Attested presence of Caucasian people in Northern Africa goes up to Paleolithic times. From the archaeological record it has been proposed that, as early as 45,000 years ago (ya), anatomically modern humans, most probably expanded the Aterian stone industry from the Maghrib into most of the Sahara . More evolved skeletal remains indicate that 20,000 years later the Iberomaurusian makers, replaced the Aterian culture in the coastal Maghrib. Several hypothesis have been forwarded concerning the Iberomaurusian origin. They can be resumed in those which propose an arrival, from the East, either from the Near East or Eastern Africa, and those which point to west Mediterranean Europe, either from the Iberian Peninsula, across the Gibraltar Strait, or from Italy, via Sicily, as their most probable homeland . Between 10,000 and 6,000 ya the Neolithic Capsian industry flourished farther inland. The historic penetration in the area of classical Mediterranean cultures, ending with the Islamic domination, supposed a strong cultural influx. However, it seems that the demic impact was not strong enough to modify the prehistoric genetic pool.
Linguistic research suggests that the Afroasiatic phylum of languages could have originated and extended with these Caucasians, either from the Near East or Eastern Africa and that posterior developments of the Capsian Neolithic in the Maghrib might be related to the origin and dispersal of proto-Berber speaking people into the area . Nowadays, the Berber speakers, scattered throughout Northwest Africa from the Atlantic to the Lybic desert and from the Mediterranean shores to the south of the Sahel, are considered the genuine descendants of those prehistoric colonizers. Some important issues are pending of resolution to clarify the past and present of the North African Caucasians: To which extent the Neolithic waves substituted the Paleolithic recipients? Which is the most probable origin of these prehistoric occupants? Did they come from Europe, East Africa, Southwest Asia or are they a result of an "in situ" evolution? Is there a correspondence between the Afroasiatic diversification and the spread of Caucasians?
Recently, molecular genetic research on North African populations has contributed new data to test the major issues proposed on archaeological, anthropological and linguistic grounds. The studies based on uniparental genetic markers have been particularly informative. Both, mitochondrial DNA (mtDNA) sequences [4, 5], and Y-chromosome binary markers [6, 7] detected specific North African haplotypes that confirm an ancient human colonization for this area and a sharp discontinuity between Northwest Africa and the Iberian Peninsula. From a mtDNA point of view, the most informative of these genetic markers is the North African clade U6. On the basis of complete mtDNA sequences, it has been proposed that U6 lineages, mainly found in North Africa, are the signatures of a return to Africa around 39,000–52,000 ya . This stresses the importance of its detailed study in order to trace one of the earliest Caucasian arrivals to Africa. Although in moderate frequencies, the geographic range of this clade extends from the Near East to the Canary Islands, along the Atlantic shores of Northwest Africa and from the Sahel belt, including Ethiopia, to the southern Mediterranean rim. Out of this area, U6 has only been spotted in the Iberian Peninsula [9–12], Sicily , in the north European Ashkenazic Jews , and in Ibero-America. The presence in the latter is, most probably, the result of the Spanish and Portuguese colonization [15, 16].
In order to construct an unambiguous phylogeny for this clade and infer precise ages for the whole group and for its derivatives, we have fully sequenced eleven mitochondrial lineages representing the main branches of U6. Subsequently, we analyzed the geographic distribution range and relative diversity of these subclades, to deduce their most probable expansion origins based on sequence information of the first hypervariable segment (HVSI) of the mitochondrial control region and on new RFLPs, discovered to be diagnostic for them.