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Author Topic:   Evolution Requires Reduction in Genetic Diversity
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(1)
Message 935 of 1034 (759829)
06-15-2015 1:25 PM
Reply to: Message 933 by Faith
06-15-2015 11:24 AM


Re: Back to HBD's Chart
I only have a few minutes because I actually have work to do today
I'm still having problems with the "between" factor that should be dealt with before moving on.
This is why I suggested that we use "genetic differences" to discuss this chart. I realize it doesn't quite get across what you are trying to say in your argument, but it is what we are actually interested in when we study population genetics - how the genetic diversity of populations change over time.
HBD writes:
Over time the populations will become increasingly different; that is, diversity will increase.
We're talking about one mutation in one of them, right? ...
HBD writes:
Or maybe they will become more similar and so diversity will decrease.
Similar how? Again, isn't genetic diversity the number of alleles or "allelic possibilities?" Over time low-frequency alleles may drop out of a population altogether and that could cause a decrease in genetic diversity in one and therefore in the combination of the two, but I think you'd have to specify that this is happening, it can't just be assumed.
These two statements I made are general, overall observations. Imagine two populations that are identical in genetic make up. If those populations are isolated from one another they will become increasingly different in their genetic makeup. This is pretty much a biological fact. (And by this, I am not referring to micro or macro evolution. Genetic divergence can lead to micro or macro evolution, but we can discuss change without inferring those processes) Population genetics is concerned with how and why those populations become different.
This is still hard to grasp.
What if I rewrite your sentence, "The question the chart addresses is how does the factor in question affect this diversity between these populations of the two populations combined?
Imagine you have two populations that are completely homogenous (that is, every individual has the same genetic makeup). And let's say that the alleles are ordered like this:
Pop 1: A B C D E F G H I J
Pop 2: A B C D E F G H I J
Both populations are identical, there is no genetic differences between them
D1=10; D2=10;D1-2=0 (D1 is #alleles in pop 1; D2 is # alleles in pop 2; D1-2 is difference in alleles between 1 and 2)
Now let's say there is a mutation in pop 2 in gene 'D' so that it becomes allele 'd'. Now the genes look like this.
Pop 1: A B C D E F G H I J
Pop 2: A B C D d E F G H I J
D1=10; D2=11;D1-2=1
The diversity IN pop 2 has increased from 10 to 11; the difference BETWEEN pop 1 and pop 2 has increased from 0 to 1.
Yes, this is very hypothetical and yes, I realize it probably doesn't fit what you are trying to argue. I am simply trying to illustrate what this chart is saying about how these factors affect genetic diversity.
but I think you'd have to specify that this is happening, it can't just be assumed.
Right now this is rather theoretical, I realize that. However, this chart has been developed by making observations of natural and experimental populations. But before we go into the evidence for it, we should understand the principals first.
By the way I like "allelic possibilities" as a way to say what I mean by genetic diversity. But if it's confusing I'll forget about it.
It's OK. That is one way to think of genetic diversity, but not the only way. As I said, genetic diversity is kind of an abstract concept and how we measure it or think about it depends on what question(s) we are asking about the populations being studied.
I better stop here. Hope that provides some clarity.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 933 by Faith, posted 06-15-2015 11:24 AM Faith has replied

Replies to this message:
 Message 938 by Faith, posted 06-15-2015 7:50 PM herebedragons has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 936 of 1034 (759832)
06-15-2015 1:41 PM
Reply to: Message 932 by Admin
06-15-2015 8:50 AM


Re: Back to HBD's Chart
I think it might be more clear if the diversity within a population were referred to simply as diversity, while the diversity between populations were referred to as diversity difference.
I proposed such terminology, but Faith didn't like it. Not really sure why but I tried to stick with a term she is comfrotable with since I didn't feel it was that much of a issue.
HBD writes:
Mutation will only affect the loci that mutates, not other loci.
I know you're trying to keep it simple, but can't mutations cross loci boundaries?
Yes, trying to keep it simple, but I did use the plural "loci" which would indicate that it could affect more than one locus. However, the sense of "mutates" was not consistent, so that might have caused some confusion. My sentence should have read:
"Mutation will only affect the loci that mutate, not other loci."
And it might help to be clear that you only mean mutation's direct impact on nucleotide sequences, not the downstream effects, for instance, regulatory genes that turn other genes on and off.
Yes, especially to keep things simple. Understanding how mutation, selection, ect. affect genetic networks can quickly become extremely complicated.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 932 by Admin, posted 06-15-2015 8:50 AM Admin has seen this message but not replied

Replies to this message:
 Message 937 by Faith, posted 06-15-2015 7:45 PM herebedragons has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 942 of 1034 (759900)
06-15-2015 9:22 PM
Reply to: Message 937 by Faith
06-15-2015 7:45 PM


Re: Back to HBD's Chart
I thought you were equating genetic diversity with "difference" or "difference in diversity" or something like that. I can't see how they are the same.
The point is that we just cannot measure and report total genetic diversity in any kind of absolute way. We need to make comparisons between populations, so that is exactly what we consider - the differences. Genetic diversity and genetic difference are not the same exact thing, but for the purposes of this discussion we can consider differences to be an indication of diversity.
But now it seems the chart is asking for the difference between the genetic diversity in each of the two populations. Is this right?
Yes. More precisely the chart is talking about changes in genetic diversity.
That's a lot easier to understand, but it also implies needing to know what the genetic diversity of each was before the mutation or other event on the chart took place. Yes or no?
We don't need the absolute value to know what the change will be. The change in diversity is what we are concerned about.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 937 by Faith, posted 06-15-2015 7:45 PM Faith has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 943 of 1034 (759904)
06-15-2015 10:24 PM
Reply to: Message 941 by Faith
06-15-2015 8:31 PM


Re: Back to HBD's Chart: Migration
Of course
Not sure what the eyeroll is for.
Vice versa? So this is two-way migration? Affecting both populations?
When considering the effect of migration you need to consider that the effect could go both directions. In nature it doesn't have to be the case - migration could be in one direction only.
Now it sounds one-way. But the phrase "between populations A and B" continues to confuse.
I used migration in one direction only to illustrate the principle. I could have said that individuals from population A were migrating to B and individuals from B were migrating to A; but that makes the situation a bit more confusing, I think.
But OK I get that for whatever reason the emphasis is on the "differences between."
The reason is that we are trying to understand what happens to the diversity of populations when these different factors are at work - which should ultimately give us a clue as to how two populations become genetically distinct.
For example, let's say we have a subpopulation that has broken off the main population and is stranded on an island for 100 years. It has only a subset of the alleles that the original population has. This population begins to look distinctly different than the parent population.
Now, after 100 years the water that kept the island separate dries up and individuals are able to migrate back and forth from the mainland. What will happen to the island population as alleles from the mainland get introduced into that population? It will begin to look more and more like the mainland population. The difference in diversity between the populations will decrease. Right?
Why not say, just as diversity within population B is increased, diversity within population A is decreased?
It is possible that as individuals move out of a population that they take some rare alleles with them and that could eliminate those alleles in that population, but that kind of situation would be rare (drift would be more likely to eliminate rare alleles). The TREND will be that migration out of a population would not be a factor, it is bringing alleles INTO a population that does not already have them that is the chief concern. Of course, if large portions of a population move out of a population, as in the scenario you have been describing there could be enough change in alleles that it could reduce the diversity of the original population. But that would be a special case rather than the trend.
That is something to keep in mind here, that deviations from the trend are often what gives us clues as to what happened in the history of a population.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 941 by Faith, posted 06-15-2015 8:31 PM Faith has replied

Replies to this message:
 Message 964 by Faith, posted 06-17-2015 3:47 PM herebedragons has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 974 of 1034 (760235)
06-18-2015 10:47 PM
Reply to: Message 964 by Faith
06-17-2015 3:47 PM


Re: Back to HBD's Chart: Trying New Wording
Sorry, I've had a lot going in the last week. I thought things were going to slow down for me this summer, but I can't seem to catch a break
If I use my own words I think I get it better, but you can tell me:
I think you pretty much get the gist of it. I want to go back and explain a little more about drift, particularly the idea of sampling error.
SELECTION: My first take:
Selection replaces one trait with another or its allele with another, so it subtracts diversity from B = DECREASE IN DIVERSITY WITHIN B
A doesn't change so there is an INCREASE IN THE DIFFERENCE BETWEEN A and B
But it's apparently more complicated than that, as you say, which I'll copy here and come back to it later:
Most of the time this is how selection works. There are exceptions though that can reverse these trends, that is why the chart says "Increase/Decrease." But those exceptions are generally rare and the net effect is that most of the time the two populations will become increasingly different.
You asked somewhere what all this has to do with your argument, and I guess I will just say that what I hope to be able to do is to show how populations (and their diversity) are currently studied and what those studies tell us about diversity.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 964 by Faith, posted 06-17-2015 3:47 PM Faith has not replied

Replies to this message:
 Message 980 by NoNukes, posted 06-20-2015 3:05 AM herebedragons has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 975 of 1034 (760236)
06-18-2015 11:04 PM
Reply to: Message 972 by Faith
06-18-2015 6:45 AM


Re: Back to HBD's Chart: Trying New Wording
For some reason the effect on only one population is considered on the chart.
You could add another column for Population A, but it would be the same as for population B. Perhaps the assumption we could make here is that A is a larger population so the effects would not be as noticeable as they are in the smaller, population B.
It seems the only factor where it is not clear to you that A and B would be the same change in diversity is migration, it seems as if one population increases the other must decrease. But I think Percy and PaulK have cleared that up. ALL the individuals with a particular allele would have to leave a population in order to decrease the diversity of that population, whereas only ONE individual with a new allele would have to migrate into population in order to increase the diversity of that population. It should be clear what the TREND would be.
But HBD's chart has Increase/Decrease and Increase/Decrease so he's going to have to explain some more.
Some examples have already been given of how selection can increase diversity in a population. These situations are rare (but very interesting) and for the most part, selection reduces diversity within a population and increase diversity between populations.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 972 by Faith, posted 06-18-2015 6:45 AM Faith has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(1)
Message 976 of 1034 (760238)
06-18-2015 11:39 PM
Reply to: Message 969 by PaulK
06-17-2015 5:16 PM


Re: Back to HBD's Chart: Trying New Wording
As a consequence selection is positive when the allele is rare and negative when it is common. (It requires some thought but it does work out)
I think this describes frequency dependent selection, not heterozygote advantage. I have been trying to figure out how that would work, but I'm not sure what you had in mind.
For heterozygote advantage the allele frequency is dependent on the fitness of the homozygotes. If the relative fitness of both homozygotes is equal, the frequency of each allele will be 0.50. If the fitness of one homozygote is higher than the other, the allele frequency will be skewed toward the allele in the more favored homozygote.
Another point regarding heterozygote advantage is that the selection pressure against each of the homozygotes (and therefore the relative fitness) comes from different environmental factors. So in the case of sickel cell, the wild-type homozygote is only disfavored in the presence of malaria pressure, so in the absence of malaria there is no fitness disadvantage and there will be selection against the sickel cell allele. Another example is warfarin resistance in rats. Susceptible rats (SS) will be killed by warfarin but homozygote resistant (RR) are vitamin K deficient. So, heterzygotes (SR) have an advantage over either homozygotes. However, in the absence of warfarin or if a sufficient supply of vitamin K can be obtained, the advantage is negated.
Anyway, negative frequency dependent selection (when fitness increases as a genotype gets rarer) is another way, in addition to heterozygote advantage) that diversity can be maintained or even increased.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 969 by PaulK, posted 06-17-2015 5:16 PM PaulK has replied

Replies to this message:
 Message 977 by PaulK, posted 06-19-2015 3:26 AM herebedragons has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 978 of 1034 (760252)
06-19-2015 7:35 AM
Reply to: Message 977 by PaulK
06-19-2015 3:26 AM


Re: Back to HBD's Chart: Trying New Wording
Perhaps I have misunderstood the terminology, but it seems to me that heterozygote advantage must describe a case where the heterozygote has an advantage over both homozygotes, which is exactly the situation with sickle-cell in malarial regions. If that is not correct I think the term needs to be carefully explained when introduced because it is not obvious.
Sorry, you got the description of heterozygote advantage right and sickel-cell is an example. I was commenting only on the part I quoted...
PaulK writes:
As a consequence selection is positive when the allele is rare and negative when it is common. (It requires some thought but it does work out)
which doesn't fit heterozygote advantage
I have thought a little more on the matter and it does seem that in this case diversity measured by the proportion of heterozygotes would increase, although diversity measured by the number of different alleles would not.
It will push allele frequency to an equilibrium point that is dependent on the relative fitness of the homozygotes rather than Hardy-Weinberg, so it could increase allelic diversity until that equilibrium is reached.
I am sure this could be modeled mathematically but I would have to look it up (I will if anyone is interested)
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 977 by PaulK, posted 06-19-2015 3:26 AM PaulK has replied

Replies to this message:
 Message 979 by PaulK, posted 06-19-2015 11:23 AM herebedragons has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(3)
Message 983 of 1034 (760328)
06-20-2015 9:54 AM
Reply to: Message 980 by NoNukes
06-20-2015 3:05 AM


Adaptive landscapes and selection (also for Faith)
Perhaps I am looking at a wording problem that you find insignificant, but selection does not replace anything.
Yea, I struggled a little with the wording but decided not to make an issue of it at this time. I didn't think she had meant replace as in "substitutes" but rather as in "becomes more prevalent," so I just ignored it. The important thing at this time was just making the chart clear.
Selection is operates on traits already present and favors animals with trait over animals with variations not including the trait.
Right. In reality, selection acts on variation within a population and shifts the mean of that variation to a different optimum. Strong selection (especially when coupled with drift) can push a trait or an allele to fixation, but it is typically beneficial to the population to maintain some variation. Since environmental conditions and therefore selection pressures are rarely static, maintaining variation allows the population to respond to changing selection pressures. In addition, traits that are controlled by a single locus are more likely to go to fixation because of selection than polygenic (influenced by multiple genes) traits. Since the majority of traits are plolygenic, fixation of a trait is difficult.
If you are familiar with the concept of an adaptive landscape (or fitness landscape), I think they are great for helping to visualize the concept of selection. The thing that an be confusing is that it can be easy to look at them as representing spacial relationships, but they don't. These "maps" have nothing to do with how close individuals are to one another but how combinations of alleles or traits are favored by selection and how those combinations change over time.
Below is a dynamic landscape where the optimum of a trait is shifting back and forth.
The X and Y axis can be the combination of alleles or some measure of a trait. The Z axis is fitness with up being increased fitness. This could represent the peppered moths whose color morphs shift back and forth depending on environmental conditions. Notice how the variation never goes away, it just shifts to a new mean when there is a new optimum.
The adaptive landscape below shows a situation where there are multiple fitness peaks and the population evolves up only one of those peaks.
Notice a smaller population begins to climb the peak on the left but disappears? This could be due to genetic drift but gene flow is probably involved as well. As one subset of the population climbs higher up on the fitness peak, it's combination of alleles are more fit and would be "replacing" or more appropriately, displacing alleles at those lower fitness levels by interbreeding.
I wish I could stop the .gif image at a specific spot so you can see exactly the point I am talking about, but watch the image as the population splits into two groups - one on the left and one on the right. (Again, this is not a spatial representation - it can be hard to keep that in mind). Now if an individual high up on the right hand peak mates with an individual in the group on the left, a portion of the offspring will have this more fit combination of alleles and so will become part of the group on the right. In this way, the combination of alleles or traits in the group on the left is being displaced.
Theoretically, the groups could climb the different peaks and so would be differentiated (sympatric speciation), but as long as there is gene flow between those groups it is unlikely because of the situation I described above.
These adaptive landscape .gifs also visually show selection acting to reduce variation WITHIN the population. You can especially see it in the dynamic model when selection is released, the variation in the population increases until it begins moving up the adaptive peak.
HBD
--------------
Author of .gif fitness landscape maps: "Visualization of a population evolving in a dynamic fitness landscape" by Randy Olson and Bjrn ‘stman - Own work. Licensed under CC BY-SA 3.0 via Wikimedia Commons -

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 980 by NoNukes, posted 06-20-2015 3:05 AM NoNukes has seen this message but not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 985 of 1034 (760717)
06-24-2015 11:59 PM
Reply to: Message 944 by Faith
06-16-2015 8:32 AM


Re: Back to HBD's Chart: Drift
How does this show up in actuality. That is, can you recognize drift just by looking at a population, of, say, a herd animal? And what would you see?
Drift shows up as random fluctuations in allele frequency. In order to see the effects of drift, you would need to look at several generations. Since most traits are polygenic (that is, controlled by more than one gene and having a continuous distribution), it would be difficult to see changing allele frequencies over a few generations without doing genetic samples. You could easily see the effect with an annual flower in which flower color is controlled by a single gene. What you would see is a fluctuating number of colored flowers - one year there would be more blue flowers than white; the next year white would be more prevalent, ect.
I've had the general picture in mind of a subpopulation forming within a population but apparently this isn't correct?
Well, in theory a subpopulation could form within a larger parental population, but how often that actually happens is debatable. Moreover, drift would probably not be the factor involved; rather it would be selection and mutation.
The concept of "sampling error" has never made any sense to me although I've encountered it many times in reading about drift. I don't know what to picture.
The easiest way to picture sampling error is flipping a coin. A coin could land either heads or tails so there is a 50% chance that it will land on heads. If we flip it 10 times in a row we would expect that it would land on heads 5 times and tails 5 times. However, there is in fact only a 25% chance that if you flip a coin 10 times you will get 5 heads. There is actually a 21% chance that you will get either 4 or 6 heads. This would be a 10% error from the expected value. If you flip the coin 100 times, there is only an 8% chance that you will get 50 heads and only a 1% chance that you will get only 40 or 60 heads (10% error).
The effect of this sampling error on organisms is that the offspring of a generation vary in allele frequency from the expected frequencies. The effect is more pronounced in small populations than in large populations.
Below are binominal distributions for n=10, n=100 and n=1000.
Notice that as sample size increases the probability of having exactly 50% success rate (heads) decreases from ~25% (n=10) to ~8% (n=100) to ~2.5% (n=1000). Also the range of error decreases from 20% (n=10) to 10% (n=100) to 5% (n=1000).
What is another source? How much occurs at the gamete level?
Another source of drift can be when individuals are removed from a population by serendipitous events such as natural disasters. Imagine a population of birds on an island when a hurricane strikes and kills half of them. Chances are that allele frequency after the event will be different from the frequencies before. This is a type of drift, yes, and often what the common perception of drift is. However, it is not really where the majority of drift comes from.
Some gametes fail to fuse with another gamete (for example, think of how many sperm are produced in mammals with only 1 or 2 that fertilize the egg) and of those that do form zygotes, only a small proportion may survive. Think about a fish that may lay thousands of eggs but most of them are eaten when they are still fry. This "sampling" is likely to result in a different allele frequency than that of the parent population.
And yet this is normal, it's how the reproductive system works, so why is there this apparently to-be-expected "error?"
How could there not be this sampling error considering how the reproductive system works?
Here is an image of experimental populations of Tribolium (flour beetles) that shows the result of drift.
If the beetle is homozygous for the wild-type allele (b+), it is black. If it homozygous for the mutant allele (b), it is red. The heterozygotes are brown and can be easily identified.
Populations were founded with 10, 20, 50 and 100 heterozygote individuals (5, 10, 25 and 50 breeding pairs) and each generation was maintained at that population level by randomly selecting the next generation. Each population size had 12 replicate populations and 240 individuals from each generation were rated as bb, bb+ or b+b+. The frequency of the wild-type allele (b+) for each population and each generation are plotted on the chart.
Notice for the population with n=10, that 6 populations fixed the b+ allele (went to 100%) and 1 population fixed for the b allele (went to 0%). But for the n=100 no populations fix for either allele. Notice also that allele frequencies bounce around, especially in the smaller populations. Also notice the trend in increase of the wild-type allele. This appears to be due to selection or a disadvantage to the mutant allele.
I hope that helps to better explain how drift works.
Also, if you haven't already, check out Message 983 about selection.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 944 by Faith, posted 06-16-2015 8:32 AM Faith has replied

Replies to this message:
 Message 986 by Faith, posted 06-25-2015 7:42 AM herebedragons has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 987 of 1034 (760741)
06-25-2015 8:23 AM
Reply to: Message 986 by Faith
06-25-2015 7:42 AM


Re: Back to HBD's Chart: Drift
You've put up a lot of information to digest but for a while I'm not going to have the time for it.
Understandable. As you can see, I am not able to post consistently either.
most of it looks to be peripheral at best to the argument I've been pursuing.
It is peripheral in that it is background information. The argument you have been pursuing looks nothing like what we see when we study the genetic diversity of natural populations. But there is just no simple answer to your argument without explaining how we actually study diversity and what the results of those studies imply. One of the creationist claims is that we are all working with the same data, just interpreting it differently. But we are NOT working with the same data here - not at all. I am trying to explain what the data is that we work with; which tells a completely different story than the one you are arguing.
So, do we all work with the same data and just interpret it different... or are creationists happy to only consider a tiny piece of the information available and draw conclusions from just that?
The Fitness Map is just going to drive me crazy though.
Why? Because it looks like it represents spacial distribution? That's understandable. Think of it as a genetic diversity map. Each individual on the map represents a particular genotype, a particular combination of alleles or traits. The landscape is how that genotype (or phenotype) interacts with the environment. The individuals higher up on the landscape will bear more offspring than those lower on the landscape because of this interaction between genotype (phenotype) and environment.
Also remember that these models are computer simulations. They are meant to be illustrations of a concept, not representations of some specific data.
I hope to be able to discuss some ways we actually measure diversity and how we analyze and use that data. To analyze total genetic diversity of a population (that is the total number of alleles at all loci) is impractical at best and essentially impossible with our current capabilities. So understanding how we actually measure and analyze diversity is important to this discussion. This background information is important to understanding how and why we make certain predictions about diversity and the signals we are looking for when we analyze it.
Taking our time is not a problem.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 986 by Faith, posted 06-25-2015 7:42 AM Faith has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 988 of 1034 (760745)
06-25-2015 8:44 AM
Reply to: Message 979 by PaulK
06-19-2015 11:23 AM


Re: Back to HBD's Chart: Trying New Wording
For cases like sickle-cell where selection maintains a balance between alleles it must be the case. Maybe there are cases where it isn't true, and it may depend on relative finesses but I'm pretty sure that it is for sickle-cell.
I realized what the wording was that I took issue with. It was that selection was dependent on whether the allele was "rare" or "common" which isn't quite right. Here is my description of heterozygote advantage again for clarity:
HBD writes:
For heterozygote advantage the allele frequency is dependent on the fitness of the homozygotes. If the relative fitness of both homozygotes is equal, the frequency of each allele will be 0.50. If the fitness of one homozygote is higher than the other, the allele frequency will be skewed toward the allele in the more favored homozygote.
Another point regarding heterozygote advantage is that the selection pressure against each of the homozygotes (and therefore the relative fitness) comes from different environmental factors. So in the case of sickel cell, the wild-type homozygote is only disfavored in the presence of malaria pressure, so in the absence of malaria there is no fitness disadvantage and there will be selection against the sickel cell allele. Another example is warfarin resistance in rats. Susceptible rats (SS) will be killed by warfarin but homozygote resistant (RR) are vitamin K deficient. So, heterzygotes (SR) have an advantage over either homozygotes. However, in the absence of warfarin or if a sufficient supply of vitamin K can be obtained, the advantage is negated.
So in the case where the fitness of both homozygotes is equal and the equilibrium frequency is 0.50, if the frequency of one allele falls to 0.49 (the other would be 0.51), selection would work to push the frequency back to 0.50. Which I guess you could describe as "rare" or "rarer," but I don't think it accurately describes the situation.
Maybe Faith is right and I am a "pedantic nitpicker," but hey, that's what we scientists do .
But I didn't comment so much as to say you were wrong, but to give a better and more complete description of how heterozygotic advantage works and why.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 979 by PaulK, posted 06-19-2015 11:23 AM PaulK has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(1)
Message 990 of 1034 (769842)
09-25-2015 1:15 PM
Reply to: Message 986 by Faith
06-25-2015 7:42 AM


Moving discussion from Fossil thread
Message 154
HBD writes:
While major structural changes may be impossible for "tape-reader genetics," they are not so for the intricate, mega-networks of real genetics.
Faith writes:
Show me that ANY structural changes occur in normal genetics.
Essentially you have framed this request so that it cannot be answered satisfactorily. First of all, what is "normal" genetics? I am pretty sure our understandings of "normal" genetics are quite different. By "normal" genetics do you mean the kind that leads to "genetic depletion?" Cause I don't think that is normal. And I am pretty sure the kinds of things we look at genetically when trying to unravel issues like this will not seem "normal" to you. Heck, we could barely get past the basics of selection, drift, mutation and migration; how could we move into the deeper water of developmental genetics?
Secondly, I am pretty sure that what you have in mind for "structural change" is beyond the scope of what we observe in the course of "normal" genetic studies. Most of the examples we have from experimental studies are relatively minor compared to what we see in the fossil record, and I imagine to you it will be a matter of "it's still a fish; a bacterium; a plant, etc..." I fell like you are expecting the proverbial dog turning into a cat right before our very eyes; and that just doesn't happen. However, we have documented flies that have developed legs where their eyes should be, which I would say is a major structural change, but somehow I don't think that is what you have in mind either.
What the examples we do have show is how these kind of changes can arise. They show how turning on and off different switches can affect development and how those effects can lead to significant structural changes. But by all means we have not unraveled but a small, small portion of the secrets of developmental biology. There is much work to be done, but we do have enough evidence to suggest that the kind of changes we see in the fossil record are not only possible but are also probable.
I will try to post a couple examples this weekend, but I doubt you will be all that impressed.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 986 by Faith, posted 06-25-2015 7:42 AM Faith has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(2)
Message 1016 of 1034 (770097)
09-29-2015 1:01 PM
Reply to: Message 1014 by Faith
09-29-2015 11:00 AM


Re: Moderator Clarifications Provided and Requested
The mechanisms and results are the same no matter what the cause of the reproductive isolation.
Wrong. The effects of the different evolutionary forces are different and leave a different "signature" in the population.
Natural selection in operating on the phenotype reproductively isolates that phenotype from the other phenotypes in the population, thereby creating a subpopulation with its own gene frequencies, the highest frequency alleles in this case being those for those traits that are selected for.
Unless you are saying that each individual is a separate subpopulation, this makes no sense. Organisms with a favored trait can still mate with organisms without the favorable trait. There is no isolation involved.
Other traits will also be affected by the new allele frequencies due to the reproductive isolation of the individuals that possess the selected trait or traits.
There is a phenomenon that describes an effect like this, it is called linkage, but I don't think that is what you are describing or that you have in mind.
Functionally there is no difference between the effects of natural selection and those of the random selection of genetic drift and population split.
We discussed this issue in this very thread, Faith. If you want to go against what is currently known about population genetics you should present some experimental results that support your understanding. You are simply imagining a scenario that supports your conclusions.
Genetic drift for whatever reason is the random reproductive favoring of some individuals over others and their traits come to dominate the subpopulation simply randomly. The isolation is brought about simply by the random favoring of those individuals, random "selection."
Not the current understanding of genetic drift. See Message 985 for a better explanation.
Natural selection isolates the individuals it selects by selecting them, reproductively favoring them, increasing their numbers relative to the parent population. The unselected are less reproductively favored, don't proliferate, may even die out.
Not the current understanding. See Message 983 for a better explanation.
Present some research on these subjects and show how your interpretation fits the evidence better.
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 1014 by Faith, posted 09-29-2015 11:00 AM Faith has not replied

  
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