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Author Topic:   No genetic bottleneck proves no global flood
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 31 of 140 (720333)
02-21-2014 3:23 PM
Reply to: Message 26 by Tangle
02-21-2014 11:54 AM


But what DNA tests really show genetic diversity?
ps Faith, note that genetic diversity was not lost by isolation - in this case at least.
Unfortunately I don't understand the test they did to prove this. They looked at something called microsatellite loci but I have no idea what that would be expected to show.
I've come to understand that the best genetic test would involve looking at the percentage of heterozygosity at the particular genes that can be shown to be involved in the development of new phenotypes in the new population (such as for blue versus black wildebeests for example, but rabbits may be different), which should be expected after enough generations that the population has acquired a new look of its own.
I haven't read through everything but so far I didn't see any report on how the new population of rabbits may have varied phenotypically from the original population. I've been arguing that there should be observable variation from population splits (blue versus black wildebeests for example), simply due to the new gene frequencies, and especially when the founding number is so low, and that this should start to show up within a few generations. Rabbits producing new generations rapidly should bring this about more rapidly than other creatures would too.
If the focus is on those particular genes that underlie the new phenotypes and fewer alleles are found for those, and especially if homozygosity is found, which really ought to occur with such a low number of founding individuals, then mutations wouldn't interfere with the test, since the likelihood that they'd show up at those loci should be quite low.
ABE: (I can't imagine why a rapid increase in population should increase genetic diversity unless they mean the overall number of mutations in the population. But consider that the elephant seal, whose genetic diversity is KNOWN to be extremely low because it was reduced almost to extinction at one point, also very rapidly increased in population when protected. Theoretically the population should have a greatly increased number of mutations, but what affect has that had on the actual genetic diversity that affects the creature's chances for survival?}
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 26 by Tangle, posted 02-21-2014 11:54 AM Tangle has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 32 of 140 (720339)
02-21-2014 5:46 PM


To coin a phrase Faith, they're still rabbits.
There's no more reason to expect rabbits in Australia to change their fur colour or physiology than those in Belgium. It would take an environmental cause to select for a fur colour change in a population. Remember the peppered moth?

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.

Replies to this message:
 Message 33 by Faith, posted 02-21-2014 11:42 PM Tangle has replied

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


Message 33 of 140 (720349)
02-21-2014 11:42 PM
Reply to: Message 32 by Tangle
02-21-2014 5:46 PM


There's no more reason to expect rabbits in Australia to change their fur colour or physiology than those in Belgium. It would take an environmental cause to select for a fur colour change in a population. Remember the peppered moth?
I'm surprised that these days so little is made of the effect of changing gene or allele frequencies on such things as the fur color of a rabbit population, and the fact that this kind of change comes about simply by isolating a population of anything.* I don't think the idea has been abandoned in population genetics circles, and it makes a lot of sense. Fewer of some alleles, more of others should come about from such a new mix based on fewer individuals, and that simple fact ought all by itself to begin to produce a new look to the organism over the generations, first a new set of individual phenotypes and then after many generations a sort of blending of all of them into something that can be distinguished from the original population. I've come to like the wildebeests for an example because they are divided basically into two geographically isolated herds, the black and the blue types. Each population should be distinguished from the other genetically by its different gene frequencies. (This blending probably depends on breeding patterns eventually mixing the whole population. This would certainly be the case with herd animals, but rabbits may go their separate ways so it may not be the case with them. Still I'd expect some changes over time by comparison with the original population.)
Natural selection has to have something to act upon, some quality that is either very beneficial or very detrimental to the organism. In the case of a new population of rabbits it would act on the new phenotypes as they are brought to expression, if any of them had such beneficial or detrimental qualities. But as you say there shouldn't be any real selection pressure on such superficial characteristics as distinguish, say, the black from the blue wildebeests, all that's needed is the new gene frequencies. If natural selection does act in a population it would of course affect the ultimate character of the population, but selection isn't necessary: to get a new characteristic throughout a new population, again, all that is required is the new gene frequencies that are the natural result of the population split.
And that would have to occur before any selection would take place anyway. The peppered moth had the genetic options of being light colored, which was beneficial against normal tree bark, or dark colored, which hid them against soot covered tree bark. But it starts with genetic options. If those aren't available there is no selection -- except of course the "selection" of extinction.
But I'm not proposing selection in the case of the rabbits. if there is a reason for black or gray rabbits to be selected they will be, but under the typical circumstances there shouldn't be any reason for that, as you say.
Again, selection is not necessary. Changed gene frequencies are all it takes to change the character of an organism, which is the result of nothing but the fact of a population split, most especially in the case when a new population is formed from a small number of founders. It would take some number of generations to work the new characteristics throughout the whole population, but there should be recognizable new characteristics.
Sorry, I know I'm repeating myself.
-------------------------
*Perhaps there's something different about rabbits but I don't see why there should be. The something different would have to be that they haven't lost as much genetic diversity as other species over the last few millennia. Perhaps they have less "junk DNA" than other species. Someone else would have to tell us if so.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : punctuation problems corrected.
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 32 by Tangle, posted 02-21-2014 5:46 PM Tangle has replied

Replies to this message:
 Message 34 by Tangle, posted 02-22-2014 3:31 AM Faith has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(1)
Message 34 of 140 (720356)
02-22-2014 3:31 AM
Reply to: Message 33 by Faith
02-21-2014 11:42 PM


The paper answers your question.
In fact, the current pattern of genetic variation in Australia is most likely a result of multiple factors including mutation, genetic drift and geographical differentiation. The absence of reduced genetic diversity is almost certainly a result of the rabbit's rapid population expansion at the time of establishment in Australia. These results highlight the importance of population growth following a demographic bottleneck, which largely determines the severity of genetic loss.
The population grew so fast - from 13 individuals to 10 billion in 60 years - that all the known methods of genetic change happened very quickly and recovered genetic diversity.
But the rabbits couldn't have bred that quickly if they were under any selection pressure and we don't expect radical changes in form if an animal is as obviously fit for its environment as the rabbit was/is in Australia.
Regardless, what this study shows is that bottlenecks aren't found in all species that undergo one and isolating a small group of animals does not necessarily lead to long term loss of genetic diversity.

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.

This message is a reply to:
 Message 33 by Faith, posted 02-21-2014 11:42 PM Faith has replied

Replies to this message:
 Message 35 by Faith, posted 02-22-2014 3:46 AM Tangle has replied

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


Message 35 of 140 (720357)
02-22-2014 3:46 AM
Reply to: Message 34 by Tangle
02-22-2014 3:31 AM


Well, I already answered or at least questioned all of that, which you apparently chose not to address.
The main thing I argued at length was that there was no selection pressure and selection was not a part of my thinking, that any change would be brought about strictly by the change in gene frequencies. I gather you didn't read any of that or if you did it went in one ear and out the other.
Another thing I said was that recovering genetic diversity through rapid population growth could only be referring to the accumulation of mutations, which would have to occur at the loci of the changing traits to have any impact on the phenotype, which can hardly be expected of a random process, so that it wouldn't affect the changes through gene frequencies anyway. THAT IS, you'd have to show that the mutations actually DID anything at all at the phenotypic level even to argue that they contribute to genetic diversity.
And I questioned their method of determining genetic diversity or its loss, wondering how that method is expected to demonstrate that, which wasn't explained and I gather you don't know either. And then I gave my own expectation of how genetic diversity would best be shown by DNA analysis, which would be by looking for reduced heterozygosity at those gene loci where the phenotypic change is occurring if there is any.
Otherwise if there is something about rabbits that changes this overall picture that would be about rabbits and not the basic idea I'vew been promoting anyway. In which case it would be interesting to know what it is about rabbits that makes the difference. I suggested that perhaps they have higher genetic diversity to begin with. You didn't address that either.

This message is a reply to:
 Message 34 by Tangle, posted 02-22-2014 3:31 AM Tangle has replied

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 Message 36 by Tangle, posted 02-22-2014 4:26 AM Faith has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(1)
Message 36 of 140 (720358)
02-22-2014 4:26 AM
Reply to: Message 35 by Faith
02-22-2014 3:46 AM


The reason I didn't rub your face in all the mistakes you made in your first post was because you were making so many and it would have been unkind. I hoped that quoting the piece that I did would be enough. However, if you insist
Faith writes:
The main thing I argued at length was that there was no selection pressure and selection was not a part of my thinking, that any change would be brought about strictly by the change in gene frequencies. I gather you didn't read any of that or if you did it went in one ear and out the other.
No Faith I chose to disregard it because change in gene frequency is the very definition of evolution; I suspect you are confusing this phrase with one of the methods by which a change in gene frequency comes about which is genetic drift.
Genetic drift is hypothesised by the paper as one of the mechanisms of recovering genetic diversity in the isolated population as well as mutation, which is why I quoted that section again for you.
Another thing I said was that recovering genetic diversity through rapid population growth could only be referring to the accumulation of mutations,
Which is incorrect and is why I quoted you that passage again.
And I questioned their method of determining genetic diversity or its loss, wondering how that method is expected to demonstrate that, which wasn't explained and I gather you don't know either. And then I gave my own expectation of how genetic diversity would best be shown by DNA analysis, which would be by looking for reduced heterozygosity at those gene loci where the phenotypic change is occurring if there is any.
Phenotypic change is not necessary to show genetic diversity - the rabbits are still rabbits, remember? You're confusing and conflating dozens of half understood terms.
And as you haven't the first clue about how you would go about deciding the genetic diversity of rabbits I didn't think it worth commenting on, preferring to take the word of those who actually do the work and know which way up to hold a pippette. But as you've pushed me, they used a method called microsatellite loci analysis (again, stated in the Abstract)
Microsatellites, also known as Simple Sequence Repeats (SSRs) or Short Tandem Repeats (STRs), are repeating sequences of 2-6 base pairs of DNA.[1] It is a type of Variable Number Tandem Repeat (VNTR). Microsatellites are typically co-dominant. They are used as molecular markers in STR analysis, for kinship, population and other studies. They can also be used for studies of gene duplication or deletion, marker assisted selection, and fingerprinting.
If you wish to know more, you're going to have to do some work but i'm afraid it will only confuse you more.
Microsatellite - Wikipedia

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.

This message is a reply to:
 Message 35 by Faith, posted 02-22-2014 3:46 AM Faith has replied

Replies to this message:
 Message 38 by Faith, posted 02-22-2014 2:20 PM Tangle has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 37 of 140 (720359)
02-22-2014 5:06 AM


Another study on rabbits and bottlenecks, this time in the UK where myxomatosis killed 99.9% of rabbits, comes to the same conclusions:
It is often assumed that, when a population goes through a severe bottleneck, random genetic drift will induce a massive loss of genetic variability. Despite the extremely large mortality induced by myxomatosis, much variation is still observed within rabbit populations, with average heterozygosity being 0.520. The reduction in heterozygosity induced by a population bottleneck depends not only on bottleneck size but also on the rate of population growth after the bottleneck, with rapid growth limiting the severe effects of drift to a few generations. However, the loss of alleles is largely dependent on bottleneck size only (Nei et al., 1975), because the bottleneck tends to eliminate many low-frequency alleles from the population. It is proposed that the rabbit's short generation time, together with high fecundity leading to a rapid population growth rate, could account for the degree of heterozygosity observed in present populations, despite the severity of the bottleneck. On the other hand, despite the degree of variation still observed in European wild rabbit populations, there can be no doubt that a disease such as myxomatosis resulting in the death of 99.9% of a population must have a significant effect on the genetic structure of that population.
This time the full paper is available in Heredity, but sadly above my pay grade.
Population structure and genetic variation of European wild rabbits (Oryctolagus cuniculus) in East Anglia | Heredity
It's quite interesting that this paper talks of genetic drift creating 'massive loss of diversity' following a bottleneck due to the loss of low frequency alleles. Which seems contradictory.
Edited by Tangle, : No reason given.
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.

Replies to this message:
 Message 39 by Faith, posted 02-22-2014 3:03 PM Tangle has replied

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


Message 38 of 140 (720389)
02-22-2014 2:20 PM
Reply to: Message 36 by Tangle
02-22-2014 4:26 AM


The reason I didn't rub your face in all the mistakes you made in your first post was because you were making so many and it would have been unkind. I hoped that quoting the piece that I did would be enough.
As I said, I didn't know what the quote referred to or how it demonstrated genetic diversity, and I still have the impression you don't know either.
However, if you insist
Faith writes:
The main thing I argued at length was that there was no selection pressure and selection was not a part of my thinking, that any change would be brought about strictly by the change in gene frequencies. I gather you didn't read any of that or if you did it went in one ear and out the other.
No Faith I chose to disregard it because change in gene frequency is the very definition of evolution; I suspect you are confusing this phrase with one of the methods by which a change in gene frequency comes about which is genetic drift.
No, Tangle, I am specifically talking about change in gene frequency BECAUSE it is how evolution comes about, which is what I'm talking about. Evolution happens all the time, the only bone of contention is how far it goes, not that it occurs. And yes, I'm aware that genetic drift is one of the ways it comes about, but clearly I'm not talking about genetic drift, I'm talking about what happens when you have a new population based on a small number of founders. The population split all by itself brings about a change in gene frequencies, which I would think you would also recognize.
Genetic drift is hypothesised by the paper as one of the mechanisms of recovering genetic diversity in the isolated population as well as mutation, which is why I quoted that section again for you.
The problem is that genetic drift is one of the mechanisms that brings about phenotypic change, otherwise known as evolution, like population splits, like selection, that ultimately reduces genetic diversity, and since there is no explanation HOW it would supposedly recover it I have a feeling you don't know yourself how it would. It does change gene frequencies but when that happens there's always the possibility that alleles will be lost from the evolving population, and that's a decrease, not an increase, in genetic diversity. Such processes cannot add alleles, only remove them, or if the founding population is large enough perhaps simply retain all the original alleles so that there is no change in that regard at all. Decreased genetic diversity is the more likely the smaller the number of founding individuals.
Mutation, as I said, is the only way genetic diversity could be recovered, but I mentioned the organisms that have suffered extreme genetic depletion, such as the cheetah and the elephant seal, to indicate that mutation has not yet recovered them from their vulnerable situation. One population did regain population quite rapidly, the seals, though not as fast as rabbits of course, but without recovering genetic diversity, not where it is needed in any case, and the other simply doing rather well getting along though no mutations have come along where they are needed.
Another thing I said was that recovering genetic diversity through rapid population growth could only be referring to the accumulation of mutations,
Which is incorrect and is why I quoted you that passage again.
Well, according to that passage it's incorrect, but in reality genetic drift is just another of the mechanisms that brings about evolution by changing gene or allele frequencies which always tends toward ultimate decrease in genetic diversity, so I have to think the writers of that paper got it wrong. I know, who am I to say anything about a scientific paper, but think about it yourself. Genetic drift can't add anything, it can only subtract, just as all the other mechanisms that bring about evolution do, with the exception of mutation. And again, mutation hardly ever shows up where it's needed, at the fixed loci of the genetically impoverished creatures, assuming it ever has any beneficial effect at all, which is another subject.
And I questioned their method of determining genetic diversity or its loss, wondering how that method is expected to demonstrate that, which wasn't explained and I gather you don't know either. And then I gave my own expectation of how genetic diversity would best be shown by DNA analysis, which would be by looking for reduced heterozygosity at those gene loci where the phenotypic change is occurring if there is any.
Phenotypic change is not necessary to show genetic diversity - the rabbits are still rabbits, remember? You're confusing and conflating dozens of half understood terms.
Not really, I'm simply focusing on observable traits because they ARE observable and they are what should be expected of a population of anything founded on low numbers, and the low founding numbers usually imply reduced genetic diversity.
And as you haven't the first clue about how you would go about deciding the genetic diversity of rabbits I didn't think it worth commenting on, preferring to take the word of those who actually do the work and know which way up to hold a pippette. But as you've pushed me, they used a method called microsatellite loci analysis (again, stated in the Abstract)
Yes, and if you read my first response to that post, you'd know I asked how that method determines genetic diversity, which you didn't answer. The abstract doesn't explain how. So I gave my own understanding of how to assess genetic diversity from the DNA, which is by looking at the percentage of heterozygosity at the evolving gene loci.
Microsatellites, also known as Simple Sequence Repeats (SSRs) or Short Tandem Repeats (STRs), are repeating sequences of 2-6 base pairs of DNA.[1] It is a type of Variable Number Tandem Repeat (VNTR). Microsatellites are typically co-dominant. They are used as molecular markers in STR analysis, for kinship, population and other studies. They can also be used for studies of gene duplication or deletion, marker assisted selection, and fingerprinting.
If you wish to know more, you're going to have to do some work but i'm afraid it will only confuse you more.
Microsatellite - Wikipedia
Yes, I had already looked up the definition myself. Besides being written in technical language which is hard for me, nothing there explains how genetic diversity can be shown by this method.
And I still get the impression you don't know either. Anyway I'm not discussing these things with Wikipedia, and it would help if you'd just explain anything you DO understand, in your own words.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 36 by Tangle, posted 02-22-2014 4:26 AM Tangle has replied

Replies to this message:
 Message 40 by Tangle, posted 02-23-2014 4:27 AM Faith has replied

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


Message 39 of 140 (720393)
02-22-2014 3:03 PM
Reply to: Message 37 by Tangle
02-22-2014 5:06 AM


Another study on rabbits and bottlenecks, this time in the UK where myxomatosis killed 99.9% of rabbits, comes to the same conclusions:
It is often assumed that, when a population goes through a severe bottleneck, random genetic drift will induce a massive loss of genetic variability. Despite the extremely large mortality induced by myxomatosis, much variation is still observed within rabbit populations, with average heterozygosity being 0.520.
Yes, this is VERY interesting, I'm very glad you found this paper and thanks for posting it. It's also technically beyond me but I get the basic idea. For one thing it confirms that heterozygosity is how genetic diversity is determined, but at those microsatellite loci, the significance of which again I don't understand.
But rabbits do appear to be different in having such high heterozygosity. That number IS over 50% heterozygosity, I'm not misreading it am I? That's enormous. That's what I've guessed might have been the percentage on the Ark for most creatures as well as the people, or as high as 70%, (for people it's now around 7%) but of course that's just a guess. Whatever it was should have decreased since then for most creatures, but apparently rabbits maintain their genetic diversity or don't lose it as rapidly as other creatures do. This makes rabbits very interesting to think about.
The paper also discusses the fact that rabbits do form small family groups, which makes them very different from the herd animals that would blend their alleles over many generations. Rabbits keep on forming new small populations instead. This would explain why a new phenotype would not develop. Instead there should be many individual differences that don't get blended into the main population.
The reduction in heterozygosity induced by a population bottleneck depends not only on bottleneck size but also on the rate of population growth after the bottleneck, with rapid growth limiting the severe effects of drift to a few generations.
OK I see what they are saying. Yes, a small number of founding individuals would risk losing the low-frequency alleles altogether, as they go on to say, but a rapid increase in population would increase their incidence and keep them in circulation. The bottleneck itself would already have eliminated the low frequency alleles of the parent population, but at least they are saved the loss through subsequent genetic drift.
However, the loss of alleles is largely dependent on bottleneck size only (Nei et al., 1975), because the bottleneck tends to eliminate many low-frequency alleles from the population.
Yes, such a small number of founding individuals would not have brought over the low-frequency alleles from the parent population.
It is proposed that the rabbit's short generation time, together with high fecundity leading to a rapid population growth rate, could account for the degree of heterozygosity observed in present populations, despite the severity of the bottleneck.
But they must also have had much greater genetic diversity than most animals to begin with. Probably due to their habits this paper is highlighting.
On the other hand, despite the degree of variation still observed in European wild rabbit populations, there can be no doubt that a disease such as myxomatosis resulting in the death of 99.9% of a population must have a significant effect on the genetic structure of that population.
That does have to be expected, but with such enormous genetic diversity to begin with they are able to recover a lot more easily than other creatures might.
This time the full paper is available in Heredity, but sadly above my pay grade.
Population structure and genetic variation of European wild rabbits (Oryctolagus cuniculus) in East Anglia | Heredity
It's quite interesting that this paper talks of genetic drift creating 'massive loss of diversity' following a bottleneck due to the loss of low frequency alleles. Which seems contradictory.
Well, no, the other paper has it wrong, this one has it right. Genetic drift SHOULD create massive loss of diversity by losing the low frequency alleles because that's what happens with all the processes that bring about phenotypic change by creating daughter populations, and the smaller the founding number the greater the loss of genetic diversity. Genetic drift is simply one of the ways this happens. But rabbits have interesting features and habits that apparently mitigate the effects of genetic loss.
Bottom line: They are losing genetic diversity but at a much slower rate than other creatures.
Edited by Faith, : Last line

This message is a reply to:
 Message 37 by Tangle, posted 02-22-2014 5:06 AM Tangle has replied

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 Message 41 by Tangle, posted 02-23-2014 5:34 AM Faith has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(1)
Message 40 of 140 (720415)
02-23-2014 4:27 AM
Reply to: Message 38 by Faith
02-22-2014 2:20 PM


All of this has been gone over many times with you but you just keep making the same assersions and errors.
Population splits/isolations/speciation events do not necessarily lead ultimately to a loss of genetic diversity. That's just one of your fantacies and it's shown here very clearly that even in extreme bottlenecks, it's possible for a species to recover extreemly quickly if the circumstances are right.
I'm simply focusing on observable traits because they ARE observable and they are what should be expected of a population of anything founded on low numbers, and the low founding numbers usually imply reduced genetic diversity
Phenotypic trait changes are NOT to be expected in a population of low numbers - it takes environmental pressure to select for a change or genetic drift over great periods of time. We would actually expect a population of low numbers to die out quickly but if they survived in circumstances like the rabbits we would expect them to reproduce in the normal way and produce rabbits just like their parents.
Yes, I had already looked up the definition myself. Besides being written in technical language which is hard for me, nothing there explains how genetic diversity can be shown by this method.
Besides it being the method used by geneticists to measure genetic diversity you mean? The fact that it's hard for you isn't an argument.
And I still get the impression you don't know either. Anyway I'm not discussing these things with Wikipedia, and it would help if you'd just explain anything you DO understand, in your own words.
Of course I don't know, i've said exactly that. I'm not a practicing geneticist, but unlike you, I have the sense not to declare things wrong that i don't understand just because i don't like the conclusion. Have a bit of humilty for god's sake.
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.

This message is a reply to:
 Message 38 by Faith, posted 02-22-2014 2:20 PM Faith has replied

Replies to this message:
 Message 42 by Faith, posted 02-23-2014 1:50 PM Tangle has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(1)
Message 41 of 140 (720416)
02-23-2014 5:34 AM
Reply to: Message 39 by Faith
02-22-2014 3:03 PM


Faith writes:
But rabbits do appear to be different in having such high heterozygosity. That number IS over 50% heterozygosity, I'm not misreading it am I? That's enormous.
Heterozygosity is measured between 0 and 1 so a measure of .5 seems average to me - but like you, I have no real clue.
Meanwhile, another paper with deer, showing roughly the same effect. I'd love someone who actually knows this stuff to comment.
Background
Within-population genetic diversity is expected to be dramatically reduced if a population is founded by a low number of individuals. Three females and one male white-tailed deer Odocoileus virginianus, a North American species, were successfully introduced in Finland in 1934 and the population has since been growing rapidly, but remained in complete isolation from other populations.
Methodology/Principal Findings
Based on 14 microsatellite loci, the expected heterozygosity H was 0.692 with a mean allelic richness (AR) of 5.36, which was significantly lower than what was found in Oklahoma, U.S.A. (H = 0.742; AR = 9.07), demonstrating that a bottleneck occurred. Observed H was in line with predictions from an individual-based model where the genealogy of the males and females in the population were tracked and the population's demography was included.
Conclusion
Our findings provide a rare within-population empirical test of the founder effect and suggest that founding a population by a small number of individuals need not have a dramatic impact on heterozygosity in an iteroparous species.

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.

This message is a reply to:
 Message 39 by Faith, posted 02-22-2014 3:03 PM Faith has not replied

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


Message 42 of 140 (720442)
02-23-2014 1:50 PM
Reply to: Message 40 by Tangle
02-23-2014 4:27 AM


Phenotypic trait changes are NOT to be expected in a population of low numbers - it takes environmental pressure to select for a change or genetic drift over great periods of time.
No, you are wrong about this. All it takes is the change in gene frequencies to produce new phenotypes.

This message is a reply to:
 Message 40 by Tangle, posted 02-23-2014 4:27 AM Tangle has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(1)
Message 43 of 140 (720443)
02-23-2014 2:09 PM


Yes Faith a change in gene frequency is the very definition of evolution but we don't expect to see phenotypic change - rabbits turning blue - just because there's been a bottleneck.
What we expect to see are rabbits being born that are like their parents.

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.

Replies to this message:
 Message 44 by Faith, posted 02-23-2014 6:19 PM Tangle has replied
 Message 45 by RAZD, posted 02-23-2014 7:21 PM Tangle has not replied

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


Message 44 of 140 (720446)
02-23-2014 6:19 PM
Reply to: Message 43 by Tangle
02-23-2014 2:09 PM


Sorry, Tangle, you've apparently missed the entire argument. The first generation of course looks like its parents --though never identical you know -- and the second and third may also not produce much difference either though maybe a striking individual. But after a few generations in an inbreeding reproductively isolated population new phenotypes should start to show up because of the changed gene frequencies, some alleles having dropped out completely, others having a higher percentage in the population. A complete new mix, new combinations etc.
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.
AND both the articles you posted do make it clear that reduced genetic diversity is certainly expected from a bottleneck although the point they are making is that there are circumstances that mitigate this effect. They can't reverse it though.
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 43 by Tangle, posted 02-23-2014 2:09 PM Tangle has replied

Replies to this message:
 Message 46 by Tangle, posted 02-24-2014 3:38 AM Faith has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(2)
Message 45 of 140 (720448)
02-23-2014 7:21 PM
Reply to: Message 43 by Tangle
02-23-2014 2:09 PM


Yes Faith a change in gene frequency is the very definition of evolution but we don't expect to see phenotypic change - rabbits turning blue - just because there's been a bottleneck.
What we expect to see are rabbits being born that are like their parents.
And now you will be lectured with Faith's fantasy ... where hidden phenotypes suddenly pop up because they were never mixed that way before ...

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This message is a reply to:
 Message 43 by Tangle, posted 02-23-2014 2:09 PM Tangle has not replied

  
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