Evolution Requires Reduction in Genetic Diversity

Just saying that there is a reduction of genetic diversity doesn't make it true you know. In order to make that statement you require evidence for its own sake but also because science is against you. A ring species would be exactly the wrong place to look for a bottleneck as there is no apparent difference between populations at any single point in the chain. If you compared both ends of the chain, logically you would not find reduced genetic diversity in one or the other - and you wouldn't even know which end of the chain to expect it in.

In this you are clearly wrong. What are called the "classical" racial traits are very clearly linked to the local environments. This has been known for decades.The traits that don't link to the environment are those such as fingerprint patterns and blood types.

With all respects but I can't make any sense out of this.
Interbreeding an artificial category?????
Nothing to add here. Until now we only see a GAIN in the number of alleles for those traits.
The max. number of ANY gene in the Adam & Eve population is just 4.
Nowadays we observe genes that count as much as 59 alleles. The human gene with the most alleles is HLA-DRB1. It is one of the genes in the human leukocyte antigen complex. It plays a central role in the immune system so it's a very crucial gene.The point is to look for evidence of this reduction from population to population? Well DO IT then and show us the empirical results.
I am STILL awaiting it 4 to 5 posts in a row. To me it suffices that all subpopulations of a ring species are able to interbreed while two of them won't. It would be nice to identify such instance by genetic DNA analysis but it is only a bonus.Rng species give evidence for evolution. there is no way around that.

In the first place he didn't suppose that. I've read his book "Why Evolution is True" very well. There he explains genetic drift quite extensively. So basically a straw man here. Not "by" the reduction of genetic diversity but resulting in dispersion of genetic diversity.Do you happen to have actual EVIDENCE for your supposition that any of the subspecies actually have more or less genetic evidence?We can suppose EVERYTHING, even most reasonable and even evidently - but in the end you have to provide the empirical evidence.

So it seems there was some geological isolation and then the groups rediscovered each other in the hybrid zones. Not as neat as before, but still not a total loss, imho, as they still show genetic variation around the ring and they still show how speciation can occur -- the major driver being species divergence between daughter populations.Also I am not surprised that they found hybrids of the two nothern variants, as it was pretty evident to me that the barrier was sexual selection and not genetic incompatibility. Brings to mind an old study that showed the longer a male went without breeding the more he tried to mate with things that looked less and less like their ideal mate (done with stickleback minnows).As far as I can see the only real difference is that divergence around the ring is clumpy rather than smooth, and I don't really understand why smooth would be expected: genetic change is essentially clumpy -- you don't really get a mixing of parental genes but a mosaic of genes and how they are expressed. After all that's why Mendelian genetics works.Enjoy

You remember how in every example we've looked at, evolution works how geneticists think it works and not how you think it works?Why do you think that is?

No, it's reading out of context on your part. My comment was a response to his blog where he specifically said the changes are the result of adaptations, the blog that was linked in Tangle's post.Genetic drift? What's that got to do with this discussion?I've read his book too. I say "by." It's not your job to correct my opinion. Do you? I've seen a lot of assumptions and claims that appear to be based on the phenotypic appearance rather than the DNA -- not real evidence. So pony up.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

My attention span is ~10 minutes at this point, what with coughing, headaches, congestion and the effects of the medications ... I'll try to make a more viewable version when I get to it below (or in following posts).I am also going to try to be brief and hit the important points.When it comes to human selection or natural selection ... Agreed: variation and selection and isolation of populations to maintain those variations. And our time is best spent on zeroing in on where your argument differs from evolutionary models.For the evolutionary model variation develops from mutations in the species, and this occurs whether we are talking about the whole species or isolated populations. Whether or not isolated populations start with the same number of alleles, or not, depends on the size of the population.For your model - as I understand it - variation occurs through either removal of some alleles from the population or by mutations that deteriorate the alleles, and this occurs whether we are talking about whole species or isolated populations, however you also argue that when a population divides that one or the other or both will not have a full set of alleles, but a subset of them ... and thus less genetic variation. Generally speaking this is true (except that a large number are neutral and can become beneficial later.However, all the identical twins I know do have some variations in appearance, and also in behavior\temperment. These differences must arise from development variations as they started with identical genes from a single zygote. This development is controlled by the DNA interaction with hormones\chemicals during development.There are many examples of developmental mutations causing single generation variations -- from missing or additional fingers or toes to siamese twins to fatally deformed fetuses. There are genes called HOX genes that control the development of the fetus and any alteration to those genes will show immediate results. This is part of evo-devo evolution.The upshot is that there are several mechanisms that result in variations available for selection, some that are not deleterious nor necessarily beneficial, just different.Nor are these differences necessarily advantageous or deleterious (depending on how extreme they are).Nor do they necessarily challenge your hypothesis -- it is just evidence that mutations happen.I have to stop nowEnjoy

Part of the problem is that you seem to be using definitions or have an understanding of certain concepts that are foreign to most of us. It makes it hard when we are talking past each other trying to argue from our own understanding of a term or concept. Like the quote above, my understanding of phenotypic diversity and genetic diversity would suggest that genetic diversity is much, much greater than phenotypic diversity. Even when there is little or no phenotypic diversity there can be a significant amount of genetic diversity. We are able to separate phenotypically indistinguishable populations by their genetic diversity. However, this seems to go against the point you are trying to make, so I am unsure what you mean by genetic diversity.It would therefore be helpful for you to describe what exactly do you mean by "genetic diversity." Here are some questions that should consider for your answer:1. Do only alleles that have a detectable variation in phenotype count as separate alleles? In other words, what if two alleles differ by 1% of their coding sequence but do not produce any visible effect on phenotype... would they be two separate alleles or the same?2. Would changes in non-coding regions count as genetic diversity? For example, one of the most commonly sequenced regions in fungi is the ITS (internal transcribed spacer) region. This region lies between the ribosomal RNA (rRNA) subunits and is transcribed into mRNA with the subunits but is not translated into protein along with the rRNA. rRNA sequences are highly conserved and so serve as excellent "flanking" regions where your PCR markers are located - that way they express in many types of fungi. However, the ITS region is highly variable and this variability can be used to identify individual species. So, does the ITS region count as genetic diversity?3. Does multiple copies of the same gene count as genetic diversity? Gene copies are quite common, particularly for "house-keeping" genes and copy numbers are variable even between closely related species. So one species may have two copies of a particular gene, a sister taxa may have 5 copies of a gene. Even though they may be the same exact sequence, does it count as genetic diversity? What if each copy has small, but distinguishable differences?4. Does changes in regulatory regions count as genetic diversity? So, an example would be that you have two copies of a gene that are both expressed in all tissue types in species A. Then there is then a sub-population that breaks off and afterwards experiences a change in the regulatory region of one of those copies which is now expressed in only one tissue type (so there is one gene expressed in all tissues and one that is only expressed in a single tissue type). Would that be an increase in genetic diversity?5. Is it only overall genetic diversity that matters or is it individual loci that must have reduced genetic diversity? So, if the original creature had 3,000 genes and 2 alleles per gene for a total of 6,000 alleles should a sub-population have fewer alleles regardless of what happens at an individual loci, say 5,900 total alleles? Could an individual loci increase in the number of alleles as long as the total number goes down? Would that still be reduced genetic diversity?There's more, but I think I better stop there. If you can answer the questions above, I think it will give everyone a much clearer picture of what you mean by genetic diversity and what it means for a speciation event to require a loss in genetic diversity. And also how your concept of genetic diversity relates to our own understanding of the concept.HBD

FWIW, I don't think Faith's position on the sheep species is that far off. There is some disagreement about the proper relative classification of O. orientalis and O. aries.The definition of speciation might be fairly clear, but the fit between the term speciation and our classification scheme is not totally consistent.Also as you suggest, Faith's discussion is short on examples of anything except breeding. Perhaps a different example might be worth considering.In my opinion, a single dominant mutation, such as a mutation giving humans functioning 'proto-wings' or 'proto-gills' would be sufficient basis to call a large population with those features a new species even if the group were interfertile with human beings. If you disagree then let's call that group a grouping rather than a species.And over time, I don't see any reason why that group could not become every bit as diverse as humanity is now. The only requirement for the new species is that it have the new feature. Variation in ear lobe shape, skin color, hair straightness, susceptability to desease and blood chemistry would not interfere with forming the species and thus new mutations or even interbreeding with baseline humans can still add diversity to the new grouping.If on the other hand, someone wants to claim that humans with gills are still of the same species as those without, then that person has not defined away evolution. They are simply ignoring evolution. Change is happening despite their dictionary, and the change is not limited by exhausting diversity.On the other hand the theory that animals not being able to breed together must or usually? comes from loss of diversity is total BS. Chromosonal count differences, for example, that have little to nothing to do with diversity, are completely capable of interfering with inter species breeding. Is the inability of dogs and cats to breed together connected to diversity in any way?Edited by NoNukes, : No reason given.Edited by NoNukes, : No reason given.

Yes I WILL correct your opinion when it's WRONG. That's debate for.
The correct way to conceive evolution in ring species is NOT "....you are getting a series of subspecies by the reduction of genetic diversity from subpopulation to subpopulation rather than "speciation" at any point as evolution defines it. "BUT: "....you are getting a series of subspecies by the dispersion of genetic diversity among the subpopulations and eventually resulting in "speciation" as evolution defines it."THAT is what REALLY happens.I explained that the genetic dispersion among subspecies or breeds of the original diversity is the RESULT, not the MECHANISM as you falsely conceive it.And my arguments on it HAVE NOT BEEN ADDRESSED until now.
And I am awaiting for 8,9 posts by now. I beg your pardon but SINCE when do I have to back up the evidence FOR YOUR CLAIMS????????And in case you didn't notice: I actually am the only one of both of us who comes up with empirical evidence. Like the Lenski experiment. Discarded by you without any ado let alone a sound argument.So pony up INDEED.Edited by Denisova, : No reason given.Edited by Denisova, : No reason given.

You can't tell that until you find genetic innovation in one of the O. aries' breeds (subspecies). If you find such examples, Faith's opinion is stone-dead.Faith's supposition is that all species some 6,500 years ago (at the moment of creation by God) had super-genomes, those since then deteriorating, leaving ever greater parts of the genome ruined in the shape of junk DNA.Furthermore, Faith does not accept genetic innovation to happen.
Because genetic innovation would replenish the gene pool and thus compensate for possible genetic deterioration. Faith thinks the phenotype variation we spot in O. aries, is solely the result of activating already (or should I say STILL) present genetic diversity or just of Mendelian mechanisms.The whole debate here, boils down to these two crucial points.That's also why it is difficult to get in the same line with her (implicit) definitions of concepts like speciation, as well as her ideas about the differences between phenotype and genotype and the sort.Faith's position on O. aries versus O. orientalis also rests on these two basic suppositions. As soon as anyone can prove that any of the traits of any of the O. aries ones are caused by fixed mutations, her whole position will be falsified. Or, for that matter, in any other bred species. SO LET'S HAVE THE EMPIRICAL EVIDENCEI asked Faith several times to provide empirical evidence for her suppositions. Until now nada. Accompanied by just refusing to face or address the contra-evidence provided.Now, by absence of Faith's own evidence, let's test her supposition of phenotype variation in breeds or subspecies to be solely the activation of genetic diversity still lurking in the genome or by Mendelian mechanisms. In other words, "no genetic innovation allowed".Let's have a look at the Dachshund, that fierce and proud little creature..... (...sorry, I was distracted a bit by my weak-spot for these utterly lovely quadrupeds, pardon for this little whim).

The beer belongs to my master

In their genetic analysis geneticist Ostrander and her team looked for the genetic factor causing the short, stumpy limbs of Dachshunds and other stump-legged dog breeds. They found out that a mutation in the gene FGF4 (short for fibroblast growth factor 4), which plays an important role in bone growth, was copied and reinserted into a new site in the dog genome.Ostrander examined 835 dogs across 76 different breeds, including 95 short-legged individuals, and found the genetic signature to be unique to these stunted animals.Source: Researchers Discover Evolutionary Event Underlying the Origin of Dachshunds, Other Dogs With Short Legs | National Institutes of Health (NIH).Now that's not an old luring gene getting expressed, nor Mendelian reshuffling of alleles. It is mutation by gene duplication and frame shifting.I was wondering how high the odds were for such genetic change also to occur in O. aries breeds. Let me have a guess: VERY HIGH. AS LONG AS this question is not answered, we are just manoeuvring in the dark.I also pointed her out to the Lenski experiment which unequivocally demonstrates genetic innovation occurring in E. coli bacteria. For any unknown reason Faith refuses to address it. Well, actually, I have a hunch.... EVIDENCE FOR DETERIORATING GENOMESI also asked Faith to provide her evidence for deteriorating genomes.
Until now, no answer.But by default of any attempts by Faith, let me elaborate myself on that too.
Actually someone actually did try to substantiate the supposition of deteriorating genomes scientifically: John Sanford with his concept of genetic entropy.Now there is not much left of Sanford's concept in current genetics. the reasons are plain: a lack of empirical foundation, an abundance of empirical evidence for the opposite and, unfortunately common among creationists, major misinterpretation of what evolution theory actually has to say and implies as well as, even worse, distortions of the work of others.A neat and decisive article on Sanford is to be found here, written by Scott Buchanan: STAN 4 | Letters to Creationists, the "JOHN SANFORD’S GENETIC ENTROPY AND THE MYSTERY OF THE GENOME" section down the page after the Behe section.First, Sanford backs up his claim of genetic entropy by referring to an empirical study by Kimura. Kimura there skips the beneficial mutations out of his observations. Sanford would have his readers believe that Kimura was so dismayed by the evolutionary implications of having only small numbers of beneficial mutations that Kimura did not dare treat the subject. But, actually, he reason Kimura omitted beneficial mutations was not that they have too little effect (as Sanford implies), but that in his model they would have TOO much effect. He just ruled them out as a bias to his actual methodological aims: when one wants to study the relationship between A and B, factor C which may also take part as a causal factor, needs to be sorted out.This was the distortion part.Secondly, the actual evidence for beneficial mutations. I quote the article: "The literature is rife with examples of helpful new mutations becoming fixed in a population which is exposed to a new environment". Buchanan refers to the studies no. 4 - 9 in the References section of his article. Many of those involve studies on emergence of resistance against antibiotics or pesticides and most of them find genetic change due to mutations.Thirdly, Sanford claims that natural selection does not have enough "selective power" to counterbalance the accumulation of deleterious mutations. In his reply Buchanan provides a series of empirical studies showing Sanford to be factually wrong. among those Lenski's long term experiment on E. coli (in that very long term one should observe deterioration in fitness which didn't happened - on the contrary), as well as several mutation accumulation experiments with eukaryotes, including Drosophila melanogaster, yeast and beetles. Those studies are also listed in the Reference section of his article.Buchanan ends up this section with the inevitable conclusion of all these experiments: "when natural selection is not operating, the population genome deteriorates, and when natural selection is operating, the average genome of the population does not deteriorate", as well as:
"This is so simple and so obvious, that we must ask: How can Sanford possibly claim what he claims, when decades of experimental studies clearly show the exact opposite? As a genetics researcher, he was certainly familiar with MA studies and their implications. This is another example of deceit in Genetic Entropy, and it is a whopper."Fourthly, Buchanna also directly addresses Sanford's claim of genome deterioration by mentioning several empirical studies which indicate this to be incorrect. see his Reference list again for those. FINAL CONCLUSIONSIn other words, the one occasion when one creationists tried to empirically substantiate claims for genome entropy, it actually ended up in being made minced meat out of it. If anyone here knows other attempts, of course be free to introduce it.The empirical evidence does not favour deteriorating genomes. It falsifies that notion.Until Faith doesn't solve these problems with her claims, we are all making feints and diversions in the shimmery realm of unsubstantiated propositions, discussing all kinds of neat details but evading the core points.Edited by Denisova, : No reason given.Edited by Denisova, : No reason given.

Actually, you cannot make the call even then. Genetic innovation is not necessarily a reason to declare animals separate species. We know for example that some dog breeds possess mutations not present in other dogs, but all dogs are considered to be of the same species.

I know that - but my point was that finding examples of genetic innovation will falsify Faith's supposition that breeds in O. aries are only exhibiting phenotype variance because of Mendelian mechanisms and already existent genes re-expressing and no genetic innovation is involved. And until that moment, any discussion about taxonomy and speciation makes no sense and only leads to manoeuvres in the dark.

To move discussion forward I'd like to introduce simple definitions for species and genetic diversity. People are free to use other definitions, certainly species has no one definition, but they should clearly define the definition they are using. But I think these definitions should serve very well most of the time.

• Species: A group of individuals capable of breeding with one another to produce fertile offspring. Obviously this definition doesn't apply everywhere, most obviously to asexual species, but it is by far the definition people most often have in mind when discussing evolution.
  ​
  In particular this should resolve a recent issue where Faith wanted to claim that two individuals could be of the same species yet not be able to interbreed, see Message 441 and Message 443, particularly this sentence in the latter:
  ​
  Faith writes:

  ​

  Yes I do want to claim that two populations that can't interbreed are the same species.
  ​
  Redefining words that already have a clear definition is a sure road to confusion, something this moderator will work hard to avoid. True, the definition of species is long and nuanced and full of qualifications, but not for populations of sexual species. Faith's attempted redefinition of species for sexual populations is hereby disallowed.
  ​
• Genetic Diversity: I'm open to discussion about this, but unless there are some objections and/or better ideas I'd like to propose the following definition for general usage. For a population, genetic diversity is the number of loci (a locus is a particular gene at a particular location on a particular chromosome) and the number of alleles for each loci across all individuals of that population. For example, if across all individuals there are 38,500 different genes (even if not all individuals have all genes), then that's the number of genes in the population. If that number should rise to 38,501 then that would represent an increase in genetic diversity. Or if across all individuals there are a total of 1,500,000 different alleles across all genes (though of course no individual would have all the alleles), then that's the number of alleles in the population. If that number should rise by one to 1,500,001 then that would represent an increase in genetic diversity.