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Are there any estimates of both the modern human and Neanderthal population sizes over the last, say, 100 k years? Since "purebread" Neanderthals are extinct, their population has to hit zero; that happened sometime around 30 k years ago. We have good estimates of both the Neanderthal (zero) and modern human (millions, billions) population sizes in the recent past -- what I'm wondering is what the numbers were (roughly) when modern humans and Neanderthals came into contact. How many people were there in each group? How many interbred? Is there any reliable way to estimate those numbers given what we know today? If not, would it be possible, if we sequenced the genomes of a large number of Neanderthal fossils, to get a sense of how much variation there was in their gene pool, and use that to estimate the size of their population? Could we also look at how much of that variation survives today in the homo sapiens gene pool?

In Why Did 6 Great Ape Species Survive But Only 1 Hominid Species? the poster states that "following the eruption of the Toba volcano 70,000 years ago, there were between 1,000 and 10,000 mating pairs of Homo sapiens left." Was the Neanderthal population of a similar order at that time? Was it ever larger than the modern human population? We'll never know the exact numbers -- and the exact numbers don't really matter. I'm interested in orders of magnitude. When homo sapiens and Neanderthals interbred, did sapiens already outnumber them, or were the populations roughly equal? Were the number of Neanderthal - sapiens crosses tiny relative to both populations, or were they perhaps large relative to the smaller of the two populations?

A related question: Of the Neanderthals living, say, 100 k years ago, what fraction have descendants who are alive today? Is that a question we can answer either now or in the near future, after sequencing more Neanderthal genomes? According to http://www.nature.com/scitable/knowledge/library/what-happened-to-the-neanderthals-68245020

recent research on Neanderthal nuclear DNA has found evidence for limited admixture: a small portion (up to ~4%) of the genomes of non-Africans so far examined may derive from Neanderthals, suggesting that interbreeding probably occurred in the Near East during the earliest dispersal of modern humans out of Africa, but prior to their arrival in Europe (Green et al. 2010). Demographic modeling of admixture combined with territorial expansion, however, indicates that this level of introgression would be produced under very low (<2%) interbreeding rates and strong barriers to reproduction between Neanderthals and modern humans, arguing against assimilation (Currat & Excoffier 2011). Pending the completion of the Neanderthal genome and ancient DNA analyses of early modern Europeans dating to the Upper Paleolithic, and following the recent discovery of a third possibly coexisting species from Denisova cave (Krause et al. 2010), it is premature to conclude that the currently observed level of admixture constitutes assimilation.

That would suggest that the fraction of Neanderthals with living descendants is very small -- most Neanderthal lineages died out. What evidence would it take to conclude the reverse -- to conclude that the Neanderthal population was very small, and was largely assimilated?

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    $\begingroup$ Just to clarify: in the second part of your question, I think you're asking about neanderthals with living descendants, rather than ancestors. I would make the edit myself, but you've used the term 'ancestors' twice, so I want to make sure I understand correctly. $\endgroup$ – bshane Oct 18 '15 at 11:59
  • $\begingroup$ You're absolutely right, I meant descendants in both cases. $\endgroup$ – Adrian Oct 18 '15 at 13:11
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Briggs et al. 2009, using mtDNA report an estimate of 3500 females. They failed to offer any estimate of the male population size. Their estimates is much lower than previously thought. They report two hypotheses of why their estimate is so low:

Hypothesis 1 - Low population size

H. neanderthalis population size was indeed really low. After all, they mostly had to live in harsh ice age conditions.

Hypothesis 2 - Slow decline in population size

H. neanderthalis population size were quite high at some point and their population size slowly decreased in size up to the point of being completely wiped out. Such low decline in population size may explain the low level of genetic diversity observed (yielding to an estimate of small population size) in their sample. If the decline of H. neanderthalis was sudden, then even the last survivors of the lineage would have shown quite a high level of genetic diversity. Their decline may have started about 40,000 years with the arrival of Homo sapiens in Europe but this is just a speculation. This second hypothesis is congruent with the evidence of a rather rapid rate of evolution observed in H. neanderthalis

In short, we don't really know what the population size of H. neanderthalis was but it might have been as low as 3500 females only

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