The most important source of gene flow to North Africa from the Neolithic Era onwards was from Western Asia, whereas the Sahara Desert to the south and the Mediterranean Sea to the north formed barriers to gene flow from the rest of Africa (sub-Saharan Africa) and parts of Europe in prehistory. North Africa is connected to Western Asia via the Isthmus of Suez and the Sinai Peninsula, while at the Straits of Gibraltar, North Africa and Europe are separated by only , similarly Malta, Sicily, Canary Islands, Lampedusa and Crete are close to the coasts of North Africa, with the indigenous Guanche people of the Canary Islands being North African Berbers.
North Africa is a genetically heterogenous and diverse region, and is characterized by its diverse ethno-linguistic groups, the main ones being Arabic and Berber-speaking people. Although historically and sociologically this consideration is assumed, no genetic differences have been reported between Arabs and Berbers when analyzing individual genetic markers. North African populations show a complex and heterogeneous genetic structure that has been described as an amalgam of at least four different ancestral components from the Middle East in particular, sub-Saharan Africa, Europe and also indigenous North Africans who are genetically distinct from these three. Although North Africa has experienced gene flows from the surrounding regions, it has also experienced long periods of genetic isolation. Some genetic studies have been criticised for their interpretation and categorisation of African genetic data."It is not clear to what degree certain genetic systems usually interpreted as non-African may in fact be native to Africa. Much depends on how "African" is defined and the model of interpretation. The various genetic studies usually suffer from what is called categorical thinking, specifically, racial thinking. Many investigators still think of "African" in a stereotyped, nonscientific (evolutionary) fashion, not acknowledging a range of genetic variants or traits as equally African".
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 Middle Paleolithic (300,000 years ago), as attested by the by Jebel Irhoud 1. Without morphological discontinuity, the Aterian was succeeded by the Iberomaurusian industry. The Iberomaurusian industry was succeeded by the heavily West Asian influenced Capsian industry (8000 BC to 2700 BC) in the eastern part of North Africa (Egypt, Libya, Tunisia, eastern Algeria and Malta).
DNA studies of Iberomaurusian peoples at Taforalt, Morocco, dating to around 15,000 years ago have found them to have a distinctive Maghrebi ancestry, formed from a mixture of Near Eastern component (related to the Natufian culture) and an ancestral North African component (that diverged from Sub-Saharan Africans around the same time as the out of Africa population), which is widespread among early Holocene North Africans, and is still found as a part of the genome of modern Northwest Africans. Individuals from Takarkori cave in southern Libya, dating to 7,000 years ago, are in contrast primarily of ancestral North African ancestry. There is evidence of a small amount (few %) of gene flow from European western hunter-gatherers into some eastern Maghreb hunter-gatherers during the late Mesolithic-early Neolithic (c. 8000 years ago). Later during the Neolithic, from around 7,500 years ago onwards, there was a migration into Northwest Africa of European Neolithic Farmers from the Iberian Peninsula (who had originated in Anatolia several thousand years prior), as well as pastoralists from the Levant, both of whom also significantly contributed to the ancestry of modern Northwest Africans.
After migrating to North Africa in the 1st millennium BC, Semitic Phoenician settlers from the cities of Tyre, Arvad, Ekron and Sidon in the Levant established over 300 coastal colonies throughout the region (as well as the Iberian Peninsula, Sicily, Malta, Sardinia, Corsica etc.) and built a powerful empire that controlled most of the region from the 8th century BC until the middle of the 2nd century BC.
In the 7th century AD, the region was conquered by Muslim Umayyad Arabs from the Arabian Peninsula. Under the relatively brief Arab-Umayyad conquest and the later arrival of nomadic Bedouin, Levantine Arabs and Arabized peoples from the Near East in Western Asia and the arrival of some Sephardi Jews and Iberian Muslims fleeing the Spanish Catholic Reconquista of Iberia, a partial population mix or fusion may have taken place and have resulted in some further genetic diversity among some North Africans, increasing the significant already long established West Asian input. The trans-Saharan slave trade which began in the 8th century AD has resulted in increased levels of Sub-Saharan African ancestry in North Africans in Medieval and modern times relative to earlier periods.
A recent study from 2017 suggested that the Arab migrations to the Maghreb was mainly a demographic process that heavily implied gene flow and remodeled the genetic structure of the Maghreb, rather than a mere cultural replacement as claimed by older studies. Another study found out that the majority of J-M267 (Eu10) chromosomes in the Maghreb are due to the recent gene flow caused by the Arab migrations to the Maghreb in the first millennium CE as both southern Qahtanite and northern Adnanite Arabs added to the heterogenous Maghrebi ethnic melting pot. The Eu10 chromosome pool in the Maghreb is derived not only from early Neolithic dispersions from Western Asia but to a much greater extent from recent expansions of Arab tribes from the Arabian Peninsula. While acknowledging the genetic impact of Arabization of Northwest Africa during the Islamic period, other authors have suggested that earlier migration processes, such as the arrival of Neolithic Revolution era famers from Western Asia and Southern Europe together with Bronze Age and Iron Age input from Mesopotamia and the Levant were ultimately more genetically impactful.
Y-chromosome
Previous works with Y-chromosome markers have shown that North Africa is highly heterogenous, the Y lineages found in the region are: A, B, E-V38, E-M78, E-M81, E-M123, G, F, H, I1, I2, J1, J2 and R1b. E-M81 reaches an average frequency of 40% across the region. J-M267 is the second most-frequent haplogroup, accounting for around 30% of North Africans and assumed to have spread out of the Arabian Peninsula or Levant into North Africa.
Haplogroup E is thought to have emerged in Africa or Eurasia, and would have originated, or later dispersed into North Africa. Common subclades include E1b1b1a, E1b1b1b and E1b1b1*. E1b1b1b is distributed along a west-to-east cline with frequencies that can reach as high as 80 per cent among Hassani Arabs and 1% among Siwa Berbers. E1b1b1a has been observed at low to moderate frequencies among Berber populations with significantly higher frequencies observed in Northeast Africa relative to Northwest Africa. Loosdrecht et al. 2018 demonstrated that E1b1b is most likely indigenous to Levant and migrated from Levant to North Africa during the Paleolithic.
Haplogroup J-M267 is another very common haplogroup in the Maghreb, being the second most-frequent haplogroup after haplogroup E. Haplogroup R1 has 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 E1b1b main haplogroups) is largely of West Asian origin, which suggests that their introduction in this part of the world was to a great extent the result of a migration of recent Semitic pastoralists from the Middle East, although more recent papers have suggested that this date could have been as long as ten thousand years ago during the Neolithic, with the transition from the Oranian to the West Asian originating Capsian culture in North Africa. Another study concluded that the J-M267 chromosome pool in the Maghreb is derived not only from early Neolithic dispersions from Levant, Mesopotamia and Anatolia but to a much greater extent from recent expansions of Arab tribes from the Arabian Peninsula during the Arab migrations to the Maghreb.
Keita (2008) examined a published Y-chromosome dataset on Afro-Asiatic populations and found that a key lineage E-M35/E-M78, sub-clade of haplogroup E, was shared between the populations in the locale of original Egyptian and Libyan speakers and modern Cushitic speakers from the Horn of Africa. These lineages are present in modern Egyptians, Berbers, Cushitic speakers from the Horn of Africa, and Semitic speakers in Western Asia. He noted that variants are also found in the Aegean and Balkans, but the origin of the M35 subclade mutation was in Egypt or Libya, and its clades were dominant in a core portion of Afro-Asiatic speaking populations which included Cushitic, Egyptian and Berber groups, and in Semitic speakers, but showed a decline in frequency among Semites going west to east in the Levantine-Syria-Mesopotamia region. Keita identified high frequencies of M35 (>50%) among Omotic populations, but stated that this only derived from a small, published sample of 12. Keita also wrote that the PN2 mutation was shared by M35 and M2 lineages and he believed this paternal clade originated from prehistoric East Africa. He concluded that "the genetic data give population profiles that clearly indicate males of African origin, as opposed to being of Asian or European descent" but acknowledged that the biodiversity does not indicate any specific set of skin colours, racial types or facial features as populations were subject to microevolutionary pressures.
E1b1b1b (Haplogroup E-M81); formerly E3b1b, E3b2
E1b1b1b (E-M81) is the most common Y chromosome haplogroup in North Africa, dominated by its sub-clade E-M183. It might have originated in North Africa. The parent clade, E1b1b, has been found among Prehistoric Levantines, Mesopotamians, Anatolians and North-Africans. This haplogroup has been found at high levels in Medieval Berber people from Al-Andalus and among Canary Islands which were inhabited by Berber Guanche people, with lower but significant amounts also in Portugal, Southern Spain, Southern Italy and the Provence region of France. As a result of European colonization, E-M81 is found in parts of Latin America,See the remarks of genetic genealogist Robert Tarín for example. We can add 6.1 per cent (8 out of 132) in Cuba, ; 5.4 per cent (6 out of 112) in Brazil (Rio de Janeiro), "The presence of chromosomes of North African origin (E3b1b-M81; Cruciani et al., 2004) can also be explained by a Portuguese-mediated influx, since this haplogroup reaches a frequency of 5.6 per cent in Portugal (Beleza et al., 2006), quite similar to the frequency found in Rio de Janeiro (5.4 per cent) among European contributors.", among Hispanic in USA.2.4 per cent (7 out of 295) among Hispanic men from California and Hawaii, This sub-clade of E1b1b1 has also been observed at 40 per cent in the comarca Pasiegos from Cantabria.
In smaller numbers, E-M81 carrying individuals can be found in Malta, Northern Sudan, Cyprus and among Sephardic Jews.
There are two recognized sub-clades, although one is much more common than the other. Sub-clades of E1b1b1b (E-M81): E1b1b1b1 (E-M107). found in one sample from Mali. E1b1b1b2b (E-M183). Most individuals belong to this subclade.Y-DNA Haplogroup E and its Subclades - 2008 E1b1b1b2 (E-M165). found in one Middle Eastern sample.