Evolution Requires Reduction in Genetic Diversity

What a dishonest way to debate. You could care less about evidence nor could you understand [ABE sorry, bad form. You don't lack the ability to understand; what you lack is the desire to understand. You would not put any real effort into reading and understanding a research article I post related to these issues] the research I would present. To demonstrate that my previous post is not just my assertion**, should I recommend a good book on population genetics?How about I give an example from my own research?The primary organism I work with is a pathogenic fungus, Rhizoctonia solani. R. solani is in the Basidiomycota, which includes the true mushrooms, the rusts and the smuts. These fungi do have a sexual stage but they spend most of their life as a dikaryon. The diploid stage of R. solani only lasts for a very short time, and as far as I know, has never been isolated in the field.Another of the characteristics of the Basidiomycota is that they have clamp connections. Below is a diagram of a clamp connection and how it regulates nucleus segregation during cell division (each nucleus shown is haploid and they divide by mitosis and are segregated into the growing cell so that each cell contains one of each nucleus). Interestingly, R. solani does not have clamp connections. It is the only member of the Basidiomycota without clamp connections (I think it is the whole genus but anyway...) Without clamp connections the regulation of nucleus segregation is poorly controlled and because of this, R. solani is multinucleate; that means it can have 4 to 12 nuclei per cell. These nuclei can have different alleles, and as many as 6 different alleles at a single marker gene have been found in a single isolate - 6 alleles for a single gene in one isolate!This does not happen in closely related basidiomycetes. They are (mostly) binucleate, that is they have 2 haploid nuclei per cell. So, they only have 2 alleles for any given gene.In addition, R. solani is further divided into subgroups based on the ability of the hyphae to fuse. These groups are called anastamosis groups (AG). These groups can be identified by genetic markers, or in other words, they each have unique genetic fingerprints. Furthermore, the AGs are further subdivided into interspecific groups (ISGs) which can also be identified by molecular markers. I am working on the diversity of the ISGs in one of the AGs in regard to host range, virulence and temperature response. The genetic groups have already been identified by a collaborator of ours and we want to see if there is anything significant (as it relates to plant pathology) in those groupings.So... how does your model make sense of this kind of genetic diversity???If R. solani diverged from the rest of the Basidiomycota and lost its clamp connection (which would be what is expected of a loss of function mutation) then the group gained genetic diversity over the course of time by adding multiple nuclei per cell (up to 6 alleles per isolate). If it went the other way and the diversity of the multinucleate state was lost to the other basidiomycetes, not only would that require an incredible amount of diversification it would require a gain of function mutation in the way of clamp connections.Your model is so overly simplistic that it is totally useless. It does not explain nor can it account for real-world observations regarding genetic diversity. The model I work with does make sense of it. It provides a framework with which I can further our knowledge of how plants and pathogens interact and how we can breed resistant crops and develop management strategies. All yours does is support your personal belief system.HBDEdited by herebedragons, : Clarification at **Edited by herebedragons, : bad form, sorry

Give me a break. You don't want to get it. I explained the terms that were unique to the organism I was talking about - like clamp connections. I read back through it and I don't see anything that is too highly technical; give an example. You can't understand this simple presentation yet you still know that population geneticists who work on these issues everyday are wrong and you have discovered the "true theory" of how organisms evolve. That is what is a joke. So, your model of speciation only works on ~1% of all the species on earth, but the rest of the 99% evolve by the regular old ToE? That is what is a flimflam. Fungi do have traits, they are sexually reproducing, R. solani does not reproduce asexually (many others do, but not R. solani). You rejected bacteria as an example because they don't reproduce sexually, you reject fungi because they don't have tails... That's actually the problem. The ToE works on all organisms not just the 1% that have fur and tails. Your theory needs to work accross the board, not just on your cherry-picked examples. To which your response is: Yes, shame on me for trying to define things properly. I know what you are saying, Faith. I know what your argument is and it is so overly simplistic, relies on a general misunderstanding of basic genetic principles, and fails to account for real world observations. The evidence against your overly simplistic nonsense is that the world is full of organisms with incredible amounts of genetic diversity. Diversity is not being depleted to some kind of end point where further diversification cannot occur. Rhizoctonia must be ancestral to other Basidiomycetes, and yet where is the reduced genetic diversity? It has gained diversity by having multi nuclei per cell.If your hypothesis can't be applied to anything but those organisms with fur and tails, it is utterly worthless to a biologist. If organisms continue to have significant amounts of genetic diversity despite speciation events, then we need to understand why. "Evolution requires a reduction in genetic diversity" doesn't do it.HBD

Yes.Go back and respond to Message 754 properly. If there is not an understanding of what is meant by genetic diversity, how can we decide that it has been reduced? My points were not just assertions but a description of some of the complexities and challenges related to defining and measuring genetic diversity. For example Go back and deal with Message 723 properly.I did not propose to "redefine" genetic diversity, but to use the term "genetic differences" temporarily for the purposes of discussing the chart I presented. Your Message 727 was a ridiculous way to respond as if I am the one who has no understanding of basic population genetics. No counter argument, just a 'no reason to take it seriously' attitude.And obviously I am not the only one who complains about the way you respond to arguments.So yes, I am saying that you are not debating in good faith.HBD

You are just trying to define yourself into being right. If a daughter population has lost the ability to interbreed with the parent population and is distinctly different from the parent population, then we would recognize it as a separate species. Calling it a subspecies that has lost its ability to interbreed is just word play.So this "end point" is the point where a fish would grow legs or a dinosaur would sprout wings right?Let's try this... Population A has the alleles R, Q and S. These alleles are co-dominant so that combinations produce intermediate phenotypes. The genotype combinations would be: RR, RQ, RS, QQ, QS, and SS. 6 combinations of alleles exist in this population.Now suppose that population B splits off of population A and is isolated. However, it is a small population so not all of the alleles are represented in the new population; only alleles R and Q are represented in the new population. So the combinations in population B are: RR, RQ and QQ - only 3 allele combinations are in the new population.So... a reduction in genetic diversity right? 6 combinations in the original and only 3 in the daughter. So far so good.Now these populations breed among themselves and their alleles get all mixed up and shuffled around. So now there is:population A: RR, RQ, RS, QQ, QS, and SSpopulation B: RR, RQ and QQWait... what has changed? The same allele combinations. Hmmm... Also note that the combinations in the daughter population already exist in the parent population. Kinda disappointing, but OK, still loss of genetic diversity.Now imagine there is a mutation in allele R in population B, lets call it r. There is a deletion of a small section of DNA, creating a stop codon and a truncated protein. This protein is non functional, but it is also recessive since the other alleles are dominant. So as long as it is paired with a dominant allele the organism is viable. Thus this recessive allele can "hide" in heterozygotes and spread through the population.So now we have alleles R, Q and r in the daughter population. So now the allele combinations in population B are:RR, RQ, Rr, QQ, Qr (we can assume that rr will be non-viable) - 5 allele combinations.Now what happens if there is another mutation? Let's say that allele Q has a substitution and this substitution changes the amino acid coded for but doesn't change the function of he protein. We can however detect this allele when we sequence it. Let's call it Q*. So now the combinations we have are:RR, RQ, Rr, RQ*, QQ, Qr, QQ*, Q*r, Q*Q* 9 allele combinations!We see no phenotypic change but there IS an increase in genetic diversity. At least I would call this:RR, RQ, Rr, RQ*, QQ, Qr, QQ*, Q*r, Q*Q*more genetically diverse than this:RR, RQ, RS, QQ, QS, and SSMaybe you say it doesn't constitute an increase in genetic diversity because it doesn't change the phenotype. Oh wait, you are talking ONLY about genetic diversity not phenotype diversity. Hmmm...I know, I know...HBD

Yes, I have proved that mutations add diversity. You complained that we were confusing phenotypic diversity with genotypic diversity but that you were only referring to genotypic diversity. Now I find out that you are really meaning phenotypic diversity. Yes, it is hypothetical; it is meant to be an illustration. But yes it has happened and is something we find in natural populations all the time. It is often how we identify different groups of organisms that cannot be distinguished morphologically. In fact, even with furry critters with tails that can be distinguished morphologically we will sequence genetic markers to see how they group genetically. Often we find that morphological differences are not supported by genetic groupings and we will refer to the groups as morphs rather than separate species or subspecies. Here's the genotypes in my example immediately after the population splitpopulation A: RR, RQ, RS, QQ, QS, and SSpopulation B: RR, RQ and QQWhere are the new phenotypes in population B? The same phenotypes were already in population A, nothing new here. No possibility of incompatibility, the same genotypes exist in both populations. Indeed. But we are discussing genetic diversity, not phenotypic diversity, right? So what I am pointing out is how genetic diversity is affected by the four evolutionary factors; in this case mutation.So here's our table again...

	Diversity within pop B	Diversity between A and B	Affect all loci
Mutation	increase	increase	No
Migration	increase	decrease	Yes
Drift	decrease	increase	Yes
Selection	increase/decrease	increase/decrease	No

And the diagram. Now, here is our genotypes before and after mutation.population A: RR, RQ, RS, QQ, QS, and SSpopulation B before: RR, RQ and QQPopulation B after: RR, RQ, Rr, RQ*, QQ, Qr, QQ*, Q*r, Q*Q*Compare population B before and after. Did the genetic diversity decrease or increase? Our chart says that the diversity within population B should increase.Now compare population A with population B after. Did the genetic diversity increase or decrease? Our chart says diversity between population A and B should increase.The final question we ask, in regards to the chart, is does the mutation affect all loci? The answer is no. The mutation occurred at one locus and does not affect the other loci.If that is clear, I will move on to migration.HBD

I only gave you the example of the fungi to point out how complex the genetic situation really is. I didn't expect you to understand it per se, except to realize that in the real world of population genetics things are very, very complex. Your overly simplistic idea just can't cut it in real population genetics.So, forget about the fungus. Just recognize that the things we deal with regarding genetic diversity are much more complex than you are imagining. And why is that when you have been studying this for 10 years? Could it be... is it possible... that this process of speciation is much more complex that you are trying to pass it off as?I would just like you to respond to one point from Message 754You are claiming heterozygosity and number of alleles per locus are synonymous with genetic diversity, so which population described above is the most genetically diverse according to your measures?HBDEdited by Admin, : Spelling correction, "per say" => "per se".

Arabidopsis thaliana is a model organism and used in all kinds of genetic research. It is native to Europe and ranges from Italy to Sweden - some 2400 km apart. As you may know, Italy has a much warmer climate than Sweden. So the question is, are these populations adapted to their particular climate? The way to test this is to do a reciprocal transplant. How this works is you take some of the Swedish population and plant them in Italy and take some of the Italian population and plant them in Sweden and measure their fitness (I believe they used number of seeds produced). What they found was that the fitness of the Italian plants grown in Sweden was about 60% compared to Swedish plants grown in Sweden. The Swedish plants grown in Italy had 18% fitness when compared to Italian plants grown in Italy.What this shows is that each population is adapted to their specific climate.What is the basis for this adaptation?Well to answer this, the researchers developed a series of RILs (recombinant inbred lines - we have talked about this before) and planted them at each location (a total of 16,736 plants/year for three years yielding a total of 565,000 fruits). Then they plotted fitness onto the known genotype of each RIL and this yielded 7 QTLs that were associated with freezing tolerance (QTLs are when a particular phenotypic trait is statistically correlated with specific genetic loci). one of the QTLs had a large effect, 25% so they considered this to be a candidate freeze tolerance gene.So they sequenced this gene (named CBF-2) and found that the Italian population had a deletion of 13 nucleotides which resulted in a stop codon and a truncated protein (sound familiar?). When they inserted the Italian CBF-2 allele into a Swedish genetic background (all other loci were of Swedish origin except the Italian CBF-2 allele) the plant lost its freeze tolerance. SO we have a Swedish CBF-2 allele that helps the plant tolerate freezing temperatures and an Italian CBF-2 allele that does not have freezing tolerance.Here we have two populations that are adapted to their specific climate and they differ by at least a 13 nucleotide deletion at a freeze tolerance gene.No, they have not speciated. However, that's even better for illustrating how this process occurs because there is not a huge difference between these populations (they can still interbreed). Looking back on speciation can be difficult, but here we have the very beginning steps. Now what would happen if these two populations were isolated so that all gene flow stopped? Has there been a reduction in diversity? Now that's just not so is it? What is your real evidence?HBDSources in case you're interested Reciprocal transplants demonstrate strong adaptive differentiation of the model organism Arabidopsis thaliana in its native range
QTL mapping of freezing tolerance: links to fitness and adaptive trade-offs

Two populations. One adapted for cold, one adapted for warm. The researchers found a gene involved in cold tolerance and sequenced it. The population in the warm climate had an allele that produced a non-functional protein and the plant was not cold tolerant. Here is a partial sequence showing the region of the deletion. Yea, so you think a gene that produces a truncated, non-functional protein was part of the original creation? And it is just now being expressed by a change in allele frequency? Plus there is not a population split involved in this case - the species' range is continuous between Italy and Sweden.The specifics of how and why are really not addressed by these papers, but the Swedish allele is probably ancestral and the ancestral range was not so far south. The mutation allowed the population to expand its range further south.One thing I didn't address in my previous post (because I thought it might be too much detail) is that there are adaptive tradoffs involved with cold resistance. So if the plant has the cold resistant allele, it doesn't do well in a climate where it doesn't need it. Read the papers that present the data and make your own judgement.HBD

Where did the non-functional allele come from in the first place? Here is the sequence alignment. HBD

Percy already addressed this, but yea, I didn't just declare it I demonstrated it. I could give you dozens of examples like that; genetic diversity is very, well... diverse.Whats more... you failed to respond to my direct question, again! So what is it? How would you rate genetic diversity in this case?Anyone else have an idea?HBD

HBDEdited by herebedragons, : No reason given.

To which you respond HBD

At the risk of going off topic... I think this is hilarious This olive tree survived the flood ripping all the sediments from the surface of the earth and redepositing them over 1 to 2 miles deep, and then was able to survive being underwater for almost a year. Laughable.

So all this is about virtually NOTHING. "Genetically different" species are not included in your "hypothesis?" Only genetically identical creatures with fur and tails that cannot interbreed or maybe than can, they just look different. (However, interbreeding is not important to your argument) Also not included are bacteria, asexually reproducing animals, or fungi - which are more than 90% of the species on earth.How do you think we might explain the origin of genetically different species, such as the grey wolf and the coyote? Every genetically different species was on the ark?HBDEdited by herebedragons, : clarity

I realize part of the problem is we are working with two different paradigms. That does make it difficult and I try to be sensitive to that. Sure. The metapopulation would indicate that both populations are the same species and can interbreed. Yes, 'A' and 'B' are separated by some type of geographical barrier. In order to talk about migration, we should not think of this barrier as complete, but will allow some level of migration between populations. The important thing is that these are independent populations.What is the relationship between them? I am not sure how it matters. The diagram is rather abstract and simply represents a population that has been split by some geographical barrier. Maybe population 'B' got blown by a storm to an island; or a road was put in that separated a population of snails; or they are just in fields far enough away from each other that they rarely come in contact, ... any imaginable scenario.A better question may be that if we sampled these populations how would we tell which was the parent and which was the daughter population? Could we even tell which was which? You hypothesis is that the population with the least amount of genetic diversity would always be the daughter population. No. I want you to say you understand what the chart is telling us about how these factors affect genetic diversity with and between populations (same applies with the other 3 factors). If you understand and agree, great. If you understand and disagree, no problem - but you need to then explain why you don't agree and justify it with observational data. If you still don't understand what the chart is saying, then we continue discussing it.All your questions seem to be very similar in what they are asking, so I will address them all in a general way before discussing the specifics. Within populations: Population 'A' has a certain amount of genetic diversity. What the chart indicates is how that particular factor affects the genetic diversity within the population. A mutation in population 'A' would add an allele to the pool and so would INCREASE diversity. Between populations: Population 'A' and 'B' both have a certain amount of genetic diversity. The question the chart addresses is how does the factor in question affect this diversity between these populations. Over time the populations will become increasingly different; that is, diversity will increase. Or maybe they will become more similar and so diversity will decrease. So "between populations" addresses how these factors will affect the differences, or the diversity, between the two populations. A mutation in either population (assuming the exact same mutation does not occur in both populations) will INCREASE the diversity between the populations. Affect all loci addresses how the factor affects the loci. Does it affect them all equally or does it only affect some loci and not others? Mutation will only affect the loci that mutates, not other loci. It means migration between populations 'A' and 'B'. Remember that to properly consider migration, we need to think of it as gene flow, not just individuals moving around. So, migration would be a member of population 'A' mating and having offspring with a member of population 'B' (or visa versa). So what happens to the diversity of population 'B' when a member of population 'A' migrates to population 'B'? It will tend to INCREASE diversity within population 'B' because it would introduce alleles that exist in population 'A' that do not exist in population 'B'. It will tend to DECREASE diversity between populations 'A' and 'B' because alleles that exist in population 'A' that don't exist in 'B' will be moved into 'B' and will reduce the differences between populations. Migration affects all loci because individuals are moving and introducing their whole genome into the other population. Genetic drift results when individuals are removed from the population regardless of their relative fitness. It is the result of serendipitous events and can eliminate even the most fit individuals. So genetic drift refers to fluctuations in allele frequency solely by chance as a result of sampling errors. (Note: The frequency of an allele is also the probability that the allele will be selected at random).The most significant source of genetic drift comes from the fact that only a small proportion of all available gametes are used to create the next generation. Some gametes fail to fuse with another gamete (for example, think of how many sperm are produced in mammals with only 1 or 2 that fertilize the egg) and of those that do form zygotes, only a small proportion may survive. Think about a fish that may lay thousands of eggs but most of them are eaten when they are still fry. This "sampling" is likely to result in a different allele frequency than that of the parent population.The ultimate result of drift is that alleles can be fixed purely by chance. This could allow slightly deleterious alleles to become fixed. This effect can be very pronounced in small populations.So drift tends to DECREASE diversity with a population because it is randomly removing alleles from the population. Drift tends to INCREASE the diversity between the populations since it is a random process it cannot be expected that each population will be "drifting" in the same direction. It will affect all loci because it involves whole individuals and their whole genome, not just specific loci. Increase OR decrease. Selection is kind of a difficult one. It will probably take more explaining that I have time for now, but I will at least explain the chart.Some alleles would tend to be favored and would increase in frequency, some alleles would be less favorable and would tend to decrease in frequency. As selection continues to act on the population the tendency would be that diversity within that population will DECREASE as the population moves towards an optimum fitness. However, there are situations where diversity can INCREASE such as with heterozygote advantage (where the heterozygote is more fit that either homozygote).If different selection pressures are operating on each population we would expect diversity between the two populations to INCREASE as in each population different alleles or combinations are being favored. However, if two populations are already slightly diverse and the same selection pressure begins to act on both populations, then they will become more similar, or diversity will DECREASE.It does not affect all loci because, in general, only loci that are being selected for or against will be affected.Like I said, selection is not quite as straight forward as the others and is a bit more difficult to grasp. But depending on the situation, either a decrease or an increase can be expected (not both at the same time).Also keep in mind that these are all TENDENCIES. This is what these factors TEND to do. The opposite effect may occur for short periods of time or under special circumstances.Hope that helps clear it up. I realize selection will need to be dealt with more vigorously, but hopefully the others make sense.HBD