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Author Topic:   Genetic 'Bottlenecks' and the Flood
Mammuthus
Member (Idle past 4986 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 5 of 59 (16216)
08-29-2002 4:32 AM
Reply to: Message 4 by John
08-28-2002 3:45 PM


Hi John,
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.

Cheers,
Mammuthus

quote:
Originally posted by John:
quote:
Originally posted by Me:
I was hoping to get some idea of the difficulties and costs involved.

It should be easy enough to do. The data is probably already available. If you could find five or six species with a bottleneck at 6000bce, the snowball would start rolling and no-one could stop it.

Just challenge the Creationists orgs to find ten species with such a bottleneck.



This message is a reply to:
 Message 4 by John, posted 08-28-2002 3:45 PM John has responded

Replies to this message:
 Message 6 by John, posted 08-29-2002 5:23 AM Mammuthus has not yet responded
 Message 7 by Me, posted 08-29-2002 6:15 AM Mammuthus has not yet responded

  
Mammuthus
Member (Idle past 4986 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 10 of 59 (16244)
08-29-2002 12:25 PM
Reply to: Message 8 by Quetzal
08-29-2002 7:06 AM


Hi Quetzal,
I am aware of the more recent bottleneck examples as well as much older bottleneck examples i.e. Homo sapiens. Many of my colleagues worked for the WCS (wildlife conservation society) so I got to see lots of seminars on the subject of bottlenecks. I had thought Steve O'Brien had put the cheetah bottleneck in recent historical times with one single breeding pair owned by a Maharaja who kept exotic pets and bred the cheetahs (I could be wrong...I read it somewhere about 12 years ago). But an example of a bottleneck really spot on dating to the mythical flood has not been demonstrated to my knowledge.

Me, however, is very correct in saying that creationists with no background in biology, genetics, or any other science will say that the methods used for determining bottlenecks or lack thereof are wrong so in effect it does not matter. On the other hand I am very certain if an example dating to the mythical flood were found for
even one species of landsnail the creationists would jump up and down about how the same methods they don't believe in vindicate their position

Of course there are plenty of species that underwent such a strong bottleneck that that went extinct long before the mythical flood such as Mammuthus primigenius

Cheers,
Mammuthus

quote:
Originally posted by Quetzal:
There IS evidence from at least one species of a genetic bottleneck around (very roughly) the right approximate timeframe. The cheetah (Acinonyx jubatus) is every conservation biologists' favorite example. The bottleneck equated to a reduction of the species to less than seven (some people claim a single pregnant female) individuals. I wonder if this corresponds to the cheetah being put on the ark as 7 specimens? Anyway, cheetahs are some 97% genetically monomorphic(the same as genetically “pure” strains of lab mice). The bottleneck is variously dated from a low of 4000 ya to 10-12,000 ya. The latter figure is probably most accurate. The point, of course, is that something similar MUST be observed in all/nearly all organisms for the massive genetic bottleneck represented by the ark to be even remotely possible.

Here’s a good on-line discussion of the ~10k date
Menotti-Raymond, M. and O’Brien, S.J. 1993. Dating the genetic bottleneck of the African cheetah. PNAS 90.

There are several other organisms that exhibit evidence of more recent genetic bottlenecks, including the Canadian grizzly (see, Implications of preliminary genetic findings for grizzly bear conservation in the central canadian rockies), the northern elephant seal, the baleine whale, florida panther, Illinois prairie chicken, black-footed ferret, etc. However, as would be expected by a standard evolutionary explanation, these bottlenecks are widely separated in time and wildly variable in causation – meaning there’s no way possible to attribute the collection of bottlenecks to a single, one-year-long point event like a global flood. There’s lots of good info in “Conservation Biology” and “Conservation Ecology” journals, as well as all over the web if anyone's interested in this issue (which has significant implications for conservation, preservation, and reintroduction of species). A fascinating topic.

[edited for grmayr an speeling]

[This message has been edited by Quetzal, 08-29-2002]


Fixed links (I think) - Adminnemooseus

[This message has been edited by minnemooseus, 09-20-2002]


This message is a reply to:
 Message 8 by Quetzal, posted 08-29-2002 7:06 AM Quetzal has responded

Replies to this message:
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Mammuthus
Member (Idle past 4986 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 18 of 59 (16418)
09-02-2002 10:21 AM
Reply to: Message 17 by Quetzal
09-02-2002 9:53 AM


Is it not fantastic to finally realize that cheetahs and sea monkeys and chia pets are all related by the carnivores running amok on a boat 6000 years ago I'm glad that phylogenetic tree of life has finally been resolved here once and for all

[QUOTE]Originally posted by Quetzal:
[B][QUOTE]Originally posted by Me:
I think we have established a new view on living conditions in the Ark with as much assurance as the creationists usually work with. We have now 'proved' that the Ark was launched, but that the predators got out of control and ate all the specimens, leaving a single cheetah pair surviving. They probably climbed the mast while the carnage was taking place below, and ate all the monkeys. Perhaps we could start our own religion on the strength of this astounding insight![/B][/QUOTE]

That is a seriously good idea! The only problem I see is showing how one pair of cheetahs "microevolved" into the 11+ million species of life (including plants) alive today in only 4000 years. Oh, why not? It works for the creationists...

[/B][/QUOTE]


This message is a reply to:
 Message 17 by Quetzal, posted 09-02-2002 9:53 AM Quetzal has not yet responded

  
Mammuthus
Member (Idle past 4986 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 31 of 59 (41457)
05-27-2003 11:38 AM
Reply to: Message 20 by Alec
05-25-2003 10:30 PM


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.

M: That study was disputed
Nat Genet 1998 Feb;18(2):109-10 Related Articles, Links

Comment on:
Nat Genet. 1997 Apr;15(4):363-8.

Mitochondrial mutation rate revisited: hot spots and polymorphism.

Jazin E, Soodyall H, Jalonen P, Lindholm E, Stoneking M, Gyllensten U.

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

An empirical genetic assessment of the severity of the northern elephant seal population bottleneck.

Weber DS, Stewart BS, Garza JC, Lehman N.

Department of Biological Sciences, University at Albany, State University of New York, 12222, USA.

A bottleneck in population size of a species is often correlated with a sharp reduction in genetic variation. The northern elephant seal (Mirounga angustirostris) has undergone at least one extreme bottleneck, having rebounded from 20-100 individuals a century ago to over 175,000 individuals today. The relative lack of molecular-genetic variation in contemporary populations has been documented, but the extent of variation before the late 19th century remains unknown. We have determined the nucleotide sequence of a 179 base-pair segment of the mitochondrial DNA (mtDNA) control region from seals that lived before, during and after a bottleneck low in 1892. A 'primerless' PCR was used to improve the recovery of information from older samples. Only two mtDNA genotypes were present in all 150+ seals from the 1892 bottleneck on, but we discovered four genotypes in five pre-bottleneck seals. This suggests a much greater amount of mtDNA genotypic variation before this bottleneck, and that the persistence of two genotypes today is a consequence of random lineage sampling. We cannot correlate the loss of mtDNA genotypes with a lowered mean fitness of individuals in the species today. However, we show that the species historically possessed additional genotypes to those present now, and that sampling of ancient DNA could elucidate the genetic consequences of severe reductions in population size.

In any case, population genetic studies of hundreds of species of plants and animals have been done and there is no indication of a common bottleneck much less one that happened at a time corresponding to the mythical flood.


This message is a reply to:
 Message 20 by Alec, posted 05-25-2003 10:30 PM Alec has not yet responded

  
Mammuthus
Member (Idle past 4986 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 34 of 59 (41952)
06-02-2003 10:52 AM
Reply to: Message 32 by Alec
05-29-2003 10:04 PM


quote:
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.

Um, this is a case of differential methylation in a non-fertile hybrid..this is known for Drosophila as well i.e. hybrid dysgenesis caused by transposons called P elements. However, this does not imply an increase in mutation...the tranposons can serve as a species barrier..not as magic diversifier or a way of speeding up the mutation rate.

quote:
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..


Um..the paper you cite does not show an increased mutation rate. It just shows that there was selection either for or against one of the two mtDNA haplotypes in mice in the Chicago area. Both types are still present. And this does not actually address the coalescence time since the last common ancestor of the haplotypes which would have preceded the bottleneck event that was recorded.

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.

cheers,
M

[This message has been edited by Mammuthus, 06-02-2003]


This message is a reply to:
 Message 32 by Alec, posted 05-29-2003 10:04 PM Alec has not yet responded

  
Mammuthus
Member (Idle past 4986 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 38 of 59 (46826)
07-22-2003 5:18 AM
Reply to: Message 35 by Alec
07-21-2003 8:13 PM


Hi Alec,

I missed this so sorry for the late response.

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...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. 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.
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 markers´, SNP studies of lots of individuals of a species...and none of these are consistent with a flood induced bottleneck.

cheers,
M


This message is a reply to:
 Message 35 by Alec, posted 07-21-2003 8:13 PM Alec has not yet responded

  
Mammuthus
Member (Idle past 4986 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 42 of 59 (47005)
07-23-2003 5:24 AM
Reply to: Message 41 by Alec
07-23-2003 3:20 AM


Hi Alec,
No problem....sometimes I bail out of here completely for lack of time myself.

I have selected a few articles that I hope you can get access to regarding several of the species I mentioned...I will post the abstracts along with them.

Humans have a long genetic history, the cheetah bottleneck correlates with the mass extinctions at the end of the Pleistocene..elephant seals were hunted almost to extinction recently so looking at ancient DNA one can see that they were more diverse prior to this (not surprisingly), I will try to find some info on cervids in north America since they apparently started to increase at the end of the Pleistocene.

Annu Rev Genomics Hum Genet. 2000;1:361-85. Related Articles, Links

Genetic perspectives on human origins and differentiation.

Harpending H, Rogers A.

Department of Anthropology, University of Utah, Salt Lake City, Utah 84112, USA.

This is a review of genetic evidence about the ancient demography of the ancestors of our species and about the genesis of worldwide human diversity. The issue of whether or not a population size bottleneck occurred among our ancestors is under debate among geneticists as well as among anthropologists. The bottleneck, if it occurred, would confirm the Garden of Eden (GOE) model of the origin of modern humans. The competing model, multiregional evolution (MRE), posits that the number of human ancestors has been large, occupying much of the temperate Old World for the last two million years. While several classes of genetic marker seem to contain a strong signal of demographic recovery from a small number of ancestors, other nuclear loci show no such signal. The pattern at these loci is compatible with the existence of widespread balancing selection in humans. The study of human diversity at (putatively) neutral genetic marker loci has been hampered since the beginning by ascertainment bias since they were discovered in Europeans. The high levels of polymorphism at microsatellite loci means that they are free of this bias. Microsatellites exhibit a clear almost linear diversity gradient away from Africa, so that New World populations are approximately 15% less diverse than African populations. This pattern is not compatible with a model of a single large population expansion and colonization of most of the Earth by our ancestors but suggests, instead, gradual loss of diversity in successive colonization bottlenecks as our species grew and spread.

Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3172-6. Related Articles, Links

Dating the genetic bottleneck of the African cheetah.

Menotti-Raymond M, O'Brien SJ.

Biological Carcinogenesis and Development Program, National Cancer Institute, Frederick, MD 21702.

The cheetah is unusual among fields in exhibiting near genetic uniformity at a variety of loci previously screened to measure population genetic diversity. It has been hypothesized that a demographic crash or population bottleneck in the recent history of the species is causal to the observed monomorphic profiles for nuclear coding loci. The timing of a bottleneck is difficult to assess, but certain aspects of the cheetah's natural history suggest it may have occurred near the end of the last ice age (late Pleistocene, approximately 10,000 years ago), when a remarkable extinction of large vertebrates occurred on several continents. To further define the timing of such a bottleneck, the character of genetic diversity for two rapidly evolving DNA sequences, mitochondrial DNA and hypervariable minisatellite loci, was examined. Moderate levels of genetic diversity were observed for both of these indices in surveys of two cheetah subspecies, one from South Africa and one from East Africa. Back calculation from the extent of accumulation of DNA diversity based on observed mutation rates for VNTR (variable number of tandem repeats) loci and mitochondrial DNA supports a hypothesis of an ancient Pleistocene bottleneck that rendered the cheetah depauperate in genetic variation for nuclear coding loci but would allow sufficient time for partial reconstitution of more rapidly evolving genomic DNA segments.

Curr Biol. 2000 Oct 19;10(20):1287-90. Related Articles, Links

An empirical genetic assessment of the severity of the northern elephant seal population bottleneck.

Weber DS, Stewart BS, Garza JC, Lehman N.

Department of Biological Sciences, University at Albany, State University of New York, 12222, USA.

A bottleneck in population size of a species is often correlated with a sharp reduction in genetic variation. The northern elephant seal (Mirounga angustirostris) has undergone at least one extreme bottleneck, having rebounded from 20-100 individuals a century ago to over 175,000 individuals today. The relative lack of molecular-genetic variation in contemporary populations has been documented, but the extent of variation before the late 19th century remains unknown. We have determined the nucleotide sequence of a 179 base-pair segment of the mitochondrial DNA (mtDNA) control region from seals that lived before, during and after a bottleneck low in 1892. A 'primerless' PCR was used to improve the recovery of information from older samples. Only two mtDNA genotypes were present in all 150+ seals from the 1892 bottleneck on, but we discovered four genotypes in five pre-bottleneck seals. This suggests a much greater amount of mtDNA genotypic variation before this bottleneck, and that the persistence of two genotypes today is a consequence of random lineage sampling. We cannot correlate the loss of mtDNA genotypes with a lowered mean fitness of individuals in the species today. However, we show that the species historically possessed additional genotypes to those present now, and that sampling of ancient DNA could elucidate the genetic consequences of severe reductions in population size.

: Mol Biol Evol. 2001 Feb;18(2):214-22. Related Articles, Links

Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1.

Yu N, Zhao Z, Fu YX, Sambuughin N, Ramsay M, Jenkins T, Leskinen E, Patthy L, Jorde LB, Kuromori T, Li WH.

Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.

Human DNA variation is currently a subject of intense research because of its importance for studying human origins, evolution, and demographic history and for association studies of complex diseases. A approximately 10-kb region on chromosome 1, which contains only four small exons (each <155 bp), was sequenced for 61 humans (20 Africans, 20 Asians, and 21 Europeans) and for 1 chimpanzee, 1 gorilla, and 1 orangutan. We found 52 polymorphic sites among the 122 human sequences and 382 variant sites among the human, chimpanzee, gorilla, and orangutan sequences. For the introns sequenced (8,991 bp), the nucleotide diversity (pi) was 0.058% among all sequences, 0.076% among the African sequences, 0.047% among the Asian sequences, and 0.045% among the European sequences. A compilation of data revealed that autosomal regions have, on average, the highest pi value (0.091%), X-linked regions have a somewhat lower pi value (0.079%), and Y-linked regions have a very low pi value (0.008%). The lower polymorphism in the present region may be due to a lower mutation rate and/or selection in the gene containing these introns or in genes linked to this region. The present region and two other 10-kb noncoding regions all show a strong excess of low-frequency variants, indicating a relatively recent population expansion. This region has a low mutation rate, which was estimated to be 0.74 x 10 per nucleotide per year. An average estimate of approximately 12,600 for the long-term effective population size was obtained using various methods; the estimate was not far from the commonly used value of 10,000. Fu and Li's tests rejected the assumption of an equilibrium neutral Wright-Fisher population, largely owing to the high proportion of low-frequency variants. The age of the most recent common ancestor of the sequences in our sample was estimated to be more than 1 Myr. Allowing for some unrealistic assumptions in the model, this estimate would still suggest an age of more than 500,000 years, providing further evidence for a genetic history of humans much more ancient than the emergence of modern humans. The fact that many unique variants exist in Europe and Asia also suggests a fairly long genetic history outside of Africa and argues against a complete replacement of all indigenous populations in Europe and Asia by a small Africa stock. Moreover, the ancient genetic history of humans indicates no severe bottleneck during the evolution of humans in the last half million years; otherwise, much of the ancient genetic history would have been lost during a severe bottleneck. We suggest that both the "Out of Africa" and the multiregional models are too simple to explain the evolution of modern humans.


This message is a reply to:
 Message 41 by Alec, posted 07-23-2003 3:20 AM Alec has not yet responded

  
Mammuthus
Member (Idle past 4986 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 44 of 59 (48139)
07-31-2003 5:31 AM
Reply to: Message 43 by Alec
07-30-2003 12:36 PM


Hi Alec,
When you come back I can summarize the findings of the MBE and Current Biology articles...it really sucks that they don't make archive files free....but that is a beef that I and a lot of other scientists have with academic publishing.

Anyway back on topic...the 1993 paper is still relevant and has not been refuted. I will point out two things...the HGP is irrelevant to the study of genetic bottlenecks. The sequence is a map of where all the genes, pseudogenes, telomeres, centromeres etc are...it says nothign about any sequences variation in the population.

Second, you won't find a paper about lack of bottlenecks...you will find papers about the high genetic diversity, relationships to other species, and timing of splits of one group from another. Papers on bottlenecks only show up when it is noticed that there is a lot less genetic diversity in a species than expected or relative to other related species. This usually comes out when one is studying the population genetics of a group for some other reason.

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.

cheers,
M


This message is a reply to:
 Message 43 by Alec, posted 07-30-2003 12:36 PM Alec has not yet responded

  
Mammuthus
Member (Idle past 4986 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 47 of 59 (52604)
08-28-2003 4:08 AM
Reply to: Message 46 by sfs
08-27-2003 11:12 PM


Greetings steve,
Excellent post..unforunately Alec is offline at the moment and nobody else seems to be interested in this thread...hopefully he will return soon and continue the discussion.

Cheers,
M


This message is a reply to:
 Message 46 by sfs, posted 08-27-2003 11:12 PM sfs has not yet responded

  
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