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Author Topic:   Genetic 'Bottlenecks' and the Flood
Alec
Inactive Member


Message 20 of 59 (41324)
05-25-2003 10:30 PM


Me:

quote:
I understand that mitochondrial Eve need not necessarily have been the only woman alive at the time, but do not some of the theories suggest a very small breeding group of humans at some time in the past?

It is true that the evidence from mtDNA does not necessarily prove that one woman was alive at the time, but simply means that only one woman's mtDNA has prevailed. However, it is consistent with Genesis also.

Evidence in the human genome is suggesting a very significant population bottleneck (a period in time when a population was almost wiped out, but then rebounded). This evidence is called long-range linkage disequilibrium (LD). LD simply means that genes are inherited together--they're not evenly shuffled out. Because they're inherited in large haplotypes (basically, chunks of them), and because we find this evidence in humans, it means that they underwent a recent population bottleneck. Because the genes aren't very shuffled, there hasn't been a great deal of time since this event.

quote:
The dates of such a bottleneck ought to match those for Noah and his family. Furthermore, there should be a similar bottleneck for all other animals, except fishes, matching the human dates.

We know the bottleneck must have been relatively recent because of the long range of the LD. However, a specific date would require a known recombination rate, and this is somewhat random.

I haven't studied bottlenecks in other animals, but I do know that low genetic diversity is present within animals such as the cheetah, elephant seal, and some rhinos, for example. Koalas alos have low genetic diversity in their mtDNA.

Mammuthus:

quote:
I don't believe that would prove much if you found 6 species with evidence of a bottleneck 6K years ago. How would a flood at that time account for all the species that show no evidence of genetic bottlenecks? Take for example Pan troglodytes. Chimps have at least 4 times the nuclear and mtDNA variation as a group as humans. Gorillas are also highly genetically diverse. There are other exceptions as well. For such a test to have any relevance EVERY single species on Earth would have to have a genetic bottlneck and a coalescence time of 6000 years before present. Actually, out of curiosity, can anyone find a single example of a species that has been identified where the genetic bottleneck dates back to 6000 years ago? There may be but it is nothing I have looked for or seen widely reported.

There has been talk of animals not having evidence of a population bottleneck. What genomes have been mapped that do not? Also, wouldn't the bottleneck be for about 5,000 years ago, the supposed time of the Flood? I do know that Mitochondrial Eve has been dated back to about 6000 years, using faster, actualy measured mutation rates, in an artice in Science.

John:

quote:
Conversely, even one species that does not show such a bottleneck derails the whole thing.

Not necessarily. For example, species of amphibians, fish, and insects would not necessarily have genetic evidence of a bottleneck in them because they wouldn't have all died during the Flood of Noah. It is significant to note that the animals that would have gone on the ark--mammals, reptiles, and bird--have a lower averge heterozygosity than the animals that wouldn't have needed to go on the ark.

I'm just throwing around ideas here that I think would be fun to discuss.

-Alec


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Alec
Inactive Member


Message 25 of 59 (41417)
05-26-2003 6:50 PM


Crashfrog:

quote:
Actually, for reasons that have been covered a few times, they would have died if they weren't on the ark.

Woodmorappe [1996, pp. 143-144] discusses some evidence he believes contradicts this assertion. I quote (a long quote):

"... fish can gradually become accustomed to a wide range of ambient salinities... For example, goldfish will die within two to three hours if place suddenly in half-strength salt water [35 parts per thousand], but will survive indefinitely in that medium if gradually acclimated to it. There are also some salt water mollusks which, if allowed to acclimate to waters of decreasing salinity, will tolerate pure fresh water [fewer than one-half of one salt part per thousand], and some fresh water mollusks which, if transferred gradually, will tolerate full-strength salt water. Amphibians also have greater salinity tolerances if allowed to acclimate gradually to waters of different salinities..."

He also discusses other animals which live in both salt and fresh water. There is even a great deal of variation in salinity among species of the same genus. In addition to this he notes of amphibians:

"... there are many reports of amphibians being found in brackish water or even seawater...salinity tolerances of amphibians vary even within species; as within populations of Rana sphenocephala, Salamandra salamandra, and species of Batrachospes. ... the relatively salt-tolerant populations of Salamandra can live in waters ahving as much as 44% of the salinity of salt water, whereas their conspecifics, living inland and away from salt waters, can tolerate only 27% of the salinity of salt water [pp. 151-152]."

He also notes that amphibians could have survived the Flood by (a) mimicking aquatic organisms and living freely in the water, (b) riding as passengers on floating objects (for example, salamanders have been found attached to wooden objects out at sea), or (c) frogs, for example, could have been transported as eggs on mats at sea, etc. If you'd like references for any one fact he gives, I'd be happy to give you the ones he cites. Keep in mind also that I haven't done any research on that issue myself, so I don't know a great deal.

WJ:

quote:
Please provide a citation to support this assertion.

Certainly: Ann Gibbons, "Calibrating the Mitochondrial Clock," Science 279(5347):28-29, 2 January 1998. She gets her information in part from an article which I have not yet been able to get ahold of: T.J. Parsons, et al., "A High Observed Substitution Rate in the Human Mitochondrial DNA Control Region," Nature Genetics 15:363-368, 1997.

The quote from Gibbons is this: ".. researchers have calculated that 'mitchondrial Eve'--the woman whose mtDNA was ancestral to that in all living people--lived 100,000 to 200,000 years ago in Africa. Using the new clock [based on new observed mutation rates], she would be a mere 6000 years old." She immediately qualifies this by saying that at the moment nobody believes this is the actual age, and I think the reason that nobody does is apparent. Also, the experiments were not 100% conclusive--research still needs to be done. However, I believe this is quite interesting evidence regarding mt Eve.

Andya:

quote:
Chimps have a greater heterozygosity than humans, which were "obviously" on the ark. Would that mean chimps can survive a flood without taken aboard the ark?

What is this estimate based on? I'm not questioning you, but I know that we don't know near as much about the chimp genome. Perhaps there are mechanisms that aid diversification. Also, I know that the human reference database has alot of people like Koreans and Europeans--both not very diverse--but very few Africans, who are much more diverse. For example, Nigerians are more diverse than other humans, and LD is less-ranging in them.

Reference:

Woodmorappe, John, Noah's Ark: A Feasibility Study, (ICR, 1996).


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Alec
Inactive Member


Message 26 of 59 (41418)
05-26-2003 6:53 PM


Also, I've been hearing that there's new evidence that mtDNA could also be inherited paternally. Does anyone know a reference for this that I could look up (preferrably in Science, Nature, or PNAS)?

  
Alec
Inactive Member


Message 28 of 59 (41429)
05-26-2003 11:54 PM


crashfrog:

quote:
Yeah, some fish might have survived. That's a long, long way from all species of fish. Or even most. So far you've got mullusks, goldfish, and salmon. It's pretty apparent that the ability to survive multiple levels of salinity is a specific adaptation in most species, not the rule.

Coral reefs die if the temperature or salinity change by more than a fraction of a percent. And they grow so slowly that it's ludicrous to suggest that modern coral reefs are younger than 4000 years.


Multiple levels of salinity is an adaptation--exactly. As is, in the creationist model, the adjustment to one level of salinity. Woodmorappe cites these example to show that it is possible to be adapted to both conditions. It then follows that in a creationist model these animals would have had the adaptation to different conditions in the past. Fish have since adapted to certain environments.

Coral reefs are a good point: you've got me there. I haven't studied them at all, so I don't know.

quote:
Is that consistent with a sudden, global deluge? It doesn't seem so to me.

I think it is. The salt would not have all been immediately stirred up in the Flood, to my knowledge. It would have been more gradual, and it's possible that different depths would have different salinities.

quote:
Also you didn't address insect populations. Many insects have lifespanse shorter than a year, and need specific, dry places to lay their eggs. A year's global flood would have wiped out the vast majority of insect species.

I also don't know much about this. It occurs to me that many insects could have survived on or in the water, on meaning on mats, etc. There also seems no reason to me that insects couldn't have simply gotten on the ark, hitching a ride with other animals that came came on, in the food supply, in the cargo, etc. Beyond that, good point also.

quote:
There's so many inconsitencies with the flood/ark model I don't know where to begin. The ark's too small to result in speciation on the scale we see it today unless you're willing to grant rates of mutation and speciation totally at odds with what we see today. There's no room for all the food that those animals would have consumed. There's no way that such small populations could survive in the post-flood world - a virtual waterlooged wasteland. There's no way an ark constructed with "antidiluvian" technology could have survived - and there's certainly no reason one big ark would have been the sole survivor, especially among fishing communities.

As far as speciation: We're finding different mechanisms all the time of rapid speciation that could have happened post-Flood. For example, introns (usally labelled Junk DNA) could have played a role. Depending on where the cell begins transcription, different genes can be produced. The founder effect also stimulated variation, for example it alters pleiotropic balance, and founder populations have a great range of variation. Inbreeding depression would have selected for animals that would have been more fit early, also. Genes are highly interactive, and rapid post-Flood variation would have been possible.

Fossils are not my field. I do know, for instance, that we find marine fossils near the top of Everest, for example. As far as the lack of bottlenecks in most species, that can't be asserted. We haven't mapped a great deal of genomes, and making accurate conclusions without doing so is questionable.

I would think that Flood myths all over the world lend support to the historical fact of a literal, global Flood. It must have its roots in history, don't you think?

-Alec


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Alec
Inactive Member


Message 32 of 59 (41752)
05-29-2003 10:04 PM


Crashfrog:

quote:
That doesn't make sense. It takes far, far longer for a species to lose functionality (the adaptation to multiple salinity environments) than it does to gain it because there's no selection pressure for losing things unless their presence is somehow detrimental.

Exactly. In the creation model, the farther back you go in history (towards creation), the more genetically diverse organisms are. They were created with ultimate genetic diversity, and adaptation by natural selection--becoming specialized for an environment--only limits genetic variation. Therefore, because fish, etc., have become adapted to certain, specialized environments does not mean they didn't have this capability in the past and, as some evidence shows, does not mean that such variation is non-existent today.

quote:
Why would fishes have lost their adaptation to multiple salinities? What's the disadvantage in having it?

Why are there pseudogenes in the genome--what's the disadvantage in having real genes? You see the flaw in your argument? Mutations are not always driven by environmental factors, though I believe they certainly can be. Mutations are almost always known for their detrimental effects, and even though it would be advantageous for the organism to keep its function, a mutation can change that.

quote:
Fish may have lost the ability to adapt to different salinities but it would have taken a lot longer than 4000 years. There's just no selection pressure for it.

I'll discuss the speed of mutation, etc., in a moment. As for the selection pressure--if a species of fish has taken up freshwater lakes as its habitat, adaptation to multiple salinities would be irrelevant. And if the ability to cope with multiple salinities is advantageous is this certain situation, why don't we find more fish with this ability today?

quote:
In a vast, churning miasma? I don't find that reasonable.
There's a thread here <www.evcforum.net/cgi-bin/dm.cgi?action=page&f=7&t=43&p=4 -->www.evcforum.net/cgi-bin/dm.cgi?action=page&f=7&t=43&p=4">http://www.evcforum.net/cgi-bin/dm.cgi?action=page&f=7&t=43&p=4> that discusses how the flood would have had to have been simultaneously incredibly violent to deposit sedimentary layers in the way we see them, yet also pretty calm to allow a 600-year-old man and his boat full of animals to survive. The flood explanation just isn't self-consistent.

The original issue was over population genetics, and I certainly don't know much about geology. The Flood was violent, probably accompanied by volcanic activity and the like. The dimensions of the ark, I have read, are such so that it could still righten itself if it was tipped 60 degrees. The dimensions are the optimum for ships--used today, if fact. I don't know what this has to do with self consistency. The Bible says the Flood would destroy what was on the face of the Earth, which it did--and the vessel which 8 humans were saved on was built to task.

quote:
Are you sure about this? I don't see how a founder population of two (or even seven) could have any significant amount of genetic diversity - certainly not enough to explain the diversity we see today. ... In a population of two, any selection at all ends the species.

Many genes are pleiotropic--they affect many different traits [Ridley 1999, p. 66]. This can account for rapid diversification. The opposite is also true: some single traits are affected by many different genes. This can aid rapid diversification also. Think of genes not as written-in-stone codes, by highly interactive bits of DNA. For example, "jumping genes" (transposons), can move to different parts on the same chromosome, or another chromosome altogether. Supressor genes can move, thus possibly either turning a gene on, or another off, or both. They may even play a part in antibiotic resistance. It is possible that the cell may be able to control transposition, also. As far as such polymorphism arising quickly, Woodmorappe [1996, p. 192] again cites a relevant example: "A very small number (probably a single pair) of macaques had been introduced to Mauritius island by Dutch sailors some 400 years ago. the presently-large population exhibits low MtDNA diversity when compared with the macaques on the Philippines. Yet (H), the average heterozygosity, as measured by allozymes, is greater than that found among the macaques on the Philippines." He cites the following reference: S.H. Lawler, et al.. 1995. Mitochondrial DNA of the Mauritian macaques (Macaca fascicularis): an example of the founder effect. American Journal of Physical Anthropology 96:133-141.

In addition to this, I mentioned splice variants in my last message, which opens a whole new world of possibilities. Therefore, "exons may be combined in alternative ways, creating distinct but related mRNAs... The resulting proteins may differ only slightly [in shape] but nevertheless have entirely distinct roles [Zweiger 2001, p. 48]." This shows the fine-tuning of a proteins shape (which determines its function). Other complex processes have been discovered--for example, protein encoding by both DNA strands, not just the one. This "rasies new questions regarding genome complexity and evolution [Labrador et al. 2001]."

Of course, mtDNA can also mutate very quickly. Just eight days ago, Nature published an article on this very fact. MtDNA was extracted from white-footed mice (in museums) which were caught in the Chicago area in 1855. They compared five collection sites, using a 340-bp polymorphic region. Only one mouse today had the A haplotype. Quote, "We found a consistently similar directional change of mouse genotype over this period at each of five collection sites that were separated by 10-70 km. The genotype most common 100 years ago is no extremely rare, indicating that the mammalian mitochondrial genome can undergo rapid evolution [Pergams et al. 2003]." Besides showing that mutation can happen very fast, this could also have significant results for the molecular clock.

Another example: "Recent studies were prompted by the curious case of a 'Benny', a hybrid between two different species--the tall swamp wallaby and the tubby tamar wallaby. Benny's chromosomes were found to have been seriously disfigured. Some of the centromeres... were tne times as long as normal; part of an arm of chromosome 2 has been moved to chromosome 7, and part of the X chromosome had been reversed. Analysis of Benny's DNA showed that it was "dramatically under-mathylated'. Methylation of DNA is a mahor method of controlling gene expression, so 'dramatically under-methylated DNA' means DNA that is 'out of control'. The researcher involved called it 'very extreme, and quite shocking'. ... Benny's experience led to the idea that perhaps a similar mechanism [as jumping genes from retorovirus DNA] has influenced wallaby speciation. A follow-up study of the Queensland rock hoppers turned up trumps. Dramatic changes of a similar kind were found, leading to an equally dramatic conclusion--'something that we thought might take 50 million years might take 5 minutes instead [Williams 2003]." The reference he cited is as follows: D. Fox, Wallaby nations, New Scientist, 3 August 2002, pp. 32-35.

So, fast genetic change is known to take place. As to any selection at all of pairs ending life, perhaps much of that did happen. Inbreeding depression may have been less severe in the past, also, as animals would have been more genetically diverse. Also, animals could have been interbreeded to remove all of the un-fit organisms, thus ensuring that death due to inbreeding depression would not happen. Numerous possibilities exist.

quote:
Plate tectonics - ever heard of it? Mount Everest used to be a lot shorter. Used to be under a sea, in fact. (Plates colliding, and all.) I'll wager that you certainly don't find any contemporary sea life on the top of Everest. No whales, for instance.

However, marine fossils on top of Everest are a direct prediction of the creation model, too. I honestly don't know about the whales part.

quote:
We don't have to map the genomes of every animal. We just have to map the genome of one animal that would have had to have been on the ark to disprove the ark story. I haven't looked, and I'm no geneticist, but I'd be very surprised indeed if there wasn't a mammal (for instance) with no recent genetic bottleneck.

I really don't know if an example exists or not. Cattle are an interesting example:

quote:
Another interesting detail comes from a mitochondrial Eve study in cattle. The mtDNA sequences point to at least 200 000 years fro the most recent common ancestor of cattle. This date was calculated by using convetional values for mtDNA substitution rates [emphasis mine; this is important] derived from human mitochondrial Eve studies and paleontological divergence dates of cattle and bison. On the other hand, archaeological evidence indicates no domesitcations earlier that 10 000 years BP. To resolve this conflict, Luftus et al. postulated independent domestication events of callt.e However, if Loftus's phylogenetic tree of cattle is correct and domestication was recent, about 23 substitutions would have occurred in the sequenced 915 bp D-loop regions during the past 10 000 years, which corresponds to 2.5 substitutions/site/million years. The similarity to Parsons' calues is striking, even if evolutionary rates in man and cattle are probably different. Perhaps it is worth rethinking domestication history of cattle with Parsons' high subsititution rates in mind [Loewe and Scherer 1997].

So a recent domestication of cattle is possible based on actual, measured mutation rates. Really, there is so much debate over the molecular clokc in the scientific literature that I don't believe anything can be known at all for sure at the moment.

In humans, the mutation rate has been found using the assumption that (a) humans diverged from chimps, and (b) this took place 5 million years ago (which is a debate in and of itself). By finding the differences between humans and chimps, an avergae mutation rate per year is found using the 5 million year assumption. Significant to note is that when mutation rates are actually measured, the rate seems much more rapid in many organisms [Gibbons 1998, Pergams et al. 2003].

quote:
The flood model raises way more questions than it addresses, is self-contradictory, and simply fails to be reasonable. I don't really see how it can be taken as anything but a myth.

Okay.

NosyNed:

quote:
It seems to me that this crys out for quantification. How long, days, hours, weeks in "gradually" in the first one? ANd how "sudden" is the second?

I really don't know the exact figures--they can be found in Comparitive Biochemistry and Physiology 28:1427. And I think it is self-evidence how sudden the global deluge was.

quote:
Certainly, we understand that evolution can happen pretty quickly under some circumstances. But there are at least a couple of problems with the idea.
1) The raw speed of the speciation. I've seen some creationist sites that have "kind" at the family level. For there to be no historic record of this happening the full range of speciation would have to have been complete sometime well before 2000 years ago.
2) Why did it stop? There is no suggestion of a mechanism that can turn on and off that extremely.
I'm afraid that an arm waving explanation like this isn't going to hold up under any kind of close examination.

Firstly, I specified my "arm-waving" above, as well as answered that such mechanisms exist today. I really don't at all understand what you're trying to say in your first point.

Mammuthus:

I will have to see if I can find the Nature Genetics article you cited.

quote:
Regardless, the other examples you provided like elephant seals and cheetahs are known to have undergone recent bottlenecks because of hunting pressure...and they don't coalesce to 5 or 6K years ago i.,e
Curr Biol 2000 Oct 19;10(20):1287-90 Related Articles, Links

What do they coalesce to, and how are we certain of hunting pressure as the cause? I don't have access to that journal. Also, as I previously stated, I don't believe the molecular clock can be heavily relied on at the moment (especially old ages) in light of evidence of rapid mutation rates, such as that discussed in Pergams et al..

quote:
A bottleneck in population size of a species is often correlated with a sharp reduction in genetic variation.

The example of macaques I give above could contradict this statement. Additionally, a bottleneck can cause a rare genotype to be expressed by eliminating the more common genotypes.

Sorry, but I'm out of time. Exams next week--gotta study.

-Alec

References:

Gibbons, Ann, "Calibrating the Mitochondrial Clock," Science 279(5347):28-29, 2 January 1998.

Labrador, Mariano, "Protein Encoding by Both DNA Strands," Nature 409(6823):1000, 22 February 2001.

Loewe, Laurence, and Siegfried Scherer, "Mitochondrial Eve: The Plot Thickens," Trends in Ecology and Evolution 12(11):422-423, 11 November 1997.

Pergams, Oliver R.W., et al., "Rapid Change in Mouse Mitochondrial DNA," Nature 423(6938):397, 22 May 2003.

Ridley, Matt, Genome (Perennial, 1999).

Williams, Alexander R., "Jumping Paradigms," TJ 17(1):19-21, 2003.

Woodmorappe, John, Noah's Ark: A Feasibility Study (ICR, 1996).

Zweiger, Gary, Transducing the Genome (McGraw-Hill, 1999).


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Alec
Inactive Member


Message 35 of 59 (46775)
07-21-2003 8:13 PM


Crashfrog and Mammuthus,

I'm sorry, I intended to respond to this and then forgot completely.

Firstly, I've read the study by Jazin et al., and Thomas Parsons and Mitchell Holland responded to their criticisms and explained why the results of their study may have not been in line with their own. Additionally, the results of the original Parsons study has seemed to be confirmed in more recent research (for example, Tully et al. 2000).

Crashfrog:

quote:
I don't think you understand my objection. My point is that, since there's no pressure to lose temperance to changing salinity, there's no way most fish would have lost it in only 4000 years or so. That kind of genetic change takes far, far longer.

New species of, say, salmon have arisen under the observation of humans. I don't think this kind of change requires that long of a time. We really can't know; some evidence does suggest rapid speciation after a bottleneck.

quote:
The mechanisms of mutation and natural selection are very well understood, and unless you can posit a potential survival advantage for an inability to tolerate different salinities, those mechanisms preclude such a change from happening in anything close to 4000 years.

Since when do mutations need a selective advantage to occur and proliferate? If a species of fish was living in fresh water, mutation affecting salinity tolerance would be more like 'genetic drift', perhaps unaffected by natural selection, unless it was in favor of an only-salty environment. There would be selection of the only-fresh water fish over the fish more adapted to multiple salinities.

quote:
Actually they're almost always known for their neutral effects, for instance the four to fifty mutations you have, somewhere in your genetic code.

According to one of my newer textbooks, "most mutations are deleterious, but the neutral theory asserts that the selective advantages or disadvantages of most molecular mutations are so small that selection on them is too weak to offset the influences of genetic drift (Purves et al. 2001)." So I suppose you're right in the sense that the negative effects of most mutations are so small as to seem neutral.

As far as the whole salinity issue, I must admit I was taken off-guard and hardly know anything about it; I'm trying to be a reasonable person also .

Mammuthus:

quote:
If you hypothesize that ALL animals in the world were reduced to a single breeding pair, their would be genetic evidence of such a bottleneck in ALL species regardless of the rate of the molecular clock. This is not the case...not even in primates that are closely related to us like chimps which have 4 times the genetic diversity as Homo sapiens in both mtDNA and nuclear markers. They do not show evidence of a any severe bottleneck much less one the magnitude of proponents of the ark myth.

We haven't even mapped the chimp genome yet, said to be our most recent ancestor. Other animals also have much higher mutation rates, for example rodents and perhaps hominids other than humans [Eyre-Walker and Keightley, 1999]. The difference between species, for example, human/chimp DNA similarity, depends on what is being compared; for exmaple, when indels are included in the comparison of the major histocompatibility complex, the similarity drops to 86.7 from the commonly touted ~98% [Anzai et al. 2003]. Indeed, "Sequence divergence estimates between human, chimpanzee and gorilla nuclear genome do not adequately respresent fine changes in genome organization [Hacia 2001]."

I'm sorry but I'm leaving in a few minutes and I must go now; I will check with this forum again soon!

-Alec

References

Tatsuya Anzai, et al., "Comparative Sequencing of HUman and Chimpanzee MHC Class I Regions Unveils Insertions/Deletions as the Major Path to Genomic Divergence," PNAS 100(13):7708-7713, 24 June 2003.

Adam Eyre-Walker and Peter D. Keightley, "High Genomic Deleterious Mutation Rates in Hominids," Nature 397(6717):344-347, 28 January 1999.

Joseph G. Hacia, "Genome of the Apes," Trends in Genetics 17(11):637-645, November 2001.

William K. Purves, et al., Life: The Science of Biology (Sinauer and WH Freeman, 2001), pp. 439-440.

Lois A. Tully, et al., "A Senitive Denaturing Gradient-Gel Electrophoresis Assay Reveals a High Frequency of Heteroplasmy in Hypervariable Region 1 of the Human mtDNA Control Region," Am. J. Hum. Genet. 67(2):432-443, August 2000.


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Alec
Inactive Member


Message 40 of 59 (46992)
07-23-2003 3:16 AM


quote:
Chimpanzees are NOT our ancestors - they are our closest LIVING relatives.

True. We are said to have diverged from them about 6 million years ago, so I guess 'ancestor' just came out. I will try to be more careful with my words, because I agree that makes a difference.

quote:
So why are you responding to the point that chimpanzees do not show the genetic bottleneck implied by the ark story by talking about the similarities between human and chimpanzee genes?

Mammuthus spoke of "primates that are closely related to us like chimps." I thought that perhaps the information would be relevant. It really doesn't have a great deal to do with genetic bottlenecks though, I agree.

quote:
There is a difference between the mutation rate and the genetic diversity among primates. However, the mutation rate is still irrelevatn to the point I made...

I was discussing mutation rates in the mitochondrial genome because you cited the Jazin et al. study before as if it somehow discredited the Parsons study. At least that's the impression I had until I read it, and I wished to clarify.

quote:
...if there was a world wide flood in biblical times, regardless of the mutation rates, you would see a coalescence of genetic diversity at that point due to the genetic bottleneck.

Firstly, I was in part discussing mutation rates because of the previos mtEve discussion. Additionally, if mutation rates are faster in an animal, they will become more genetically diverse faster. The study I cited on hominid mutation rates regarded nuclear DNA.

quote:
This is not observed. Elephants don't show this, whales don't..the mammalian model of bottlenecks, the cheetah does not, elephant seals do not, chimps don't..., fish do not, plants don't.

Really, I've only studied the human genome and don't know much about other animals. I take your word for it.

quote:
Sequencing of genomes is entirely irrelevant to the study of genetic bottlnecks in its current form. What does the sequencing of a single representative individual tell you about the population gentic history of the species? Nothing. The types of studies that do are smaller scale sequencing projects of loci like mtDNA or micro and mini satellite markersĀ“, SNP studies of lots of individuals of a species...and none of these are consistent with a flood induced bottleneck.

Linkage disequilibrium and low genetic diversity is, to my knowledge, the reason for the inference of a bottleneck in human history. I really don't know what to say because I'm not sure about everything you're referring to. What I think you should do is pick a study in a journal that I can go and read, and we can discuss it. Right now I do not know of any examples so I am in a difficult situation.

quote:
I can state with certainty that he would be quite dismayed that you are using his text as some sort of indication that evolution has some fundamental problems that indicate a global flood.

That is not what I was doing at all, but I do not doubt he would be dismayed. I simply stated that most mutations are deleterious and was challenged, and cited his textbook as evidence. The more complete view you cited is good. However, whether or not mutations are usually 'bad or good' does not really form the basis of my present arguments, nor did I intend for it to be the issue; I simply clarified my position. I'm not sure what you believe I'm 'making him out to say,' and I would like to know so that I could perhaps clarify further. That issue came up while we were discussing how fish could have lost adaptation to multiple salinities. Another stated that "Actually they're almost always known for their neutral effects, for instance the four to fifty mutations you have, somewhere in your genetic code." and I answered that. The only thing I intended for the quote was to show that mutations are most often deleterious (in other words, exactly what it stated). Therefore, the only misconception that could arise is if the quote is wrong, which I doubt. I certainly didn't make the claim that his quote somehow gives an 'indication that evolution has some fundamental problems'--that's a bit far out, I would say. Additionally, I did not claim that his quote in any way 'indicate[s] a global flood'. Therefore, I believe contacting William K. Purves is largely unecessary; however, if you believe that would aid this discussion you of course may do so.

Regards,
Alec


  
Alec
Inactive Member


Message 41 of 59 (46993)
07-23-2003 3:20 AM


Also, Mammuthus, it is I who should be apologizing. I have trouble finding the time to get on here and provide anything resembling a thorough response; I do appreciate your promt-ness and will attempt to do my best also.

-Alec


Replies to this message:
 Message 42 by Mammuthus, posted 07-23-2003 5:24 AM Alec has not yet responded

  
Alec
Inactive Member


Message 43 of 59 (48044)
07-30-2003 12:36 PM


Mammuthus,

I don't have access to the journals Molecular Biology and Evolution or Current Biology. I looked at the one by Harpending and Rogers but it was too long for me to photocopy in the few minutes I had at the college last night. I found the cheetah one, also, and will read it as soon as I can. I do remind you though, that this is dated to 1993. Even the Harpending and Rogers one was written before the completion of the HGP. Additionally, when I looked through it I did not see the mention of a lack of bottlenecks in other animals, which is what I thought we were tlaking about--perhaps I missed it (most likely).

I'll try to be as punctual as possible! Many thanks!

-Alec


Replies to this message:
 Message 44 by Mammuthus, posted 07-31-2003 5:31 AM Alec has not yet responded

  
Alec
Inactive Member


Message 45 of 59 (48264)
07-31-2003 9:46 PM


Mammuthus,

quote:
...the HGP is irrelevant to the study of genetic bottlenecks

Didn't the HGP complete a SNP map, which is used to find LD, which provides evidence of human bottlenecks?

quote:
Second, you won't find a paper about lack of bottlenecks...you will find papers about the high genetic diversity

Well then, high genetic diversity. I would think that studies would publish about low-ranging LD, though.

quote:
I'll look around and see if I can find some review articles on the subject so you don't have to go chasing around after individual papers.

Thank you I'm leaving for Idaho for a week tomorrow, I may or may not have time to get back on before then. I do plan on lots of reading! See you...

-Alec


Replies to this message:
 Message 46 by sfs, posted 08-27-2003 11:12 PM Alec has not yet responded

  
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