Natural Limitation to Evolutionary Processes (2/14/05)

I can't see the sense in this. Any decrease in frequency of one allele is going to be balanced by an increase in frequency of another allele.TTFN,WK

Genetic drift is a general term for non-selective change in allele frequencies. It includes things like bottlenecks (where the cause is NOT selective) and the founder effect (which needn't be due to "destruction" at all - the classic example is colonising a new habitat, like an island). But drift doesn't need a reduction in population - statistics guarantees that some degree of drift will happen whatever the populations does.As for mutation let me stress the reason that it is referred to as only one of the mechanisms of evolution is because it acts only as a source of variation for selection (and drift). I find it odd that you weren't aware of that - or even aware that scientists recognised that there was a need for a source of new variation.On the other hand I haven't noticed anyone claiming that there is an improbable "great rate" of mutation - just a rate high enough to compensate for losses (which as I have pointed out can be qute low, due to feedback effects). So it seems that your claim relies on an implicit assumption that there is a "great" rate of loss of variation - but I haven't seen any support for that claim.As to your talk about "alleleic variation" the term as I understand it refers to variations already present. If that is what you meant you've already seen examples refuting that as an explanation of all variations.THe fundamental problem of your argument is that it relies on comparing two rates but estimates neither. Rather it just assumes that one rate must be "great" without any support or without any estimation of the actual rate (or even a theoretical look at the issue of negative feedback leading to dynamic equilibrium which I raised). Yet this assumption is the core of the argument. At this stage your argument is not so much refuted rather, it is shown to be an unsupported assumption

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Yes, again, it does seem odd to me that the scientists who inspire these lists define them as change in frequencies rather than decrease in frequencies.

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I can't see the sense in this. Any decrease in frequency of one allele is going to be balanced by an increase in frequency of another allele.

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OK, that makes sense. As some alleles are eliminated from a population, or their frequencies reduced, others are increased. So I'm apparently arguing with the wrong thing. But when there is a population reduction that reduces or eliminates some alleles there is a reduction in the overall capacity for variation in the new population, simply because some allelic opportunities have been lost or reduced. That's what I'm trying to get at. Yes, frequencies of alleles is independent of this effect. In fact frequencies of some alleles will increase along with the decrease in variability. So I should keep my focus on the decrease in variability and not confuse it with the frequencies of alleles. Decreased NUMBERS of allelic possibilities is really what I'm getting at. For some to increase others have to be eliminated. When this is drastic, as in the degree of natural selection that brings an antibiotic-resistant bacterium to the fore, or a poisonous newt, or bottlenecked creatures, some allelic frequencies are increased enormously, but the overall effect is a drastic decrease in allelic variation.This message has been edited by Faith, 02-16-2005 07:08 AM

As I see it the problem here is your use of terms such as 'capacity' and 'possibilities'. In terms of extant allelic variation you are correct that much of the time selection leads to a restriction of variation even to the point of fixation. The problem is that in terms of capacity and possibility there is no restriction, the genes are still perfectly capable of producing any possible allelic variation as a result of mutation.In terms of producing novelty mutation, in a relatively broad sense, pretty much is everything. This depends very much on the initial prevalence of the selected trait, if the selection is very strong and the trait at very low abundance then you may see a drastic reduction in population and genetic variability, if on the other hand the selected trait is already fairly evenly distributed then there is a good chance that much of the genetic variability of the population can be maintained, except for at the particular locus under selection.TTFN,WK

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Genetic drift is a general term for non-selective change in allele frequencies. It includes things like bottlenecks (where the cause is NOT selective) and the founder effect (which needn't be due to "destruction" at all - the classic example is colonising a new habitat, like an island).

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It is hard then to sort out the various processes, as "migration" would seem to define that circumstance just as well. And the example of Noah -- is that a bottleneck or a founder effect? But thanks for the clarification that the REASON for the change in allele frequencies (such as "non-selective") is intended by some terminology. I tend to focus only on the effect and ignore the cause. Actually I don't see the relevance or importance of the cause now that I think of it.

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But drift doesn't need a reduction in population - statistics guarantees that some degree of drift will happen whatever the populations does.

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So the causes of drift are, say, differences in breeding patterns within the population over time, or mutation?

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As for mutation let me stress the reason that it is referred to as only one of the mechanisms of evolution is because it acts only as a source of variation for selection (and drift). I find it odd that you weren't aware of that - or even aware that scientists recognised that there was a need for a source of new variation.

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Not sure I'm getting you. You mean scientists had noticed that the theory of evolution WOULD fail because of the overall tendency to reduction in variability from all the selective processes, and therefore had to suppose input from somewhere to balance out or overcome these processes?

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On the other hand I haven't noticed anyone claiming that there is an improbable "great rate" of mutation - just a rate high enough to compensate for losses (which as I have pointed out can be qute low, due to feedback effects). So it seems that your claim relies on an implicit assumption that there is a "great" rate of loss of variation - but I haven't seen any support for that claim.

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Because all the processes of evolution except immigration and mutation tend in that direction. Rate doesn't seem crucial if this is the overall tendency and these processes are operating as frequently as SEEMS to be understood to be the case. But I understand that the Hardy-Weinberg principle was formulated because of the observation of overall reduction in genetic diversity through all the processes of reduction, needing to account for the fact that in reality such drastic reduction in diversity doesn't occur as rapidly as would be expected if those were the only processes in operation.Any rate of mutation sufficient to be a counterforce to the processes of reduction of variability seems to me to be a great rate.

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As to your talk about "alleleic variation" the term as I understand it refers to variations already present. If that is what you meant you've already seen examples refuting that as an explanation of all variations.

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Yes, your bacterium. But still in my mind are the examples from the PBS program that called the process of selection of the poisonous newt and the antibiotic-resistant tuberculosis "mutation" while nevertheless ILLUSTRATING the process by diagrams showing that the adaptive trait was present in the beginning of the process. Surely that is not mutation, that is simply an already-present allelic variant. And such a case makes the whole question of mutation very iffy.

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THe fundamental problem of your argument is that it relies on comparing two rates but estimates neither. Rather it just assumes that one rate must be "great" without any support or without any estimation of the actual rate

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I have trouble with the whole idea of mutation, a random input that follows no law but somehow manages to be a beneficial effect in some cases. The probabilities against anything that would increase survivability would seem to have to outstrip any rate of such random changes whatever but yes, I'm no mathematician and would rather keep away from rates and estimates. I don't think they are really necessary. If you are right you are right that mutations provide enough variability to overcome all the processes that decrease variability, which seem to me to be happening all the time just because death happens all the time and allelic potentials must disappear from genomes at some noticeable rate simply because of death. It's slower than one might think, for various reasons including the Hardy-Weinberg principle, which says that the processes of reduction aren't always happening, but it seems to me inevitable. Rate isn't crucial to the idea.

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(or even a theoretical look at the issue of negative feedback leading to dynamic equilibrium which I raised). Yet this assumption is the core of the argument. At this stage your argument is not so much refuted rather, it is shown to be an unsupported assumption

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If I've missed the "core of the argument" I will have to go back and review.This message has been edited by Faith, 02-16-2005 07:48 AMThis message has been edited by Faith, 02-16-2005 07:50 AM

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But when there is a population reduction that reduces or eliminates some alleles there is a reduction in the overall capacity for variation in the new population, simply because some allelic opportunities have been lost or reduced. That's what I'm trying to get at.

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As I see it the problem here is your use of terms such as 'capacity' and 'possibilities'. In terms of extant allelic variation you are correct that much of the time selection leads to a restriction of variation even to the point of fixation. The problem is that in terms of capacity and possibility there is no restriction, the genes are still perfectly capable of producing any possible allelic variation as a result of mutation.

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And mutation is random input? Of what from where? In fact, please define mutation.

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In terms of producing novelty mutation, in a relatively broad sense, pretty much is everything.

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For some to increase others have to be eliminated. When this is drastic, as in the degree of natural selection that brings an antibiotic-resistant bacterium to the fore, or a poisonous newt, or bottlenecked creatures, some allelic frequencies are increased enormously, but the overall effect is a drastic decrease in allelic variation.

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This depends very much on the initial prevalence of the selected trait, if the selection is very strong and the trait at very low abundance then you may see a drastic reduction in population and genetic variability, if on the other hand the selected trait is already fairly evenly distributed then there is a good chance that much of the genetic variability of the population can be maintained, except for at the particular locus under selection

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OK, but the OVERALL tendency, leaving aside mutation and equilibrium when no selecting processes are operating, is a reduction in variability. Without the input of mutation over time the net effect of all the selection processes would be reduction in variability, often to the point of fixation. This may occur only in SOME traits but that may be enough to fix the "species" past the point where further variation is possible. In other words the processes may be quite slow, and I assume they are, but the accumulated overall effect is a loss of enough alleles in a population, or reduction in variability, to complete contradict any idea of evolution -- EXCEPT if mutation does increase variability in a beneficial way overall to such an extent that the processes of selection and reduction are overcome.

The "founder effect" specifically refers to the founding of a new population. Migration is more general - IIRC you yourself used it to refer to new alleles being brought into an existing population.The Noachic Flood would be a severe bottleneck for the affected species since (depending on the reading) even "clean" species are reduced to not more than 14 individuals and "unclean" species to 2.The difference between selection and non-selection is in fact very important in evolutionary theory. And as I pointed out the slower pace typical of drift actually leads to a consequence of greater variation than selective change would. So even the effects are different altough it requires some analysis to see that.Drift requires some variation to be present and therefore requires mutation to replace lost variation. Aside from that there is no specific cause. As I said it's a general term and ordinary statistical fluctuations are included. The "mitochondrial Eve" is largely a consequence of drift (i.e. matrilineal lines are interrupted if a woman has no daughters - and this is largely a chance effect at the appropriate level of analysis).You are however correct to note that evolution requires a source of new variations - and as I have pointed out Darwin devoted a chapter of his work to dealing with the issue (he was largely wrong but not unreasonably so given the state of scientific knowledge at the time).But you are badly wrong to insist that there must be a huge number of mutations based on the number of processes reducing variation and even more wrong to insist that rate is unimportant. In this discussion everything BUT the rates is peripheral. Either the rate at which new variation enters a populations is sufficient to balance out the loss or - as you claim - it isn't. That's it. And I don't see how you can make your point without dealing with actual rates - your only hope would be to make a theoretical argument along the liens of the one I made earlier pointing to equilibrium as the expected state, but I don't think that such an argument is available to you.You're even wrong to claim that the Hardy-Weinberg equation always points to declines in variation - it can also point to equilibrium situations (as it does in the case of sickle-cell anaemia).Finally I think you've missed the point that the experiments with bacteria started with a clonal population. Any genetic variation has to be the product of mutation. That it occurred before the selective influence was added doesn't help your position at all - because your position is that that could not happen.

Mutation is a general term for a heritable change, most mutations in terms of evolution and genetics are thought of in terms of changes to the DNA sequence, either within the primary sequence (A,C,G and Ts) or in terms of the location of sequences or even large scale rearrangements of the chromosomes up to complete genome duplications.There are also some more recently studied examples of heritable traits which are not connected to the primary DNA sequence, but these are peripheral to the question you are considering.So for our purposes a mutation is an alteration in DNA from a simple single base substitution up to large scale chromosomal rearrangement. The causes of mutation are also many and varied, some are mere mistakes in the normal replication process, others are the result of environmental factors such as mutagenic chemicals, UV light or radiation. This isn't neccessarily the case, there are some forms of selection which act to maintain diversity in a population. Some traits work best in a heterogeneous population or when they only represent a particular proportion of the population, in which case selection can maintain the frequencies of different alleles.You don't really seem to be very familiar with the basics of molecular genetics, population genetics or evolutionary mechanisms. Here is a section from a genetics textbook covering the origin of variability in mutation and the effect of selective mechanism on reducing variability.TTFN,WKThis message has been edited by Wounded King, 02-16-2005 09:12 AM

Hi Faith. I think part of the problem here is that some of the ways certain terms are being bandied about here may be a bit misleading (or unclear). Maybe I can help out - I don't want you to think we're "ganging up" on you.1. Genetic drift. This refers to random fluctuations in the frequency of alleles within a population. The fluctuation is not due to selection at all, rather to stochastic (statistical) effects. The alleles do not differ on average in fitness - as was mentioned, this is the heart of "neutral theory". If there's no effect on fitness, the alleles are not acted upon by natural selection. Drift could also be considered sampling error (more on this later in conjunction with founder effects). Think of it this way: if you have a population of "A" alleles, and an "a" single mutation occurs, what happens when the population reproduces? Say only two offspring survive. AA x Aa yields a probability of 25% that the "a" allele will be lost in the first generation (AA = 1/2 x 1/2 = 1/4). However, looking at multiple alleles in multiple populations with multiple offspring, the probability distribution, somewhat counterintuitively, of the neutral allele doesn't vary around the mean distribution. There is an equal probability of the frequency of this allele either increasing or decreasing randomly. This is called the "drunkards' walk" (or "random walk"). You can graph this fairly easily if you're interested. The simple version of the relevant equation is V = p(1-p)/2N, where V is variance in frequency, p is probability distribution for a single population, and N is the number of gene copies (2N indicating haploid, with two alleles for each gene in the adults). It is obvious that the size of the initial population will also have a great deal of effect - genetic drift occurs faster in small populations than large ones. If you plot the drift of multiple neutral alleles over time, the graph comes out looking like a plate of spaghetti as lines criss-cross back and forth, disappear, rise to fixation, etc.Adding to this, which should be obvious from the equation, a rare allele (p close to zero) will be more likely to "walk off the end of the pier" and disappear than a more common allele. Of course, things get a bit more complicated when you're dealing with metapopulations (populations of populations), but that's the simplest way of looking at it.Drift drives evolution by changing the frequency of alleles in a population, irrespective of any selection pressures. It may drive an allele to fixation (p = 1), but alternatively may cause it to disappear completely (p = 0). It does NOT automatically reduce variation.2. Other factors: Something that is taken into consideration in more complex treatments is the effect of other non-deterministic factors, like accidents. If you have a small population which is polymorphic for a neutral allele with a low frequency, accidents can change the frequency of this allele downward. Consider: a group of 10 organisms of which 8 are homozygous (AA), and two are heterozygous (Aa). If one of the Aa individuals is eaten before it reproduces, the frequency of "a" is reduced. OTOH, accidents can increase the frequency of "a" by an AA getting eaten. (Apologies to all for the gross oversimplification).3. Bottleneck. A bottleneck is simply where a population is reduced to a very few individuals, and hence a very few alleles. If the population survives, we say it has passed through a bottleneck. One effect of bottlenecks is to homogenize a population - every member of the population shares identical alleles, whether through drift, selection, or even just sampling error. As an interesting aside, bottlenecks can actually counteract selection by reducing the population to such an extent that drift may cause fixation of a deleterious allele, causing the population to actually move from one fitness peak to the "valley" in its adaptive landscape - allowing it (assuming it survives) to climb to another adaptive peak. This is something that selection cannot do. IOW, in the context of your argument, reduction in variability caused by a bottleneck can in fact impel an increase in variability or even fitness when the population rebounds. Bottlenecks may be caused by selection pressures, but they are NOT selection pressures - they are a possible result. In addition, bottlenecks are NOT evolution, they are simply a term describing the effect of population reduction where the population subsequently returns to a larger size over time (and hence increased variability).4. Founder effect. This is actually a special type of bottleneck. It is NOT caused by selection. Founder effects occur when a small (often just a few individuals or even one pregnant female) subset of a population arrives in a new habitat cut off from the parent (or "source") population. In this case, the founding population will likely be unrepresentative of the source population, in terms of the alleles present in the source. IOW, it is a form of sampling error - the probability that a rare allele carried in the source population will appear in the new population is very low (actually, the likeliehood is identical to the p of the allele in the source population). Just like any other bottleneck, founder effects show similar genetic markers (homogeneity, etc). Indeed, drift can have a significant effect on founder populations because they are so small.Note, however, founder populations are significant for evolution (just like mass extinctions) - not because of the genetics - but because of the potential for the population to divide and divide again in subsequent generations due to the availability of new, unoccupied niches (see "adaptive radiation").To sum up: drift has nothing to do with selection, but does drive evolution. Bottlenecks and founder effects have nothing to do with selection, and also have nothing intrinsically to do with evolution - they are descriptions of population dynamics.Hope this helped.

First off, great string of posts! It is rare to see a creationist that actually has the ability to admit that their argument might be flawed and who can think for themselves independent of the organized creationist's information stream. Mutation always happens. You are not an exact copy of half your father and half your mother. Certain parts of your genetic makup are unique to you independent of your parents and that is a fact. The vast majority of these mutations do absolutly nothing. Some have a small negative or positive effect on your survivability depending on the environment you live in. Some that are unlucky enough to happen in an important piece of your genetic code may cause you to have a severe genetic defect. Luckly this is rare and due to decreased survivability these mutations are rarely passed on to offspring. Hence selection.Mutation is the primary source of variability in a population. Selection ensures that bad mutations do not permeate the population and that good mutations will. Along with all the good and bad there are the neutal mutations that may or may not get passed on based on nothing more than random luck. Hence genetic drift. Scientists do not suppose input in variability. Scientists did not invent the "concept of mutation". It is a fact that you are not a discrete representation of 1/2 of each of your parents genes. You have genetic variability that you did not recieve from your parents. Mutations happen and are observed.In the bacteria monoculture, children of the original bacterium had genetic differences that they did not inherit from their parent. This genetic difference must have come from somewhere. Others on this site have tried to argue that the differences are a result of some kind of programmed mutation but have done so unsuccessfully. Either way, we know that changes in genetic variability in a new creature happen independently of its parent(s). And now I see the source of your main argument. You currently have an assertion that the combination of all the different types of selective pressures always constitutes a reduction in genetic variability. I would like to point out that this is an assertion and you must now provide evidence to show that is it more than such. Notice the "seems to me to be" portion of your quote. In order for your argument to be credible it needs to "actually be". If you can show that the rate that genetic variability being lost by selection is greater than the rate of genetic variability being introduced by mutation then you have a platform for your argument that evolution has limits.Even if you can establish that the amount of mutation required to keep up with selection needs to be "great" in whatever metric you choose, you also need to show that such a "great" rate of mutation is detrimental. What is "great"?Given that a not insignificant number of mutations happen each time an organism reproduces I am not convinced that selective pressures reduce the amount of genetic variability faster than mutations can put it back. To clarify further about the bacteria experiment. If the population is decendent from a single genetic source then any trait that one individual has different from the source must have come from a mutation. If mutations could not produce genetic variability then there is no way that the child of a bacterium could attain a trait that was not also held by the parent.In the particular experiment there were numerous bacteria that were genetically different enough from the original bacterium to be resistant to the anti-biotic. In fact, if I remember correctly, the mutation that conferred the resistance happened often, independent of heritability. In other words, it wasn't just one bacterium that gained the resistance and passed it on but rather many who independently gained the resistence off and on while the culture was not exposed to the anti-biotic. Someone else may be able to provide more details in the form of a source I hope. The random input is only beneficial because of selection. The best source of new information is a random number generator according to certain aspects of information theory.In the case of the bacterium, the resistance to anti-biotics was only beneficial once the culture was actually exposed to teh anti-biotic. Before that the mutations were just part of the populations variability.If you don't want to consider rates then you might want to reconstruct your argument because, when rigerously defined, your entire argument depends on rates. The "tendency" to reduce genetic variability is a rate. If your argument is that selection will "tend" to always reduce the genetic variability of a population despite mutation then you are already in the realm of rates!Thanks,

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By the way, for a fun second-term drinking game, chug a beer every time you hear the phrase, "...contentious but futile protest vote by democrats." By the time Jeb Bush is elected president you will be so wasted you wont even notice the war in Syria.
-- Jon Stewart, The Daily Show

I'm not sure what you mean by "normal allelic variation", but I thought I would point out that sexual reproduction creates new phenotypic variation, but not actually new allelic variation. I thought that might be germaine to the discussion.

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You're even wrong to claim that the Hardy-Weinberg equation always points to declines in variation - it can also point to equilibrium situations (as it does in the case of sickle-cell anaemia).

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Why do Hardy and Weinberg get the credit (or the blame) for all of population genetics? Hardy-Weinberg describes the relationship between allele frequencies and genotype frequencies in the case of an infinite population, random mating and no selection, nothing more. In Hardy-Weinberg equilibrium, variation does not decline (nor does it increase), nor do allele frequencies change, in response to selection or anything else. No real population achieves Hardy-Weinberg equilibrium, of course, but it is a useful approximation for many purposes.

Hey Faith, I also appreciate that you are willing to learn and keep an open mind. Perhaps, but evolution does NOT only proceed by such drastic events that kill off the majority of the population. I tried to explain this to you on page one of this thread with a frog example, but perhaps you missed it. I'll try again:An individual animal is born with a mutation that makes it slightly better at catching prey, and thus slightly more fit than the rest of the population. This does not mean that the rest of the population will now die off en masse. Instead, the frequency of that mutated allele may increase over generations in the population, since individuals carrying that allele are more fit and thus more likely to have offspring. As the frequency of the mutated allele increases, the frequency of the original alleles for that gene decreases. The mutated allele becomes fixed in the population, replacing previous allelic diversity for that gene with a single allele (a state which I'll call "zero allelic diversity").But here is the important part, that I fear you are missing: Even though the success of the mutated allele drops "diversity" for its gene to zero, the organisms within the population have NOT reduced the allelic diversity for the other 20,000 genes in their genome. Thus, fixation of an allele for one gene generally has neglible effects on the allelic diversity for the other 99.99% of the genome. Genes coding for any other trait the population have retained their allelic diversity.Is that clear?Also - you seem hung up on the bacteria-mutation example, which is a good example because monoculture allows the experiment to begin with zero allelic diversity. However, that is not the only example of documented mutations (I gave you another one - the Baldwin mutation that appeared in a closed population several years ago and results in hairless (and I think darn cute) guinea pigs.)I worked in mouse genetics for several years - mouse geneticists have established "inbred" mice that are homozygous for every gene, which means they have zero allelic diversity, not unlike bacterial monoculture. Mutations occur on a very regular basis in closed populations of these inbred, zero-allelic-diversity-mice. A simple example is an inbred mouse strain that happened to have black fur. One day white-furred mice began appearing in the population, and the mutation that caused this difference was identified. Examination of the DNA of the great-grandparents of the white-furred mice did not reveal the same mutation. There was no source of the white-furred gene except for mutation, since there was zero allelic diversity at that gene in the grandparents of the mice with the mutation.

The rates of mutation don't need to be high in order to maintain variation because much of variation is protected from selection. For traits that are affected by genes at many different loci, low mutation rates can maintain a populations variability. Many different genotypes generate intermediate phenotypes that are favored by stabilizing selection. If the individuals within a population are all just as likely to survive and reproduce, then a lot of variation is protected from selection. When a large number of loci affect a single trait, only a small fraction of the genetic variability present in the population is expessed phenotypically. Selection removes variation from the population very slowly, if this happens. Recombination and reshuffling will expose these hidden variation to natural selection in later generations. Because of this protection from selection, a low mutation rate can maintain variation despite natural selections tendency to decrease variation.Hidden variation is always present in continuously varying traits.This is the reason that we can get different forms of species via artificial selection. A chihuahua(sp?), which is smaller than the smallest wolf, has been and could be selected for by humans over a very short period of time because within the genes of wolves, there must have been these hidden variations!

(My bold)But the fact is that novel mutations DO take place and breeders do USE them in breeding. There are different breeds of domestic cats which came about due to some novel mutation.For example:

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On a sunny day in June 1981 in Lakewood, California, a longhair silky black female kitten with unusual ears wandered up to the doorstep of Joe and Grace Ruga. Joe scrutinized the situation and determined that the most effective solution to this stray kitten problem was to ask Grace not to feed the kitten. Grace, not abiding by her husband's wishes but listening to her heart instead, left a bowl of food on the porch. The affectionate black kitten quickly worked her way into the Ruga's hearts (especially Joe's) and they named her Shulamith, which means "black but comely". Such are the beginnings of the American Curl as it is known today. True American Curls must trace their pedigree back to Shulamith, the foundation female.

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In December 1981, Shulamith delivered her first litter of kittens. Out of four kittens, two had the same curly ears as Shulamith. A geneticist was contacted to study this phenomenon and he confirmed that this unusual ear was a genetic trait and was inherited in every case, causing it to be labeled a dominant gene, with no deformities attached to it. Referred to as a spontaneous mutation, the gene that causes the ear to curl appeared to be following a single dominant pattern.

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From: Cat Fanciers Website