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Author Topic:   Molecular Population Genetics and Diversity through Mutation
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


(3)
Message 1 of 455 (784814)
05-23-2016 7:59 PM


Originally, as I was mulling over a new topic for EvC, I was going to offer a rebuttal to Faith’s argument that creationism can indeed work as an explanatory model for horizontal gene transfer and phylogenetic incongruences.
However, I’ve decided to instead tackle Faith’s argument in the The Science in Creationism thread that evolution always reduces genetic variability, which is the opposite of what evolution needs. This argument seems to have been floated by Faith way back in 2005 (and earlier), in the thread titled Natural Limitation to Evolutionary Processes.
I wasn’t around EvC at that time, but the argument presented by Faith seems come back again and again, most lately in The Science in Creationism thread. I believe that thread has mostly outlived its usefulness, so I will just propose a new topic. It also seems that there’s been some difficulty coming up with a viable mathematical approach to understanding the subject.
Thus, my refutation of Faith’s argument here will take a molecular population genetics approach. Most of the material discussed below is pretty standard introductory content in evolutionary biology courses, and can be found online, as well. Only high school algebra, high school probability theory, and a smattering of Mendelian genetics should be needed to grasp the basis of my argument.
I will begin by noting that genetic drift eliminates diversity in a population. Genetic drift, of course, is basically a sampling error -- there are a number of cool images on the web that can help you visualize why genetic drift, by itself, removes genetic diversity in a population.
So both genetic drift and selection eliminate diversity in a population; both of these processes weed out alleles at a given locus. As both of these processes remove genetic diversity in a population of organisms, I will focus on genetic drift. Note that my argument holds perfectly well for selection; however, the mathematics for selection are slightly more intricate, so I will go there only if necessary.
Now comes the math. Why does genetic drift weed out diversity? For starters, let G = the probability that 2 alleles (from the same locus) randomly chosen from the population are identical.
Thus, G = how much genetic variation there is in the population. If G = 1, then there is absolutely no variation at that locus; all the alleles are the same. When G = 0, every single allele (from that locus) in the population is different. Perhaps they differ by a few nucleotides here, and a few there -- but they are all different if G = 0.
So far so good. A quick side note: from now on, whenever I say 2 alleles or 2 identical alleles or the 2 alleles are different, or whatever, I mean 2 alleles of the same loci. And by locus, of course, I mean the chromosomal location of the allele under consideration, or Where in the genome you can find this allele.
Now, then, let G’ = the probability of randomly picking 2 identical alleles from the population after one generation, or one round of more-or-less random mating.
The value of G’ = 1/2N + (1-1/2N)*G.
You might think Where the actual freak did that come from?
So let me explain.
There are basically only two ways for 2 alleles picked at random to be identical. First, 2 alleles could be identical because they share an immediate ancestor -- a parent -- in the previous generation. The probability of 2 randomly picked alleles being identical because of this is 1/2N.
Here, N = the size of the mating population. But 2N is used because we are dealing with diploid organisms, so there are 2 allele copies per organism. So when you think about it -- yes, if I’m looking at one allele, and I want to randomly find an identical allele that has the same parent, then the probability of doing that successfully is 1/2N.
The other way for 2 alleles to be identical is if they do not share a parent, but if the immediate ancestors of each allele have identical alleles. So, for example, let’s say A and B are two identical alleles, with different parents. A and B can be identical if the parent allele of A is identical to the parent allele of B. Think through it and it will make sense.
So what’s the probability of 2 alleles being identical through this way? It’s (1-1/2N)*G. Why 1-1/2N?
Well, say you have 2 identical alleles. The probability that they are identical is 100%, or 1. There are two basic ways for them to be identical: they share the same immediate ancestor in the prior generation (1/2N), or they are identical because both their parents were identical. These must add up to 1, so the probability of the alleles being identical because their parent alleles were identical must be 1-1/2N. But 1-1/2N must be multiplied by G to get the actual probability of the alleles being identical because their parent alleles were identical; this is because G = the probability that 2 alleles randomly chosen from the population are identical.
G is independent from 1-1/2N, so the two are multiplied together to get the actual probability of 2 alleles (picked randomly from the population) being identical because their parent alleles were identical.
Then we add 1/2N to (1-1/2N)*G to get the value for G’, which is the probability of randomly picking 2 identical alleles from the population after one generation. This brings us to the equation above:
G’ = 1/2N + (1-1/2N)*G
Now, let’s take this equation out for a test drive.
Suppose N = 100, and the initial probability of two alleles being identical = 50%. After 1 generation, G’ = 1/200 + (1-1/200)*.5 = 50.25%. In other words, the probability that the two alleles, drawn at random from the population, will be identical has increased. We can carry this on through for several generations.
G2 = 1/200 + (1-1/200)*.5025 = 50.5%. The probability keeps increasing, inching the population towards homozygosity. After 10 generations, we’re at 52.6%. Eventually, it will reach 100% in a real population. In other words, all the alleles will be identical -- so there is no genetic diversity in the population.
But now let’s take a look at the role of mutation in this.
Mutation puts variation into a population at the rate 2Nu, where u = the mutation rate for selectively neutral alleles. Why 2Nu? Well, there are 2N gene copies per generation, and u = mutation rate, so these are multiplied together to get the overall rate at which variation enters the population.
More precisely, u = the mutation probability for a given allele. So u = the probability that an allele in a given locus of a gamete will have a mutation. When mutation rate is taken into consideration, then, we must revise the equation for G’. Remember, G’ is the probability of 2 alleles picked at random from the population will be identical after one generation; if G = 1, all alleles are the same; if G = 0, no alleles are the same.
So the new equation, taking mutation into consideration, is this:
G’ = (1-u)^2 * [1/2N + (1-1/2N)*G]
What is 1-u? The factor 1-u is the probability that a mutation did not occur in one allele. But remember these are diploid organisms (2 allele copies), so the probability that a mutation didn’t take place in either allele is (1-u)^2 -- it is multiplied by itself (the two events are independent, so a la basic probability theory, they are multiplied instead of added). Why 1-u? Well, u = the probability that a mutation does happen; u must necessarily be less than 1, so 1-u is the probability of the allele not having a mutation.
Okay, now let’s plug in some numbers. Say the mating population size is 100 and G = 50%. Let’s say the mutation rate is 10^-5 (pretty standard mutation rate for a number of diploid organisms). That means there’s a 1 in 100,000 chance that a given allele will mutate. After one generation, G’, the probability of 2 alleles being identical (picked randomly from given loci) is: 50.248995%, which is extremely close to the 50.25% reported above, where mutation was NOT taken into consideration. However, what happens when the population size is increased?
When the population size is 100,000 (instead of a mere 100), the probability of randomly picking 2 identical alleles begins decreasing. After one generation, it’s 49.99925%. Each generation, the probability inches closer to 0. In other words, because of mutation, the probability of randomly picking out 2 identical alleles increasingly becomes 0. This, in turn, means that there’s an enormous amount of genetic diversity in the population. In short, mutation has an effect that can and does counter both genetic drift and the forces of selection.
The challenge is for Faith to show that:
(1) The mathematics undergirding these processes become irrelevant in isolated founding populations, which represent a sampling of the allele frequency of the ancestor population. Clearly, if founding populations are quite small and geographically isolated, then genetic drift and selection will work to eliminate genetic diversity. Often, the result will be extinction. But if the founding population is sufficiently large, then mutation will be enough to continue adding diversity to the gene pool, generation after generation -- despite selection and genetic drift.
(2) Most mutations are too detrimental for any of this to be of real meaning in biology, or beneficial mutations too rare for positive selection to have something to work on.
(3) While mutation can overcome the reduced diversity wrought by genetic drift, selection is necessarily always strong enough that mutation cannot overcome its reductive effects.
Any questions, just ask!
Note: when I say "parent" in the above piece, I mean "parent allele," of course.
Edited by Genomicus, : No reason given.
Edited by Genomicus, : No reason given.
Edited by Genomicus, : Clearing up typos n' stuff.

Replies to this message:
 Message 4 by Faith, posted 05-24-2016 6:04 AM Genomicus has replied
 Message 11 by caffeine, posted 05-24-2016 4:56 PM Genomicus has replied
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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 17 of 455 (784856)
05-24-2016 6:41 PM
Reply to: Message 11 by caffeine
05-24-2016 4:56 PM


Re: Nitpick alert
Certain types of selection can work to maintain diversity, such as in cases of heterozygote advantage.
You are right, of course, so your nitpick is well-taken

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


(2)
Message 18 of 455 (784858)
05-24-2016 7:51 PM
Reply to: Message 4 by Faith
05-24-2016 6:04 AM


Re: But I'm just as mathematically challenged as ever
If necessary, I'll endeavor to walk you through the math. For now, though, I'll stick with word-based reasoning. Here's what I'm going to respond to:
Well, now I see that you are saying the same thing I’ve answered many times in this argument already: it doesn’t matter how much new genetic variability you can put into, or put back into, a population, when it is evolving a new population of new phenotypes, a new look, the trend is going to be to loss of genetic diversity, no matter how much new diversity may have been added. As I put it above, you can't get the phenotypic changes without removing the genetic diversity. So if you are adding genetic diversity, you are obviously not removing genetic diversity.
The processes that bring about the new phenotypes, that is, that are actively evolving the population, have to get rid of whatever genetic diversity doesn’t support the new phenotypes, and the end is going to be the same no matter how much diversity is added: a subspecies with reduced genetic diversity, and if many daughter populations succeed one another eventually the loss of genetic diversity should be quite dramatic. And if during all these evolutionary changes new genetic diversity is added, all that can do is interfere with the formation of the phenotypes that is underway. It can happen, of course, but then it isn’t evolution.
You state that the process giving rise to novel phenotypes "have to get rid of whatever genetic diversity doesn’t support the new phenotypes." I'm not sure if this is a typo on your part or a genuine misunderstanding of terminology. The only process that gives rise to new phenotypes (barring epigenetic mechanisms) is mutation; natural selection and genetic drift only determines the distribution of that new phenotype in the population.
That being said, your argument is fatally flawed, and here's why.
It is indeed true that while a new trait is increasing in frequency throughout the population, there is a loss in heterozygosity among the relevant alleles (that is, the alleles which encode the specific proteins that constitute the novel trait on a molecular level). There are some exceptions, as caffeine noted, but these aren't relevant here and the exceptions would further refute your argument anyway.
So, from that perspective, you're right: as a new trait is evolving, there is a decay in heterozygosity among the relevant alleles. However, what you apparently fail to take into consideration is the entire diversity of the population's gene pool. In other words, while one set of alleles might become increasingly homozygous in the population by virtue of so-called "active evolution" of a trait, there are literally thousands of other chromosomal loci which are witnessing an increase in allelic heterozygosity (that is, an increase in diversity). What you have failed to demonstrate is that while a given trait is evolving, ALL alleles must necessarily tend towards homozygosity (even if these alleles have little to do with the trait under consideration).
The experimental facts of life, however, demonstrate that as one beneficial phenotype gains in frequency in the population, plenty of other selectively neutral phenotypes will emerge in the population -- phenotypes which are not related to the function of the beneficial phenotype. And these selectively neutral phenotypes, too, will -- fueled by mutation -- spread through the population according to the statistics of population genetics. These phenotypes, then, provide the "raw genetic material" -- or the genetic diversity -- for further evolution to continue. In short, while one particular beneficial trait will gain in frequency at the expense of other alleles, selection will only "weed out" the alleles which are selectively relevant to the function of the beneficial trait.
Edited by Genomicus, : No reason given.

This message is a reply to:
 Message 4 by Faith, posted 05-24-2016 6:04 AM Faith has replied

Replies to this message:
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 Message 27 by Faith, posted 05-25-2016 12:18 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 22 of 455 (784871)
05-24-2016 10:05 PM
Reply to: Message 20 by NoNukes
05-24-2016 9:22 PM


Re: But I'm just as mathematically challenged as ever
Hey NoNukes,
The only process that gives rise to new phenotypes (barring epigenetic mechanisms) is mutation
That's probably not a correct statement.
Phenotype - Wikipedia
I believe you will find my original statement correct in the light of this explanation:
1. While I have a disdain for quoting from Wikipedia, here's Wikipedia's definition of phenotype:
"A phenotype (from Greek phainein, meaning "to show", and typos, meaning "type") is the composite of an organism's observable characteristics or traits, such as its morphology, development, biochemical or physiological properties, phenology, behavior, and products of behavior (such as a bird's nest)."
So what kind of processes can give rise to new phenotypes? Well, as I stated, barring epigenetic mechanisms, only mutations can result in new phenotypes. In the Wikipedia quote you cited, it is stated that phenotype results from genes and the influence of environmental factors. If a new phenotype is to arise, then (a) it is the result of changes in genes (mutation), or (b) the result of environmental factors (or a combination of the two). If it is the result of environmental factors -- e.g., diet affecting DNA methylation patterns -- then these are epigenetic mechanisms.
Having said that, I should also add that new phenotypes can arise through novel allele combinations in a diploid organism, so this wouldn't technically be a mutation. But it's not like genetic drift or selection produces new phenotypes; these only impact the distribution of phenotypes in the population.

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 38 of 455 (784923)
05-26-2016 12:22 AM
Reply to: Message 27 by Faith
05-25-2016 12:18 AM


Re: But I'm just as mathematically challenged as ever
However, what you apparently fail to take into consideration is the entire diversity of the population's gene pool. In other words, while one set of alleles might become increasingly homozygous in the population by virtue of so-called "active evolution" of a trait, there are literally thousands of other chromosomal loci which are witnessing an increase in allelic heterozygosity (that is, an increase in diversity). What you have failed to demonstrate is that while a given trait is evolving, ALL alleles must necessarily tend towards homozygosity (even if these alleles have little to do with the trait under consideration).
Well, no, I haven't failed to take into account that there are plenty of other genes that are being affected at the same time although it’s true I don’t spend time focusing on them. You stymied me for a while with your statement that an increase in allelic heterozygosity is an increase in diversity. It took a while for me to see that you made a mistake there: you are confusing gene frequency with genetic diversity. The former is just an increase in the quantity of an allele, the latter would be an increase in kinds of alleles, which isn’t going to happen in a reproductively isolated population, except by mutations of course.
No, an increase in allelic heterozygosity is an increase in genetic diversity. Heterozygosity at a locus under consideration is a pretty standard way to measure genetic diversity in a population. See here (warning: it's a PDF; it's a "primer" on population genetics which you might find easier to understand than standard pop gen textbooks).
If a given locus exhibits a high degree of heterozygosity within a population, it means that there's whole range of different, diverse allelic combinations at that locus. Ipso facto, there's an increase in genetic diversity when there's an increase in heterozygosity (and here, when I say "increase," I do not mean an increase in frequency of a particular allelic combination; I mean an increase in diverse allelic combinations throughout the population).
What you have failed to demonstrate is that while a given trait is evolving, ALL alleles must necessarily tend towards homozygosity (even if these alleles have little to do with the trait under consideration).
Not sure what you are saying. Do you mean my argument requires ALL alleles to tend towards homozygosity or do you mean that this is to be expected in reality?
Your argument appears to require that the allelic sites become increasingly homozygous. For if allelic sites, or chromosomal loci, do not become increasingly homozygous while a novel trait is evolving, then the population has plenty of genetic diversity -- even if novel traits are evolving. And if the population has this genetic diversity, your argument falls apart.
But to the general point, the whole genome should have new gene frequencies as a result of the population split, except for any that are always fixed, which you would know more about than I do, and just like the ones that are making the major changes in the look of the population by working through the population from generation to generation, all the alleles throughout the genome should have undergone the same changes: some higher frequency than they were in the original population, some lower, including many also not changed or much changed in frequency. Most of them probably wouldn’t affect the phenotype, but there should be some differences that do contribute to the change in appearance of the new population in relation to the original population.
So what's the problem here? You're basically just saying that there's going to be a change in allele frequency when the population splits, but that's not any kind of "limit" to continued evolution of the species.
In any case the decrease I have in mind is specifically due to the high frequency traits that will dominate the appearance of the new population.
As a novel, beneficial trait gains in frequency throughout the population, than the alternative allelic combinations for that trait will decrease in frequency. That is correct, yes, but the problem here is what exactly?
But as to mutations: in every discussion I've ever read, mutations are treated as sort of an article of faith, their actuality not being demonstrated...
Umm, we know mutations actually happen. Do you deny that mutations occur?
...or the mere presence of a newly expressed phenotype gets it called a mutation without warrant.
Umm, maybe among lay people, but if you actually read the scientific literature and biology papers, we don't assume any new phenotype is the result of a mutation. New phenotypes can arise through epigenetic mechanisms, so usually molecular genetic techniques are employed to determine the actual cause of a new phenotype in a population. It's very, very often mutation, by the way -- and this can be verified with nucleotide sequence data.
It’s science that describes them as so predominantly either deleterious or neutral and so extremely rarely of any value to the organism, but the obvious conclusion isn’t drawn from those facts.
Most mutations in Metazoan genomes are selectively neutral; this is the present consensus among geneticists, evolutionary biologists, and others in the field given the preponderance of evidence which points to that conclusion.
And as I suspected, your argument does really end up boiling down to the notion that beneficial mutations are too rare to fuel Metazoan evolution.
Not only is a beneficial mutation rare, it’s even rarer in the sex cells where it might have an impact on offspring...
Actually, beneficial mutations happen all the time. While the ratio of beneficial mutations to selectively neutral ones may make it seem like beneficial mutations are rare, this is no way means that beneficial mutations are so rare as to not be a driver of the emergence of novel morphological, physiological, or biochemical systems. You have yet to demonstrate otherwise.
...and the time frame required can be so enormous — as I keep noting, the cheetah has been waiting around forever for a mutation to get it out of its genetic purgatory...
Wut? A single mutation won't add significant genetic diversity to the cheetah population. What's needed is an elevated rate of mutation in the cheetah population if they are ever to get out of their "genetic purgatory." The equations in the OP demonstrate very nicely why there's extremely low genetic diversity among cheetahs; the small population size, coupled with a not-very-high mutation rate, means that genetic drift and inbreeding (which is basically just an extension of the sampling error that genetic drift is) will continue to decrease the diversity of the cheetah gene pool. So I have no idea where this "waiting around for a mutation to get them out of their 'genetic purgatory'" comes from, since it's not like a single mutation will do that.
that I didn't make up, that most are by far deleterious or neutral and anything at all beneficial is rare to the point of vanishing, means to me that mutations contribute nothing to the evolution of new varieties.
See above. Beneficial mutations aren't so incredibly rare that they are unable to contribute to the evolution of new species and higher taxa. This is something that you have made up without any empirical basis.

This message is a reply to:
 Message 27 by Faith, posted 05-25-2016 12:18 AM Faith has replied

Replies to this message:
 Message 39 by Faith, posted 05-26-2016 3:03 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 74 of 455 (785113)
05-28-2016 2:01 AM
Reply to: Message 39 by Faith
05-26-2016 3:03 AM


Re: But I'm just as mathematically challenged as ever
See Message 3 of the Great Debate thread.
Edited by Genomicus, : No reason given.

This message is a reply to:
 Message 39 by Faith, posted 05-26-2016 3:03 AM Faith has not replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 163 of 455 (785498)
06-06-2016 8:32 AM
Reply to: Message 162 by Faith
06-06-2016 7:37 AM


Re: Mt DNA vs microsatellites vs chromosomal DNA as measures of genetic diversity
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.
Have been busy with non-EvC stuff, but I'm presently working on an excoriation of your last posts in the Great Debate thread, and wanted to respond to this bit here. You do realize that microsatellite sequences consists of chromosomal DNA, right? This is pretty basic stuff, so c'mon, you shoulda known that.
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?
Umm, what good is answering a question that doesn't have a reliable way to see what point you're referring to that you don't remember? Do the work and look it up and present the actual, relevant data.
Edited by Genomicus, : No reason given.

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 166 of 455 (785503)
06-06-2016 9:18 AM
Reply to: Message 165 by Faith
06-06-2016 9:08 AM


Re: Mt DNA vs microsatellites vs chromosomal DNA as measures of genetic diversity
Here's the point you wanted me to look up, found on page 79 of the journal...
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.

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 Message 165 by Faith, posted 06-06-2016 9:08 AM Faith has replied

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 Message 167 by Faith, posted 06-06-2016 9:30 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 168 of 455 (785506)
06-06-2016 9:41 AM
Reply to: Message 167 by Faith
06-06-2016 9:30 AM


Re: Mt DNA vs microsatellites vs chromosomal DNA as measures of genetic diversity
I'm not even totally sure what it means. Phenotypically different?
It means that microsatellite sequences for one breed pair are more divergent than mtDNA sequences for that pair.
So your notion explains this how?
But what interests me is why MtDNA and microsatellite data disagree.
Why should they agree all the time?
Edited by Genomicus, : No reason given.

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 Message 167 by Faith, posted 06-06-2016 9:30 AM Faith has replied

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 Message 169 by Faith, posted 06-06-2016 9:45 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 170 of 455 (785510)
06-06-2016 10:15 AM
Reply to: Message 169 by Faith
06-06-2016 9:45 AM


Re: Mt DNA vs microsatellites vs chromosomal DNA as measures of genetic diversity
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.
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?
I have NO idea what this means:
It means that microsatellite sequences for one breed pair are more divergent than mtDNA sequences for that pair.
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.

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 Message 169 by Faith, posted 06-06-2016 9:45 AM Faith has replied

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 173 of 455 (785513)
06-06-2016 10:45 AM
Reply to: Message 171 by Faith
06-06-2016 10:35 AM


Re: Mt DNA vs microsatellites vs chromosomal DNA as measures of genetic diversity
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?
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?
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)?
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.

This message is a reply to:
 Message 171 by Faith, posted 06-06-2016 10:35 AM Faith has replied

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 Message 174 by Faith, posted 06-06-2016 10:56 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 176 of 455 (785516)
06-06-2016 11:19 AM
Reply to: Message 174 by Faith
06-06-2016 10:56 AM


Re: Mt DNA vs microsatellites vs chromosomal DNA as measures of genetic diversity
I have NO idea what this means. How can completely unrelated short sequences of DNA say anything about the overall heterozygosity of the genome?
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.
What does "a low level of sequence divergence among their various genes and other genomic regions" mean?
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.
I have NO idea what this means.
It means that pre-bottleneck elephant seals had more nucleotide diversity than post-bottleneck elephant seals.

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 Message 174 by Faith, posted 06-06-2016 10:56 AM Faith has replied

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 179 of 455 (785536)
06-06-2016 2:28 PM
Reply to: Message 177 by Faith
06-06-2016 1:08 PM


Re: Mt DNA vs microsatellites vs chromosomal DNA as measures of genetic diversity
I've never been talking about any kind of diversity except GENETIC diversity and that's about heterozygosity...
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.
...which I've understood to have to do with the health of a species...
Yeah, and so does nucleotide diversity have to do with the health of the species.
...so that the elephant seal's being so low on THAT kind of diversity is what threatens it...
Yes, and the low nucleotide diversity also threatens the health of the species.
Your measurement found high genetic diversity which is some kind of delusion.
Wut?
Nucleotide diversity wouldn't help that problem as far as I can see...
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?
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.
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.

This message is a reply to:
 Message 177 by Faith, posted 06-06-2016 1:08 PM Faith has replied

Replies to this message:
 Message 180 by Faith, posted 06-07-2016 3:07 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 181 of 455 (785560)
06-07-2016 7:12 AM
Reply to: Message 180 by Faith
06-07-2016 3:07 AM


Re: Mt DNA and microsatellites as measures of genetic diversity
I know you don't like Wikipedia but here it comes...
Wikipedia isn't exactly a scholarly source. Anyway, here's Clark et al. who use single-nucleotide polymorphisms (= nucleotide diversity) as a measure of genetic diversity. Please don't cite Wikipedia when it comes to definitional terms as there is a robust scientific literature on the different ways of measuring genetic diversity.

This message is a reply to:
 Message 180 by Faith, posted 06-07-2016 3:07 AM Faith has not replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 190 of 455 (785600)
06-07-2016 5:02 PM
Reply to: Message 189 by Faith
06-07-2016 4:38 PM


Re: Mt DNA and microsatellites as measures of genetic diversity
Just FYI, "polymorphic loci" also often refers to the nucleotide sequence variation among the alleles at a locus. Highly polymorphic loci have highly variable nucleotide sequences. This meaning of "polymorphic loci" goes way back to the dawn of the genomics revolution; see, e.g., this 1975 paper.

This message is a reply to:
 Message 189 by Faith, posted 06-07-2016 4:38 PM Faith has replied

Replies to this message:
 Message 191 by Faith, posted 06-07-2016 7:11 PM Genomicus has not replied

  
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