A new study in Nature Genetics by a group of Icelandic scientists has found a 900kbp inversion whose origin appears to be 3 million years before present, i.e., during the time that Homo erectus existed on earth, or even before that time. The mutation is found in Caucasoids (~20%) almost absent in Mongoloids, and rare in Negroids. The authors also discovered that the presence of the mutation has an effect on women having more children and higher recombination rates [the two have been found to be related].
The presence of such an ancient mutation is still a mystery, but two alternative explanations are proposed. The first one is that the polymorphism has been maintained in the human gene pool through balancing selection, which would indicate that its fitness benefits in heterozygotes might have corresponding fitness costs in homozygotes, which remain to be discovered. Since the polymorphism is more frequent in Europeans, it may be the case that there is something in the European environment which allows the fitness benefit to manifest itself, similar to the malarial environments in many places of the world which allow sickle-cell alleles to persist.
The second explanation -which is more likely in my opinion- is that ancestral Caucasoids underwent admixture with a different type of hominin which survived in Western Eurasia and which partially interbred with incoming modern sapiens humans. The mutation subsequently may have spread in the Caucasoid population by balancing selection (since it has not been fixed), and its absence in other populations may indicate simply that they did not interbreed with the different type of hominin.
As far as we know, during the radiation of anatomically modern Homo sapiens, the only candidate species for hybridization with it would be Homo neandertalensis. It's possible then that this was the source of the mutation in question, but since Neanderthals are also a relatively young species (less than 1 million years old) it may be the case that they also received it from a previous hominin species.
After the contested Flores hominin and the recent discovery of possible hybridization of Mongoloids with Homo erectus, this new study presents a new mystery about the origin of modern humans. It remains to be seen how these developments will eventually affect the current picture about human origins which insists on a recent African origin for our species. mtDNA research on humans and Neanderthals suggests no significant hybridization between the two species, and the arguments of the multiregionalists have been severely criticized, but I suspect that in the end the Out-of-Africa theory will have to accommodate the presence of (at least limited) admixture from older forms of Homo in the origins of modern humankind.
For more info Genes Promoting Fertility Are Found in Europeans, Scientists Find Effect of Natural Selection on Human Genome, Gene Arrangement Makes Some Europeans More Fertile.
Nature Genetics (published online)
A common inversion under selection in Europeans
Hreinn Stefansson et al.
A refined physical map of chromosome 17q21.31 uncovered a 900-kb inversion polymorphism. Chromosomes with the inverted segment in different orientations represent two distinct lineages, H1 and H2, that have diverged for as much as 3 million years and show no evidence of having recombined. The H2 lineage is rare in Africans, almost absent in East Asians but found at a frequency of 20% in Europeans, in whom the haplotype structure is indicative of a history of positive selection. Here we show that the H2 lineage is undergoing positive selection in the Icelandic population, such that carrier females have more children and have higher recombination rates than noncarriers.