. Allelic Diversity quote: This is a rather rudimentary estimate of expected heterozygosity (proportion of individuals heterozygous at a locus), basically like an order of magnitude calculation, as it doesn't include the number of alleles involved. Note that this is looking at only one locus, one gene, and the number of alleles for that one locus\gene. The number 2N is the number of DNA strings in the population size N, and the maximum possible number would be obtained when there is a different allele in each DNA strand for that locus\gene. Next they look at how this stacks up for different numbers of alleles in the original population for the various loci, and the math, unfortunately, gets a little more involved:
quote: To break it down, n is the original population number of alleles at a loci, pj is the frequency of the jth allele at that loci, and (1-pj)2N is the probability of that allele being in the number of DNA strands (2N) of the bottleneck population, The probability of each allele, from 1 to n, is calculated and then they are all added up and this sum is subtracted from the original population number of alleles at a loci, n, to derive the expected number of alleles, n', in the bottleneck population. Applying this to a simplistic example where N = 2 again, and using n = 2, with each allele having the same frequency (pj = 0.5) in the original population, we get:
With N = 2 and n = 3 we get n' = 2.41With N = 2 and n = 4 we get n' = 2.73 And this is STILL only one loci of the genetic sequence \ DNA strands \ genes.
quote: For our first example this would be: A = (1.88-1)/(2-1) = 0.88For our second example this would be: A = (2.41-1)/(3-1) = 0.70 For our third example this would be: A = (2.73-1)/(4-1) = 0.58 So there is significant variation depending on the numbers of alleles. For just one loci.
quote: Certainly when the original number of alleles, n, is greater than the number of DNA strings in the bottleneck population, 2N, there has to be some loss in allelic diversity, as it is mathematically impossible to have more alleles than strings. From what I can see the black dots for the expected heterozygosity are just pasted on the curves at their values and don't have any calculated relationship to the original number of alleles. And we can see that the proportion of heterozygosity is different from the expected allelic diversity, and the larger the number of original alleles the greater this difference will be. Further, to get an idea of the overall effect these calculations would need to be repeated for every gene\loci and the results averaged. A lot of calculations. They go on to calculate the effect over several generations (see graphs) and conclude:
quote: So the expected heterozygosity is best used for initial evaluations, and more long term evaluations should use allelic diversity for a more accurate picture. Genetic diversity, which would include evaluation for each gene\loci and integrating them into an overall picture would be even more complex a calculation. If you have g genes do you multiply all the A values and then take the gth root? Do you average all the A values? Or is there some other metric that is used? I don't know yet. Edited by RAZD, : formula instead of hard to see image Edited by RAZD, : ..by our ability to understand Rebel American Zen Deist ... to learn ... to think ... to live ... to laugh ... to share. Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)
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Tangle Member Posts: 9514 From: UK Joined: Member Rating: 4.8 |
Wake me up when you do ;-)
Life, don't talk to me about life - Marvin the Paranoid Android "Science adjusts it's views based on what's observed. Faith is the denial of observation so that Belief can be preserved."- Tim Minchin, in his beat poem, Storm.
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