No genetic bottleneck proves no global flood

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.

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.

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.

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. 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. 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. 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. 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. 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. 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.

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. 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. Yes, such a small number of founding individuals would not have brought over the low-frequency alleles from the parent population. 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. 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. 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

No, you are wrong about this. All it takes is the change in gene frequencies to produce new phenotypes.

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.

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.

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.

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. 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. 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 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. "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.

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.

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. 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.. 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. 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. 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. I have NO idea how you are getting such an idea out of my reply. 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.

Yes there could have been all those varieties in the original population, but the effect of a change in gene frequencies is that you DO get more of some and less of others and you DO get completely new combinations, more mottled fur with fewer green eyes or whatever. The point isn't that you get something that never existed before but that you get combinations that now CHARACTERIZE this new population and distinguish it from the mother population, a new "look," not brand new traits. "Suddenly" is not a word I've used; "sorted into certain individuals" also reflects nothing I've said; and you have it backwards, saying that after such sorting "then" these "sorted individuals" "become reproductively isolated," which gets everything out of order that I've been talking about. Reproductive isolation of a portion of a population is the FIRST thing that happens in my scenario, although in reality there may not be such perfect isolation; but isolation all by itself should produce the effects I'm talking about, because it gives you new gene frequencies that now work their way through the new isolated population.I thought it was pretty well understood that a change in gene frequencies is a definition of evolution so that merely from such a change you should expect new phenotypes; it's rather surprising to see this foundational principle challenged and misrepresented. New combinations that form a new characteristic look to a subpopulation are not necessarily "mathematically rare," at least the components of the combinations are not although the particular combination MAY be brand new, based on as many as half a dozen or more traits in a combination that didn't occur in the parent population, or maybe very occasionally did but was overwhelmed by combinations that occurred in greater frequency there. The new "look" is based on a new mix of alleles. This is elementary, RAZD, you really shouldn't be fighting it.You may or may not ALSO have positive selection working on the population. You'll get a new population whether you do or don't. In a population of mice, or any small creature vulnerable to predators, or other circumstances that challenge the fit between creature and environment, selection may well be a big factor, but it is possible to get a new population without positive selection. In fact it is inevitable as long as the genetic diversity in the original population was reasonably good.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

With a bottleneck you can get such depleted genetic diversity that breeding with other members of the pseices has become impossible, unless the others are reintroduced very soon after the bottleneck. But in the examples I focus on I've specifically ruled out immigration because that is only putting back formerly lost genetic material, it is not new genetic material. I've specifically said this many times. Gene flow keeps genetic diversity up. I'm trying to highlight what happens when the processes that bring about evolution are happening, the isolating and selecting processes. That's when you get reduction of genetic diversity, through the processes of evolution. Sure you can prevent loss of genetic diversity in many ways, and that's what conservationists try to do when a species has low genetic diversity, they try to reintroduce others of the species to bring it back up.There is only ONE process that supposedly adds new genetic material, new alleles, and that's mutation, which I don't believe does any such thing.I don't understand any of gthat about microsatellite loci, still have to spend some time on it.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

All the processes of evolution bring about that isolation you acknowledge does cause decrease in genetic diversity. Natural selection produces a new population in much the same way as geographic isolation would, only without moving the population; it simply forms a new population of the selected types. Isolation is more random, but it still forms a new population of the randomly "selected" types as it were. Genetic drift is another form of reproductive isolation, within the population, where unknown or random factors bring about a subpopulation with its own characteristic genetic frequencies, which often involves the elimination of some alleles, just as the other processes do.Immigration simply remixes the genes that belong to the species already. It's important for recovering genetic diversity when a species is threatened with extinction through a bottleneck.Again, the ONLY process that could bring about actual increased genetic diversity is mutation, or the formation of new VIABLE genetic sequences or new alleles. It is claimed this happens. I doubt it.Edited by Faith, : No reason given.