Explaining the Neandertal admixture paradox via long-running but very infrequent admixture

This seems like an interesting theory that might explain two facts that do not appear to gel well with existing models of a single (or few) short and intense periods of admixture during Out-of-Africa. These are:

• The complete absence of archaic Eurasian Y chromosomes and mtDNA in the modern human gene pool
• The fact that Neandertals did not appear to have gotten morphologically more different than modern humans over most of their late history, but rather the opposite, they became ever-more similar to modern humans

It would also have three added benefits:

• it would be a very natural consequence of my favored scenario that modern humans (living probably in northern and eastern Africa) had Neandertal neighbors living in the Near East and southern Europe from which they were separated by geographical barriers, making admixture likely but not routine. The authors consider the idea that the admixture took place in the Near East, and even if some of it did not, I'd say most of it must have taken place there, since that is where maximal evidence of temporal co-existence between the two demes exists.
• it would not require an unlikely scenario of large-scale hybridization between very divergent demes: occasional gene flow could still occur, and could spread adaptations back and forth (explaining the phenotypic non-divergence), but the tendency of people to marry those like themselves (homogamy) would be preserved. 
• It would be consistent with the re-writing of Out-of-Africa thanks to the halving of the autosomal rate. This would necessitate an early OoA and thus a longer occupation of parts of Asia by both sapiens and Neandertals.during which they may have occasionally interbred. So, not only were modern humans and Neandertals neighbors in Asia, but modern Eurasians are not descended from a fresh ~50ka Out-of-Sub-Saharan Africa expansion that would have rendered these long neighborly relations in the Near East irrelevant.

Note that this does not appear to be inconsistent with recent dating of the modern human-Neandertal admixture by Sankararaman et al. since that involved only the latest period of admixture. It is also not inconsistent with the idea that archaic African admixture may be contributing to the D-statistic evidence for non-African/Neandertal similarity, since, presumably, modern humans could experience low-level gene flow both with their northern Neandertal neighbors, and their southern archaic African ones.

So, all in all, I'm fairly sympathetic to this model, and I'd be interested to see how it is received by experts in this field.

PLoS ONE 7(10): e47076. doi:10.1371/journal.pone.0047076

Extremely Rare Interbreeding Events Can Explain Neanderthal DNA in Living Humans

Armando G. M. Neves, Maurizio Serva

Considering the recent experimental discovery of Green et al that present-day non-Africans have 1 to 4% of their nuclear DNA of Neanderthal origin, we propose here a model which is able to quantify the genetic interbreeding between two subpopulations with equal fitness, living in the same geographic region. The model consists of a solvable system of deterministic ordinary differential equations containing as a stochastic ingredient a realization of the neutral Wright-Fisher process. By simulating the stochastic part of the model we are able to apply it to the interbreeding ofthe African ancestors of Eurasians and Middle Eastern Neanderthal subpopulations and estimate the only parameter of the model, which is the number of individuals per generation exchanged between subpopulations. Our results indicate that the amount of Neanderthal DNA in living non-Africans can be explained with maximum probability by the exchange of a single pair of individuals between the subpopulations at each 77 generations, but larger exchange frequencies are also allowed with sizeable probability. The results are compatible with a long coexistence time of 130,000 years, a total interbreeding population of order individuals, and with all living humans being descendants of Africans both for mitochondrial DNA and Y chromosome.

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