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Author Topic:   Genetic 'Bottlenecks' and the Flood
sfs
Member
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 46 of 59 (52574)
08-27-2003 11:12 PM
Reply to: Message 45 by Alec
07-31-2003 9:46 PM


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

Not exactly. The SNP map was produced by three efforts. Two found SNPs in data taken from the HGP by lookng for differences between two human clone inserts where they overlapped. The third was a joint public-private resequencing operation run by TSC (The SNP Consortium), which compared a lot of random sequencing reads to the HGP consensus sequence. The TSC project overlapped with the HGP a lot in institutions and personnel and the overlap projects used HGP data, but none was officially part of the HGP. (The SNP map was, however, published in the same issue of Nature as the genome.)

As for the substance of your question, SNPs from the map have been used to measure LD. What the LD shows is
1) There's more LD in Africans than one would expect from their genetic diversity, given known recombination rates, and
2) There's much more LD in Europeans and Asians (East Asians, anyway) than there is in Africans.
(2) implies one or more bottlenecks in the population(s) that left Africa, but doesn't say anything about the human population as a whole. (1) suggests that eirhter our understanding of human demographic history is wrong in some undefined way that no one has been able to figure out yet, or that our understanding of recombination is wrong. As it happens, there's also independent evidence that the simple models of recombination that were used to make predictions were seriously flawed; models that look more like reality are consistent with the diversity data and don't suggest a bottleneck.

A severe bottleneck within the last couple of hundred thousand years would have left a variety of traces behind: very low diversity (lower than we see), a highly distorted allele frequency spectrum (many very rare alleles and many common alleles, with almost none at intermediate frequency), and a probability that an allele is ancestral that almost independent of allele frequency (in contrast to the nearly linear relationship we see, and which we would expect from a constant-sized population). We don't see these traces.

Steve (a newcomer who just wandered by looking for genetics questions)


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Replies to this message:
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Mammuthus
Member (Idle past 3919 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


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roxrkool
Member (Idle past 340 days)
Posts: 1493
From: Nevada
Joined: 03-23-2003


Message 48 of 59 (53877)
09-04-2003 2:50 PM
Reply to: Message 46 by sfs
08-27-2003 11:12 PM


I watched a show on super volcanoes the other week and there was a segment regarding a genetic(?) bottleneck happening approximately 72,000 years ago, which happened to coincide with a super volcano eruption. Have you heard anything about this?
This message is a reply to:
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Asgara
Member
Posts: 1780
From: Wisconsin, USA
Joined: 05-10-2003


Message 49 of 59 (53887)
09-04-2003 4:41 PM
Reply to: Message 48 by roxrkool
09-04-2003 2:50 PM


Hi Rox,

I watched that show also. They suggested that the population of hominids was as low as 5k. I'm at school and do not have the notes I took on that program concerning the location and such. When I get home tonight I'll post the info if no one else has by then.

------------------
Asgara
"An unexamined life is not worth living" Socrates via Plato


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Brad McFall
Member (Idle past 2476 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 50 of 59 (53890)
09-04-2003 5:18 PM
Reply to: Message 48 by roxrkool
09-04-2003 2:50 PM


I can not get the NOTION of "genetic bottleneck" out of my hearing Mr. Will Provine EXPLAIN his idea of a "constriction" during the 'modern synthesis' historically which SINCE I, as a herpetologist, KNEW WAS NOT A MODIFICATION FROM A SQUAMATE subjectivity immediately objectived my own ear to the meaning ONLY TO FIND WILL DISCUSSING NOT THE CONTENT OF BIOLOGY BUT THE CONTEXT, namely the reduction in the reading materials a student of evolution had to master AFTER THE SYNTHESIS.

This historical event seems to be misssing not only from the current teaching of biology but also its dissemination. I guess 'bottle necks' could be generalized outside of this finished hearing but there is so much little used biological lingusitcs that choosing what to instantiate is difficult for even someone interested in apply the axiom of choice. The electronic media seems oriented more towards atomic describability and less to set theory.


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Asgara
Member
Posts: 1780
From: Wisconsin, USA
Joined: 05-10-2003


Message 51 of 59 (53929)
09-04-2003 9:36 PM
Reply to: Message 49 by Asgara
09-04-2003 4:41 PM


I found some of the info, the last "super volcano" was Toba in Sumatra approximately 75kya. It had 10,000 times the explosive power of Mt. St. Helens.

The huge caldera that makes up Yellowstone park is swelling and I have read estimates that say it is long overdue to blow.

------------------
Asgara
"An unexamined life is not worth living" Socrates via Plato


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sfs
Member
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 52 of 59 (54299)
09-07-2003 12:17 AM
Reply to: Message 49 by Asgara
09-04-2003 4:41 PM


While it's certainly possible that a massive volcanic eruption caused a bottleneck in the human population, there really isn't the resolution in the genetic record to spot such a bottleneck, or to date it accurately if it could be identified.
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Adminnemooseus
Director
Posts: 3795
Joined: 09-26-2002
Member Rating: 3.6


Message 53 of 59 (54355)
09-07-2003 2:26 PM


Possible relevent info elsewhere
I have just closed down, as being off-topic, the thread "The flood and Ancient Chinese Documents". I there included a reference to this topic.

Readers of this topic might also find something of interest at the above cited topic.

Adminnemooseus


    
akilo55
Junior Member (Idle past 3513 days)
Posts: 1
Joined: 08-15-2007


Message 54 of 59 (416481)
08-15-2007 10:18 PM
Reply to: Message 46 by sfs
08-27-2003 11:12 PM


Steve -- perhaps you could look at the discussion at http://babysafari.us/main-1_000003/ (Default Options) and expand on your comment which is posted there (at the end). A couple of references (and your last name) would be very helpful. My email address is snowwater3@netzero.com. Also your comments about why human babies are fat at http://babysafari.us/main-1_000011/ would be very welcome. Many thanks. Frank Hodgson
This message is a reply to:
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Nuggin
Member
Posts: 2965
From: Los Angeles, CA USA
Joined: 08-09-2005


Message 55 of 59 (416635)
08-17-2007 3:13 AM
Reply to: Message 9 by Me
08-29-2002 11:53 AM


No need to wonder, it's obvious
I wonder why creationists are not citing the cheetah as an example of the Ark's cargo - it looks like it could have been the only one!

The creationists aren't citing it because they know if they do they'll get slammed.

The very existance of the "Cheetah bottleneck" is proof AGAINST the flood.

The fact that we can look at the cheetah's genetics and say - "Oh, this is different" means that there is something we are checking it against.

In other words, the only reason we know that there is a "cheetah bottleneck" is because the vast majority of species don't have the bottleneck.

If every species had the same bottleneck (as would be predicted by the Ark) then that would be our baseline and the cheetah's genetics wouldn't stand out at all.

What's more, if the creationists start hoisting the genetics flag, they quickly find themselves in big trouble since the vast vast vast majority of genetic data clearly contradicts their myth.


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Dr Adequate
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Posts: 15936
Joined: 07-20-2006
Member Rating: 3.4


(1)
Message 56 of 59 (671856)
08-30-2012 10:41 PM


Bump For Foreveryoung
This seems a better thread then the one on chromosome 2 to discuss fey's question.

Edited by Dr Adequate, : No reason given.


  
foreveryoung
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Posts: 879
Joined: 12-26-2011


Message 57 of 59 (671857)
08-30-2012 10:51 PM


The thread was closed where I posted this question earlier. What would be the result if all human life was destroyed except for 7 humans? I am referring to noah and his family. What would the genetics look like after 6000 years?
Replies to this message:
 Message 59 by Coyote, posted 08-30-2012 11:14 PM foreveryoung has acknowledged this reply

    
Dr Adequate
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Posts: 15936
Joined: 07-20-2006
Member Rating: 3.4


(1)
Message 58 of 59 (671858)
08-30-2012 10:55 PM


Answer For FEY
I've been looking around for answers to fey's question. One relevant paper would seem to be Francisco J. Ayala, Ananias Escalante, Colm O'hUigin and Jan Klein, "Molecular Genetics of Speciation and Human Origins," Proc. Natl. Acad. Sci, USA, 91: pp6787-6794, July 1994, p. 6787-6788. Addresssing the question of whether there was a bottleneck 100,000-200,000 years ago, they calculate from the present level of heterozygosity that there can't have been fewer than 4000 breeding individuals at that time.

Now the effective population would have to be larger the closer in time the bottleneck was, so if we put it at a mere ~4000 years ago, it would have to be so large it would hardly be a bottleneck at all ... certainly not as small as 8 people.

Edited by Dr Adequate, : No reason given.


  
Coyote
Member
Posts: 5864
Joined: 01-12-2008
Member Rating: 4.0


Message 59 of 59 (671860)
08-30-2012 11:14 PM
Reply to: Message 57 by foreveryoung
08-30-2012 10:51 PM


What would be the result if all human life was destroyed except for 7 humans? I am referring to noah and his family. What would the genetics look like after 6000 years?

I addressed this question on another thread Message 22.

Edited by Coyote, : No reason given.


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 Message 57 by foreveryoung, posted 08-30-2012 10:51 PM foreveryoung has acknowledged this reply

  
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