Evolution Requires Reduction in Genetic Diversity

Evidently and crystal clear, but: Do you mean the 10% functional part of the genome affected by those indels, or, to be precise: do you mean that 10% of the indels have functional effects?Hence: Why should it? (again the question!)
Because 85-88% (after ENCODE) of the genome is merely junk.
When one of those parts is deleted by an indel, nothing happens with selective effects.
When something is inserted there, nothing happens as well unless the very rare instance this newly inserted chunk is immediately functional. Such insertions might get functional only after more future mutations. But measured just after the moment of insertion, no selection will be detected.My contention was: Now why would we need to see indels having selective effects in 100% of the genome when such effects are only to be expected in the 12-15% functional part of the genome? Moreover, indels may have direct effects too. If an indel deletes parts of the gene that encodes for cytC, for instance, it's over and out and a very strong selective effect takes place. Now, I wasn't referring to these direct indels. I was referring to indels that ONLY hit the (rather tiny) parts of the spacer DNA that separate genes.To be precise: two particular genes may be separated by larger chunks of spacer DNA. Hence, my argument only counts for the instances where genes are separated by rather small parts of spacer DNA. The larger such a spacer chunk, the less the odds of it completely deleted by an indel.So, I do not understand your argument "shouldn't we see selection against indels in 100% of the genome?" Well, I said I do not know any empirical studies on the energy budget of cells in relation to the energy consumption of transcription - maybe there are some approaches but I do not know any of those - but I tried to make my case by arguing why this energy consumption should be notable.Hence, those arguments were not assertions but arguments.
And their emptiness is still to be substantiated by you! OK, I understand now what you meant with low level transcription.
But as I understood, the making of nucleotides does energetically not come very cheap.
What you say is that junk DNA tends to be low level transcribed.
The low level transcription is already incorporated in my arguments. The tendency of junk DNA to be low level transcribed is counteracted by its majority in the genome. The 76% of total DNA transcribed minus the 12-15% found to be functional. Even when, as ENCODE also found, 70% of the transcription coverage was less than 1 transcript per cell. I agree but I was curious what precise share in the total energy budget it exactly is taking away. Of course junk DNA doesn't have such features. Otherwise, like cytC, it would be functional.
The functional parts of cytC are extremely conserved, otherwise, as I mentioned, it wouldn't be possible to transplant human cytC to algae without doing the latter any harm. But I was referring to the redundant parts of cytC. The 70% of its amino acids that seem to only be freeloading.Edited by Denisova, : No reason given.

My understanding from reading other articles is that it is the same general area, but not all in one column, and they are grouped by the geological layers they are found in, the names are for groups of layers, just as is done in the Grand Canyon.There are other nearby areas that have also been excavated without finding this lineage (I can provide more if you are interested). btw the thick part of the lines represents two standard deviations within each population ... so 95% of the fossils are grouped in the thick sections at each layer. The thin part of each line represents the full range of fossils from largest to smallest at each interval\layer within the remaining 5%. Here is the transcribed chart again for reference: Yes, because the more fossils found in a layer the better representation you have for the variations within the population. Yes, they are so similar that you can mix fossils from neighboring layers that are in the same size range and then not be able to sort them back out with confidence. Curiously what you have is the data that show just that, albeit with relative age from the layers, not specific dates from any other measurements. What theory Faith? and thus the relative ages of the fossils. Which you know is not true due to the strong degree of overlap in sizes, and because of the time between deposits: why would there be 80% overlap in sizes from one layer to the next if there were some magical sorting mechanism? Why would animals the same size be sorted into different layers? How would animals the same size be sorted into different layers? No Faith, it is looking at -- reading --what the evidence tells us: similar animals in discrete time differentiated layers, layers that have to be from different times laid one on top of the other. You acknowledge that superposition means upper layers came after lower layers Again, why would there be 80% overlap in sizes from one layer to the next if there were some magical sorting mechanism? Why would animals the same size be sorted into different layers? How would animals the same size be sorted into different layers? They were differentiated by age (teeth). Those labels are arbitrary human divisions for the purpose of discussion, based on the layer time intervals. Some other documents break the lineage into more divisions (ie - P. frugivorous just below N.nunienus). It is what the data shows. We know they are related because you could mix the same sizes from adjacent layers and not be able to sort them with confidence, and we know that the upper layer was deposited after the layer below it. Agreed. Mundanely true in that the same animal cannot become two fossils. Which is at odds with the evidence. Thus your interpretation fails to explain the evidence. Also at odds with the evidence that they came from different excavations in the same general area, and that adjacent areas have fossils of similar sized near relative Copelemur fossils but not Pelycodus fossils.So I will agree that Copelemur was a contemporaneous population inhabiting different nearby locations, morphologically similar but distinct enough to separate. Riiiiiiiiiiiiight, the offspring are somehow buried below the parents??? That is what the evidence shows. All we can know is what the data shows, but after several layers of consistent shift to larger sizes and no outliers (the thin lines show the full extent from largest to smallest) we can have confidence that certain size alleles are no longer expressed. Then they would be expressed. Remember that the thick parts of the lines encompass 95% of the fossils found, that the thin lines extend to the largest and smallest fossils in the remaining 5% so the probability of single individuals being significantly outside these limits is very very small. When you consider this small probability recurring at each level the possibility becomes vanishingly small. Precisely as seen at the top of the chart where there is the initial division. Population splits can only select alleles within that population -- selection does not create alleles. That is what you see at the time of the split, but then each population continues to diverge by developing sizes that are NOT in the parent\split population. The large group continues to grow to sizes not seen in previous populations with magical new size alleles, the small group revisits the sizes of the bottom population, but not seen in intermediate populations.If we consider this a test of your hypothesis that alleles are permanently lost then the evidence shows your hypothesis to be false.On the other hand if you now hypothesize that alleles from the parent population not seen expressed in the later populations are hidden but still exist in the "collective genome", then your hypothesis become useless because nothing is truly lost it just gets magically hidden until needed. Irrelevant to your problem. There would be a founder effect, but each population is large enough that inbreeding would not be a problem. Once they have divided selection would drive them further apart to lessen competition.The problem remains that the left hand small group branch recovers alleles that should have been lost if your hypothesis were correct. It isn't necessary, but it does happen. Here we see about a 50/50 split in size but a large variation remaining in each population -- as large a variation as seen in lower populations. In other words you have made up a "get out of jail" card that you can play every time your hypothesis is shown to be falsified by empirical evidence. It is a trend that has not been observed. Ever. What we see is occasional temporary depression of diversity at the time of population division, followed by increase in diversity within each daughter population as new alleles are added. By Mutation. Even when there is a very small founding population with very few alleles.The two populations at the top each have as much diversity as the populations at the bottom. Of course, because you don't accept actual evidence in place of imagination, especially when it invalidates your imagination.Enjoy

Yes, I believe it does!! Lol!

Oh my, do we really need to explain why or how upper layers come after lower ones?
We cannot even refer to obviousness here.Weird.
And absurd.

Blessed are the simple of minds.

No, Faith does understand the law of superposition, but she has a tendency to discard inconvenient facts when the counter her thinking, as you may have noticed.Enjoy

These work for me. Isolation initiates the process and the fixation of genetic incompatibility (post-zygotic separation) completes the process.Isolation may be over many many generations and over widely separate intermediate locations, with populations accumulating mutations, but genetic incompatibility isn't a foregone conclusion, especially if there is no stress/selection to change gene functions. Indeed. With the Asian Greenish Warbler Phylloscopus trochiloides we see separation and variation\modification resulting in a low occurrence of hybrids at the ring end overlap area, due to behavior\song\mating choice, but no definitive evidence of genetic incompatibility ...... however there could be reduced viability if some alleles are lethal but others are viable, and that could be a factor in the low recording of hybrids). From your H. Allen Orr paper The Population Genetics of Speciation: The Evolution of Hybrid Incompatibilities: If the left population had some (a) mixed with some (A) alleles, and the right population had some (b) mixed with some (B) alleles, then you could get: Of these only AB is not tested and could be lethal\sterile, and if so, then reproduction would be depressed compared to normal fertility, with the degree depending on the relative proportions of a:A and b:B in the breeding populations.And of course there could also be interaction with other genes that could affect viability\fertility of the hybrid.And some could be sex-linked so male (A) could mate successfully with female (B) but male (B) would be lethal\sterile when mated with female (A).It comes down to the fixation of the mutated genes in the populations and their effect on viability\fertility when the two populations meet. Exactly. Well I think they are just different forms of isolation, and I would list it

1. genetic incompatibility
2. geological separation
3. ecological separation
4. mating choice separation

... we can agree to disagree, but the way I see it is that there are several ways that subpopulations become isolated, and that it is the isolation that is critical for further genetic divergence.An example of (3) would be your Monkeyflowers, where different pollinators enable the isolation.An example of (4) would be the Asian Greenish Warbler in the overlap zone With the Monkeyflower we see a genetic basis for isolation by causing a shift in how they interact with the ecology (pollinators) while not being genetically incompatible. With the Greenish Warbler we see a genetic basis for isolation by causing a shift in mating preferences (song and wing pattern), while not being genetically incompatible.So the genetic isolation can be initiated with a genetic change without necessarily resulting in genetic incompatibility. [qs]Genetic incompatibility can be very simple as in the case of Mimulus

quote:

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Much evidence has shown that postzygotic reproductive isolation (hybrid inviability or sterility) evolves by the accumulation of interlocus incompatibilities between diverging populations. Although in theory only a single pair of incompatible loci is needed to isolate species, empirical work in Drosophila has revealed that hybrid fertility problems often are highly polygenic and complex. In this article we investigate the genetic basis of hybrid sterility between two closely related species of monkeyflower, Mimulus guttatus and M. nasutus. In striking contrast to Drosophila systems, we demonstrate that nearly complete hybrid male sterility in Mimulus results from a simple genetic incompatibility between a single pair of heterospecific loci.

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(For clarity these are different monkeyflowers than the other paper above.)So we have m1f2 sterility but m2f1 (reduced) fertility, interesting. hmmm ... the "V" diagram above is faster growing

# subtitutions	# incompatibilities
1	0
2	1
3	3
4	6
5	10
6	15

or and it doesn't matter which branch the substitutions occur on. And the possibility that one additional substitution enables genetic incompatibility increases dramatically as the number of substitutions increases.What we don't know is how many substitutions are involved in the initial split of the two species populations.For instance if we are at (e) on one branch and have (E) on the other, then even though the other substitutions did not affect viability\fertility the latest one has 4 opportunities to do so.Thanks.

Just a couple quick notes here as I have just a little time right now. Just a point of clarification in case it is not clear to everyone reading this. In this case, (a) and (A) do not refer to dominant and recessive genes but to derived and ancestral character states. So (a) is ancestral and (A) is derived. So, the point is you only get the potential for incompatibility when there are at least two derived character states. Yes, hmmm. I went back and looked at the lecture and my professor drew his "V" diagram a bit different; he only considered derived - derived relationships - he did not include derived - ancestral, but I am not sure why. Maybe it just simplifies the situation since derived - derived incompatibilities are 3 times more likely to occur than derived - ancestral incompatibilities when rates of substitution are equal in each lineage (see bottom of page 1807). So, I think derived - ancestral makes more sense so, not sure why he only included derived - derived. I don't think we disagree, maybe just using different terminology?? I initially list 3 types of isolation:1. geological/ecological (or spacial) isolation
2. prezygotic isolation (mating choice would be a prezygotic isolating mechanism)
3. postzygotic isolation (genetic incompatibility)And yes, isolation is what is critical for further divergence, that is why geological/ecological isolation is the big player in speciation.HBD

I'm trying to avoid the situation of gene flow altogether because gene flow muddies up the point I'm trying to make. {ABE: Are you equating the emigration of some of the original population itself to its new location with "gene flow?" Why? Gene flow as I understand it is the lack of reproductdive isolation between populations so that they reproduce with each other, at least partially. /ABE} If by physical barrier you mean a geographic barrier, that's what I like to focus on, but what does that have to do with the founder effect? That's about a very small number of individuals as I understand it and I don't limit the numbers except to say the point is clearer the smaller the number. And complete isolation is the point. Any gene flow just complicates the point I'm trying to make.Migration, or emigration --out of the main population to create a new subpopulation -- seems to me to best represent ALL the ways new subpopulations form. The Wikipedia page on Speciation shows four different ways populations can split,. three of them into smaller subpopulations, only one of which really represents (e) migration as I have been using it. But all of them do the same thing: except for the first which is an equal split, they form a smaller group that becomes the new "species." All I'm focusing on is the necessary reduction in genetic diversity in the smaller group, necessary to the appearance of new traits in the smaller population. I keep being asked for evidence for this, when I'm trying to get you to see that it's inevitable if you just think about what must be happening : smaller number of individuals, new allele frequencies. DNA counts at all phases is the only direct evidence there could be and I haven't seen anything like that demonstrated. I also refer to domestic breeding as an example of the same process. It doesn't matter if the number is so small you are getting Founder effect, the same basic principle applies with any number, it just takes longer with larger numbers. You say migration has been well studied. Do they do DNA analysis of each situation? It doesn't "rest" on it, I regard it as the simplest way to show what I'm talking about and I claim they all amount to the same thing. I don't ignore any of these things, you are assuming I do, but what I'm arguing is intended to be representative and to simplify. ALL of the examples where new traits form a new population by reproductive isolation, usually through geographic isolation, HAVE to do it by reduced genetic diversity, that's the claim. If there is continued gene flow instead, that just slows down the process, can even bring it to an end so that evolution isn't happening at that point either but for a different reason. Hybridization is another way the process can come to a halt, from infertility in this case. I don't include these examples just because it gets too detailed and messy, but perhaps I should because they are also dead ends for evolution. I just like the example of complete reproductive isolation of an inbreeding subpopulation formed from new allele frequencies, just because it is where new traits are forming (microevolution) by new "selected" allele frequencies, it SHOULD be easy to follow and it should be easy to see how it has to decrease genetic diversity in the formation of new traits.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : add paragraph about gene flow

Of course it doesn't. You addressed this to Admin and I may have answre3ed it somewhere but I'm answering it again if so. When I say it takes inbreeding to bring out the new traits, this COULD be the same as your phrase "change the genotype frequency" but I'm not sure. What it does is combine the new allele frequencies into new genotypes, bringing out new traits from those new allele frequencies.Since you are using migration only in the additive sense although I use it in the sense of individuals moving out to start new subpopulations it's going to be hard to keep things clear. I have in mind how, say, there are two populations of wildebeests, the blue and the black, figuring that one was created by individuals leaving the other and becoming geographically isolated, developing its new characteristics over generations of inbreeding. That's how I use the term migration and I can't think of another word that would work for it but we need to find a way to be clear here. I don't see how "founder effect" means the same thing. What YOU mean by migration is essentially resumed gene flow: a formerly split-off population rejoins another population of the same species. Edited by Faith, : No reason given.

I couldn't figure out why you thought I was saying inbreeding changes allele frequencies. It doesn't. It makes new combinations of the new allele frequencies and that's how you get new traits.

You can get entirely new combinations from a new set of allele frequencies, not just a subset of the original. Recessives can be more frequently expressed, traits with multiple genes can have new combinations that bring out completely new traits. Some of the new traits may have shown up in the original population now and then of course, but would have been buried by the dominant traits.Inbreeding is necessary to bring the new allele combinations to phenotypic expression, which over a few generations should start to change the look of the new subpopulation compared to the original.Edited by Faith, : No reason given.

Percy is right about how I've been using the term and I can't even see how you get your use of it out of anything that has been said,.I'm talking about inbreeding within a new subpopulation that formed from another, usually much larger, population, the new population having new allele frequencies, but the individuals involved are a random mix of theformer population so there is no necessary implication of closer relationships than between any two in the earlier population. There was no reason for you to say this in the first place since nobody had said that inbreeding changes allele frequencies. There is also no other reason to say it either, that I can see. Your weird responses were driving me crazy. I'm glad I got off this thread for a while.Edited by Faith, : No reason given.

And migration as I was using the term and so on.NOBODY EVER SAID INBREEDING CHANGES ALLELE FREQUENCIES. OF COURSE no evolution occurs in these inbred lines. THIS IS EXACTLY WHAT I'VE BEEN TALKING ABOUT FOR YEARS. When you get to the point of so many fixed loci you've reached the end of any possibility of further variation, that is, the end of evolution. By stages of decreasing genetic diversity.Drift and selection (which includes my use of the term migration as a form of random selection like drift) is the evolving part, in both breeding and microevolution in the wild. Fprtunately mutation of any consequence is so rare as to be negligible or you could never maintain a breed.
/ For the lab experiment I'd like to see done you'd have to start with a population that has high genetic diversity. I wonder if it's even -possible to find one.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

So you have claimed. Show how this works. This is not an explanation. It is just an assertion, but recessives can come together in either large or small populations. You have yet to show a combination that is impossible in the large population yet possible in the small population.Make up some alleles and show an example of what you claim can occur. Or come up with your own scheme. But repeating the same assertion over and over again is not going to convince anyone.And let's say that such a thing is true? So what? The mechanism you describe isn't where the curly eared mutation came from, so what you are describing is without any question NOT the sole method of creating new traits. Therefore this entire line of argument cannot disprove the theory of evolution. Mutation remains a viable way to generate new traits without the reduction in diversity method you describe here.You don't need to respond to me on this. Ned has asked for the same thing and so have others. If you respond to them, I'll see it. Edited by NoNukes, : No reason given.