Molecular Population Genetics and Diversity through Mutation

I didn't say that, RAZD did. Please change the quote reference.

Thank you for that recitation of the Evo Creed, Article Whatever. That's all it is, just the usual Evo Statement of Faith. Cuz you do not know for sure that it didn't exist in the population already.The way added mutations could mess up a breed is by changing major characteristics. If you've been working for decades to get a perfect purebred Whozit you don't want a mutation to pop up for a Whatzit. You DO NOT WANT this new trait in your breed. What's so hard to understand about that?And this is after the Whozit breed has been pretty well established, so that it's ALREADY lost genetic diversity in its formation, which is NECESSARY to its formation. What you've got is a LARGE net decrease in genetic diversity with respect to former populations from which it was derived. The idea that one mutation could come along and increase its genetic diversity in any meaningful sense of the term is quite laughable. Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

This discussion has gone weird and I'm not up to trying to correct it. The REAL point, which I probably contributed to garbling as much or more than anyone else, is whether after you get a breed, or in nature a subspecies, the lost genetic diversity will be made up by mutations. I say isn't going to happen and if it did you wouldn't want it to if you were a breeder, from which I conclude it hardly ever happens anyway. But if it did it would never make up for what has been lost in arriving at the breed or species, which is the alleles for ALL the other breeds or subspecies of the Dog Kind or Cat Kind or cattle Kind or whatever it is. And if it did you could never hold on to a breed at all and Nature wouldn't have recognizable species at all. MEASURING GENETIC DIVERSITY:
Anyway I'd like to go on to this other issue that has been bugging me. I still don't get the point about cytochromeC, HBD, and I'm afraid to ask you to try to clarify it again. But it's related to this other question I'd also like to understand if possible, and that is how you can get any true measure of a population's genetic iversity from microsatellites or Mitochondrial DNA, both of which I understand are used for that purpose.You explained a couple of discrepancies between the studies Genomicus posted on the Great Debate thread and known facts: one study that showed no gene flow and high diversity, which was contradicted by a known rich history of gene flow, and the other study found high genetic diversity in the elephant seals although Scientific American just a few years ago discussed the plight of the seals with their known low genetic diversity despite their great population increase.I gather the discrepancy is explained by measuring Mitochrondrial DNA rather than chromosomal DNA? Right? In which case why would that be done at all? I'm sure there's some rational explanation but it completely escapes me. GENETIC DIVERSITY IN JUTLAND CATTLE:
I just went back to a very old thread and read up on the Jutland cattle which had split into four different breeds with distinctive phenotypes. Percy had introduced the subject and gave a link to this journal where you can find the article on page 75.It's full of technical terms so it's hard for me to get through it all, but it's concerned with conservation of these Danish cattle breeds, and of course that would be a concern if their genetic diversity is low, which one might expect to be the case as a result of much splitting into separate populations. I was of course interested at the time in the fact that you can get recognizable new phenotypes from such splits, showing that this can occur in a very short period of time and not take millions of years. A few decades in the case of these four populations of cattle. It also implies loss of genetic diversity, of course, since that's the concern of the conservationists. So it worked well for my argument.But reading through it now I see that they studied the genetic diversity at Mitochondrial DNA and microsatellites. (I read up on these enough at least to know where they are located and what they look like), and they found HIGH GENETIC DIVERSITY IN THESE FOUR CATTLE POPULATIONS. Which is just mindboggling to me. I suspect this is exactly the same situation I ran into with Genomicus' examples -- the high diversity is ONLY in the MtDNA and the microsatellites and NOT in the chromosomal DNA WHERE IT COUNTS.By the way the microsatellite and MtDNA results differed for two of the herds on some point I don't remember and would have to look up again. What good are methods that don't give reliable results?Or is this a fluke?SOMEBODY please explain this in ordinary English.********************************
POD MRCARU LIZARDS DON'T NEED NO STINKIN MUTATIONSABE: Just have to bring up the Pod Mrcaru lizards too because Percy said this about them: Yes I wish the phenotypic differences between the cattle populations had been described too, though enough is said to indicate that they had distinct differences. But where he goes on to say "we have to grant" that the lizards' large head and diet changes "could have been due" to drift, selection, mutation or a combination, my answer is that they were most probably due ONLY to normal recombination over some number of generations of inbreeding. Selection was accomplished by the initial numbers released on the island anyway, starting the population with a mere five pairs, drift is just a version of selection and could have been a factor in such a small population too, though not needed, and mutation is simply not needed AT ALL.The large heads and different digestive system were NOT present in the original population so how would they emerge in the new population? I would point you to Darwin's pigeons which acquired some dramatically exaggerated characteristics over a number of generations in which he selected for that particular trait. The huge breasts, for one, are not to be found at all in wild pigeons; they emerged due only to sexual recombination over some number of breeding seasons, showing that genetic changes can multiply. So you wouldn't need to have a single allele for the large heads of the Pod Mrcaru lizards either, all you would have to have is a multiplication of the alleles for size down the generations. And the new gut seems to demonstrate a design factor that links characteristics for the good of the animal, IMHO. If it's going to be munching some crunchier food with its big new jaws, it needs to be able to digest it.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

Sigh. Yes, microsatellites are chromosomal, should only have contrasted Mitochondrial DNA with chromosomal. Sigh. But they are another thing from the traits that require reduced genetic diversity and from the heterozygosity that would reflect genetic diversity, so why are these separate apparently unrelated segments of chromosomal DNA used to measure genetic diversity?The point you want me to look up was so minor and secondary I didn't want an answer to it, it was just a by-the-way. There are more important matters in that post. 'ABE: Of course we're debating but why the need to be "excoriating." What's wrong with "Understanding Through Discussion," which IS the slogan for EvC Forums despite the murderous inclinations on both sides of this issue. What's the point of playing Swashbuckling Scientist with a mere creationist? Edited by Faith, : No reason given.Edited by Faith, : No reason given.

Here's the point you wanted me to look up, found on page 79 of the journalNot sure what this meant at first. I guess it means how different or similar the phenotypes?Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

I'm not even totally sure what it means. Phenotypically different? If that's what it means it would probably have to do with the sizes of the founding populations, or the particular gene frequencies that occurred.But what interests me is why MtDNA and microsatellite data disagree.Edited by Faith, : No reason given.

I can't possibly have an answer to a question about a difference between microsatellite and MtDNA conclusions since I still haven't a clue how either of them can be used to determine genetic diversity which is normally measured by heterozygosity at OTHER loci. I'm still waiting for an explanation of the discrepancies between those different assessments.I have NO idea what this means: Why should they agree? Because they are ostensibly measuring the same thing. Sheesh.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

NO idea how anything but heterozygosity for the traits of the organism could measure genetic diversity. Sorry. That's basically the question I'm asking in this thread: how on earth do MtDNA and microsatellites give any kind of information about diversity ELSEWHERE? No idea what either of those have to do with anything. How's about you answer my original question? What does MtDNA or microsatellites have to do with genetic diversity (of the sort that elephant seals and cheetahs lack)? I know what they ARE, as far as where they are located and more or less what they look like or a basic description of them, but haven't a clue how they relate to the question of genetic diversity as I keep raising it. They seem to have nothing to do with genetic diversity so I have no idea why they are used to measure it.

I have NO idea what this means. How can completely unrelated short sequences of DNA say anything about the overall heterozygosity of the genome? What does "matrilineal diversity" have to do with anything?I started this discussion by asking the question how these things are related at all. You haven't answered any of it. What does "a low level of sequence divergence among their various genes and other genomic regions" mean? I have NO idea what this means.If you can't answer the question, perhaps someone else will come along who can. Edited by Faith, : No reason given.

Again you've attributed a quote to me that isn't mine. Kindly correct. Thank you.

Maybe you know what you are talking about (I'm really not sure, to tell you the truth), but it's all meaningless to me. I've never been talking about any kind of diversity except GENETIC diversity and that's about heterozygosity, which I've understood to have to do with the health of a species, so that the elephant seal's being so low on THAT kind of diversity is what threatens it, and still threatens it according to that Scientific American article on it. Your measurement found high genetic diversity which is some kind of delusion.Nucleotide diversity wouldn't help that problem as far as I can see, so there's no point in considering it. If your tests don't measure the usual allelic diversity I don't see any use for them.Such as the study you posted of the Sardinian population which has experienced lots of immigration over the centuries making for lots of gene flow, while your study found NO gene flow.Nothing you've said clarifies any of this, and in fact seems designed to obscure it rather than clarify it. Nothing you've said tells me why MtDNA or microsatellites contribute anything to the problem of reduced genetic diversity as I've been discussing it.All I can do is continue to argue along the lines that I DO understand, until someone comes along who can make this clear.

Utter nonsense? I made it up? This discussion is becoming less than enjoyable.I know you don't like Wikipedia but here it comes: Pretty standard definition here. Polymorphic loci, many alleles per locus I take into account as a matter of fact as where most loss of genetic diversity occurs; Heterozygosity, alleles per locus, exactly what I've been talking about. Did THEY "make it up?" Interesting that there's no mention here of MtDNA or microsatellites either. However, heterozygosity is the STANDARD indicator, it's how the genetic depletion of the elephant seals and the cheetahs are measured, and nucleotides are also not on the list above. Then it must agree with the normal ways of measuring genetic diversity or it's of no use anyway, and assuming it does agree I'll stick with heterozygosity and number of alleles per locus. Well, you can't have both high genetic diversity and low genetic diversity. Your reference on the elephant seals found high genetic diversity, which has to be some kind of delusion because Scientific American reported the normally understood situation of the seals as endangered due to extreme genetic depletion despite their population increase. In deference to your superior knowledge I'll take back any comments about nucleotide diversity. To be of any importance, however, it would have to agree with the standard measure of genetic diversity which is heterozygosity, and if it doesn't agree, heterozygosity IS the standard.And by the way, this is a debate forum that includes nonscientists. I've many times said if EvC wants all scientists they need to make that clear at the outset but that is always denied. So you can't rightly come along and one-up me on my level of science education as a debate tactic as you keep doing. I understand what I understand; it's holding up rather well against your sophistication too. Or there's something wrong with the study, same as with the study of the seals that found (how absurd) high genetic diversity; wrong in this case because it is highly improbable that all that immigration since the time of the Roman Empire would not have mingled the peoples. Besides, the term was "NO" gene flow, not insignificant gene flow. Well, so far you've been batting about zero in the debate. 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, but if it shows reduced genetic diversity at those loci, or even homozygosity, after all the steps I've been talking about have been completed: daughter population with new gene frequencies, reproductive isolation, some number of generations during which those frequencies are worked through and a pretty stable phenotype emerges -- the reasonable conclusion would be that this reduction in genetic diversity is genome-wide, because it's the gene frequencies themselves brought about by the reduced number of individuals, that leads to that reduction, and you aren't going to get different results of the same processes in different parts of the genome. Check a hundred or a few dozen loci that form the main characteristics of the species or breed, in as many breeds or species as possible. The pattern should hold up. Other parts of the genome code for more hidden elements in the species or breed, internal systems and organs perhaps. but it's the main characteristics that establish the breed or species as what it is, so looking at those loci should reveal the pattern in question. The thing is if I'm right the entire genome has to undergo reduced genetic diversity because it's also a product of the reduced number of individuals and the consequent new gene frequencies same as the main traits. Loci with a great number of alleles are still going to lose some of those alleles; homozygosity isn't always going to be the proof of this trend, but reduction will be. One thing is certain: there won't be a general increase in the genome, there could only be a general decrease. Because the whole genome has to be affected by the same processes, not different parts of it. The writers for Wikipedia aren't babies in their field are they? Why would they leave out a common practice for assessing genetic diversity?However, I'll provisionally take your word for it. Yes, because it certainly remains inexplicable why you would choose a site that is known for accumulating mutations but has nothing to do with the genetic issues under discussion, doesn't even code for anything related to the discussion. But also I did defend the focus on heterozygosity above. More of the genome could be checked of course, even though a laborious undertaking, than just the characteristic traits of the organism, just to see if I'm right. Well, efforts in that direction have yielded absolutely zip so far. Perhaps when you come back you'll do a better job of it. Meanwhile I KNOW heterozygosity measures the situation I'm talking about, and anything that contradicts it is suspect, to put it mildly. If you are going to try to convince me from MtDNA that the seals have increased genetic diversity I'm just going to wait for the reports of their going extinct. OK, but increasing genetic diversity is also delusional questionable. Yes, but this is some kind of joke if that diversity is increasing by useless mutations in a location that has absolutely nothing to do with the genetic problems the animal is facing, or even the benign loss of genetic diversity I keep describing as a result of population splits.OK, OK, I'll TRY to think maybe there could be a reasonable explanation for this... Oy This isn't just some bias of mine, I haven't yet seen the slightest reasonable explanation for using it. So is Scientific American out to deceive the public by telling us the seals are genetically in bad shape?I have yet to see any reason to think increasing diversity at MtDNA is anything more than accumulation of useless mutations. That's not genetic diversity. And that's a separate issue from how an increase in MtDNA could say anything at all about the losses of diversity we've been discussing all along.Recovery of population isn't recovery of genetic diversity, as that Scientific American article made clear.The genetic situation on the ark would have been enormously more diverse and variable than it is today after so many generations of population splits.Did you read that article about the Jutland cattle by the way? There is concern by conservationists about farm animals in general, including cattle, because of hundreds of years of fragmentation, meaning population splits, and a growing number of extinctions of breeds. Sure, but it's a reasonable wild guess from where I sit that there's something weirdly wrong about using MtDNA, microsatellites and nucleotides to measure genetic diversity. I've gone from total inability to understand any of it to suspicions born of a bit of knowledge. Now I'm suspecting too much trust in the ToE as the cause of such a weirdness. But yes, this is just my own ponderings, you can ignore me for now, carry on.Edited by Faith, : No reason given.

Before the Fall all living things were immortal, human beings as well as animals. After the Fall all died, but not immediately. They still had a great deal of vitality in them that allowed them to live enormously long lives by our standards. Before the Flood the environment would also have contributed to their vitality. After the Flood the world was less hospitable to life, but it is sin that kills us and we inherit the propensity to sin and that's why we all die. After the Flood people still lived long lives by our standards but over time the length of life was shortened until God decreed a limit or average around seventy years. People may live much longer even now both because of good genes and because of living good lives. Edited by Faith, : No reason given.

Certainly must have had a part in sustaining their immortal life. We'll have the Tree of Life again in the New Jerusalem. Couldn't eat from it as sinners or we'd be immortal sinners, incapable of salvation. Not a good idea. Christian doctrine is always derived from the Bible, and I think animal immortality IS based on the Bible because the phrasing is "By one man sin entered the world, and death by sin." So it didn't exist at all in the world until then. It also wouldn't make sense for anything to die if all things were made good. But I know some believe animals died, mostly believing that because it fits with evolution though. I don't believe it myself but I'm not going to argue with you about it.Edited by Faith, : No reason given.Edited by Faith, : No reason given.