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)
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?
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
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.
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.
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 firstname.lastname@example.org. Also your comments about why human babies are fat at http://babysafari.us/main-1_000011/ would be very welcome. Many thanks. Frank Hodgson
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?
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.