Evolution Requires Reduction in Genetic Diversity

Absolutely. I was isolating the effect of inbreeding from other factors to show that inbreeding alone did not change allele frequency. Maybe I did get a little technical for this discussion, but I thought it was important to make the point that inbreeding is not what changes the proportion of alleles; it is the other evolutionary factors - such as drift. See Message 605 and Message 615.Another point to make is that in plant breeding, when a particular trait of interest is found, breeders will produce a highly inbred line (7+ generations) starting from a single individual or a small group of individuals. The point is to produce a population that is highly homozygous (enough inbreeding and they can be homozygous at virtually every loci). They then use this population to do QTL studies and identify what marker the particular trait is associated with. Interestingly, no evolution occurs in these inbred lines. Why? because they are shielded from drift, selection and migration (you can't prevent mutation)(some animal lines such a lab mice as well are highly inbred, but I am not as familiar with animal breeding programs)HBD

Thanks, I just do not see how dividing alleles into different populations can result in genetic incompatibility. The alleles are not the genes, but just a part of them. In a population with four alleles: A, B, C and D you can have theses combinations: If we split the population into those with A and B and those with C and D then each subpopulation can have the following combinations: So then if we reintroduce the two populations to each other ... None of those offspring are any different mix than occurred in the parent population, none of those parent varieties did not occur in the parent population.Without any change to the gene how could there be genetic incompatibility?Without any change to any of the alleles, how could there be genetic incompatibility?Even with change to create a new allele, how could there be genetic incompatibility?If we assume a new allele E in population 2 then we get these possible offspring: So the recombined population would then have: There are only two new combinations between pop1 and pop2: AE and BE, so -- unless the of the gene is changed, how could there be genetic incompatibility when the populations recombine?As I see it there is the basic function of the gene, and there are variations that don't affect function but do affect the phenotype (ie alleles).As I see it, to get genetic incompatibility you need to affect the basic function of the gene.Or do I have this wrong?EnjoyEdited by RAZD, : resorted table for clarity

Is anybody going to dispute that a small population is inevitably going to develop genetic drift which DOES change allele frequencies? Granted that's not inbreeding alone. If someone answered this earlier, sorry, I know I'm jumping in late.And is anybody going to dispute that inbreeding can multiply undesirable traits simply by pairing recessive alleles (normal genetics)?But I've lost track of how this thread got onto this topic. My main point about inbreeding always was that it's necessary to bring out new traits in a recently isolated subpopulation, through the new combinations that occur due to the new gene frequencies. The newly isolated subpopulation won't look any different from the population it split from until these new combinations are worked through for some generations, though if the population is quite small some dramatic individual changes could show up sooner, maybe even in the first generation. And that's still my main interest.I did think that the new combinations could lead to a genetic mismatch preventing interbreeding in some circumstances, such as by pairing recessive alleles for instance, but it isn't important to my argument.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

Sigh. Everyone who has pushed you on this issue has been careful to give the conditions for their answer. Inbreeding increases the likelihoood of already present bad traits being expressed simply because it is more likely that both parents possess the allele for the trait. But that kind of reinforcement is not an example of inbreeding creating new traits. The same issues arise in the larger population too but at lower frequencies. If you have something else in mind, then tell us how that something else works. It is a simple matter to go back and look at the thread. There is no need to rely on your memory.New frequencies means the percentage at which the individual alleles are expressed in a population. It does NOT mean that single individual animals possess different frequencies or combinations. If you want us to believe that simply inbreeding, without doing some selection is going to make the population develop new characteristics, please explain how that works.Of course a mutation that does not even exist in the main population would obviously have the result you are trying to describe.By the way, I don't see how the procedure as you've described it would even produce a new breed of dogs. In addition to inbreeding, you have to do some selection or the offspring, and the results are going to be highly dependent on exactly what that selection process is.And by results I mean to include the diversity of the final population. There is no way to predict the even the likely qualitative characteristics of the final population without talking about selection and modeling the selection process in detail. That's one reason why nobody is going to accept that every evolutionary process is going to turn out 'just like breeding'. You'll need some math to convince me. I don't know what others will require.Let's look at it this way. The entire human population is completely isolated. There is no other source of human genetic material in the entire solar system that we can use to add to our genome save the mutations we generate in the offspring we produce. Is it your claim therefore that the current human population, regardless of what mutations occur, must decrease in diversity over time? Regardless of what selection paradigm is imposed?Show me.Edited by NoNukes, : No reason given.Edited by NoNukes, : No reason given.Edited by NoNukes, : No reason given.

OF COURSE IT'S NOT AND WHERE DID I SAY IT WAS? You are confusing two different subjects.And please get this straight. I've said it for years and years by now. It's the NEW GENE FREQUENCIES brought about by the population split that CAUSE new traits, but it takes the recombinations through inbreeding of the new subpopulation to BRING OUT the new phenotypes. Even this isn't of major importance, but it's true: you won't SEE the new traits until after a period of inbreeding.THIS GETS SO FRUSTRATING. Maybe I'll eventually read the rest of your post and all the others that are backed up but Why Bother keeps passing through my mind.Edited by Faith, : No reason given.

It is you who are confused. What was the point of posting this if it wasn't to address the topics under question? The above was not ever in dispute. It is not something that you had previously argued and received disagreement on. You have yet to demonstrate how this happens. We've been asking you for an explanation for several days now. You will notice that the title of this sub thread happens to be loss of ability to interbreed. You've also made the claim that the new gene frequencies cause that too. When are we going to get a description of a mechanism for how those things work? You don't have any answers, so you are right. Why bother? I can see that you are already using the coping mechanisms that show up when you have no answer. In this case we see you nibbling away at posts and airing frustration while ignoring most of the meat.ABE:I've noticed that my posts are not unique in pointing out problems. I'm also sensitive to the issues with your eyes. Please feel free to ignore my posts. I promise not to hold that against you.Edited by NoNukes, : No reason given.Edited by NoNukes, : No reason given.

This is of major importance because it's wrong.
As shown extensively in many posts last 2 weeks - and I am only around here for that period, let alone previous attempts - a population split cannot bring a different GENE frequency but only a different ALLELE frequency. In the population of the very same (ancestral) species there are not much differences in genes. Unless it's a typo, it is a flaw. Because a different gene frequency implies that one breed must have taken with them some genes other breed lost throughout the split event. That can't be.And it is not true that you won't see new traits until after a period of inbreeding.
MOSTLY, the accumulation of new traits CAUSES the eventual split.But the most severe flaw is just skipping an abundance of observations both in the field and the lab on genetic innovation by means of Darwinist evolution.It is indeed frustrating - if I weren't used to it when debating creationists - to experience your posts just being ignored. Why Bother indeed is what crosses my mind.Edited by Denisova, : No reason given.

Just a little while back in Message 549, and my own readings confirm this, HBD explained that the term gene frequency and allele frequency are often used interchangeably when it is allele frequency that is actually meant. I don't think Faith meant to imply that the it was actual genes whose frequencies were changing.But, and somebody please correct me if I'm wrong, I believe individuals in a population can differ as to which genes they have and how many. Some individuals may have different numbers of copies of some genes, or even possess genes other members do not. But I don't believe this is what Faith is talking about.

Congratulations, Faith, you have just discovered the founder effect! This topic got started because you want to take known evolutionary processes and ignore certain parts of them and redefine others so you don't have to acknowledge that what you are talking about IS evolution. You wanted the founder effect to be based on inbreeding alone. I made a simple, straight-forward comment about inbreeding not changing allele frequency but simply shuffling them into homozygotes and that in order for allelic frequency to change there had to be other evolutionary forces at work - like drift. But that sounds too much like evolution to you. It IS important to your argument. You don't want to acknowledge that mutations can add genetic diversity to a population so you require genetic incompatibility to come about by shuffling alleles around into different genetic combinations. Or do you have another mode of incompatibility in mind?HBD

Maybe not, but there are places where using the term "gene frequencies" has been terribly confusing. Allele frequency is much clearer. Genotypic frequencies should be used when talking about combinations of alleles. Oh, this is definitely true. Some genes, such as ribosomal genes, are particularly prone to variable copy numbers. Sub-species level organization is often identified by these types of copy number variations or extra genes, for example a pathovar may have a gene that allows it to disable the defenses of a particular host that no other members of the species has.I would just point out that to say "individuals in a population can differ as to which genes they have and how many" could give the wrong impression. For the most part genomes are very stable and we would not expect this kind of variation at the individual level. Where we usually see it is at the sub-species level. Of course, this sub-species variation undoubtedly arose from an individual, so it is not an incorrect statement.HBDEdited by herebedragons, : spelling

If something is a receipt for misunderstanding, it will be blurring of concepts, using them interchangeable when they shouldn't. The very concept of an allele is exactly to indicate that different versions of the same gene may exist. That implies the gene itself persists among its versions.I could live with it when all contributors to this thread would agree on "gene frequency may be used as a synonym for allele frequency". But imagine when a newcomer will join.So I propose to designate it "allele frequency" when such was meant. I already pointed that out to Faith but these instances of individuals of the same species having different genes are rather rare. Because too much of those and you have different species. But Faith is thinking that many genes (not alleles) of the original genome from the creation moment are silenced and became junk DNA. That is impossible because that would imply that extant humans supposedly differ thousands of genes from the original ancestral humans. That actually implies a complete other species.

Agreed. I'll rule that the term allele frequency should be used when referring to allelic percentages in a population and related concepts, and the term gene frequency should not be used as it is confusing. If someone finds they need to talk about actual gene frequencies then they need only make it clear that that's what they mean.

There are three basic categories of reproductive isolation,1) Ecological or geographical isolation
2) Prezygotic isolation - ie. different pollinators, different breeding patterns/timing, different mating habits (bird songs/displays)
3) Postzygotic isolation or hybrid incompatibilityWhat we seem to be focused on here is postzygotic isolation, which seems like it would be the most important barrier because of our general concept of species, however, it turns out that postzygotic factors usually play little role in speciation. Ecological isolation is of course the big player in allowing two subpopulations to diverge, but prezygotic isolation is really the major factor in the reproductive isolation of two subspecies - at least initially. In the case of the greenish warblers, IIRC, where the two ends of the ring meet the two species have different songs and so do not recognize each other as potential mates. Could they produce viable hybrids if forced to mate? Maybe, but does it matter?This is really a huge subject and maybe we could spin this off as a separate thread? Genetic incompatibility can come from a number of things. It could be from incompatible genes or from failure of the chromosomes to form viable pairings during recombination or from changes in regulatory networks. (I suspect that the latter to be the most common).So in theory, one mutation could result in prezygotic or postzygotic incompatibility but it is highly unlikely. It more probable that it is due to a series of incompatibilities that accumulate.ABE: I should make it clear though that I agree that shuffling alleles around is not sufficient to cause genetic incompatibility and that is the point I have been making all along. Introducing a new gene could theoretically do it, but that would require mutations not just working with the same alleles or a subset of them. /ABEHere is a good paper by Allen Orr that discusses the Dobzhansky-Muller Incompatibility. Look especially at figure 1 which shows how incompatibilities increase rapidly as the number of mutational differences increase. The population genetics of speciation: The evolution of hybrid incompatibilitiesAlso check out this paper Hybrid incompatibility and speiationWe can talk about them later.HBDEdited by herebedragons, : clarification

[This post is a response to HBD's #624, that accidentally got attached to his #628] That would be odd since I know I'm talking about evolution, MICROevolution of course, and have never claimed to be talking about anything else.I also have thought through my argument (that evolution requires reduced genetic diversity) in ways you obviously miss because you're up to your ears in the party line. I've thought it through and seen where I believe the standard explanations are wrong. If I hadn't I wouldn't bother trying to argue about it. Founder effect? I've said nothing about founder effect. Where do you get this stuff? I also don't WANT anything here, I THOUGHT sufficient genetic incompatibilities could arise to prevent interbreeding as the definition of speciation, but IT DOESN'T MATTER ONE BIT whether they do or not because speciation is a very small part of my thinking. I regard it as a potential end point of a series of subpopulations but they all are characterized by reduced genetic diversity.The reproductive isiolation I'm usually talking about, which is necessary to the formation of a new subspecies, is geographic isolation. Any kind will do because I'm trying to avoid the complications of hybrid zones and continuous gene flow to keep the argument simple. The idea of genetic incompatibilities purely from allele mixing is not wrong, however, even if they don't prevent interbreeding. Something happens in the combining of alleles that affects them in other combinations (which I gather I should refer to as genotypes.) It's only on paper that all the same allleles can combine endlessly without problems. Read about "outbreeding depression" for instance, which is similar to what I described on this thread somewhere, genetic problems caused by two different sets of COMBINED alleles (genotypes) coming together. Where are you getting all this? I had the idea that simple inbreeding could lead to genetic incompatibilities and I was right even if wrong about their causing inability to breed. I don't recall having any other idea. I certainly had no idea of changing alllele frequencies except by drift or other fiorms of selection, as I recall saying. (I was assuming drift without differentiating it from inbreeding because in a small population it seems inevitable.)And again stop imputing some fear of the concept of evolution to me. That's a big fat lie. As far as I'm concerned you've hijacked this thread for your own purposes and I'm not part of it. I guess you'll continue to argue with your phantom Faith. Oh brother, you'll make up anything. Perhaps it's important and I didn't recognize it, but I certainly wasn't intentionally pursuing a particular strategy, it's simply what I happened to think.As for other causes of incompatibility, sure, there can be enough change for preference against interbreeding to occur, but again I didn't make a decision about this for some strategic purpose. Believe it or not I've given little thought to the causes of failure to interbreed at speciation because I've been assuming some kind of genetic incompatibility arises after the formation of a series of subpopulations. But there's no problem with mutation being the cause of failure to interbreed at speciation because the new subspecies is genetically depleted beyond further evolution anyway and the mutation doesn't add diversity to any useful purpose if all it does is lead to genetic incompatibility. I'm claiming you'll find genetic depletion on DNA analysis, mutation or no mutation.You're so busy swallowing the ToE whole, including the additive processes uncritically assumed by the ToE that I'm specifically arguing against, you'll never see how any of this really works.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

If the space were important then we would see selection against indel events that would be detectable.At the same time, that is a rather rudimentary function akin to vestigial organs or the actual junk in your kitchen. The descriptor "junk" gives us additional information, that the stretch of DNA in question shows no signs of positive or negative selection. This is not true of all non-coding DNA. Also, you no more sequence non-coding DNA than you sequence junk DNA. You sequence DNA. Period. Only afterwards can you determine if a specific stretch of DNA is coding, non-coding, regulatory, junk, etc. DNA takes a tremendous amount of resources? Since when? I don't know for sure, but I wouldn't be surprised if the ATP turnover in one muscle cell from one contraction was equal to all of the ATP turnover needed to replicate the genome of that cell. The problem for the bladderwort was the availability of phosphates to make the ATP, not the energy needed to replicate the genome. Junk DNA and regulatory DNA are both non-coding DNA, and they are very different from each other. As the bladderwort genome shows, 90% of our genome may be disposible, just like the trash in your kitchen.