Neanderthals and Cro-Magnon

Here's a recent paper that discusses the bottleneck:Gabor Marth, et al, 2003, Sequence variations in the public human genome data reflect a bottlenecked population history", PNAS 100:376-381

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Single-nucleotide polymorphisms (SNPs) constitute the great majority of variations in the human genome, and as heritable variable landmarks they are useful markers for disease mapping and resolving population structure. Redundant coverage in overlaps of large-insert genomic clones, sequenced as part of the Human Genome Project, comprises a quarter of the genome, and it is representative in terms of base compositional and functional sequence features. We mined these regions to produce 500,000 high-confidence SNP candidates as a uniform resource for describing nucleotide diversity and its regional variation within the genome. Distributions of marker density observed at different overlap length scales under a model of recombination and population size change show that the history of the population represented by the public genome sequence is one of collapse followed by a recent phase of mild size recovery. The inferred times of collapse and recovery are Upper Paleolithic, in agreement with archaeological evidence of the initial modern human colonization of Europe.

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This paper puts the 4-7 fold population decline at around 40,000 years ago. Three different tests of the data showed strong evidence of severe linkage disequilibrium in Homo sapiens, at least in Europe.Mammuthus — you’re the extinction expert. Any speculations as to cause?

Hey Peter,They don't really refer to population size, per se, rather population genetic variability. Given known substitution rates, they simply didn't discover nearly enough polymorphisms. What the data DID show - again based on known substitution rates - was that the apparent homogenization in Europeans (because they were using European samples) is consistent with a bottleneck traced back to around 40 kya. As Mammuthus pointed out, there could be a lot of problems with the analysis and a lot of other factors, so there's not a "smoking gun" necessarily. It might be indicative, however, if other evidence is discovered. The article concludes with fairly high confidence on the part of the authors.

Yeah, but it sounds like if the authors were right, the Europeans came pretty close. Might be that the only thing preventing it was the fact that they WERE small-scale hunter-gatherers. IOW, lots of local population extinctions homogenizing the gene pool followed by slow recovery. Just like cheetahs and elephant seals...Hmmm, Paleolithic warfare. Sounds like the bloody Europeans haven't changed much in 40,000 years. As far as neanderthalensis still living in Europe - have you seen pictures of Ken Ham? Talk about living proof that australopithecus still exists...

Thanks for the links. I'd read the first article before. I'd like to point out that the reference I cited was from this past January, so might be either a more definitive study OR simply the next shot across the bows in the GoE/OoA war.

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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.

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My reference didn't dispute this - and in fact discussed the problems with previous studies in much the same fashion. All they tried to show was that there WAS evidence, based on SNPs, that there may have been a bottleneck in European populations - the population from which came the samples. They made no conclusions about whether this represented ALL human populations, or simply the geographical population based in Europe. So, IMO, they weren't trying to get in on the other debate. I'm relatively impressed with the way they handled and presented the data - since it was based on sequences derived from the Human Genome Project, they weren't actually in the lab. And they made a pretty good case for the way they chose and manipulated the data. Not conclusive, of course, but pretty indicative.

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We suggest that both the "Out of Africa" and the multiregional models are too simple to explain the evolution of modern humans.

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This is probably a pretty valid conclusion. After all, various populations - even widely distributed across continental Europe, for instance - could easily have suffered a genetic bottleneck without effecting other regional populations in the slightest.And the debate goes on...[This message has been edited by Quetzal, 05-20-2003]

Ah, you don't know what you've been missing. Presented for your edification: Ken Ham, founder, president, and CEO of Answers in Genesis (and living proof that Australopithecus robustus still lives - or alternatively, the close relationship between Pan and Homo):

This ought to light some fires! Everybody from taxonomists (Pan into Homo), to anthropologists with their favorite subspecies/species, to fundies with the "I ain't related to no monkey". Whee! Fun times were had by all... I personally always thought that chimps should have been in the same genus as humans, but of course no one ever listens to me...

Weeelll, I don't know about "all the data". Certainly a number of the references I've read seem to indicate that. As to the discussion of "European" (vs everybody else - and whatever the hell that means), I'm only going by what the authors state:

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Our third-order analysis indicates that the dominant effect in our data is a collapse ca. 40,000 years ago (1,600 generations), consistent with the timing of the initial appearance of anatomically modern humans in Europe. To which population do our results refer? The ethnic composition of the DNA donors of the public human genome is not described, but genotyping of diallelelic, insertion-deletion type polymorphisms mined from the same BAC overlaps (27) suggests that the majority of these sequences represent donors of European origin. Similar patterns resulting in reduction of diversity and extension of linkage disequilibrium in European samples (26, 28-31), and reports of long invariable regions in the human genome (32) have been published. If our results indeed describe European chromosomes, then our estimated time of collapse is in good agreement with expansion time estimates from mitochondrial mismatch distributions.

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Which is about all they say on the subject, actually.Here are the references quoted in the above paragraph, in case you want to look 'em up (some of them are probably on-line):26. Reich, D. E. , Cargill, M. , Bolk, S. , Ireland, J. , Sabeti, P. C. , Richter, D. J. , Lavery, T. , Kouyoumjian, R. , Farhadian, S. F. , Ward, R. , et al. (2001) Linkage disequilibrium in the human genome Nature 411, 199-20427. Weber, J. L. , David, D. , Heil, J. , Fan, Y. , Zhao, C. & Marth, G. T. (2002) Human diallelic insertion/deletion polymorphisms Am. J. Hum. Genet. 71, 854-86228. Kimmel, M. , Chakraborty, R. , King, J. P. , Bamshad, M. , Watkins, W. S. & Jorde, L. B. (1998) Signatures of Population Expansion in Microsatellite Repeat Data Genetics 148, 1921-193029. Pereira, L. , Dupanloup, I. , Rosser, Z. H. , Jobling, M. A. & Barbujani, G. (2001) Y-Chromosome Mismatch Distributions in Europe Mol. Biol. Evol. 18, 1259-127130. Goldstein, D. B. & Weale, M. E. (2001) Population genomics: linkage disequilibrium holds the key Curr. Biol. 11, R576-R57931. Gabriel, S. B. , Schaffner, S. F. , Nguyen, H. , Moore, J. M. , Roy, J. , Blumenstiel, B. , Higgins, J. , DeFelice, M. , Lochner, A. , Faggart, M. , et al. (2002) The Structure of Haplotype Blocks in the Human Genome Science 296, 2225-222932. Miller, R. D. , Taillon-Miller, P. & Kwok, P. Y. (2001) Regions of low single-nucleotide polymorphism incidence in human and orangutan xq: deserts and recent coalescences Genomics 71, 78-88

Hi Mammuthus.Can't the contamination problem apply to just about any "old" DNA experiment? I think you brought this up as your argument questioning the validity (during one of the interminable Borger discussions) of the Mungo Lake data. Is there some way to prevent contamination? How do you tell a "real" from a "contaminated" sequence? (In words of one syllable or less for all us non-molecular biology types... )