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Author Topic:   Genetic 'Bottlenecks' and the Flood
Member (Idle past 918 days)
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

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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Member (Idle past 918 days)
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.

This message is a reply to:
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