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Author Topic:   The Great Debate: Molecular Population Genetics and Diversity in Evolution
Genomicus
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Message 1 of 30 (785012)
05-26-2016 4:48 PM


This is the Great Debate thread on genetic diversity and the limits of evolution, between myself and Faith.

The purpose and scope of this topic is the material and overarching themes I discussed in the OP of "Molecular Population Genetics and Diversity through Mutation".

Instead of regurgitating our few exchanges on that thread and posting them here, here I've listed the relevant messages to look at in order to get caught up.

Message 1, OP, by Genomicus.

Message 4, response by Faith.

Message 18, response by Genomicus.

Message 27, response by Faith.

Message 38, response by Genomicus.

Message 39, response by Faith.

If this topic gets approved, I will simply start by responding to Message 39 and perhaps adding a bit of material on the key points I intend to demonstrate.

Moderator, let me know if there's anything that needs to be changed with this.


  
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Message 2 of 30 (785014)
05-27-2016 10:08 AM


Thread Copied from Proposed New Topics Forum
Thread copied here from the The Great Debate: Molecular Population Genetics and Diversity in Evolution thread in the Proposed New Topics forum.
    
Genomicus
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(1)
Message 3 of 30 (785114)
05-28-2016 2:06 AM


The Biological Evidence
In this discussion, I intend to demonstrate that the limits to evolution as perceived by Faith are non-existent in the real world of biology. While it is indeed true that evolutionary forces and dynamics can sometimes lead to morphological, physiological, or biochemical dead-ends, this is in no way a necessary outcome of evolutionary development and emergence. Thus, I intend to show that Faith's argument is not a viable critique of the plausibility of the modern evolutionary synthesis or the theory of universal common ancestry.

Here I will marshall an array of observations, evidence, and arguments from phylogenetics and phylogeography, molecular population genetics, bioinformatics, and functional genomics, which collectively refute Faith's argument.

***
I will begin my responding to Message 39 of Faith, in the "Molecular Population Genetics and Diversity Through Mutation" thread.

No, an increase in allelic heterozygosity is an increase in genetic diversity. Heterozygosity at a locus under consideration is a pretty standard way to measure genetic diversity in a population. See here (warning: it's a PDF; it's a "primer" on population genetics which you might find easier to understand than standard pop gen textbooks).

Funny, I've known that and yet forgot it in this exchange: I've even said that the way to measure genetic diversity to test my argument is by looking for increases in homozygosity. Iíve saved the link and skimmed through it. There may be too much math there for me, however.

You said heterozygosity can increase from parent to daughter and I accepted that possibility but I would still expect that the overall trend would be to increasing homozygosity, which would show up more clearly after a series of population splits such as in ring species.

Then let's compare your expectation of an overall trend in increasing homozygosity to biotic reality -- to what really see in nature. For this example, I will look to the classic case of a ring species: the Larus gulls.

A phylogenetic tree of mtDNA sequences of various Larus gull taxa (Liebers-Helbig et al., 2010, Figure 7, page 11) has established the "ring order" of these gulls. By "ring order," I simply mean which gulls are representative of the original population, and which arose later in a ring-like manner.

This phylogenetic analysis shows that:

1. Larus canus are the oldest, or "original" population, that represent the very "start" of the ring species formation.

2. L. argentatus and L. hyperboreus are slightly younger taxa than L. canus, but are still considerably old, so they also represent the early parts of the formation of this ring species.

3. L. schistisagus, L. glaucescens, L. glaucoides, are all considerably younger taxa than those in #1 and #2, and so represent the latest "end" to the ring species.

Thus, by your expectation, Faith, there should be an increasing trend of homozygosity from L. canus to L. argentatus and L. hyperboreus to L. schistisagus, L. glaucescens, and L. glaucoides. Significantly, this trend should "show up clearly." But does it?

Answering that question a decade ago -- when you first floated this argument -- may have been difficult, but progress in biotechnology has yielded an explosive amount of genomic data. A study by Sonsthagen et al. (2012) examined levels of heterozygosity in all of the above gull taxa (see Table 1 in their paper). Here are the averaged observed heterozygosity values observed in the previously mentioned taxa:

Larus canus: 61.04

L. argentatus: 50.4
L. hyperboreus: 45.6

L. schistisagus: 59.5
L. glaucescens: 50.77
L. glaucoides: 47.0

Interestingly, the only part of your expectation that holds up is that L. canus (representing the earliest part of the ring species formation) has the highest level of heterozygosity, at 61.04; but after that, your expectation completely falls apart.

First, L. schistisagus, one of the latest-evolving species at the end of the ring, has a heterozygosity value (59.5) well above the heterozygosity values of either of the older, earlier-evolving gull taxa (L. argentatus and L. hyperboreus). In fact, all of the later-evolving gull species have more heterozygosity within their populations than the earlier-evolving L. hyperboreus species. Second, these later-evolving taxa also have greater heterozygosity than the earlier-evolving species L. argentatus, with the exception of L. glaucoides.

This completely upends any notion that there is some kind of "trend" here, wherein "the overall trend would be to increasing homozygosity, which would show up more clearly after a series of population splits such as in ring species."

Importantly, this data on heterozygosity was acquired from microsatellite sequences. The study also looked at heterozygosity values from nuclear introns and mitochondrial DNA. So what kind of trend does your model predict we should find in these genomic regions?

And why, if your argument is actually biologically valid, do we not see the trend toward homozygosity exactly where you say we should find this trend -- in ring species?

But yes, increased homozygosity is THE sign of reduced genetic diversity. The question now is whether the fact that heterozygosity can increase in some cases is enough to overcome the predicted trend to increased homozygosity.

Well, clearly in the gull ring species, mutation, gene flow, and population growth is sufficient to overcome any trend towards increased homozygosity. So we have biological evidence that this trend doesn't actually do much to impede a reversal towards heterozygosity and genetic diversity.

If a given locus exhibits a high degree of heterozygosity within a population, it means that there's whole range of different, diverse allelic combinations at that locus. Ipso facto, there's an increase in genetic diversity when there's an increase in heterozygosity (and here, when I say "increase," I do not mean an increase in frequency of a particular allelic combination; I mean an increase in diverse allelic combinations throughout the population).

The question, again, is whether this increase in heterozygosity could occur in a geographically / reproductively isolated daughter population to any extent to offset the trend to homozygosity or reduction of alleles.

And the answer to that question is a resounding "yes." To further bolster this answer, I will draw an example from human genomics.

In particular, let's look to a small island in the Mediterranean, Sardinia. The human population in Sardinia has grown in size generation over generation, without immigration (so it's been an isolated population), as evidenced by sequence analyses of the D loop region of the mitochondrial genome and nuclear DNA polymorphisms (see references 18 and 19 in Di Rienzo et al., 1994).

So to re-quote you:

"...the question, again, is whether this increase in heterozygosity could occur in a geographically / reproductively isolated daughter population to any extent to offset the trend to homozygosity or reduction of alleles."

In fact, there is an excess in the number of alleles in the population (this is known as "allelic richness," and is another measure of genetic diversity), compared to the proportion of individuals who are heterozygous at a given site (see Cornuet and Luikart, 1996). In other words, while there isn't a striking degree of heterozygosity, there is a high prevalence of the number of different alleles in the population at a given chromosomal locus, which in turn means that mutation -- coupled with population growth -- has fueled the rise of new alleles. And that means that far from witnessing a decrease in genetic diversity, this geographically isolated human population has seen an increase in genetic diversity.This makes sense, of course, from a population genetics perspective -- for if the population steadily grows over time, then mutation plays an increasingly major role in shaping genetic diversity than genetic drift or selection does. That mutation has increased genetic diversity in the Sardinian population is evidenced by the high ratio of allelic richness to heterozygosity. This is exactly what we would predict if the Sardinian population has grown over time, without immigration, as other lines of independent evidence demonstrate.

And this uncovers a lethal blow to your argument: namely, population growth is a very simple mechanism that can relatively easily offset an increase in homozygosity in a reproductively isolated population. Both the equations of population genetics, and real-world observations, demonstrate this.

Put differently, a reproductively isolated population might initially have a low amount of genetic diversity, but by growing in size generation after generation, the number of different, diverse alleles steadily increase (due to mutation) -- providing the increase in genetic diversity that can further drive evolution.

You are describing a situation that starts out with high genetic diversity in general, which I suppose to generally increase the farther back you go along any evolving line, and where that is the case there should still be a trend to increased homozygosity all down the evolving chain of daughter populations, but it wouldnít be particularly dramatic until you have less genetically diverse populations splitting into daughter populations, especially into significantly smaller populations.

See the microsatellite heterozygosity data from the gull ring species, above, which is contrary to the expectations of your idea. That being said, you have yet to demonstrate that (1) population growth, and (2) mutation is not sufficient to reverse any trend towards homozygosity. There is absolutely no reason why these processes cannot, under any biological or evolutionary circumstances, increase genetic diversity in a reproductively isolated population (as measured by heterozygosity, nucleotide sequence divergence, or allelic richness).

In any case I think youíd be very hard-pressed to demonstrate that Iím wrong about the TREND to decreased genetic diversity, or to make a case for an actual increase. Population splits do very much what natural selection does as far as changing gene frequencies goes, and youíve agreed that natural selection reduces genetic diversity. A daughter population is a sort of selected population, randomly selected in this case, and even if some increase can occur over that of the parent at some loci thereís no way that could be the trend of change, because of the principle you have also already agreed with, that developing new phenotypes requires the loss of competing alleles. (Even in the case of our new high frequency Bís there is a reduction of the bís after all.)

Sure, the fixation of a novel phenotype in the population does mean that the competing alleles are lost. So what? There's still plenty of other chromosomal loci which will be increasing in diversity due to mutation, and this provides a "fresh batch" of diversity which natural selection can operate on when the environment changes. And this increase in genetic diversity in the numerous chromosomal loci which are not under strong selective pressure means that further population splits can recover genetic diversity simply through mutation and population growth.

OK, I see, and this is so as a TREND and with respect to the salient characteristics of the subspecies that is developing. There could still be great diversity for other characteristics of the creature that donít show up in the new phenotype.

So if there can still be great diversity for other characteristics that aren't relevant to the phenotype that's being fixed in the population, then what's the problem here? Why can't this increased genetic diversity also happen in daughter population that successively split off from each other?

The estimate of heterozygosity for human beings now is something like 7% IIRC, but taking a wild guess back a few thousand years it could have been as much as 50% or 70% or higher, and some loci could have retained a higher percentage than others even now.

Are you willing to stake your idea on the notion that a few thousand years ago human heterozygosity was as high as 50%? What about overall nucleotide sequence diversity? Do you think there has been an increase or decrease in nucleotide sequence diversity over the course of human history?

For if allelic sites, or chromosomal loci, do not become increasingly homozygous while a novel trait is evolving, then the population has plenty of genetic diversity -- even if novel traits are evolving. And if the population has this genetic diversity, your argument falls apart.

No it doesnít, it just means, as I say above, that the loss is a trend over time.

Nope, because the trend can become reversed by mutation and population growth.

There was a lot more genetic diversity in the past, that has been decreasing over time...

You state this as if it is an empirical observation. It is not; quite the contrary, in fact -- human genetic diversity, on the whole, has increased over time. Would you like me to provide the consilience of independent lines of biological evidence for an increase in human genetic diversity over time? In the meantime, you can present your evidence that human genetic diversity has been decreasing. If you do not have such evidence, then your argument is little more than an anti-evolutionary fantasia.

None of this changes my argument that homozygosity will be the trend down any line of evolving subpopulations, slow or fast, dramatic or hardly discernible, but always the trend.

Do you have any evidence that this "trend" cannot be reversed or counterbalanced by sufficient mutation or population growth?

The idea that a mammal evolved from a reptile assumes enormous continuing or growing genetic diversity (over hundreds of millions of years yet)...

Well, we have evidence that speciation can occur followed by an increase in genetic diversity. See the microsatellite heterozygosity data on the gull ring species, above.

And, of course, there's nothing stopping mutation and population growth from adding genetic diversity to a population, even while a few phenotypes are being fixed. There will still be plenty of chromosomal loci which will see an increase in heterozygosity or allelic richness, and there's nothing stopping that.

But if selection reduces genetic diversity then itís going to treat any source of genetic diversity the same way...

No, because plenty of loci won't be under any significant selection pressure.

Wut? A single mutation won't add significant genetic diversity to the cheetah population. What's needed is an elevated rate of mutation in the cheetah population if they are ever to get out of their "genetic purgatory." The equations in the OP demonstrate very nicely why there's extremely low genetic diversity among cheetahs; the small population size, coupled with a not-very-high mutation rate, means that genetic drift and inbreeding (which is basically just an extension of the sampling error that genetic drift is) will continue to decrease the diversity of the cheetah gene pool. So I have no idea where this "waiting around for a mutation to get them out of their 'genetic purgatory'" comes from, since it's not like a single mutation will do that.

OK, so any genetically compromised species will face the same kind of problem, and if thatís what ďspeciationĒ amounts to, weíve got a deteriorating system that isnít going to be able to reverse itself.

Speciation doesn't amount to a "genetically compromised" population. Cheetahs underwent a significant population bottleneck; but if a founding population is sufficiently large, then there is nothing of necessity preventing mutation and population growth from replenishing the genetic diversity of the population.

Sometimes the population is too small, and the mutation rate to small, that extinction results. Other times the population size is not too small, and the mutation rate is sufficiently large, that genetic diversity can increase. This not only makes perfect sense from the mathematics of population genetics, but it's also what we see in biology.

Your error is in assuming that all founding populations are equal, all mutation rates are equal, and all selective pressures are equal. They are not.

Your argument not only makes a failed prediction (see ring species example of gull taxa), it also ignores perfectly valid and demonstrated principles of genetics.

Edited by Genomicus, : No reason given.


Replies to this message:
 Message 4 by Faith, posted 05-28-2016 3:44 AM Genomicus has responded
 Message 5 by Faith, posted 05-28-2016 4:11 AM Genomicus has not yet responded
 Message 10 by Faith, posted 05-29-2016 2:56 AM Genomicus has not yet responded
 Message 11 by Faith, posted 05-29-2016 10:30 AM Genomicus has not yet responded

  
Faith
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Posts: 24846
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 4 of 30 (785120)
05-28-2016 3:44 AM
Reply to: Message 3 by Genomicus
05-28-2016 2:06 AM


Re: The Biological Evidence
So I've got to read that paper?

Just a couple questions:

Are hybrid zones and gene flow between populations also taken into account?

You've agreed that selection reduces genetic diversity. So what else is going on here genetically to account for this supposed contrary information?


This message is a reply to:
 Message 3 by Genomicus, posted 05-28-2016 2:06 AM Genomicus has responded

Replies to this message:
 Message 7 by Genomicus, posted 05-28-2016 5:40 AM Faith has responded

    
Faith
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Posts: 24846
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 5 of 30 (785123)
05-28-2016 4:11 AM
Reply to: Message 3 by Genomicus
05-28-2016 2:06 AM


Re: The Biological Evidence
Well I see I didn't read far enough, but I'd expect to have to spend a fair amount of time on this since your intent is obviously to swamp me.

But I just read this little gem of a sentence:

Well, clearly in the gull ring species, mutation, gene flow, and population growth is sufficient to overcome any trend towards increased homozygosity. So we have biological evidence that this trend doesn't actually do much to impede a reversal towards heterozygosity and genetic diversity.

Um, "gene flow" is of course specifically the main reason one would NOT get the trend I'm talking about, as I believe I've said many many times. That right there makes this study utterly irrelevant.

If there's actual evidence of mutation AFTER the new species has developed that's something else to consider as an interference with the expected loss. ANYTHING that adds to the genetic diversity will prevent the situation I'm talking about from developing. The REAL history of these gulls is obviously not accurately expressed in these numbers.

Ah well. You should concede that you're wrong about this example now.


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Faith
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From: Nevada, USA
Joined: 10-06-2001
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Message 6 of 30 (785124)
05-28-2016 4:34 AM
Reply to: Message 5 by Faith
05-28-2016 4:11 AM


Gulls don't meet the specs
ABE: Why do you think I insist on REPRODUCTIVE ISOLATION?

It's because that's where we see the processes of evolution most clearly. If you have gene flow that has to interfere. Same with mutation, although I really don't think mutation occurs as is so often claimed.

But again, I'm only talking about the situation of selection and reproductive isolation, the processes that bring about evolution itself, that make the changes we call evolution, bring out new phenotypes from new gene frequencies, etc etc etc. Adding genetic diversity will of course interfere with these processes. Reality is usually a lot messier than my idealized argument, of course, in reality there is often continued gene flow or resumed gene flow or hybrid zones and whatnot, but they are the opposite of the processes that bring about evolutionary change.

It's because of this sort of confusion that I think a lab setup is probably the only way to know for sure what happens in a series of reproductively isolated daughter populations.


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Genomicus
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Posts: 815
Joined: 02-15-2012
Member Rating: 4.7


(2)
Message 7 of 30 (785125)
05-28-2016 5:40 AM
Reply to: Message 4 by Faith
05-28-2016 3:44 AM


Re: The Biological Evidence
So I've got to read that paper?

Well, yes, if you want to verify that what I'm saying is accurate.

You've agreed that selection reduces genetic diversity. So what else is going on here genetically to account for this supposed contrary information?

I've concurred that selection at a locus under consideration reduces the genetic diversity of that locus. That there is a variety in heterozygosity in daughter populations in ring species is exactly what we'd expect if genetic diversity is determined by a combination of mutation rate, population size, genetic drift, and selection. Population growth and mutation rate are sufficient to add genetic diversity to daughter populations.

Well I see I didn't read far enough, but I'd expect to have to spend a fair amount of time on this since your intent is obviously to swamp me.

I also expect you to have to spend a fair amount of time on this, inasmuch as I spent a considerable amount of time assembling various lines of evidence. However, the intention is not to swamp you, but rather to be thorough -- as all too often threads turn into nitpicking back-and-forth from a lack of comprehensiveness. Take all the time you need, of course.

Well, clearly in the gull ring species, mutation, gene flow, and population growth is sufficient to overcome any trend towards increased homozygosity. So we have biological evidence that this trend doesn't actually do much to impede a reversal towards heterozygosity and genetic diversity.

Um, "gene flow" is of course specifically the main reason one would NOT get the trend I'm talking about, as I believe I've said many many times. That right there makes this study utterly irrelevant.

And that right there is a concession that this trend you speak of can be overcome by counteracting biological processes, such as gene flow. Or mutation. Or population growth combined with mutation. Or horizontal gene transfer. In other words, there are so many "exceptions" that this so-called trend doesn't become a problem for the Neo-Darwinian synthesis.

And, as a side note, you do realize that there will almost always be a degree of gene flow among the taxa of a ring species, yes?

If there's actual evidence of mutation AFTER the new species has developed that's something else to consider as an interference with the expected loss.

Yes, there is that evidence, right in the paper I cited. Here's a look at the mean values ofnucleotide diversity of the various gull taxa (the closer these values are to 1, the greater the amount of nucleotide diversity):

Larus canus: .00380

L. argentatus: .00418
L. hyperboreus: .00383

L. schistisagus: .00300
L. glaucescens: .00329
L. glaucoides: .00500

Once again, this pattern reveals absolutely no trend towards decreased genetic diversity in daughter populations. But why do we think this diversity is the result of mutation after the origin of the species? Because:

1. This nucleotide diversity data comes from nuclear intron sequences, and there is no evidence that there has been significant gene flow among nuclear DNA genes in various Larus species (see Pons et al., 2014).

2. If this nucleotide diversity was the result of significant gene flow, then it would totally confuse any molecular phylogenetic construction of the Larus species. For if there has been significant gene flow among nuclear regions -- enough to account for this diversity -- then that gene flow would result in multiple shared polymorphisms among divergent Larus taxa. And, this in turn, would lead to weird, conflicting branching patterns in molecular phylogenies of these taxa -- which we don't observe. In other words, the best explanation for this nucleotide diversity is mutation.

The REAL history of these gulls is obviously not accurately expressed in these numbers.

Yes, actually, these numbers very nicely demonstrate the real phylogenomic history of these taxa.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 4 by Faith, posted 05-28-2016 3:44 AM Faith has responded

Replies to this message:
 Message 9 by Faith, posted 05-28-2016 9:08 AM Genomicus has responded

  
Genomicus
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Posts: 815
Joined: 02-15-2012
Member Rating: 4.7


Message 8 of 30 (785126)
05-28-2016 6:03 AM
Reply to: Message 6 by Faith
05-28-2016 4:34 AM


Gulls Troll Faith's Specs but Evolve Anyway
ABE: Why do you think I insist on REPRODUCTIVE ISOLATION? It's because that's where we see the processes of evolution most clearly.

No, we see particular processes of evolution more clearly with reproductively isolated populations. Other evolutionary processes are better captured by, e.g., ring species.

If you have gene flow that has to interfere.

So basically gene flow refutes your whole notion that evolution is necessarily limited under all biological circumstances.

Same with mutation, although I really don't think mutation occurs as is so often claimed.

I'm not going to get into a debate about the nuances of mutations quite yet. That may be an interesting discussion for the future, however.

But again, I'm only talking about the situation of selection and reproductive isolation, the processes that bring about evolution itself, that make the changes we call evolution, bring out new phenotypes from new gene frequencies, etc etc etc.

For evidence that genetic diversity can increase in reproductively isolated populations, see the genomics data I reference in Message 3 regarding the human population on Sardinia.

Adding genetic diversity will of course interfere with these processes. Reality is usually a lot messier than my idealized argument, of course, in reality there is often continued gene flow or resumed gene flow or hybrid zones and whatnot, but they are the opposite of the processes that bring about evolutionary change.

No, these processes are evolutionary change.

*Gene flow increases the heterozygosity of a population, which in turn means that there are a greater number of variants possible which can elevate the fitness of the population. A.k.a., evolution.

*Mutation adds new variants in the population, and increases the genetic and therefore morphological distance between a daughter population and a parent population. A.k.a., evolution.

*Horizontal gene transfer can completely alter genomes which are better suited to a new environment, so these new genomes spread throughout a population. A.k.a., evolution.

And so on.

It's because of this sort of confusion...

Honestly, I'm pretty sure you're the only one who's confused. Anyhew, if you want a fancy lab setup, then the short generation time of bacteria would seem to offer an excellent way to test your idea. Now, you will object here likely because you know bacteria refutes your idea. So you're going to say that the organisms used need to be animals. But why is that the case? If your argument were actually valid, it would apply equally well to "reproductively isolated" bacteria (that is, bacteria which are not exposed to other bacterial populations) and reproductively isolated Metazoa. So why shouldn't we test your idea with bacteria?

Edited by Genomicus, : No reason given.


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 Message 6 by Faith, posted 05-28-2016 4:34 AM Faith has not yet responded

  
Faith
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Posts: 24846
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 9 of 30 (785136)
05-28-2016 9:08 AM
Reply to: Message 7 by Genomicus
05-28-2016 5:40 AM


Re: The Biological Evidence
Well, I did want to take my time with this but we seem to be on our way whether I'm ready or not. I skimmed your post last night and made my first brief post between watchings on Netflix. Gene flow, hybrid zones, interfere. Yes they do. Then I came back and skimmed again and found that statement that gene flow IS included in the calculations. Didn't expect that, did think you knew reproductive isolation is essential to my argument. It's already piling up here but maybe I can still get back to the earlier stuff I skipped.

Skimming your posts today I see a lot of this is going to be definitional. Well, I DO need to take my time with this. I just saw this statement of yours I have to respond to before putting that time in on the whole project:

I've concurred that selection at a locus under consideration reduces the genetic diversity of that locus. That there is a variety in heterozygosity in daughter populations in ring species is exactly what we'd expect if genetic diversity is determined by a combination of mutation rate, population size, genetic drift, and selection. Population growth and mutation rate are sufficient to add genetic diversity to daughter populations.

Yes of course, "if genetic diversity is determined by a combination of mutation rate, population size, genetic drift, and selection" you'll get increased heterozygosity. But that isn't evolution, that isn't how new species come about. That's a see-saw between adding and subtracting that overall gets called evolution but it's only the subtractive processes that form the new species. I think it's in your next post that you talk about new phenotypes spreading in a population and I agree that is also evolution, and for that to happen requires the competing alleles to drop out. THAT's what makes it evolution.

That is by way of condensing my argument, which is of course what I'll continue to be arguing in this thread. The idea that adding and subtracting genetic diversity, one step forward, two steps back etc., is any way to run a theory of evolution is not exactly what Darwin had in mind, or anybody else for that matter...

ABE: Why not bacteria? Because they're weird, they're ugly and they don't sexually reproduce. And I don't think they behave in exactly the same way as diploid animals at all. That's why it's got to be mice or something I can talk to and pet.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 7 by Genomicus, posted 05-28-2016 5:40 AM Genomicus has responded

Replies to this message:
 Message 12 by Genomicus, posted 05-29-2016 5:12 PM Faith has responded

    
Faith
Member
Posts: 24846
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 10 of 30 (785198)
05-29-2016 2:56 AM
Reply to: Message 3 by Genomicus
05-28-2016 2:06 AM


You've still got two competing processes both calling themselves evolution
So I'll try to do more justice to your posts now, regretting my slapdash approach while preoccupied with a film last night.

In this discussion, I intend to demonstrate that the limits to evolution as perceived by Faith are non-existent in the real world of biology.

OK, then I need to state my contrary view that there is one particular limit I've identified and it follows from certain premises, many times reiterated already.

There are four processes or mechanisms that are identified as evolutionary processes: mutation, migration (gene flow), genetic drift and natural selection. Of this list, two are additive, adding genetic diversity by either adding new alleles (mutation) or keeping alleles in play or reintroducing alleles lost in former population splits (migration); and two are subtractive, reducing genetic diversity by losing alleles: genetic drift changes a population from the inside by increasing a particular phenotype until it supplants others, also losing the alleles for the others; natural selection also loses alleles while favoring a particular phenotype.

Although these four are all identified as ďevolutionary processesĒ They do entirely different things. The additive processes contribute to genetic diversity in a haphazard way, adding a variety of phenotypes to a population for a motley appearance, while the subtractive processes select and bring out a new homogeneous collection of phenotypes, even a completely new subspecies, which is what I mean by active evolution.

While it is indeed true that evolutionary forces and dynamics can sometimes lead to morphological, physiological, or biochemical dead-ends, this is in no way a necessary outcome of evolutionary development and emergence. Thus, I intend to show that Faith's argument is not a viable critique of the plausibility of the modern evolutionary synthesis or the theory of universal common ancestry.

None of the ďdead endsĒ listed relates to my argument except ďbiochemical dead endsĒ which I suppose may refer to loss of genetic diversity.

Here I will marshall an array of observations, evidence, and arguments from phylogenetics and phylogeography, molecular population genetics, bioinformatics, and functional genomics, which collectively refute Faith's argument.

***
I will begin my responding to Message 39 of Faith, in the "Molecular Population Genetics and Diversity Through Mutation" thread.

ÖThen let's compare your expectation of an overall trend in increasing homozygosity to biotic reality -- to what really see in nature. For this example, I will look to the classic case of a ring species: the Larus gulls.

And here you go on to give the information about the gulls, which of course I answered as not meeting the specifications of my argument, meaning particularly absolute reproductive isolation. The high heterozygosity and lack of a declining series of percentages naturally prompted me to wonder whether gene flow was excluded, and I found out quickly that it wasnít

Larus canus: 61.04

L. argentatus: 50.4
L. hyperboreus: 45.6

L. schistisagus: 59.5
L. glaucescens: 50.77
L. glaucoides: 47.0

Interestingly, the only part of your expectation that holds up is that L. canus (representing the earliest part of the ring species formation) has the highest level of heterozygosity, at 61.04; but after that, your expectation completely falls apart.

Actually I usually consider the possibility that the originating population could have lost enough alleles even to have fewer than later populations. It all depends on size of the daughter relative to the parent populations. But I suppose the most typical situation would be that the parent remains the larger.

This completely upends any notion that there is some kind of "trend" here, wherein "the overall trend would be to increasing homozygosity, which would show up more clearly after a series of population splits such as in ring species."

It would upend it if in fact the conditions I give in my argument applied, but they donít. Absolute reproductive isolation after the population split is essential to my prediction of this overall trend.

And why, if your argument is actually biologically valid, do we not see the trend toward homozygosity exactly where you say we should find this trend -- in ring species?

I thought I was clear about the requirement for reproductive isolation but as often happens I donít get the whole thing stated in one place. I did expect gene flow and hybrid zones to occur in ring species, between some of the daughter populations for instance, which would interfere with the trend I expect to see, but I also didnít expect to see so MUCH of that kind of interference. I thought there must be some portion of a chain of species where reproductive isolation was maintained, where the decline in genetic diversity could be seen. If not then it isnít any kind of test of my prediction. Back to the lab idea.

But yes, increased homozygosity is THE sign of reduced genetic diversity. The question now is whether the fact that heterozygosity can increase in some cases is enough to overcome the predicted trend to increased homozygosity.

Well, clearly in the gull ring species, mutation, gene flow, and population growth is sufficient to overcome any trend towards increased homozygosity. So we have biological evidence that this trend doesn't actually do much to impede a reversal towards heterozygosity and genetic diversity.

This is where you revealed that reproductive isolation was not maintained between the gull populations. Also when I allowed that heterozygosity might increase in some circumstances I had in mind the conditions of my argument, mainly absolute reproductive isolation. The idea is that even in this situation heterozygosity might increase at some loci just from the new gene frequencies, though I thought it would have to be a rare occurrence. Nevertheless NOT due to gene flow or mutation or even population growth.

If a given locus exhibits a high degree of heterozygosity within a population, it means that there's whole range of different, diverse allelic combinations at that locus.

It MAY mean that but not necessarily. If one or more of these alleles are high frequency in the new population so that a particular phenotype emerges from those particular alleles, the others are most likely going to drop out eventually. And if they instead are low frequency by comparison with the parent population itís most likely only a few of the allelic possibilities came over to the new population anyway, and any that are very low frequency will certainly drop out.

Ipso facto, there's an increase in genetic diversity when there's an increase in heterozygosity (and here, when I say "increase," I do not mean an increase in frequency of a particular allelic combination; I mean an increase in diverse allelic combinations throughout the population).

But frequency canít be ignored here because frequencies are what change with the formation of a daughter population. To get an increase in heterozygosity over homozygosity from the parent to the daughter population means that you are getting more individuals that are heterozygous at a given locus than was the case in the parent population. Itís all about frequencies. And you arenít going to get an increase in those ďdiverse allelic combinations throughout the populationĒ unless they too came over to the new population in greater numbers than they existed in the parent population.

The question, again, is whether this increase in heterozygosity could occur in a geographically / reproductively isolated daughter population to any extent to offset the trend to homozygosity or reduction of alleles.

And the answer to that question is a resounding "yes."

Canít be since your example of the gulls was NOT of geographically / reproductively isolated daughter populations.

To further bolster this answer, I will draw an example from human genomics.

In particular, let's look to a small island in the Mediterranean, Sardinia. The human population in Sardinia has grown in size generation over generation, without immigration (so it's been an isolated population), as evidenced by sequence analyses of the D loop region of the mitochondrial genome and nuclear DNA polymorphisms (see references 18 and 19 in Di Rienzo et al., 1994).

So to re-quote you:

"...the question, again, is whether this increase in heterozygosity could occur in a geographically / reproductively isolated daughter population to any extent to offset the trend to homozygosity or reduction of alleles."

In fact, there is an excess in the number of alleles in the population (this is known as "allelic richness," and is another measure of genetic diversity), compared to the proportion of individuals who are heterozygous at a given site (see Cornuet and Luikart, 1996). In other words, while there isn't a striking degree of heterozygosity, there is a high prevalence of the number of different alleles in the population at a given chromosomal locus, which in turn means that mutation -- coupled with population growth -- has fueled the rise of new alleles. And that means that far from witnessing a decrease in genetic diversity, this geographically isolated human population has seen an increase in genetic diversity.This makes sense, of course, from a population genetics perspective -- for if the population steadily grows over time, then mutation plays an increasingly major role in shaping genetic diversity than genetic drift or selection does. That mutation has increased genetic diversity in the Sardinian population is evidenced by the high ratio of allelic richness to heterozygosity. This is exactly what we would predict if the Sardinian population has grown over time, without immigration, as other lines of independent evidence demonstrate.

This would be more convincing if you knew the original state of allelic richness in the population. As it is, thereís no real way of telling if these things are an increase over time, such as by mutation, or reflect the original situation as it played out over the generations. In fact how much is known about the original settlers anyway? How far back does the history go?

And this uncovers a lethal blow to your argument: namely, population growth is a very simple mechanism that can relatively easily offset an increase in homozygosity in a reproductively isolated population. Both the equations of population genetics, and real-world observations, demonstrate this.

Yes, IF mutations really do contribute to the genetic diversity of a population, and IF this occurs after a new subspecies has developed from its own set of gene frequencies due to a population split, then youíll lose your subspecies as the mutations interfere with it, which is something Iíve said many times too. Youíll get your increased genetic diversity but that means interfering with the processes of evolution that brought about the new species or subspecies. Getting a new species or subspecies is what Iím trying to keep in focus, and that comes about by losing the alleles for the emerging new phenotype or phenotypes in the new isolated population. This is why I like the examples from domestic breeding, at least as it used to be done, which rather drastically selected the preferred traits, losing all the genetic material for every other trait possible at the chosen loci. Thatís how you get the striking breeds, by losing the genetic diversity that underlies all the other breeds. If you then throw a mutation or three into the mix, at least where it can affect the selected traits, you wreck your breed. As people keep telling me, Nature doesnít care, and of course that is true, but Nature does happen to produce new subspecies, itís quite a common situation, ring species do a lot of that, and if thereís a lot of gene flow or mutations youíre not going to get or keep recognizable species, theyíre going to go all motley. So ring species preserve their characteristic traits only where the additive processes are limited.

Put differently, a reproductively isolated population might initially have a low amount of genetic diversity, but by growing in size generation after generation, the number of different, diverse alleles steadily increase (due to mutation) -- providing the increase in genetic diversity that can further drive evolution.

Well, this is clearly what the ToE implies and everybody here seems to assume, but in fact this increase only occurs over the dead body of evolution as it were. That is, you cannot keep a breed or a new species if new genetic diversity keeps being added to it, because getting a new species REQUIRES a loss of genetic diversity. Now if this should occur youíll definitely have your increased genetic diversity as a new motley collection of phenotypes within your population, but evolution will have ceased. UNTIL some form of selection occurs again, either a population split or even just drift, and youíll get a new phenotypic appearance due to losing the alleles for other phenotypes. And maybe youíll get a new species again. But again if genetic diversity increases at that point, bye bye new species. This isnít anything the ToE ever had in mind. Because the fact of loss of genetic diversity to bring evolution about isnít recognized.

You are describing a situation that starts out with high genetic diversity in general, which I suppose to generally increase the farther back you go along any evolving line, and where that is the case there should still be a trend to increased homozygosity all down the evolving chain of daughter populations, but it wouldnít be particularly dramatic until you have less genetically diverse populations splitting into daughter populations, especially into significantly smaller populations.

See the microsatellite heterozygosity data from the gull ring species, above, which is contrary to the expectations of your idea. That being said, you have yet to demonstrate that (1) population growth, and (2) mutation is not sufficient to reverse any trend towards homozygosity.

Well, I made that case again for the umpteenth time above. It COULD reverse the trend of course, but by interfering with evolution (meaning the production of a new species or subspecies, i.e. a population thatís mostly or completely homogeneous in its shared traits that differentiate it from all other populations of the same Species or Family or whatever the relevant reference group is). I donít think population growth does that by itself, but mutations, if they really occur as you expect, would do it. The point is that it's active evolution I'm talking about always, of course it has to have genetic diversity to work on but if it's added at the wrong point you can't get evolution, meaning you can't get new species or subspecies, or you'll undo them after you get them, and that is just not evolution.

There is absolutely no reason why these processes cannot, under any biological or evolutionary circumstances, increase genetic diversity in a reproductively isolated population (as measured by heterozygosity, nucleotide sequence divergence, or allelic richness).

That may be true, but itís interesting then that it doesnít happen much if at all in established domestic breeds where reproductive isolation is carefully maintained. And again, if it did it would only destroy the breed, just as it would the subspecies in the wild, interfering with all the hard work done by the evolutionary subtractive processes in the service of bringing about the new species, subspecies, variety or breed.

There's more to this post but I'm going to have to come back to it later.

The thing about the gull ring species is that you do get some evolution, you do get new species, but the continuation of gene flow means that it's a sort of compromise. Continuing or increased genetic diversity doesn't contribute to the evolution itself, though it may contribute a few traits to the mix, and evolution really doesn't need any such additions. There's quite enough in the original collection of gene frequencies to create a whole new subspecies from that alone if reproductive isolation is maintained. Nature of course doesn't care if it gets gulls with gene flow or in perfect isolation, and the more gene flow the more species you can get too because the loss of genetic diversity is slowed. Slowing it is probably a good thing for the gulls of course, the way new breeding practices of including other breeds in your selected breed is good for its health; but that doesn't change the fact that evolution itself REQUIRES a loss of genetic diversity to get the changes called evolution. The point is that the ToE stands or falls on the claim that the production of new phenotypic variations has no stopping point. But it clearly does when it's doing its thing in isolation.


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Faith
Member
Posts: 24846
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 11 of 30 (785202)
05-29-2016 10:30 AM
Reply to: Message 3 by Genomicus
05-28-2016 2:06 AM


Re: The Biological Evidence
THE REST OF MESSAGE 3.
Certainly didn't expect this to take so much time, and I know I'm being repetitive too, but it seems necessary. Anyway this should finish Message 3, then there are a couple more posts to respond to.

================================

In any case I think youíd be very hard-pressed to demonstrate that Iím wrong about the TREND to decreased genetic diversity, or to make a case for an actual increase. Population splits do very much what natural selection does as far as changing gene frequencies goes, and youíve agreed that natural selection reduces genetic diversity. A daughter population is a sort of selected population, randomly selected in this case, and even if some increase can occur over that of the parent at some loci thereís no way that could be the trend of change, because of the principle you have also already agreed with, that developing new phenotypes requires the loss of competing alleles. (Even in the case of our new high frequency Bís there is a reduction of the bís after all.)

Sure, the fixation of a novel phenotype in the population does mean that the competing alleles are lost. So what?

Thatís way too specific. Wherever there are new high frequency alleles in the daughter population youíll get new phenotypes emerging and other alleles being lost, with the general trend to increased homozygosity.

Although I agreed that there could be increased heterozygosity in the new population at a locus that was predominantly homozygous in the parent population while more of the heterozygous genotypes came over to the new population, Iím really unsure of that. And itís not likely to be a very common situation anyway. If there is a trend to homozygosity overall then some heterozygous genotypes will become homozygous in the new population.

So what? There's still plenty of other chromosomal loci which will be increasing in diversity due to mutation,

Again if you are relying on mutations to keep occurring in the population you are not getting a clearcut species, which is the whole point of evolution. Same as if you are developing a breed of cattle and that population keeps getting mutations, youíre never going to get the true breed breeders are always looking for. Or used to be looking for. Mutations do not further evolution, they slow it down at best and completely prevent it at worst. If you want a true breed you do not want mutations; same in the wild: youíll get the clearest new species where you have ZERO gene flow or mutations. I guess you could ask if evolution really depends on getting such clearcut species, but what Iím going on is the usual idea that change or variation is open-ended and goes right on through microevolution into macroevolution producing an entirely different species, a not-dog from a dog etc. Over millions of years of course. But if the way evolution works is by reducing genetic diversity to get the new species, then itís going to come to an end at the boundary of the Kind before you get to macroevolution; in fact that end should be the definition of that boundary. And if you keep adding mutations all youíll do is slow down the evolution so it takes a lot longer to get to that point; and if you slow it down enough so that you never get to that point then you have no breed or species at all and how is evolution possible at all in that case?

and this provides a "fresh batch" of diversity which natural selection can operate on when the environment changes.

Or random selection can work on for no particular reason at all except that Nature seems to like variety. But anyway, again, same refrain here: yes if mutations really do occur as claimed and really do increase useful genetic diversity, youíll get new phenotypes for selection to work on. But you wonít get a new species or variety until selection DOES work on it, increasing some and losing others, which can occur whether the gene pool was built in or created by mutations (which always seems like a totally unnecessary redundancy to me but oh well Iím just a nutty creationist). So youíve got your gene pool and selection works on it, changing gene frequencies to create the new species and losing alleles in the process, which must happen to get a new species. Otherwise with all those mutations popping up in your population all youíll have is a scattering of new phenotypes within the population, a motley collection. It has to be selected and reproduced down the generations to start to get a new homogeneous look or a new subspecies.

And this increase in genetic diversity in the numerous chromosomal loci which are not under strong selective pressure means that further population splits can recover genetic diversity simply through mutation and population growth.

And lose their character as homogeneous species or breeds in the process, thus preventing evolution. Evolution can get stopped by adding genetic diversity which interferes with species formation, or it can get stopped by operating in reproductive isolation which will form a nice clear species which requires loss of genetic diversity and THAT will bring evolution to a halt. Either way evolution is a lost cause.

OK, I see, and this is so as a TREND and with respect to the salient characteristics of the subspecies that is developing. There could still be great diversity for other characteristics of the creature that donít show up in the new phenotype.

So if there can still be great diversity for other characteristics that aren't relevant to the phenotype that's being fixed in the population, then what's the problem here? Why can't this increased genetic diversity also happen in daughter population that successively split off from each other?

Well, with each new daughter population you are losing genetic diversity throughout the genome just because you are starting with fewer individuals each time. Even if greater diversity remains in other parts of the genome that too is getting reduced though perhaps not to the extent of the salient traits.

The estimate of heterozygosity for human beings now is something like 7% IIRC, but taking a wild guess back a few thousand years it could have been as much as 50% or 70% or higher, and some loci could have retained a higher percentage than others even now.

Are you willing to stake your idea on the notion that a few thousand years ago human heterozygosity was as high as 50%? What about overall nucleotide sequence diversity? Do you think there has been an increase or decrease in nucleotide sequence diversity over the course of human history?

I wouldnít know how to judge that. As for insisting on any particular percentage at any given time thatís not possible either, itís a guess extrapolated back from the loss of genetic diversity that accompanies the formation of new species. If my argument is at least generally correct then itís a good guess. Best I can say.

For if allelic sites, or chromosomal loci, do not become increasingly homozygous while a novel trait is evolving, then the population has plenty of genetic diversity -- even if novel traits are evolving. And if the population has this genetic diversity, your argument falls apart.

Hardly. That increase in genetic diversity is absolutely useless to evolution as Iíve tried to show above.

No it doesnít, it just means, as I say above, that the loss is a trend over time.

Nope, because the trend can become reversed by mutation and population growth.

Which Iíve argued above prevents evolution from happening. That may be a good thing for biological systems, but it doesnít bode well for the ToE.

And of course population growth itself accomplishes nothing, except supposedly this wishful opportunity for mutations to increase genetic diversity. But I think this expectation is truly wishful and not real, which is proved by the situation of the elephant seals which have increased enormously in population size in a condition of genetic depletion that shows no signs of being mitigated by any increase in mutations.

There was a lot more genetic diversity in the past, that has been decreasing over time...

You state this as if it is an empirical observation.

Yes, I suppose I should always remember to say, ďaccording to my theoryÖĒ

It is not; quite the contrary, in fact -- human genetic diversity, on the whole, has increased over time. Would you like me to provide the consilience of independent lines of biological evidence for an increase in human genetic diversity over time? In the meantime, you can present your evidence that human genetic diversity has been decreasing. If you do not have such evidence, then your argument is little more than an anti-evolutionary fantasia.

You are welcome to provide your evidence, keeping in mind that if it is over my head thereís no point. Youíve been doing a pretty good job of keeping to explanations in English so if you can give your evidence with the same clarity we can see what comes of it.

None of this changes my argument that homozygosity will be the trend down any line of evolving subpopulations, slow or fast, dramatic or hardly discernible, but always the trend.

Do you have any evidence that this "trend" cannot be reversed or counterbalanced by sufficient mutation or population growth?

Just the argument that mutation would interfere with developing species, which I think Iíve made pretty clear, and that population growth in itself doesnít increase genetic diversity anyway.

I will say that interfering with the evolutionary processes is probably a very good thing and seems to be the aim of conservation efforts anyway. Just as breeders no longer aim for pure breeds because of genetic depletion, conservationists try to interfere with the same situation of genetic depletion in nature. I read about a population of salmon in which a few individuals got lost in a tributary and developed a new highly undesirable subspecies with a great reduction in genetic diversity. Conservationists had the job of reincorporating them with the main population, increasing gene flow. If speciation has occurred and interbreeding is no longer possible then nothing can be done to improve the situation. Itís BECAUSE evolution tends to genetic loss that measures need to be taken to counteract it.

The idea that a mammal evolved from a reptile assumes enormous continuing or growing genetic diversity (over hundreds of millions of years yet)...

Well, we have evidence that speciation can occur followed by an increase in genetic diversity. See the microsatellite heterozygosity data on the gull ring species, above.

Well, be careful of your terminology. Did ďspeciationĒ actually occur, in which interbreeding with other population had become impossible? Or was gene flow still going on so that the drastic loss of genetic diversity was impeded?

And, of course, there's nothing stopping mutation and population growth from adding genetic diversity to a population, even while a few phenotypes are being fixed. There will still be plenty of chromosomal loci which will see an increase in heterozygosity or allelic richness, and there's nothing stopping that.

I certainly hope Iíve put that idea to rest by now.

But if selection reduces genetic diversity then itís going to treat any source of genetic diversity the same way...

No, because plenty of loci won't be under any significant selection pressure.

The mere formation of a daughter population, which is a form of random selection, will reduce the genetic diversity at all loci if it has fewer individuals, which is the usual case, or even reduce it but to a lesser degree if the populations are about equal in size.

Wut? A single mutation won't add significant genetic diversity to the cheetah population. What's needed is an elevated rate of mutation in the cheetah population if they are ever to get out of their "genetic purgatory." The equations in the OP demonstrate very nicely why there's extremely low genetic diversity among cheetahs; the small population size, coupled with a not-very-high mutation rate, means that genetic drift and inbreeding (which is basically just an extension of the sampling error that genetic drift is) will continue to decrease the diversity of the cheetah gene pool. So I have no idea where this "waiting around for a mutation to get them out of their 'genetic purgatory'" comes from, since it's not like a single mutation will do that.

OK, so any genetically compromised species will face the same kind of problem, and if thatís what ďspeciationĒ amounts to, weíve got a deteriorating system that isnít going to be able to reverse itself.

Speciation doesn't amount to a "genetically compromised" population. Cheetahs underwent a significant population bottleneck; but if a founding population is sufficiently large, then there is nothing of necessity preventing mutation and population growth from replenishing the genetic diversity of the population.

The problem is that speciation seems to be the product of a population split, and since it produces inability to interbreed with other populations it suggests a condition of genetic reduction to depletion to me. Perhaps there are some cases where itís not as compromised as that, but as for the idea that mutations are going to come along and save the day, again wishful thinking seems to be the ďevidenceĒ for that, and even if it occurred it would mess up your brand new species so whatís the point of a Speciation Event anyway?

Sometimes the population is too small, and the mutation rate to small, that extinction results.

Yes, the cheetah is remarkable for having survived at all in its genetically depleted condition.

Other times the population size is not too small, and the mutation rate is sufficiently large, that genetic diversity can increase. This not only makes perfect sense from the mathematics of population genetics, but it's also what we see in biology.

Well, I have my serious doubts but you are welcome to try to prove it. In ordinary English please.

Your error is in assuming that all founding populations are equal, all mutation rates are equal, and all selective pressures are equal. They are not.

I think perhaps a lot of what Iíve said above should show that I donít assume such things.

Your argument not only makes a failed prediction (see ring species example of gull taxa), it also ignores perfectly valid and demonstrated principles of genetics.

I think Iíve shot down the gull example, and as for the supposedly demonstrated principles Iím ignoring, youíve failed to show me any such thing.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 3 by Genomicus, posted 05-28-2016 2:06 AM Genomicus has not yet responded

Replies to this message:
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Genomicus
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Posts: 815
Joined: 02-15-2012
Member Rating: 4.7


Message 12 of 30 (785207)
05-29-2016 5:12 PM
Reply to: Message 9 by Faith
05-28-2016 9:08 AM


Re: The Biological Evidence
I've concurred that selection at a locus under consideration reduces the genetic diversity of that locus. That there is a variety in heterozygosity in daughter populations in ring species is exactly what we'd expect if genetic diversity is determined by a combination of mutation rate, population size, genetic drift, and selection. Population growth and mutation rate are sufficient to add genetic diversity to daughter populations.

Yes of course, "if genetic diversity is determined by a combination of mutation rate, population size, genetic drift, and selection" you'll get increased heterozygosity. But that isn't evolution...

That isn't evolution according to someone with little more than a high school level of understanding of biology or according to the relevant experts?

...that isn't how new species come about.

Sure it is. These are all factors that contribute to the formation of new species. Mutation + positive selection + genetic drift all work together to create new species. A population need not be geographically isolated from its parent population in order to become a novel species. The population merely must occupy a somewhat different ecological niche; genetic divergence (through mutation, drift, selection) from the parent population then, over the course of generations, leads to the emergence of reproductive barriers which define the new species.

That's a see-saw between adding and subtracting that overall gets called evolution but it's only the subtractive processes that form the new species.

No, that's not true. It is the genetic divergence between a daughter population from its parent population that eventually gives rise to reproductive barriers (as characterized by morphology or molecular/cell biology) between the two populations, and this is speciation. And what creates genetic divergence between two populations? Mutation. Genetic drift. Population growth. Selection.

From this perspective, there's no "adding and subtracting," there is only genetic divergence between populations (which can be counteracted by gene flow, though not always -- e.g., when the ecological niche selects against immigrants).

...but it's only the subtractive processes that form the new species.

Whoever or whatever gave you that idea?

ABE: Why not bacteria? Because they're weird, they're ugly and they don't sexually reproduce. And I don't think they behave in exactly the same way as diploid animals at all. That's why it's got to be mice or something I can talk to and pet.

Well, bacteria are actually freakin' beautiful, but by your description, it seems your proposed lab experiment can be done with diploid yeast populations.

Anyhew, responding to the rest of your posts later.


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 Message 9 by Faith, posted 05-28-2016 9:08 AM Faith has responded

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Faith
Member
Posts: 24846
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 13 of 30 (785211)
05-30-2016 1:20 AM
Reply to: Message 12 by Genomicus
05-29-2016 5:12 PM


The Creationist Paradigm Blues
Genomicus writes:

I've concurred that selection at a locus under consideration reduces the genetic diversity of that locus. That there is a variety in heterozygosity in daughter populations in ring species is exactly what we'd expect if genetic diversity is determined by a combination of mutation rate, population size, genetic drift, and selection. Population growth and mutation rate are sufficient to add genetic diversity to daughter populations.

Faith writes:

Yes of course, "if genetic diversity is determined by a combination of mutation rate, population size, genetic drift, and selection" you'll get increased heterozygosity. But that isn't evolution...

That isn't evolution according to someone with little more than a high school level of understanding of biology or according to the relevant experts?

Interesting how predictable it is that eventually the debate will devolve into personal attack. I wonder what I said that got to you.

I would think you would have known from everything I've said so far that I differentiate between the additive and the subtractive processes. Calling all of them collectively "evolution" is standard practice, but in reality they do different things. It's the subtractive processes that take the accumulated genetic diversity and shape it into new varieties and species, which is where what I call "active evolution" is happening, while the accumulation of diversity would never ever form a new species. That takes selection. Which I've said so many times it's rather disingenuous of you to pretend the point hasn't been made.

...that isn't how new species come about.

Sure it is. These are all factors that contribute to the formation of new species.

Yeah yeah yeah, why do you feel the need to repeat the party line which I've been at pains to divide into its relevant opposing activities because that's what makes my point? Anything to obscure my point perhaps? You don't have to like my way of dealing with the party line, but honesty should compel you to recognize the logic of it so you can follow my argument.

Mutation + positive selection + genetic drift all work together to create new species.

What's the point of debating with you if you won't acknowledge the argument I'm making? I even accept mutation for the sake of argument, merely mentioning from time to time that I don't think it contributes anything positive to the formation of species. But I do include it in my reasoning. If I'm so educationally inferior it shouldn't be hard for you to follow that reasoning and indulge me after all.

A population need not be geographically isolated from its parent population in order to become a novel species.

I emphasize it because it makes my point most clearly, but yes, drift can do it within the population, and you can get species even with gene flow, but the problem with this is that it blurs the point I'm making: that it's the selective processes that do the work of forming the species by changing gene frequencies. That includes drift, natural selection and the random selection I like to focus on for the sake of clarity. All those are the selection or subtractive processes but the formation of a separate reproductively isolated population is the clearest example of how it works.

The population merely must occupy a somewhat different ecological niche; genetic divergence (through mutation, drift, selection) from the parent population then, over the course of generations, leads to the emergence of reproductive barriers which define the new species.

Reality is messy; that's why it helps to have a model that can streamline the essential points as I'm trying to do.

That's a see-saw between adding and subtracting that overall gets called evolution but it's only the subtractive processes that form the new species.

No, that's not true. It is the genetic divergence between a daughter population from its parent population that eventually gives rise to reproductive barriers (as characterized by morphology or molecular/cell biology) between the two populations, and this is speciation. And what creates genetic divergence between two populations? Mutation. Genetic drift. Population growth. Selection.

This is just a terminologically different way of saying what I'm saying. The divergence is shown in the new set of gene frequencies. Allowed to mix through the new population for some number of generations the population can in fact arrive at a condition of genetic inability to breed with other populations. Of course I don't think mutation contributes anything to this, it's just part of the Evo Creed which must be recited from time to time, but drift, yes and selection absolutely. Population growth alone doesn't do anything genetically.

From this perspective, there's no "adding and subtracting," there is only genetic divergence between populations (which can be counteracted by gene flow, though not always -- e.g., when the ecological niche selects against immigrants).

Or the new population is sufficiently geographically isolated that immigrants don't arrive there anyway.

(Perhaps I reject too much of Evo Theory to be able to have a meaningful discussion with anyone as immersed in it as you are. I don't even think the concept of a "niche" has much to do with what actually happens in the formation of species -- some, I'm sure, but not much. I think most of it is random and accidental, that environmental differences don't affect how species form anywhere near as much as the theory requires, that natural selection or "fitness" really doesn't either except in certain extreme situations, and so on.)

...but it's only the subtractive processes that form the new species.

Whoever or whatever gave you that idea?

It's my own personal observation and if you would just follow the argument I think you'd have to get what I mean by it because I've been emphasizing and explaining it all along,

But I'm starting to think, as I say above, that you habitually think within such a different frame of reference perhaps there's just no way to bridge the gap between our different viewpoints even enough to debate them. I thought facts would just be facts but unfortunately there's really no such thing; facts naturally come with tons of theoretical baggage attached. So you can't help imposing that baggage on me and demanding that I conform my thinking to it, making anything I say that's contrary to it simply "wrong." Except that it would be nice to be able to think mathematically and have more knowledge of the current state of biological education, I don't really feel much of a lack, since the argument I'm trying to make doesn't depend on any of that. Except that more education would make me a dues-paying member of the guild, which of course has some value, I don't think it would further my argument to be able to use the lingo more fluently. Creationists who do have higher education don't get any further with their arguments either.

As for bacteria, yeah, I don't trust bacteria, that's what it comes down to. I doubt that what can be learned from them can be meaningfully applied to mammals or other higher animals.


This message is a reply to:
 Message 12 by Genomicus, posted 05-29-2016 5:12 PM Genomicus has not yet responded

    
Faith
Member
Posts: 24846
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 14 of 30 (785212)
05-30-2016 1:40 AM
Reply to: Message 11 by Faith
05-29-2016 10:30 AM


Re: The Biological Evidence
It is not; quite the contrary, in fact -- human genetic diversity, on the whole, has increased over time. Would you like me to provide the consilience of independent lines of biological evidence for an increase in human genetic diversity over time? In the meantime, you can present your evidence that human genetic diversity has been decreasing. If you do not have such evidence, then your argument is little more than an anti-evolutionary fantasia.

Can you really show INCREASE, in terms I can follow?

To show an increase would require knowledge of its level in the past, and I don't trust DNA analysis to tell us that, the same way I don't trust the "fossil record" or radiometric dating to tell me how old the earth is -- because there's no way to test the test when it's about the unwitnessed past. And I can't trust somebody who's immersed in Evo assumptions to interpret things accurately either. Sorry.

I don't think of humans as lacking in genetic diversity on the whole, but would expect it to show up in isolated populations. But the sophisticated genomics you use to prove the level of diversity is of course mystification to me. And totally untrustworthy, especially when you can pronounce my argument about ring species failed without following the conditions of the argument.

My evidence that human genetic diversity has been decreasing is more a necessary deduction from my argument than direct evidence. However, I'd include the huge amount of junk DNA in the genome as evidence myself, which isn't likely to convince you of the point because you could only believe it's explained sufficiently by Evo Theory.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 11 by Faith, posted 05-29-2016 10:30 AM Faith has not yet responded

    
Genomicus
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Posts: 815
Joined: 02-15-2012
Member Rating: 4.7


(4)
Message 15 of 30 (785234)
05-31-2016 5:28 AM


A Consilience of Genomics Evidence
At the onset of this debate, one of my stated intentions was to ďshow that Faith's argument is not a viable critique of the plausibility of the modern evolutionary synthesis.Ē Even a cursory reading of Faithís responses will reveal that far from presenting a robust critique against the modern evolutionary synthesis, she is instead focusing on a very narrowly described anti-evolutionary fantasia that is not grounded in biological reality.

As I continue to marshall the evidence that refutes Faithís notion, the keen reader will note a common, recurring theme: namely, that Faithís argument is exceptionally ineffective at making accurate predictions about the living world. So while her argument is repeated over and over again, and expectations of the argument tentatively offered up, a consilience of observations, experiments, and research from a breathtaking range of biological disciplines continue to refute her notion.

For the sake of making this discussion easier to follow, I have organized my rebuttal in topical fashion, rather than in chronological order:

I. General Responses
II. The Evidence from Human Genomics
III. The Evidence from Elephant Seal mtDNA

GENERAL RESPONSES

That isn't evolution according to someone with little more than a high school level of understanding of biology or according to the relevant experts?

Interesting how predictable it is that eventually the debate will devolve into personal attack. I wonder what I said that got to you.

That's not a personal attack in any way. It's merely highlighting the curious nature of your reality, wherein you get to decide what "evolution" means even though you don't know what electron transport chains and cytochrome c is.

...you cannot keep a breed or a new species if new genetic diversity keeps being added to it, because getting a new species REQUIRES a loss of genetic diversity.

This is not true. The emergence of a new species only implies a loss of genetic diversity at a few chromosomal loci, namely those loci with alleles directly involved with reproduction. For cladogenesis to occur, the only real, relevant requirement is that a population is not able to reproduce with the parent species.

Indeed, for some Metazoa -- such as Spodoptera latifascia and S. descoinsi -- only a couple of genes are required to change for reproductive barriers between the two populations to arise (Monti et al., 1997).

The salient point here is that you have yet to demonstrate (either via biological observation or through principles of genetics) that the emergence of a new species necessarily entails a loss of genetic diversity at most chromosomal loci. For if only a couple of genes are required to change for speciation to occur, then there are hundreds and hundreds of other loci which can continue to diversify, increasing the overall, net genetic diversity of the population even while speciation is occurring.

This alone is enough to render your argument egregiously flawed, but I will press on.

So what? There's still plenty of other chromosomal loci which will be increasing in diversity due to mutation...

Again if you are relying on mutations to keep occurring in the population you are not getting a clear-cut species, which is the whole point of evolution.

You have to demonstrate the truth of this above statement on mutations and the so-called clear-cut-ness of species. So demonstrate it.

It's relatively easily dismissed, anyway. We know mutations regularly occur in gametes, and we know that these mutations have a certain probability distribution of spreading throughout the population. So long as these mutations do not alter the reproductive capability of the individuals in which they are found, then these mutations will not make the species any less "clear-cut."

Same as if you are developing a breed of cattle and that population keeps getting mutations, youíre never going to get the true breed breeders are always looking for.

Except that mutations are often what create the phenotypes that lead to the "true breeds." Consider, for example, Belgian Blue cattle, which have been bred through multiple generations to get the desired muscular physique. This phenotype is the result of a 11 base pair deletion in the gene coding for myostatin (Kambadur et al., 1997). In other words, it is a mutation that originally gave rise to the double-muscle phenotype.

Furthermore, mutations do not of necessity "mess up" the breed. Mutations can occur anywhere in the genome, and anywhere along a chromosome. In the case of the Belgian Blue cattle, so long as extensive mutations do not occur in the myostatin gene (and functionally related genes), then the breed's desired phenotype will remain intact.

So your argument really doesn't make any sense at all.

...youíll get the clearest new species where you have ZERO gene flow or mutations.

You're right about the gene flow, but deathly wrong about the mutation part. Mutations in a new population increase the genetic distance between the parent and daughter populations, and this is really all that needs to happen for reproductive barriers between the two populations to emerge.

But if the way evolution works is by reducing genetic diversity to get the new species...

Only a few loci within the new population will lose diversity, as a consequence of reproductive system related phenotypes being fixed in the population. The other hundreds and thousands of loci can increase in diversity, and you have yet to counter this argument effectively.

And if you keep adding mutations all youíll do is slow down the evolution...

No, mutations speed up the emergence of evolutionary adaptation. Why do you think viruses are able to evolve drug resistance so rapidly? It's because of their rapid rate of mutation, coupled to rapid generation time.

So if there can still be great diversity for other characteristics that aren't relevant to the phenotype that's being fixed in the population, then what's the problem here? Why can't this increased genetic diversity also happen in daughter population that successively split off from each other?

Well, with each new daughter population you are losing genetic diversity throughout the genome just because you are starting with fewer individuals each time.

Yes, but mutations will add to the genetic diversity. You still haven't refuted this point.

*****

THE EVIDENCE FROM HUMAN GENOMICS

This would be more convincing if you knew the original state of allelic richness in the population. As it is, thereís no real way of telling if these things are an increase over time, such as by mutation, or reflect the original situation as it played out over the generations. In fact how much is known about the original settlers anyway? How far back does the history go?

A common thread you will soon discover being weaved throughout this discussion is your claim that we canít really ďtell if these things are an increase over timeĒ -- only to be confuted by numerous lines of research which mesh together in elegant concordance.

First, archaeological and census evidence indicates that the Sardinian population (which goes back thousands of years) never grew beyond about 300,000 individuals until around 1728, when the population began to grow rapidly (see CalÚ et al., 2008).

Second, sequence analysis of Sardinian mitochondrial DNA also suggests that this population was initially a small ďbottleneckĒ but has experienced growth over time (Di Rienzo and Wilson, 1991). This is further corroborated by research on allelic richness and heterozygosity, which can indicate population growth from an initial, smaller population (Cornuet and Luikart, 1996). So we have here multiple lines of independent evidence for a small founding population on Sardinia, which was followed by population growth.

There is, moreover, compelling genetic evidence from nuclear DNA polymorphisms, mitochondrial DNA sequences, and other markers that the Sardinian population has been isolated with no gene flow from outside the island (Di Rienzo et al., 1994).

Now, for the clincher. In a beautiful piece of genomics research, Caramelli and colleagues (2007) analyzed mtDNA D-loop sequences (which are basically the most variable regions of the human genome) from ancient Sardinians who lived between 3,430 and 2,700 years ago (the DNA was extracted from teeth using a highly rigorous laboratory approach). The diversity of these sequences was then compared to the mtDNA of present-day Sardinians.

The haplotype diversity (a way to measure genetic diversity, and a form of heterozygosity) of the ancient population was 0.83, compared to a haplotype diversity of .96 for modern Sardinians (the larger the number, the greater the diversity). Revealingly, too, was the discovery that the average number of indels (a form of mutation) between sequences from the ancient population was a low 1.43, whereas the mean value for indels between modern Sardinian sequences was 4.68. This neatly demonstrates, again, that the modern Sardinian population has increased in genetic diversity, despite being isolated. The study by Caramelli and colleagues also provides evidence for clear genetic continuity between the ancient population and the modern Sardinian population, indicating a lack of gene flow from the ďoutsideĒ world.

So how does your notion explain the above experimental results, Faith?

*****

THE EVIDENCE FROM ELEPHANT SEAL mtDNA

Nope, because the trend can become reversed by mutation and population growth.

And of course population growth itself accomplishes nothing, except supposedly this wishful opportunity for mutations to increase genetic diversity. But I think this expectation is truly wishful and not real, which is proved by the situation of the elephant seals which have increased enormously in population size in a condition of genetic depletion that shows no signs of being mitigated by any increase in mutations.

And yet the molecular sequence data is in direct contradiction to your above statement. Again, I must call attention to how consistently, and how often, the expectations of your argument can be immediately eviscerated by what we observe in biological reality.

In the late 1800s, the northern elephant seal population hit an all-time low, with numbers dipping below a mere 100 individuals. However, the northern elephant sealís population size has recovered, and now has over 175,000 individuals.

This situation, then, allows an empirical test of the expectations of your argument. In an analysis of mtDNA sequences, Weber et al. (2000) sought to compare the genetic diversity of northern elephant seals prior to their bottleneck, during the bottleneck, and after the bottleneck when the population recovered.

Like other studies referenced in this response, the control region of the mitochondrial genome was used, given the highly variable nature of this genomic region. In other words, changes in nucleotide and haplotype diversity would show up most clearly in the D-loop region of mtDNA.

So what were the results (from Table 1 of Weber et al., 2000)?

Haplotype Diversity, Elephant Seal Population DNA from 1892: 0.00
Haplotype Diversity, Elephant Seal Population DNA from 1980: 0.53

Nucleotide Diversity, Elephant Seal Population DNA from 1892: 0.0000
Nucleotide Diversity, Elephant Seal Population DNA from 1980: 0.0086

What do these results tell us? Both haplotype diversity and nucleotide diversity of modern northern elephant seals are significantly higher than that of the elephant seal population from 1892, when the population hit an all-time low. And unlike heterozygosity, which is not necessarily the result of novel mutations, nucleotide diversity is the result of mutations introducing new DNA changes throughout the population. Furthermore, in recent history, the northern elephant seal population has not been subjected to gene flow from other species, so the only way these observations can be explained is through mutations.

To re-quote you, Faith:

ĒBut I think this expectation is truly wishful and not real, which is proved by the situation of the elephant seals which have increased enormously in population size in a condition of genetic depletion that shows no signs of being mitigated by any increase in mutations.Ē

Yet here we have direct empirical evidence that categorically refutes that comment, and further bolsters my argument that population growth, coupled with mutation, can increase the genetic diversity of a population.

So how does your notion explain the above experimental results, Faith?

*****

My evidence that human genetic diversity has been decreasing is more a necessary deduction from my argument than direct evidence. However, I'd include the huge amount of junk DNA in the genome as evidence myself, which isn't likely to convince you of the point because you could only believe it's explained sufficiently by Evo Theory.

Explain why you think so-called junk DNA in the human genome is evidence for your position, so that I can more properly refute it.

More later on ring species, etc. I think you've got a lot to chew on here, and some experimental results to explain -- and that's an understatement.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : Multiple cups of coffee to stay awake = multiple typos.


Replies to this message:
 Message 16 by Faith, posted 06-01-2016 8:04 AM Genomicus has responded
 Message 17 by Faith, posted 06-01-2016 12:15 PM Genomicus has not yet responded
 Message 18 by Faith, posted 06-01-2016 3:56 PM Genomicus has responded

  
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