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The genetic history of North Africa has been heavily influenced by geography. The Sahara desert to the south and the Mediterranean Sea to the North were important barriers to gene flow in prehistoric times. However Eurasia and Africa form a single land mass at the Suez. At the Straits of Gibraltar, Africa and Europe are separated by only 15 km (9 mi). At periods of low sea-levels, such as during a glacial maximum, islands that are currently submerged would appear in the Mediterranean and possibly in between the Gibraltar straits.
These may have encouraged humans to "island hop" between Africa and Europe. During wetter phases of the Sahara, Sub-Saharan Africans would have expanded into North Africa. West Asian populations would have also been attracted to a wet Sahara. West Asian populations could also migrate into Africa via the coastal regions of the Mediterranean.
As a result of these geographic influences, the genetic profile of Berber populations is a complex mosaic of European, Sub-Saharan African and West Asian influences. Though North Africa has experienced gene-flow from the surrounding regions, it has also experienced long periods of genetic isolation, allowing a distinctive genetic markers to evolve in Berber populations.
Current scientific debate is concerned with determining the relative contributions of different periods of gene flow to the current gene pool of North Africans. Anatomically modern humans are known to have been present in North Africa during the Upper Paleolithic 45,000 years ago as attested by the Aterian culture. With no apparent continuity, 22,000 years ago, the Aterian was succeeded by the Iberomaurusian culture which shared similarities with Iberian cultures. The Iberomaurusian was succeeded by the Capsian, a pre-neolithic culture. About 9,000 years ago the Saharan entered a wet phase which attracted Neolithic peoples from the Near East and Sub-Saharan Africans. In historic times, North Africa was occupied by several peoples including Phoenicians (814–146 BCE), Romans (146 BCE–439 CE), Vandals (439–534 CE),and Byzantines (534–647 CE). In the 7th Century a migration of Bedouin peoples from the Arabian peninsula brought Arabic language into North Africa.
Haplogroup E is the most prevalent haplogroup amongst the Berbers accounting for up to 87 percent of Y-chromosomes among some Berber populations. Haplogroup E is thought to have emerged in East-Africa  and would have later dispersed into North Africa and Eurasia. The major sub-clades of haplogroup E found amongst Berbers belong to E1b1b1 which is believed to have emerged in East Africa. Common subclades include, E1b1b1a, E1b1b1b and E1b1b1*. E1b1b1b is distributed along a west-to-east cline with frequencies which can reach as high as 80 percent in Northwest Africa. E1b1b1a has been observed at low to moderate frequencies among Berber populations with significantly higher frequencies observed in Northeast Africa relative to Northwest Africa.
Eurasian haplogroups such as Haplogroup J and Haplogroup R1 have also been observed at moderate frequencies. A thorough study by Arredi et al. (2004) which analyzed populations from Algeria concludes that the North African pattern of Y-chromosomal variation (including both J1 and E3b2 main haplogroups) is largely of Neolithic origin, which suggests that the Neolithic transition in this part of the world was accompanied by demic diffusion of Berber–speaking pastoralists from the Middle East 
E1b1b1b (E-M81) is the most common Y chromosome haplogroup in North Africa, dominated by its sub-clade E-M183. It is thought to have originated in North Afric. 5,600 years ago. The parent clade E1b1b originated in East Africa. Colloquially referred to as the Berber marker for its prevalence among Mozabite, Middle Atlas, Kabyle people and other Amazigh groups, E-M81 is also quite common among North African groups. It reaches frequencies of up to 80 percent in some parts of the Maghreb. This includes the Saharawish for whose men Bosch et al. (2001) reports that approximately 76 percent are M81+.
This haplogroup is also found of some amounts in the Iberian Peninsula, probably due to ancient migrations during the Islamic, Roman, and Carthaginian empires, as well as the influence of Sephardic Jews. In Iberia generally it is more common than E1b1b1a (E-M78), unlike in the rest of Europe, and as a result this E-M81 is found throughout Latin America and among Hispanic men in USA. As an exceptional case in Europe, this sub-clade of E1b1b1 has also been observed at 40 percent the Pasiegos from Cantabria.
There are two recognized sub-clades, although one is much more important than the other.
Individuals receive mtDNA only from their mothers. According to Macaulay et al. 1999, "one-third of Mozabite Berber mtDNAs have a Near Eastern ancestry, probably having arrived in North Africa less than 50,000 years ago, and one-eighth have an origin in sub-Saharan Africa. Europe appears to be the source of many of the remaining sequences, with the rest having arisen either in Europe or in the Near East." Maca-Meyer et al. 2003 analyze the "autochthonous North African lineage U6" in mtDNA, and conclude that:
A genetic study by Fadhlaoui-Zid et al. 2004 argues concerning certain exclusively North African haplotypes that "expansion of this group of lineages took place around 10,500 years ago in North Africa, and spread to neighbouring population", and apparently that a specific Northwestern African haplotype, U6, probably originated in the Near East 30,000 years ago but has not been highly preserved and accounts for 6-8 percent in southern Moroccan Berbers, 18 percent in Kabyles and 28 percent in Mozabites. Rando et al. 1998 (as cited by ) "detected female-mediated gene flow from sub-Saharan Africa to NW Africa" amounting to as much as 21.5 percent of the mtDNA sequences in a sample of NW African populations; the amount varied from 82 percent (Tuaregs) to 4 percent (Rifains). This north-south gradient in the sub-Saharan contribution to the gene pool is supported by Esteban et al.
Nevertheless, individual Berber communities display a considerably high mtDNA heterogeneity among them. The Berbers of Jerba Island, located in South Eastern Tunisia, display an 87 percent Eurasian contribution with no U6 haplotypes, while the Kesra of Tunisia, for example, display a much higher proportion of typical sub-Saharan mtDNA haplotypes (49 percent), as compared to the Zriba (8 percent). According to the article, "The North African patchy mtDNA landscape has no parallel in other regions of the world and increasing the number of sampled populations has not been accompanied by any substantial increase in our understanding of its phylogeography. Available data up to now rely on sampling small, scattered populations, although they are carefully characterized in terms of their ethnic, linguistic, and historical backgrounds. It is therefore doubtful that this picture truly represents the complex historical demography of the region rather than being just the result of the type of samplings performed so far."
Additionally, recent studies have discovered a close mitochondrial link between Berbers and the Saami of Scandinavia which confirms that the Franco-Cantabrian refuge area of southwestern Europe was the source of late-glacial expansions of hunter-gatherers that repopulated northern Europe after the Last Glacial Maximum and reveals a direct maternal link between those European hunter-gatherer populations and the Berbers. With regard to Mozabite Berbers, one-third of Mozabite Berber mtDNAs have a Near Eastern ancestry, probably having arrived in North Africa ∼50,000 years ago, and one-eighth have an origin in sub-Saharan Africa. Europe appears to be the source of many of the remaining sequences, with the rest having arisen either in Europe or in the Near East."
According to the most recent and thorough study about Berber mtDNA from Coudray et al. 2008 that analysed 614 individuals from 10 different regions (Morocco (Asni, Bouhria, Figuig, Souss), Algeria (Mozabites), Tunisia (Chenini-Douiret, Sened, Matmata, Jerba) and Egypt (Siwa)) the results may be summarized as follows :
The Berber mitochondrial pool is characterized by an "overall high frequency of Western Eurasian haplogroups, a somehow lower frequency of sub-Saharan L lineages, and a significant (but differential) presence of North African haplogroups U6 and M1". And according to Cherni et al. 2008 "the post-Last glacial maximum expansion originating in Iberia not only led to the resettlement of Europe but also of North Africa".
Until recently, some papers suggested that the distribution of the main L haplogroups in North Africa was mainly due to trans-Saharan slave trade. However in September 2010, a thorough study about Berber mtDNA by Frigi et al. concluded that most of L haplogroups were much older and introduced by an ancient African gene flow around 20,000 years ago.
In January 13 th 2012, an exhaustive genetic study of North Africa's human populations was published in PLoS Genetics and was undertaken jointly by researchers in the Evolutionary Biology Institute (CSIC-UPF) and Stanford University, among other institutions.
The study reveals that the genetic composition of North Africa's human populations is extremely complex, and the result of a local component dating back thirteen thousand years and the varied genetic influence of neighbouring populations on North African groups during successive migrations. According to David Comas, coordinator of the study and researcher at the Institute for Evolutionary Biology (CSIC-UPF), "some of the questions we wanted to answer were whether today's inhabitants are direct descendants of the populations with the oldest archaeological remains in the region, dating back fifty thousand years, or whether they are descendants of the Neolithic populations in the Middle East which introduced agriculture to the region around eight thousand years ago. We also wondered if there had been any genetic exchange between the North African populations and the neighbouring regions and if so, when these took place".
To answer these questions, the researchers analyzed around 800,000 genetic markers, distributed throughout the entire genome in 125 North African individuals belonging to seven representative populations in the whole region, and the information obtained was compared with the information from the neighbouring populations.
The results of this study show that there is a native genetic component which defines North Africans. In-depth study of these markers, shows that the people inhabiting North Africa today are not descendants of either the earliest occupants of this region fifty thousand years ago, or descendants of the most recent Neolithic populations.
The data shows that the ancestors of today's North Africans were a group of populations which already lived in the region around thirteen thousand years ago. Furthermore, this local North African genetic component is very different from the one found in the populations in the south of the Sahara, which shows that the ancestors of today's North Africans were members of a subgroup of humanity who left Africa to conquer the rest of the world and who subsequently returned to the north of the continent to settle in the region.
As well as this local component, North African populations were also observed to share genetic markers with all the neighbouring regions, as a result of more recent migrations, although these appear in different proportions.
There is an influence from the Middle East, which becomes less marked as the distance from the Arabian Peninsula increases, similar proportions of European influence in all North African populations, and, in some populations, there are even individuals who present a large proportion of influence from the South of the Sahara in their genome.
Recent genetic analysis of North African populations have found that, despite the complex admixture genetic background, there is an autochthonous genomic component which is likely derived from “back-to-Africa” gene flow older than 12,000 years ago (ya) (i.e., prior to the Neolithic migrations). This local population substratum seems to represent a genetic discontinuity with the earliest modern human settlers of North Africa (those with the Aterian industry) given the estimated ancestry is younger than 40,000 years ago. North Morocco, Libya and Egypt carry high proportions of European and Near Eastern ancestral components, whereas Tunisian Berbers and Saharawi are those populations with highest autochthonous North African component.
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The general parent Y-chromosome Haplogroup E1b1b (formerly known as E3b), which might have originated in the Horn of Africa or the near east is by far the most common clade in North and Northeast Africa and found in select populations in Europe, particularly in the Mediterranean and South Eastern Europe. E1b1b reaches in Europe Greece and the Balkan region but, is not as high there as it is among African populations..
Outside of North and Northeast Africa, E1b1b's two most prevalent clades are E1b1b1a (E-M78, formerly E3b1a) and E1b1b1b (E-M81, formerly E3b1b).
E1b1b1a is the most common subclade of E1b1b and is present predominantly in North East Africa. It was originally thought to have been a marker of Neolithic migrations (perhaps coinciding with the introduction of Agriculture into Europe) from Anatolia to Europe, via the Balkans, where it enjoys the high frequency. However, Cruciani's latest study suggests that it actually arrived into the Balkans from Western Asia during the Palaeolithic, and then spread throughout Europe much later (c. 5300 years ago) due to a population expansion from Egypt. E1b1a is also found at low frequencies in this area.
A study from Semino (published 2004) showed that Y-chromosome haplotype E1b1b1b (E-M81), is specific to North African populations and almost absent in Europe except the Iberia (Spain and Portugal) and Sicily. Another 2004 study showed that E1b1b1b is found present, albeit at low levels throughout Southern Europe (ranging from 1.5 percent in Northern Italians, 2.2 percent in Central Italians, 1.6 percent in southern Spaniards, 3.5 percent in the French, 4 percent in the Northern Portuguese, 12.2 percent in the southern Portuguese and 41.2 percent in the genetic isolate of the Pasiegos from Cantabria).
The findings of this latter study contradict a more thorough analysis Y-chromosome analysis of the Iberian peninsula according to which haplogroup E1b1b1b surpasses frequencies of 10 percent in Southern Spain. The study points only to a very limited influence from northern Africa and the Middle East both in historic and prehistoric times. The absence of microsatellite variation suggests a very recent arrival from North Africa consistent with historical exchanges across the Mediterranean during the period of Islamic expansion, namely of Berber populations. A study restricted to Portugal, concerning Y-chromosome lineages, revealed that "The mtDNA and Y data indicate that the Berber presence in that region dates prior to the Moorish expansion in 711 AD. ... Our data indicate that male Berbers, unlike sub-Saharan immigrants, constituted a long-lasting and continuous community in the country".
Haplotype V(p49/TaqI), a characteristic North African haplotype, may be also found in the Iberian peninsula, and a decreasing North-South cline of frequency clearly establishes a gene flow from North Africa towards Iberia which is also consistent with Moorish presence in the peninsula. This North-South cline of frequency of haplotype V is to be observed throughout the Mediterranean region, ranging from frequencies of close to 30 percent in southern Portugal to around 10 percent in southern France. Similarly, the highest frequency in Italy is to be found in the southern island of Sicily (28 percent).
A wide-ranging study (published 2007) using 6,501 unrelated Y-chromosome samples from 81 populations found that: "Considering both these E-M78 sub-haplogroups (E-V12, E-V22, E-V65) and the E-M81 haplogroup, the contribution of northern African lineages to the entire male gene pool of Iberia (barring Pasiegos), continental Italy and Sicily can be estimated as 5.6 percent, 3.6 percent and 6.6 percent, respectively."
A very recent study about Sicily by Gaetano et al. 2008 found that "The Hg E3b1b-M81, widely diffused in northwestern African populations, is estimated to contribute to the Sicilian gene pool at a rate of 6 percent." .
According to the most recent and thorough study about Iberia by Adams et al. 2008 that analysed 1,140 unrelated Y-chromosome samples in Iberia, a much more important contribution of northern African lineages to the entire male gene pool of Iberia was found : "mean North African admixture is 10.6 percent, with wide geographical variation, ranging from zero in Gascony to 21.7 percent in Northwest Castile".
Genetic studies on Iberian populations also show that North African mitochondrial DNA sequences (haplogroup U6) and sub-Saharan sequences (Haplogroup L), although present at only low levels, are still at much higher levels than those generally observed elsewhere in Europe. Haplogroup U6 have also been detected in Sicily and South Italy at very low levels. It happens also to be a characteristic genetic marker of the Saami populations of Northern Scandinavia.
It is difficult to ascertain that U6's presence is the consequence of Islam's expansion into Europe during the Middle Ages, particularly because it is more frequent in the north of the Iberian Peninsula rather than in the south. In smaller numbers it is also attested too in the British Isles, again in its northern and western borders. It may be a trace of a prehistoric neolithic/megalithic expansion along the Atlantic coasts from North Africa, perhaps in conjunction with seaborne trade. One subclade of U6 is particularly common among Canarian Spaniards as a result of native Guanche (proto-Berber) ancestry.