nero wrote:
Another thing is that some of you do not realize that the evidence of the bottleneck is not from ancient, prehistoric DNA but from modern human genome.

*sigh* yes we DO realize that.
We also realize that it is, as Midol has tried to splain, a "statistical" observation . . .
...
Yeah, I am aware that mdiehl understood the thing, but some other people did not.
I'll jump in and add my two cents at some point. That two cents is probably about 10 years "out-of-date" and (like everyone elses) was based on the inherently flawed ethnological and archaeological data available.
Was the bottleneck an actual population bottleneck, or was it just a variability bottleneck? How would that be answered?
The thing about molecular paleobiology is that: at best it takes DECADES for a sufficient sample size and number of replicated studies to unfurl to warrant reaching conclusions. Indeed, sufficiently representative samples and generalizable results may NEVER be at hand.
I believe they now have DNA from several hundred (perhaps 1000) Neanderthal individuals? (it may be a lot less than that actually). Neanderthals existed for what? 200,000 years over virtually the entire extent of the north Old World? Maximum simultaneous population sizes probably > 500,000? Maximum total population ever perhaps 10,000,000? Can a non-random convenience sample of 0.0001% a population which changed over the course of its existence ever be considered representative of that population?
This issue is a bit different, but as far as I know, the original data on which the whole Y-chromosome paleo-variability inference models were based was TWO old Chinese brothers! TWO!

In 10 years that may be 50 pairs of brothers, and maybe in 20 years 100 pairs of brothers, at which point the margin of error (which is the actually correct technical term but close enough) for the estimates on which the model is based might be somewhat close to a bare minimum of acceptable?
It is definitely cool stuff, but they never tell the lay public the truth about this stuff: it is generally EXTREMELY speculative when it is first initiated and generally stays that way for decades. Remember as recently as 2000 there were scholars insisting that "Neanderthals are NOT US!" and they had "plenty" of empirical evidence to back up their arguments. Now, with sample sizes that have increased probably 50 or 80 fold compared to those days, we know that such claims were ludicrous. Obviously Neanderthals interbred with modern humans and Northern populations got more of the genetic material than southern ones. It is wise to be skeptical and not get too attached to any specific conclusion for a few years if not decades.
Not to say the arguments made in the article are not interesting--possible even accurate--but there is not really anyway to say at this point. More research is needed.