Molecular Population Genetics and Diversity through Mutation

How does your notion explain this discrepancy?It's very easily explained by mutation, but let's see how you can explain it. Give it a go.

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.

It means that microsatellite sequences for one breed pair are more divergent than mtDNA sequences for that pair.So your notion explains this how? Why should they agree all the time?Edited by Genomicus, : 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.

Heterozygosity is only one way to measure genetic diversity. You do realize that, yes? There are many other ways of measuring genetic diversity. E.g., based on pairwise sequence data, SNP data, etc.So, again, how does your notion explain this discrepancy in microsatellite sequences and mtDNA sequences? You supposedly know what microsatellite sequences are.You supposedly know what mtDNA sequences are.You know all the words I am using in the above statement, so what part don't you understand?Edited by Genomicus, : 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.

She knows the words but not their meanings and she can't link it all together. This is the weirdest discussion I've ever seen.Normally when someone repeatedly admits to not understanding technical issues, they shut up, listen and learn. Once they've mastered the subject, then they can argue with intelligence. They don't usually argue the toss from near total ignorance of the subject.In the peppered moth thread she thinks that her undeducated ignorance of the subject matter is somehow more impressive than the molecular geneticist's 15 year's of work resulting in a paper published in Nature. She not even concerned that she's not read it.She's a poster child for delusion. I wish you luck, but without hope.Edited by Tangle, : No reason given.

Umm, heterozygosity would only measure complete genetic diversity if you looked at heterozygosity at the whole-genome level. Microsatellite sequences can give a complete picture of genetic diversity if you look at all microsatellite sequences in the whole genome, and mtDNA can give a good picture of matrilinear diversity.So, one more time: how does your idea explain the discrepancy in mtDNA and microsatellite sequence diversity in the paper you cited? Elephant seals and cheetah lack genetic diversity in the sense that their is a low level of sequence divergence among their various genes and other genomic regions. This is expressed in the mtDNA of modern elephant seals compared to pre-bottleneck elephant seals. Edited by Genomicus, : No reason given.

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.

Who said anything about microsatellite sequences measuring heterozygosity? Read carefully. I said whole-genome analysis of microsatellite sequences can give a good picture of genetic diversity. Remember, heterozygosity only measures one kind of genetic diversity. There are plenty of other ways to measure genetic diversity. Low Level of Sequence Divergence - Pairwise Comparison of Hemoglobin Subunit Alpha from Human and Mouse:

High Level of Sequence Divergence - Pairwise Comparison of Hemoglobin Subunit Alpha from Human and Antarctic Fish:

Asterisks represent amino acid positions which are identical. Look closely at these two different figures, and you will notice that there are more differences (= higher divergence) between hemoglobin of human and the Antarctic fish than between human hemoglobin and mouse hemoglobin (= lower divergence). That is what a low level of sequence divergence is, and that is one way of measuring genetic diversity.Of course, the above example is between species, but the same can be done for the genes/proteins of individuals in the same species. It means that pre-bottleneck elephant seals had more nucleotide diversity than post-bottleneck elephant seals.

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.

Let's try and keep this in simple terms.We have a population with four alleles, A. B. C and D. The proportion doesn't matter for the sake of our example.Part of the population is separated, for whatever reason. This subpopulation only has alleles A, B and C. Over a few generations C is lost to drift. Now it only has A and B. B has a selective advantage over A in this environment, and over time B becomes fixed and all the As die out.The original population is much bigger, and B offers no special benefit in the original environment. So now we have two populations:Population 1 has alleles A, B, C and D.
Population 2 only has allele B.This is the picture you're describing, if I understand it right. Here's the reductive processes of evolution making populations distinct from one another.Now, you claim that mutation would muddle the distinctness of these gene pools and then we would no longer have distinct species, but I cannot see why.Let's imagine mutations occur in Population 1 that introduce the new alleles E and F. Meanwhile, a mutation occurs in Population 2 that introduces allele G.Now we have:Population 1, containing A, B, C, D, E and F
Population 2, containing B and G.Did these mutations muddy the distinctions between the two populations? Clearly not. They made them more distinct.

That's pretty much utter nonsense. Genetic diversity is a lot more than just heterozygosity, and your denial of that means you're making stuff up just to suit your agenda. Yeah, and so does nucleotide diversity have to do with the health of the species. Yes, and the low nucleotide diversity also threatens the health of the species. Wut? Well, that's why you should study molecular biology and related disciplines before venturing to make speculations about the wild world of biotic reality. Anyways, why do you think heterozygosity helps the situation but nucleotide diversity somehow doesn't? Yeah, that's because there wasn't any significant gene flow. I'll cover this in more depth in my rebuttal, but you do realize that immigration does not mean automatic gene flow from the migrant population to the indigenous population, yes? You do know how gene flow actually works, right? You don't have just some vague notion of how gene flow operates that you got off of Wikipedia, correct?Edited by Genomicus, : No reason given.

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.