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Author Topic:   WTF is wrong with people
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 347 of 457 (708531)
10-10-2013 7:28 PM
Reply to: Message 345 by AZPaul3
10-10-2013 7:10 PM


Re: Environment-driven evolution
Then you misunderstand what everyone has been trying to tell you for years now. Yes, allele frequency is an agent of change. The different forms of selection are agents of change since they change allele frequency. Mutation of DNA into new alleles is an agent of change since they change allele frequency . Drift is an agent of change since they change allele frequency. .....
In the end, yes, evolution is the change in allele frequency in a population. But there are different mechanisms that cause this frequency change including new alleles.
For cryin out loud I've been saying all this all along!!!!! And I JUST GOT THROUGH SAYING IT AGAIN ABOUT NATURAL SELECTION!!! What I'm adding, or emphasizing, is just that ALL these things bring about POPULATION SPLITS, which is THE FUNDAMENTAL DEFINITIVE way allele frequencies get changed. YES, THROUGH ALL THOSE DIFFERENT MECHANISMS.
Sheesh.

This message is a reply to:
 Message 345 by AZPaul3, posted 10-10-2013 7:10 PM AZPaul3 has replied

Replies to this message:
 Message 348 by Tangle, posted 10-10-2013 7:36 PM Faith has not replied
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 350 of 457 (708537)
10-10-2013 8:49 PM
Reply to: Message 349 by AZPaul3
10-10-2013 7:57 PM


Re: Environment-driven evolution
No, Faith. These mechanisms of change operate quite readily in an unsplit population.
No, YOU are wrong. All but mutations bring about population splits. Anything that acts as a selector and isolator is a population splitter. All those mechanisms act in that way, only mutations don't. Some population splits can occur WITHIN a larger population TOO, as I've also said a number of times. I believe Drift can be described that way. Whenever a particular allele or set of alleles occurs in higher frequency that does not spread through the entire larger population, THAT's the equivalent of a population split, creating its own reproductively isolated subpopulation within the larger. Natural Selection may also operate that way or it may actually just eliminate nonadaptive alleles and create a brand new population. Migration creates a completely separate population as I've understood the term, a new population that's migrated away from the mother population..
These add genetic diversity to the population.
Far from it. All you are getting is new gene/allele frequencies, and this is due to the fact that you have fewer numbers in both new populations than you did in the original population, and when you have fewer numbers you are not adding genetic diversity, you merely have new allele frequencies to combine in new ways. And Drift may eliminate any low frequency alleles altogether, and so will a subpopulation that is a great deal smaller than the original, and then you definitely have reduced genetic diversity.
Genetic diversity will not split a population.
Of course not, but it will be reduced in any new small population that splits off from it.
Only reproductive isolation causes a population split.
I've been using the terms more or less synonymously myself all along, although some population splits do not bring about complete reproductive isolation. Nevertheless they are roughly equivalent and the result is new allele frequencies and therefore new phenotypes, and very often ALSO a reduction in genetic diversity.
At that point the same old mechanisms of allele frequency change continue more or less just as always. If the initial number of the smaller split population is low then we get the cheetah situation with a higher probability of extinction of that sub-population since new diversity is also low to nonexistent.
Which is also what I've been saying all along. Where have YOU been?
If the sub-population is not too small then genetic diversity will increase with each new generation. That is what sex and mutation do for a species assuming selection allows the changes.
Sex only shuffles alleles, it does not increase genetic diversity. Mutation is the only thing that could possibly increase genetic diversity, assuming reproductive isolation, that is, where there is no gene flow with other populations.
And as I've argued, all this happens a lot faster than the ToE supposed. I think the lizard video time frame of just a few decades is probably quite typical, the long time frames are pure unevidenced theory. And with such short time frames you are not going to get enough mutation to increase diversity by much, AND even if you did, IF you then also get Selection, or Migration or anything else that further splits the population and creates a new variety, then you're back on the track to reduced genetic diversity and the end of evolution for that line of variation no matter how many mutations you have.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 349 by AZPaul3, posted 10-10-2013 7:57 PM AZPaul3 has replied

Replies to this message:
 Message 351 by AZPaul3, posted 10-10-2013 10:21 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 364 of 457 (708620)
10-11-2013 12:55 PM
Reply to: Message 346 by AZPaul3
10-10-2013 7:27 PM


Re: Environment-driven evolution
At about 2,100,000,000 mutations entering the human genome every year, that would take a whole lot of swallowing.
The entire human genome with its 2 billion mutations per year is not what loses genetic diversity. It's any particular line of subpopulations or variations that is continuing to evolve by splitting off new subpopulations. Human beings have enough genetic diversity so that any group can reproduce with any other despite great differences, but many animals don't have that much genetic diversity in any particular variety or "species" etc.
My claim has been that evolution comes to an end down a PARTICULAR LINE of variation as it continues to split into subpopulations, and ring species are probably the best example of what I'm talking about. If the last "species" in the ring can't breed with the first or other earlier populations, my guess would be the reason is the reduction in genetic diversity in the last one. Somebody wanted me to allow for other ways breeding can come to a stop, but in this kind of example the evolved genetic mismatch seems to me to be the most likely reason.
" Once Natural Selection or any other 'mechanism of change' that brings about a new subpopulation kicks in then you have the trend to reduced genetic diversity"
is just pure bullshit as you have been shown many times.
Natural Selection *selects,* that is, it creates a new subpopulation of those best adapted in a particular situation. The new subpopulation is very likely to be appreciably smaller at its founding than the original just because how many adaptive alleles or other genetic influences are you going to find in any population with respect to a particular environmental challenge? Not all NS has this drastic an effect so this can be taken as the most extreme example of how it works.
Different reasons aside, domestic breeding is the best comparison because it also selects and creates new smaller subpopulations to bring out the selected traits.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 346 by AZPaul3, posted 10-10-2013 7:27 PM AZPaul3 has replied

Replies to this message:
 Message 370 by AZPaul3, posted 10-11-2013 3:07 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 365 of 457 (708624)
10-11-2013 1:17 PM
Reply to: Message 363 by PaulK
10-11-2013 12:38 PM


Re: Environment-driven evolution
As I've been saying to Faith it mainly comes down to rates. Adaptive evolution is the combination of two processes, one generating variations, the other culling them.
I think you mean "generating genetic variability or diversity," not "variations," since it is the selective and isolating processes that generate new varieties or races or "species" etc. There is only one process that could possibly generate new genetic diversity and that is mutation, which as everybody agrees doesn't generate much in the short term. All the other processes split populations, which may not reduce genetic diversity right away if the populations are both large enough to contain the range of alleles in the original, (though it will change allele frequencies since you aren't going to get the exact same proportions of alleles in a random population split). Depends on the numbers in each and the original genetic diversity level as well.
Artificial selection drastically emphasises the culling, and in the short term it will deplete the variation needed fuel the process, because of the greatly accelerated rate of of selection.
Thank you. Now you need to admit that this happens at least in SOME situations in the wild. For the rest I realize I'll have to make the case better that it also occurs wherever you are getting new varieties since that's the main point of contention. Meanwhile, the artificial selection situation as you've described it IS my model for what happens overall, though of course it's far more drastic than the usual situation in the wild.
As a result any attempt to use the breeding process as a guide to evolution will get a very one-sided picture.
But it nevertheless provides the principle I have in mind, which I'm arguing operates wherever new varieties are being developed at a much slower and less conspicuous rate. (But slower in decades, not millennia or millions of years, and culling is still going to overwhelm the mutations at that rate).
(And, I will note, when even the limited role that mutations have played in actual breeding is denied or minimised the picture is even more one-sided and inaccurate.)
Why, when all that happens to those mutations is that they become part of the breed or not, and the breed is still characterized by very small genetic diversity? If mutations DO add alleles or anything that gets passed on, then they get treated exactly as alleles get treated when selection and isolation create small subpopulations by culling individuals from it. You've got your new trait (supposedly) but it's locked into a population of less genetic diversity.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 363 by PaulK, posted 10-11-2013 12:38 PM PaulK has replied

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 367 of 457 (708629)
10-11-2013 1:33 PM
Reply to: Message 354 by Percy
10-11-2013 7:39 AM


Re: Environment-driven evolution
That wasn't what Tangle was calling daft. What's daft is your idea that merely isolating a subpopulation will produce changes in allele frequencies sufficient for producing phenotypic change. As has been pointed out to you, if this were the case then we would see it happening in both captive and natural subpopulations over and over and over again, but we do not.
We DO see it in natural subpopulations: ring species. And anywhere else you have many "species" of a Species.
In captive populations you don't have a reproductively isolated population that you can inbreed over enough generations over enough time to see the effect. They may be introducing new mates to avoid the problems of breeding close relatives, but then not insuring that the mates become part of a reproductively isolated group that can be inbred over generations. Also you may have founders that are already genetically reduced to the point that you aren't going to see much variation anyway.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 368 of 457 (708636)
10-11-2013 1:43 PM
Reply to: Message 351 by AZPaul3
10-10-2013 10:21 PM


Re: Environment-driven evolution
All those mechanisms act in that way, only mutations don't. Some population splits can occur WITHIN a larger population TOO, as I've also said a number of times. I believe Drift can be described that way. Whenever a particular allele or set of alleles occurs in higher frequency that does not spread through the entire larger population, THAT's the equivalent of a population split, creating its own reproductively isolated subpopulation within the larger.
Oh, my lady, how can you get so much wrong in such a short amount of space.
Yes, in massive populations over an extended range the population in the eastern quarter may have an allele frequency quite different than the population in the western quarter. We already know this. Over time the eastern and western populations may diverge to the point of separate identities. But this was not caused because of some intrinsic feature of allele frequency but because of the reproductive isolation of the two populations over a large geographic region.
Seems to me where you are going to see this effect soonest and most dramatically is in the smaller subpopulations not the larger. When there is a population split, both populations are going to have different allele frequencies just because the alleles that belong to each are randomly "selected" out of the original pool in the split. You MUST get different allele frequencies. But it's going to take generations of inbreeding for their effect on the overall population to show up, and the greater the original numbers the more generations it will take.
In a small subpopulation, however, such as the ten lizards that were isolated from the main population of lizards in the Dawkins video, the effect should be obvious in a shorter time period, such as the decades recognized in that case. Certainly the proportions of alleles in the new population must be greatly different from those in the mother population, and in fact it's very probable that some alleles in the original population didn't make it at all into the new population. That would depend on how much genetic diversity was originally present, but let's assume it was fairly high.
I want to get to the rest of your post as well as others here, but I can't do it right now.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 371 of 457 (708646)
10-11-2013 3:30 PM
Reply to: Message 370 by AZPaul3
10-11-2013 3:07 PM


Re: Environment-driven evolution
Your guess would be in error. The "last" link in a ring species cannot/will not breed with the first because of the built-up genetic differences that now exist between the two. Each species has now a separate history of increased genetic diversity to the point where the two have far fewer alleles in common.
I also expect them to have far fewer alleles in common but this is most likely because of the LOSS of genetic diversity that has attended the development of each new population around the ring. You are guessing based on the ToE and not because you KNOW the situation is as you say, and I am guessing too. We are arguing two different models or theories.
The only way this could be decided is by actually examining the DNA of the various populations. I'd expect greater homozygosity for the most characteristic traits the farther you go around the ring.
Both may have the same number of, say, tail-plumage alleles, but each species may have a set of unique such alleles not carried in the other.
I would expect them to have fewer such alleles AND unique alleles for the distinctive plumage showing up from population to population and the farther you go around the ring, as I expect there to be a loss of alleles from population to population around the ring, the distinctive plumage of each being based on the alleles that are left, or are the most high frequency in each population. They are only unique with respect to their being the basis for the particular plumage in a particular population.
The situation is not so much that a breeding would not be successful but that sexual selection would preclude any such attempt.
This is a possibility in the abstract but if the situation is as I've described it then the genetic mismatch is the more likely explanation, or at least AS likely.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 370 by AZPaul3, posted 10-11-2013 3:07 PM AZPaul3 has replied

Replies to this message:
 Message 373 by AZPaul3, posted 10-11-2013 4:50 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 372 of 457 (708650)
10-11-2013 4:24 PM
Reply to: Message 370 by AZPaul3
10-11-2013 3:07 PM


Re: Environment-driven evolution
Sorry, Faith, but this is not the way NS operates. You are assuming that these fitter individuals are separated from the rest of the population they are embedded within and thus could only reproduce within this group. The way NS works is the fitter individuals create just a few more, or in extreme cases many more, offspring than the less fit members mating within the same population of available mates. This increases the number of "fitter" genomes, sets of more effective alleles, available to the population. This is the change in allele frequency we have all been talking about. Over a period of generations those "fitter" genomes with the more effective alleles may become the standard average for the population. NS has "selected" for these fitter alleles. Evolution of the population has occurred.
And it has occurred BY creating that subpopulation I was talking about. In your scenario its formation takes more time but in the end what you have is a NEW population, and yes new allele frequencies. Selection can happen faster too of course, if the selection pressure is severe. In both cases yes you have (micro)evolution, you have new allele frequencies, the unadaptive ones becoming less frequent, even dying out altogether eventually, while the adaptive ones become more frequent. And if the adaptive alleles are a much smaller number than the unadaptive ones, as I suggested will be the case, which makes sense, eventually you will have fewer alleles for the selected trait(s) than you had before (although more members of the population will possess them) as the adaptive ones will eventually replace them all, first outnumbering them and then replacing them. And that amounts to a great loss of genetic diversity over the generations it takes to fully actualize the new adapted phenotypes.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 370 by AZPaul3, posted 10-11-2013 3:07 PM AZPaul3 has replied

Replies to this message:
 Message 374 by AZPaul3, posted 10-11-2013 5:01 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 375 of 457 (708657)
10-11-2013 6:12 PM
Reply to: Message 373 by AZPaul3
10-11-2013 4:50 PM


Re: Environment-driven evolution
The only way this could be decided is by actually examining the DNA of the various populations.
I would have thought you would look this up already. It's been done. Many times. After all, a ring species scenario with its ecological divergence shows us the processes of evolution that happen in deep time without having to wait. They have been studied in great detail.
There is no point in referring me to a technical paper full of terminological mystifications. Besides which, your assumption that ring species diverge ecologically is highly questionable in my mind, certainly for some situations where there simply is no environmental divergence from population to population. Then of course your assumption that such species show "the processes of evolution that happen in deep time" is tendentious, question-begging and rife with confirmation bias. Of course if the paper were readable I'd read it and show where these errors occur in the paper itself, but I'm not sure it's readable enough for me for that purpose. I've skimmed it, saved it, and hope to check again later to see if I can answer some of it.
This one is from the perspective of finding what indicators would appear to predict reproductive isolation. Their subjects were the various populations around a ring species. Their conclusion is that genetic divergence was a stronger predictor of reproductive isolation than ecological divergence. (Gee, really?)
So far we are in agreement.
In their analysis of genetic data they looked at both nuclear DNA and mitochondrial DNA. Genetic divergence from the parent population became greater the further around the ring.
Which is exactly what I too would expect, as I've said.
Guess what? The genetic divergence seen was due to:
"new sequences nested within the clades already described for the whole species complex."
Which means new mutations of alleles that existed in the whole population, not a "loss" of alleles between the populations around the ring.
But "new sequences" in the different populations is what I would also expect, demonstrating the new high frequency alleles in the population as compared with those of the previous population. "nested within the clades" is just jargon to me so I can't make use of the concept, and "new sequences" does not suggest mutations to me, though I'm sure it does to someone with evolutionist confirmation bias.
Perhaps I'll see it differently when I try to read the paper again.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 376 of 457 (708658)
10-11-2013 6:14 PM
Reply to: Message 374 by AZPaul3
10-11-2013 5:01 PM


Re: Environment-driven evolution
No, Faith, an individual with a reproductive advantage does not constitute a "subpopulation" of the species any more than a woman with stronger leg muscles than the average constitutes a "subpopulation" of the human species.
No, Arizona Paul, I'm not talking about an individual, I'm talking about the proliferation of the adaptive alleles throughout the population in many individuals, which gradually displace all the nonadaptive alleles BECAUSE of their reproductive advantage. This constitutes a subpopulation within the original population that might even grow from generation to generation until it completely displaces the original.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 383 of 457 (708707)
10-12-2013 2:25 PM
Reply to: Message 382 by NoNukes
10-12-2013 11:56 AM


Selection does lead to reduced genetic diversity
Breeding might well lead to a loss of diversity while natural selection does not require any such thing.
I've been trying to argue why it does and must require a loss of diversity -- meaning GENETIC DIVERSITY -- In the long run at least.
Also why I've been arguing that it is merely one of the ways that lead to evolution (meaning of course microevolution) BY CHANGING ALLELE FREQUENCIES, including migration, bottleneck, founder effect, probably Drift too, and how all these share with domestic breeding the basic fact of increasing the frequency of some alleles and reducing or eliminating others, and that despite their differences it all amounts to the same thing in the end as far as getting new varieties and reducing genetic diversity goes. Allele frequencies change randomly in some of these processes, but due to particular selection in NS and domestic breeding, but the allele frequencies alone are enough to make big changes and bring about a new variety whatever the cause.
Natural selection to one degree or another eliminates alleles that are not adaptive according to what is being selected for. It doesn't matter if a breeder is doing the selecting or the environment is, whether the gazelle is selected for speed or sensory advantage and so on, WHATEVER is being selected is going to spread through the population down the generations, displacing the genetic substrate for the less adaptive traits, the slower gazelle, the less acutely sensitive gazelle. This in a sense forms a subpopulation of those better adapted, even within the original population, while those less adapted with their reproductive disadvantage become less numerous and their alleles lower frequency in the overall population. The preponderance of a particular type of allele among the reproductively advantaged forms a subpopulation that is less genetically diverse than the former population because it has ONLY those alleles that promote the adaptive trait or traits.
ALSO, there is likely to be an inadvertent effect on other genes as well, changing THEIR frequencies, just because only certain individuals are being favored with whatever their alleles happen to be for whatever traits they happen to be for. (This is very much the same situation as in a migration where alleles for all kinds of traits change frequencies, only there is a different REASON for it and it occurs within the original population instead of outside it.)
Finally if the adaptation is crucially important to the creature ALL the nonadapted individuals will have no offspring or even die out before reproductive age and all you will have left is a population of the adapted with their high frequency alleles for the adaptive traits and LOSS of the alleles for the nonadaptive traits along with the loss of alleles for whatever other traits happen to become low frequency inadvertently. If merely an advantage is conferred but it's not dire you will still have the adaptive alleles proliferating and forming this subpopulation over the generations, and that subpopulation MUST have reduced genetic diversity as compared with the mother population because its alleles for the adaptive traits are very high frequency over those for nonadaptive traits.
And in the case of Natural Selection it ought to be easy to see why all those who keep wanting to increase the inevitable reduction in genetic diversity by insisting that mutations will come in and increase it, as if that were a good thing, are really promoting a bad thing, and what I've meant about how mutations that alter the new adaptive picture only "blur" it and lose the new variety that's been developed. Losing the adaptive alleles has to be a step backward, an overall loss for the creature as well as a loss for the whole idea of evolution in the end. Do you want your adapted creature or not? Meaning does evolution depend on getting established adaptive new varieties of creatures or not?
ABE: OK, the mutations could occur at other locations for other traits but then you've got your increased genetic diversity to what purpose? NS has done its job of bringing out an adapted creature. It works, what's the point of altering it except to convince yourself that there doesn't have to be an inevitable trend to reduced genetic diversity?
I have yet to go through many posts prior to this one but this one caught my eye.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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Replies to this message:
 Message 384 by PaulK, posted 10-12-2013 2:57 PM Faith has replied
 Message 390 by Percy, posted 10-13-2013 2:15 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 385 of 457 (708710)
10-12-2013 3:25 PM
Reply to: Message 384 by PaulK
10-12-2013 2:57 PM


Re: Selection does lead to reduced genetic diversity
It should also be easy to see that mutations don't need to alter that adaptive picture at all, and don't have to alter it in a way that seriously disadvantages the traits already being selected for. They certainly don't have to cause any adaptive alleles to be lost from the population entirely - in fact that would be very, very unlikely (it wouldn't be common even for single individuals to lose an adaptive allele and it wouldn't matter much if it did happen). And besides evolution expects failures as well as successes, so even if it did happen on very rare occasions it wouldn't be a problem.
{I was apparently adding something to this effect while you were wring this post).
HOWEVER, evolution supposedly builds on established new "species" does it not? Isn't that the whole point of Natural Selection, that it supposedly can ultimately bring about a new species that can be a stepping stone to further speciation? And on and on and on out to something entirely NOT that same species at all but something new? We have to get that entire evolutionary genealogical tree into the picture here don't we?
So if you're constantly starting and stopping the process that produces these varieties -- starting with new varieties built on less genetic diversity, stopping with mutations that increase the genetic diversity -- where is evolution finally?
And keep in mind that you all want to answer Creationists who insist that microevolution occurs but not macroevolution, by saying that there is nothing to stop the one from going on to the other, as if its all a matter of addition, so if you are now acknowledging that the evolutionary processes that bring about new varieties do in fact overall reduce genetic diversity that OUGHT to be a BIG DEAL, and not something to just run on past as if it's meaningless. It effectively answers the constant refrain about there being no barrier to macroevolution.
If NS and all the other natural processes that bring about new varieties or species by changing allele frequencies actually in the long run bring about sufficiently reduced genetic diversity to interfere with further variation or speciation, then you've got less rather than more ability to evolve.
ABE: and let me add that I mean less ability to evolve down whatever line of evolution is occurring, not in the overall genome of any particular species. I keep trying to remember to say this but sometimes don't get it said. While you are breeding Dachshunds all the other dogs in the overall dog genome are not necessarily evolving (although many are). I'm talking ONLY about what happens in the line of Dachshunds. Or the third population in a ring species, or the second or fifth, or in fact any species in the wild that has formed from an isolated subpopulation off a former population.
So of course again now you want to bring in mutations to save the day. I've been struggling to say how they can't although it's intuitively obvious to me that they can't.
So you,re really going to have to stop being vague explain what you mean, because I can't come up with any interpretation that would be a plausible problem for evolution at all.
I certainly don't mean to be vague, I'm trying very hard to be as precise and specific as I can.
But I'd start here again with reminding you that IF you see what I mean about how phenotypic variation, at least if brought about through a relatively small subpopulation, MUST be built upon reduced genetic diversity and if further subdivisions should occur the effect will only increase until you have no ability to vary further, THAT should be acknowledged here. I've been working hard to get that much across.
You'd also have to consider the huge probability that these changes do NOT take "deep time" to accomplish. Let that video of Dawkins about the lizards on Pod Mrcaru be the evidence for that. If lizards can do it in 37 years there is no reason any given population in a ring species needs to take any longer, or any new "species" whatever, except those developed from much larger founding populations, and that is only going to add hundreds of years at the most for all the new allele frequencies to work through it generation by generation.
And IF you take that seriously then you also have to consider that mutations are not going to occur frequently enough anyway to make the changes you are hoping they might make.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 384 by PaulK, posted 10-12-2013 2:57 PM PaulK has replied

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 392 of 457 (708737)
10-13-2013 4:41 PM
Reply to: Message 390 by Percy
10-13-2013 2:15 PM


Re: Selection does lead to reduced genetic diversity
Faith writes:
Allele frequencies change randomly in some of these processes, but due to particular selection in NS and domestic breeding, but the allele frequencies alone are enough to make big changes and bring about a new variety whatever the cause.
You keep saying this, and it is as false as ever. The allelic frequencies of the very common alleles that define a species are going to be pretty much the same when one first creates a randomly chosen subpopulation.
I keep saying it because to me it is intuitively obvious and the objections to it make no sense to me, they seem to me to reflect a belief in the ToE and nothing much else.
Seems to me it depends on HOW common the alleles that "define a species" were in the original population whether their frequencies will remain the same when the subpopulation is first formed. Of course the alleles that define the main Species, say Cats or Dogs or Bears or Gerbils will remain the same, if those major characteristics are governed by alleles at all, but those for the particular characteristics of the first population are very likely to change, especially in a population that has fairly high genetic diversity. The first population could be characterized by pointy ears, long noses, short tails, brown coat with black markings, but the alleles will nevertheless be present in that population for variations on all those traits, floppy ears or round ears or even pointier ears, short broad noses or longer noses, broad tails or long tails or really short tails, gray or black or tan coat with white or gray or whatever markings and so on, and in a randomly created subpopulation chances are some of those are going to be higher frequency than in the original population, while the alleles for the characteristics of the original population will be lower frequency than before -- enough to make an observable difference after some generations of inbreeding so that their phenotypes become apparent and get spread through the new population.
The new allele frequencies wouldn't be apparent at the first creation of the new subpopulation, but the LOOK of the new subpopulation, that is, its phenotypic expression, would be "pretty much the same when one FIRST creates a randomly chosen subpopulation" -- my emphasis on "first." I've tried to keep this in view during the discussion, saying that you will not see the new phenotypes of a new variety or subspecies until after some number of generations of inbreeding. The first population is going to look just like the one it split off from. But the alleles possessed by the individuals may occur in much different proportions among them, and that will EVENTUALLY make a big difference in the look of the population after some generations of inbreeding.
The only allelic frequencies different in the subpopulation would be those that were uncommon in the parent population. Many of the frequencies of these uncommon alleles will drop from some low percentage like 5% or 3% or 1% all the way down to 0%. This is what accounts for the drop in genetic diversity in a subpopulation.
That could happen of course, and that too would have its effect on the phenotype eventually, but we're talking maybe half a dozen alleles for at least half a dozen traits, and it also could happen that some of the formerly lower frequency alleles are recessive and unexpressed in the original population though they occur in as much as 50% of the individuals, and then get passed on to become 70% in the new population, where they pair up more frequently over time and so on. [Some genes accumulate their effects over generations too, right? I'm thinking of some of the exaggerated traits in say Darwin's pigeons. I don't understand how that works, but if you keep breeding for a particular trait generation after generation you can get a really exaggerated version of that trait eventually even if it's based on only one or a few genes, though the first expression of it may be fairly modest, slightly more expansive tail feathers, etc. Something like this must sometimes happen in the wild too]. While other relatively low frequency alleles also become more high frequency and others even more low frequency and even drop out altogether. All the different ways they can be sorted and matched up are going to create a new trait picture in the new subpopulation.
A change in allelic frequency is necessary to bringing about a phenotypic change in a subpopulation. Without different selection pressures the allelic frequencies will remain about the same as the parent population. Only different selection pressures will cause the allelic frequencies to change.
But the subpopulation is often of much smaller numbers than the original, therefore a whole new set of allele frequencies is VERY likely. Even if the subpopulation is much larger the chances of getting the same proportions, in a genetically diverse species anyway, defies the odds. You'd have to have near 100% of alleles in the former population for that to occur, and in that case you must have a pretty depleted genetic diversity there already. The cheetah for instance is never going to produce a subpopulation with different allele frequencies, but a more genetically diverse population, that is a population that contains many alleles for many traits, although only a certain percentage of them are expressed in the dominant phenotype, would divide into subpopulations with very different frequencies. And again, the first individuals in the new subpopulation aren't going to look any different from the mother population; but after generations of inbreeding their peculiar new mix of alleles is going to combine in new ways and begin to express itself, first in new traits in individuals, then in an overall look for that population.
What are you imagining could cause allelic frequencies to change in the absence of selection pressures? In answering this question, consider a main population that becomes split right down the middle when a river changes course, and assume that the environment remains the same on both sides of the river. Let's say that one of the alleles had a frequency of 95% in the original main population, and that it begins at that level in both subpopulations. What cause of change to allelic frequency could there be that would affect one subpopulation but not the other?
First in an equal split I would expect BOTH populations to have different allele frequencies and therefore change observably over time, neither looking exactly like the original population after many generations.
Seems to me even with such a high original frequency of the one allele there is going to be some difference, maybe 99% in one of the populations and 92% in the other which could be enough over MANY generations (it would take a great many generations if the population split is about equal) to alter the look of that particular trait.
But at the same time there are many alleles for many other traits that are also going to be sorted into new frequencies in both populations, and even if the 95% high frequency allele continues more or less the same in both, other alleles for other traits originally in lower frequencies are going to be shuffled into new proportions TOO, and they are certainly going to contribute to the new trait picture for both new populations. After many generations I would expect both those subpopulations to have diverged greatly from each other and also from the original population (I hope plenty of pictures were taken of the original), all without any other cause than the new allele frequencies in each.
If the selection pressures remain the same then the main contributor to change (aside from drift, which is random and slow) is mutation.
Sure, if the mere change in allele frequencies doesn't work as I'm supposing it does, and the environment is offering no new pressures, then mutations would be the only source of change. (Seems to me that for particular mutations to come to characterize the new populations would take at least as long as Drift, since they'd have to be selected at least by reproductive advantage and so on but anyway.)
The paper AZPaul3 cited was about a chain of lizard subpopulations distributed around the perimeter of a mountain, here's the link:
Predictors for reproductive isolation in a ring species complex following genetic and ecological divergence.
Yes I've got that paper saved.
AZPaul3 already quoted one portion about the arise of new DNA sequences, and here's another portion about the cause of reproductive isolation:
Experimental studies strongly favor this view, showing that mutations in coevolving gene complexes can rapidly cause hybrid incompatibilities in closely related species.
In other words, mutations play a key role in producing reproductive incompatibility, and reproductive incompatibility must be considered the foremost of phenotypic differences in speciation processes.
The problem here for me is that mutations are so often assumed by people who subscribe to the ToE to be the cause of changes either in the DNA or in phenotypic traits, that I have to suspect that they are being assumed in any particular case where the real cause of the changes may be something entirely different. They observe changes in the DNA sequence and CALL those mutations just because that's what the ToE requires. Aside from the problems I would expect to have trying to understand a highly technical paper I don't see how I'm going to get past this suspicion. Those who believe in evolution are very good at recognizing confirmation bias in creationists, but it operates wherever there is a strong prior commitment to a way of explaining phenomena and that includes a commitment to the ToE.
And if selection pressures on the two populations do become different, then the divergent selection pressures will result in divergent allelic frequencies.
If that occurred then yes to the conclusion.
But just removing genetic interflow between two populations in the same environment will do little to produce phenotypic differences, and certainly not in a mere 37 years.
All I can say is I think you are drastically underestimating the effect of changed allele frequencies, first the inevitability of such changed frequencies in the formation of any new subpopulations, then the great effects they would have to bring about.
Again the the smaller the numbers of founders, which describes the lizards of Pod Mrcaru, the greater the differences should be, and working these through the new population really should not take more than a few decades. As you reported, those lizards produce many offspring very frequently and if they all freely interbreed with one another it shouldn't take long at all to work the new allele frequencies through to a new look for that population.
That's my argument anyway.

This message is a reply to:
 Message 390 by Percy, posted 10-13-2013 2:15 PM Percy has not replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 393 of 457 (708745)
10-13-2013 5:55 PM
Reply to: Message 391 by Percy
10-13-2013 2:59 PM


Re: Contribution of Drift
Percy writes:
I was looking for technical articles about differences emerging in small populations of the same species and came across an article about herds of the Jutland breed of cattle. I'm amazed at how often persistence can bring a free copy of an article to light which it at first appears available only for a fee, which was the case with this paper, found beginning at page 75 of this link to the journal:
Impacts of genetic drift and restricted geneflow in indigenous cattle breeds: evidence from the Jutland breed
The abstract says:
The data reflected the impacts of fragmentation and restricted gene flow in breeds with small segregated herds, and revealed the rapid differentiation of herds resulting from genetic drift.
"Fragmentation" I assume refers to the formation of the many small segregated herds?
That there was "rapid differentiation" is very interesting, which is what my theory predicts of course: all that's required is restricted or absent gene flow, that is, reproductive isolation of each new subpopulation, and you should get rapid differentiation from the other herds.
In fact this is a very interesting study for my purposes. But of course they don't even consider that each new subpopulation would have new allele frequencies from the mere fact of its BEING a new subpopulation apparently randomly created. In a way this does surprise me since I didn't know I was working with a concept that is apparently so unusual, I really thought I got it from evolutionist writings on the subject, and that being the case I'd expect it to figure in such a study.
At first I wasn't sure how to assess their explanation that genetic drift was the cause of the changes when the merely changed allele frequencies is sufficient cause, but then it occurred to me that the two are really quite compatible. That is, genetic drift is just the expectable working-through of the new frequencies down some number of generations to create the new phenotypes. Genetic drift brings about changes over generations, and that's what I'd expect too, new phenotypes showing up and eventually a particular new look or trait picture coming to characterize the whole herd. The difference is that the study isn't considering the initial new allele frequencies as the stuff the drift is working through. But genetic drift does describe the same thing I'm saying about how generations of inbreeding eventually produce a new trait picture for the whole herd from emerging new phenotypes down the generations.
The conclusion says:
Our results further demonstrate the rapid diversification of the Jutland breed herds due to limited gene flow and genetic drift.
Yes, same as what I've been saying, now that I understand genetic drift as the effect of inbreeding over generations, although they aren't considering the impact or even the existence of the new allele frequencies at the founding of each new herd.
The article also describes the contribution of mutations. They checked for allelic stuttering (repeated sequences in a portion of allele), allele drop out, and null alleles (mutation making the gene non-functional) (page 77). Subsequent discussion drops into a level of detail that would be too time consuming for me to attempt to parse.
Well, the mutations identified here, allelic stuttering, null alleles, hardly seem to be of a kind that would produce anything useful to the animal, which of course I would also expect, so claiming they make a "contribution" to the herd in any positive sense seems highly questionable to say the least. Do they really mean to say that such changes are anything but deleterious? The new phenotypes that are emerging in each herd could hardly be based on such mutations.
The article focuses primarily on genetic differences. Most of the research effort seems to have been expended on genetic analysis. But the article does make clear that there a very visible phenotypic differences, for example, this from the introduction:
As a consequence, there are high levels of phenotypic variation among indigenous breeds, a variety of adaptations to local environmental conditions and high fitness under natural conditions (Tapio et al., 2006; Dalvit et al., 2008).
Unfortunately the phenotypic differences are never described, so there is no way to tell if they're as significant as the head and diet changes of the lizards of Pod Mrcaru, ...
I would take their word for it myself, that the phenotypic differences were considerable or at least readily recognizable. As I keep arguing, the mere division into many small herds is enough to bring about such changes based on the new allele frequencies for each new herd.
...but even without this detail I think we have to grant that the phenotypic changes in these lizards could have been due either drift, selection, mutation or, most likely, some combination.
1) Drift. Although I'd never put the concepts together before, as suggested above I'm coming to think that "drift" describes the working-through of the new allele frequencies I keep claiming are the main cause of changes in new subpopulations, so I'm thinking this study confirms my expectations in that regard rather than contradicting them.
2) There is nothing in this study about selection, at least as far as you've presented it, and although I can agree that selection COULD have an effect, I still disagree that there's any reason to think so in the case of the Pod Mrcaru lizards, and even less reason to think so in the case of the Jutland cattle.
3) The mutations described above seem hardly of any use to the animal at all, simply showing the usual destructive effects I expect of mutations, nothing that could be passed on to any benefit to the new herd. And again, useful mutations seem to be merely an article of faith based on commitment to the ToE, something assumed to be the cause of new traits rather than actually in most cases shown to be. Perhaps they say more that could qualify this conclusion?
4) Some "combination" -- well maybe sort of sometimes -- but nothing in this study or the lizard video leads me to think ANYTHING more than the mere new allele frequencies is needed to produce a new variety or subspecies. There COULD be such influences but I don't see any evidence for it as presented above anyway.
I really LIKE this study of the Jutland cattle, though, since it describes the RAPID formation of MANY separate phenotypically different herds, which is EXACTLY what I'd expect.
Again, I really don't understand why changed allele frequencies aren't ALWAYS recognized as resulting from population splits and as producing great effects over time.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 391 by Percy, posted 10-13-2013 2:59 PM Percy has not replied

Replies to this message:
 Message 394 by Faith, posted 10-14-2013 8:23 PM Faith has not replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 394 of 457 (708813)
10-14-2013 8:23 PM
Reply to: Message 393 by Faith
10-13-2013 5:55 PM


Re: Contribution of Drift
Found myself pondering genetic drift. I've had only a vague idea about drift, although I've thought of it as one of the ways new phenotypes can emerge while genetic diversity is reduced in a small population. I've looked it up many times over the years, but the definition "random sampling" just doesn't convey much to me; sampling sounds like something the scientist might do to analyze the DNA of the population, but it hits me as a strange word for the effects of random breeding. Which I now understand it to be.
As I've been thinking about what happens after a new subpopulation with new allele frequencies gets started, I've been picturing random breeding over many generations working through the new frequencies until they underlie a new trait picture for the whole new population.
The fact that this random reproductive pattern would itself affect the allele frequencies, as genetic drift does, didn't occur to me.
Now I'm wondering if genetic drift only operates observably where you do have these new allele frequencies in the new subpopulation or it would operate to produce new phenotypes in any case. This raises the question whether it was still observably operating in the greater original population of Jutland cattle and if not why not. If it wasn't, that is, if it wasn't bringing out new phenotypes as it is apparently now doing in the new smaller herds, my guess would be that a stable population HAS somehow "worked through" its various different genetic possibilities and arrived at a point where new phenotypes aren't cropping up all the time as they obviously do in the new subpopulations. This thought has occurred to me many times in this overall discussion but there was never any reason to mention it before. It has seemed to me that a population can be genetically stable in this way whether it has high or low genetic diversity.
Not sure the question makes sense yet.
Anyway, I was reading the Wikipedia article on Genetic Drift and I think they made an error. Look down at the example of the marbles in the jars.
It is even possible that in any one generation no marbles of a particular color are chosen, meaning they have no offspring. In this example, if no red marbles are selected the jar representing the new generation contains only blue offspring. If this happens, the red allele has been lost permanently in the population, while the remaining blue allele has become fixed: all future generations are entirely blue. In small populations, fixation can occur in just a few generations.
This must be incorrect unless any given individual has only one generation in which to reproduce, but I'm not aware of any animal that can't reproduce over many generations or many reproductive seasons. That is, the Wikipedia writer only seems to be thinking of a particular generation reproducing among itself alone, forgetting that earlier generations may continue to reproduce for many seasons, also with members of other generations depending on the creature. So even if in one generation a particular allele is completely lost, it's lost only from that generation, not "permanently," and it could reappear in the next generation as the first generation with the equal number of both alleles is presumably still living and still able to reproduce.
Yes?
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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 Message 393 by Faith, posted 10-13-2013 5:55 PM Faith has not replied

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 Message 395 by NoNukes, posted 10-14-2013 10:25 PM Faith has not replied

  
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