The most archaic AMH remains come from Florished, South Africa; they date between 190-330 kya. Other ancient fossil evidence of AMH in South Africa come from Broken Hill (c.110kya) and the Klasis River caves (c. 65-105kya). The Khoisan early migrated into North Africa. As a result, we see shared cultural and behavioral traditions between 200-40kya among South Africans and Moroccans.
The Khoisan carry haplogroups L3(M,N). Before they reached Iberia, they probably stopped in West Africa. Granted L3 and L2 are not as old as LOd, but Gonder et al (2006)provides very early dates for this mtDNA e.g., L3(M,N) 94.3; the South African Khoisan (SAK) carry L1c, L1,L2,L3(M,N) dates to 142.3kya; the Hadza are L2a, L2, L3(M,N), dates to 96.7kya. The dates for L1,L2,L3, M,N are old enough for the Khoisan to have taken N to West Africa, where we find L3, L2 and LOd and thence to Iberia as I suggested in my paper (Winters,2011).
It is interesting to note that LO haplogroups are primarily found among Khoisan and West Africans. This shows that at some point in prehistory the Khoisan had migrated into West Africa on their way to Morocco. The basal L3(M) motiff in West Africa is characterized by the Ddel site np 10394 and Alul site np 10397 associated with AF-24. This supports my contention that Khoisan speakers early settled West Africa on their way to Iberia.
The Khoisan may have introduced the L haplogroup to Iberia. The SAK populations carry haplogroups L2, and L3. Dominguez (2005) ,noted that much of the ancient mtDNA found in Iberia has no relationship to the people presently living in Iberia today and correspond to African mtDNA haplogroups .
The SAK carry haplogroups L1c, L1,L2,L3 M,N and dates to 142.3kya; the Hadza are L2a, L2, L3, M,N, and dates to 96.7kya. The dates for L1,L2,L3(M,N) are old enough for the Khoisan to have taken N to West Africa and thence Iberia. Dominguez (2005) found that the lineages recovered from ancient Iberian skeletons are the African lineages L1b,L2 and L3. Almost 50% of the lineages from the Abauntz Chalcolithic deposits and Tres Montes, in Navarre are the Sub-Saharan lineages L1b,L2 and L3.
The appearance of phylogenetically related sequences of hg L3 present in many ancient Iberian skeletons suggest that this haplogroup may have a long history in Iberia. This would support the possibility that SAK populations early settled ancient Iberia.
The Neanderthal used Mousterian tools. These tools were also being used in Africa as early 130kya. This places Neanderthalers in North Africa. The human types associated with the Neanderthal tools found at Jebel Ighoud and Haua Fteah resemble contemporaneous European Neanderthaler tools. The presence of Mousterian tools suggest that Neanderthalers mixed with Africans because we know that anatomically modern humans were living in the area at the time.
The African Neanderthal people used the common Levoiso-Mousterian tool kit originally discovered in Europe. The Nenderthal skeletons have come from Djebel Irhoud and El Guettar in Morocco (Ki-Zerbo,1981). Later Neanderthal people used the Aterian tool kit.
It was probably in Morocco that Neanderthal and Khoisan interacted. An exception to this norm are the Khoisan who share a phylogenic relationship with Altai Neanderthals (Prufer, et al, 2013).
Many researchers claim that Africans have no relationship to the Neanderthals.But Prufer et al (2013) observed that Khoisan share more alleles with Altaic Neanderthal than Denisova. In the Supplemental section of Prufer et al (2013) there is considerable discussion of the relationship between Neanderthal and Khoisan.
In relation to the Altaic Neanderthal the non-Africans have a lower divergence rate than Africans between 10-20%. Prufer et al (2013) note little statistical difference between non-African and African divergence.
Researchers have observered a relationship between the Neanderthals, the Khoisan and Yoruba. Prufer et al (2013) detected a relationship between the Neanderthal and Mandekan. It is interesting to note that Yoruba traditions place them in Mande-speaking areas (Prufer et al,2013).
There is interesting information in Figure S7.1. In Figure S7.1 the maximum likelihood tree of bonobo, Denisova and Neanderthal, the closest present-day hmans are Africans, not Europeans. Reading the Tree Chart Graph, the neighbor joining tree of archaic and present day human individuals has the Khoisan following the Denisova. An interesting finding of Prufer et al (2013) was that Altaic Neanderthal and Denisova are estimated to have similar split times.
The divergence estimate for African Khoisan-Mandekan and Altaic is younger than the split between Africans and Denisova archaic individuals and modern African individuals. The split times between the Khoisan and Mandekan may be explained by the presence of AF-24 haplotype in West Africa. The major problem with the paper is that the Prufer et al (2013)believe that there was a back-to-Africa migration of Eurasian genomes among West Africans people.
This back migration probably did not occur. What we do know is that the ancient Kushite people belonged to the C-Group. The C-Group people spoke Niger-Congo and Dravidian languages. The Kushites founded many civilizations in Eurasia including the Sumerian and Elamite civilizations. The Kushites may have spread L3(M) and y-chromosome R haplogroup in Eurasia. This suggest that so-called Eurasian genomes are the result of admixtures of Europeans and Kushites.
In summary the Khoisan early settled Morocco. From here they interacted with Neanderthal populations. Later the Khoisan migrated into Iberia an deposited many genomes of the L clade and L3(N) macrohaplogroup.
de Domínguez E.F. Polimorfismos de DNA mitocondrial en poblaciones antiguas de la cuenca mediterránea. Universitat de Barcelona. Departament Biologia Animal, 2005 (PhD thesis).
Gonder MK, Mortensen HM, Reed FA, de Sousa A, Tishkoff SA. (2006). Whole mtDNA Genome Sequence Analysis of Ancient African Lineages. Mol Biol Evol. 2006 Dec 28.
Ki-Zerbo,J. (1981). Unesco General History of Africa Vol. 1: Methodology and African Prehistory (1981), pg.572.
Pruler,K, Racimo,F.,Patterson,N et al. (2014). The complete genome sequences of Neanderthal from the Altai, Mountains. Nature , 505/7481: 43-9. doi .10.1038/ Nature 12881.Epub.2013.Dec.18.
Scozzari, R, Massaia,A, Trombatta,B. et al.(2014). An unbiased resource of novel SNP markers provides a new chronology for human Y-chromosome and reveals a deep phylogenetic structure in Africa. Genome Research, January 6,2014, doi: 10.1101/gr./60785.113.
Winters C. The Gibraltar Out of Africa Exit for Anatomically Modern Humans. WebmedCentral BIOLOGY 2011;2(10):WMC002311 . http://www.webmedcentral.com/article_view/2311