Almost all of the Tunisian Y-DNA in the 220 man sample is either African, and within that almost all N. African, or is typical of Arab populations. One instance of Y-DNA G, six of R1b other than R1b-V88, 2 of DE*, one of R1a, 1 of Y-DNA L (most common in Pakistan), 3 of Y-DNA T, and 18 of J2 are the only exceptions. But, J2 and T aren't unusual to find mixed with J1 in an Arab or Afro-Asiatic language speaking African population.
Only 8/220 (less than 4 %), spread across three halogroups (1 G, 1 R1a, and 6 R1b xV88), are predominantly European, and none of those are entirely absent from the Near East.
(Mozabites, a Berber population of Northern Algeria has much less Arab genetic influence in its Y-DNA. Tunisa is a North African hotspot for this influence which is also much weaker in Morocco.)
The TMRCA of the Berber Y-DNA E which is modal in the sample, is about 3700 BCE. This would imply a male dominated migration, likely bringing the current Berber languages as well, just before the dawn of the historic era in Egypt and well after the likely ethnogenesis of the Chadic people ca. 5700 BCE whose Y-DNA TMCRA for R1b-V88 also corresponds well with the archaeologically calibrated date of origin of these peoples. This appears to be a sweet spot where Y-DNA mutation rate estimates appear to be pretty accurate.
The close similarities of the Berber language family dialects also supports the relatively recent 3700 BCE date, which would be Neolithic, rather than Mesolithic in this region. This is also about the time that the Green Sahara era that began ca. 8000 BCE ended in the region which from then on had roughly the same climate as it does today. The arid climate shift called the 5.9 kyr event peaked around 3900 BCE, and could easily have left to previous population ill adapted to survive in the new conditions, relative to the Berber migrants into the region.
This timing also coincides with Ethiopian domestication of Sorghum (which could have pushed out Cushitic pastoralists from the region as Sorghum farmers pushed them out of an area that had not been congenial to Fertile Crescent crops) and is long after cattle were present in the Sahara and NW Africa. It also coincides with the dawn of the Copper Age in Egypt. It probably also predates the arrival of the domesticated camel in the region.
The older TMRCA of the J1 clades (which are next most common), which make up about a quarter of the sample, at ca. 7500 BCE, probably reflects the mix of Y-DNA clades that arose in the Near East in Arab populations that arrived together in the historic era with the Islamic empire, rather than local differentiation of those clades. The Y-DNA L is likewise probably a post-Islamic empire contribution.
The non-Berber Y-DNA E (which do not look like new arrivals in the overall context), the DE* and possibly even the T may date back to the Mesolithic era or earlier. DE* was previously found only in West Africans and Tibetans. The appearance of it in North Africa further muddies the waters concerning the manner in which Y-DNA D and Y-DNA E split into an Asian and a predominantly African clade, sometime in the Middle or Upper Paleolithic era.
If there was ever a major Iberian contribution to the Y-DNA of this area, subsequent Berber and Arab male dominated migration waves largely replaced this male genetic contribution. This is at odds with an mtDNA picture for NW Africa which is more similar to Iberia, and which is much more ancient in its back migrated African components like mtDNA U6 than in its Y-DNA.
Via Bell Beaker blogger.
General background on North African genetics can be found at the relevant Wikipedia article.
The mtDNA M1, U6 and some of the mtDNA L (which the Wikipedia article cites a 2010 study a finding to be deep rooted rather than a recent arrival), along with the Y-DNA DE* may date back to the Aterian era in North Africa during the Upper Paleolithic. But, the remaining mtDNA and Y-DNA is probably no older than 10,000 years old, and a significant share of the Y-DNA is probably considerably more recent.
North African autosomal DNA has four significant components. A Maghrebi component, a sub-Saharan African component, a specifically European component (that peaks in the Basque, Sardinians, Tuscans, Russians and the French) and a broader West Eurasian component that extends not just to Europe but also to the Near East, West Asia, Central Asia and South Asia.
The Maghrebi component is predominant in NW Africans, but makes up a much smaller share of the people of Libya. It is a minor component of populations in Egypt, Ethiopia, the Near East, West Asia and Northern Italy including Tuscany. The Sub-Saharan African population is a quite minor component in Northwest Africa except in Southern Morocco, which is closer geographically to Sub-Saharan Africa. The European specific component is also very modest in Northwest Africans.
Assuming that the Basque are the best modern proxy for Bell Beaker autosomal genetic profiles, the demic contribution of the Bell Beaker people to Northwest Africa was very modest (just a few percent); a result that finds parallels in the Y-DNA data, since Y-DNA R1b xV88 is rare in Northwest Africa (although present at trace levels).
Low levels of Y-DNA and autosomal DNA associated with Bell Beaker people in Northwest Africa also suggest that the genetic commonalities between Northwest Africans and Iberians probably did not arise from either a major demic migration of Iberian Bell Beaker people to Northwest Africa, or the scenario in which Northwest Africa was a major demic source for the Iberian Bell Beaker people.
Just as the continuity of Moroccan mtDNA from pre-Neolithic periods to the present suggests, the Y-DNA and autosomal DNA evidence also suggests an early origin for most of these similarities, either in the early Neolithic or prior to the Neolithic era in Northwest Africa.
About mtDNA H
A comment about the distribution of mtDNA haplogroup H is also in order.
Berbers have very high concentrations of H1, with a population in Libya having the peak amount of this subclade. Ancient mtDNA from Morocco shows continuity from the early Holocene era through to the present in mtDNA in the region.
But, the diversity of different mtDNA H clades is much higher in Iberia where the greatest non-Berber concentrations of H1 are found, but also H2, H3, H4, H5, and H20. H1 is pretty much absent in sub-Saharan Africa, is rare in the Near East (with somewhat elevated levels in Lebanon), and absent in the Saami, despite the fact that they have strong mtDNA links of other kinds of the Berbers.
The evidence points strongly to Iberia as close to a Mesolithic source of mtDNA H to both the North and the South, with Berber mtDNA H being less diverse but receiving founder effect boosts. Notably, Iberian clades of mtDNA H overlap heavily with those found in the Caucasus, and also overlap with clades found in ancient DNA from the pre-pottery Neolithic B era. The evidence also strong favors a West Asian origin of mtDNA H ca. 25,000 years ago (from parent clade HV) from which there is no plausible "Southern route" to NW Africa.
All of this data provides powerful evidence that mtDNA H1 and V traveled from Iberia to North Africa in Mesolithic times, and not the other way around.
Many accounts attribute the Mesolithic mtDNA diversity of Iberia to the Franco-Cantabrian refuge, which is plausible, but not to be taken as the definitive truth. A Mesolithic migration of women with mtDNA HV and H (and possibly also V) only after the Last Glacial Maximum from the east along the Southern European coast, more or less, fits the data just as well and helps to explain the absence of any mtDNA type other than U in the remainder of repopulated Europe to the North (despite the fact that it would have to have emerged from the same refugia) or prior to the LGM anywhere in Europe. They may have been pre-Neolithic in their arrival in Europe, but possibly only by a couple of thousand years.
The timing and geography of the Berber expansion would be a natural fit for an Egyptian or Chadic origin to the Berber people and language. Yet, there are problems with either hypothesis.
The Berber language has much more lexical similarity to the Semitic, Chadic, and Cushitic languages than it does to ancient Egyptian (i.e. Coptic) (the Omotic languages are even less similar and do not share pastoralism related words with Afro-Asiatic languages, although they do share honey related words).
But, there is virtually no overlap between Berber Y-DNA and Chadic Y-DNA, despite the fact that the Berber ethnogenesis appears to involve a language shift driven by mass male population replacement. Y-DNA E that is dominant in the Berbers is a minor component of Semitic populations today and involves many Y-DNA clades not found in modern Berbers. And, the range of the Semitic peoples as of 3700 BCE (prior to Ethio-Semitic and Arab expansions), were remote from Berber territory relative to the Egyptians or Chadic peoples.
Several scenarios could make sense of this situation.
1. Languages in the Berber language family were widely spoken in NW Africa much earlier, perhaps from the Mesolithic era or earlier even, but when the 5.9 kyr climate event hit, one patriarchial tribe with key cultural innovations or religious fervor of some kind swept the region displacing all Berber language family dialects but their own and replacing a huge share of the male population of other Berber communities.
The Berber language family's link to other Afro-Asiatic languages may pre-date the Neolithic revolution during which Egyptian deviated lexically from other Afro-Asiatic languages due to Mesopotamian influences, but which it was strong enough to limit to word borrowing because its riverine hunter-gatherer-fisherman economy was not totally swept away by the first farmers of the Fertile Crescent as was the case in Europe, a thousand years later. The trouble with this is that Afro-Asiatic languages have a great deal of pastoral vocabulary in common suggesting post-Neolithic origins.
Also, the ergative noun case system of Berber languages, similar to Basque, Sumerian, Elamite, and Caucasian languages, and unlike all other Afro-Asiatic languages, suggests that Berber had an ergative substrate influence that was not Afro-Asiatic (as discussed below, this varies among Berber dialects in a way suggestive of possible substrate influences in NW Africa). Berber is the only ergative language in Africa (possibly also subject to caveats discussed below of a few Cushitic and Omotic languages). The only Indo-European language that is ergative, Kurdish, has a known ergative non-Indo-European substrate.
Given the genetic affinity of the first farmers and relict populations in the Caucasus mountains most exemplified by the high frequency of Y-DNA G in both populations, it is likely that the language of the first farmers of Europe was an ergative one. Also, unlike tonality, which shows strong areal effects, ergativity appears to me to be a good index of a language's deeper relationships to other languages, which makes sense given how common phonetic changes in languages over time are generally, while fundamental grammatical changes appear to be less common.
The ergative noun case system is also inconsistent with a Nilo-Saharan or Niger-Congo linguistic substrate, despite the fact that both languages were probably present in much more of the Sahara than they are today during the Green Sahara period that preceded Berber expansion.
Thus, this scenario 1 is probably wrong. Likewise, while there may be considerable mtDNA continuity in NW Africa for 10,000 years, the Berber language and ethnicity are probably only half that old.
2. Egyptian may have been much more similar to other Afro-Asiatic languages prior to the consolidation of the Egyptian state around 3500 BCE under King Scorpion II and his immediate successor, who appears to have been very strongly influenced by Mesopotamian culture.
The Coptic language, aided by the second earliest use of writing, may have reflected a highly atypical dialect of Coptic used in his court with lots of outside influences that became a national standard as a result of his unification of the Egyptian kingdom, while the Afro-Asiatic dialects spoken in Egypt during the early Neolithic prior to his reign may have mostly been much more similar to early Semitic and Berber languages. Similar dialect standardizations around the dialect spoken in a capitol city, or by a monarch in a strong state are historically known to have occurred in England and many other nation-states.
Berber and Semitic may both descend from pre-Coptic Egyptian languages of these more typical dialects that faded away in connection with the process of state formation in a strong unified Egyptian state. NW Africa, prior to Berber expansion, perhaps starting with the Iberomaurusian archaeological culture, might have been much more strongly Iberian influenced as mtDNA data points suggest, and could have involved a European derived ergative language that arrived in the Mesolithic or early Neolithic era.
But, this ergative Iberoaurusian language was quite probably not a Vasconic one since it was probably not associated with subsequent Copper Age Bell Beaker peoples who expanded out of Iberia starting around 2900 BCE and who were the likely source of Y-DNA R1b in Western Europe. The Berbers would have arrived 500 to 1000 years earlier than the earliest signs of Bell Beaker people in North Africa, so there would have been no Bell Beaker substrate for the Berber languages of Bell Beaker influenced North Africa to absorb at the time.
The source of the Iberomaurusian is a subject of debate. A 2013 study reached the following conclusions (translated from the French original at Bernard's blog), which also suggest older dates for this culture than Wikipedia's sources assign to it:
Its lithic industry is characterized by lamellar microliths and marks a profound change from the Middle Paleolithic in the Maghreb. However, very little is known about its origin.
Several theories have been proposed. The term itself connects Northwest Africa with Iberia. But since this proposal, archaeologists have rejected a possible link between the industry and iberomaurusienne southern Europe. Another theory proposed that the culture was iberomaurusienne after the Dabéenne culture Cyrenaica (Libya). However the dates of the iberomauruisenne Culture in Libya are newer than those in the Maghreb. More recently it has been proposed that the iberomaurusienne culture was connected to a broader phenomenon of lamellar stone industry in North Africa and the Middle East 20,000 to 23,000 years. However, this theory does not explain the greater antiquity of the iberomaurusienne Culture in North Africa and the differences between them and the stone industry in Egypt.
Part of the problem is related to the scarcity of accurate dating. The oldest radiocarbon dates obtained for iberomaurusienne culture were obtained Taforalt: 21,900 and 21,100 years. A Tamar Hat, 7 dates were obtained between 20,600 and 16,100 years. Cyrenaica, both dating gave a value of 16,070 and 18,620 years.
On the other hand some doubt on relations in the iberomaurusienne culture and the oldest cultures in the region. The Culture iberomaurusienne always covers the Aterian culture. However there is a debate about whether there is a temporal continuity between the two cultures, or if there is a blank period of occupation between. In Cyrenaica, iberomaurusienne culture seems to follow the Dabéenne Culture immediately. . . .
All these 54 dates provided the largest consistent set available for this period in the Maghreb. The iberomaurusienne culture and lasted about 9000 years between 21,420 and 12,698 years. In addition there is a large gap between the end of the non-Levallois industry and the beginning of the iberomaurusienne industry, about 1900 years. This non Levallois industry is different from atérienne industry that uses Levallois techniques. . . . another area of the cave Taforalt included below iberomaurusienne layer and the non-Levallois layer, a layer atérienne. A date 37,570 years was obtained for this industry atérienne matching the latest timing for atérienne culture Taforalt. This dating is dating obtained Wadi Noun, south of Morocco, which gives a value of 30,900 years and the dating obtained Mugharet el Aliya, in northern Morocco, with a value of 39,000 years. Thus, Taforalt the atérienne industry is followed by a non Levallois culture, followed by the iberomaurusienne culture.
The authors then tried to connect these dating with climatic events. The recent phase of Iberomaurusian (gray sedimentary layers) is the first interstage Greenland, which is a relatively wet period. It is also interesting to see that the transition between the old and middle stages of the match Iberomaurusian to Heinrich event 1 (HE1) [Ed. a sudden global temperature decline ca. 14,000-16,800 years BP.]. Finally the end of the non-Levallois industry seems to match the 2 Heinrich event (HE2) [Ed. a sudden global temperature decline ca. 22,000-24,000 years BP.].
This study showed that there is no cultural continuity between iberomaurusienne industry and the one before. Thus, in the northwest of Africa the transition from the Middle Paleolithic and Upper Paleolithic corresponds to the arrival of a lamellar industry around 22,000 years driven by population growth sub-clades of mitochondrial haplogroup U6 . The question is whether this event is related to the arrival of a new population in North Africa following the disappearance of the cultures of the Middle Paleolithic or not, and if it is linked to climate change.But, this archaeological uncertainty has to be tempered by the ancient DNA evidence showing significant levels of European-like mtDNA in the region which this culture was found ca. 10,000 years ago, and the lack of strong influxes of European mtDNA or autosomal DNA in the time period from 5000 years ago onwards. The subsequent Capsian culture is the only other alternative culture in which this mtDNA could have entered the NW African gene pool. So, the odds of an Iberian connection are greatly enhanced despite the indeterminate nature of the archaeological evidence.
Thinly populated NW Africa may have had less of a capacity to hold onto its pre-existing hunter-gatherer culture in the face of Neolithic migrants than the relatively densely populated and sedentary Egyptians did as a result of the abundance of the Nile's biosphere.
Berber Y-DNA is a better match to some subset of the Egyptian mix than to the Chadic peoples, or the Semitic peoples. But, it is worth observing that the Egyptian mtDNA mix, as shown in the map above, is very different from that of any Berber populations. For example, there is almost no mtDNA H in Egypt, while it is common in some Berber populations. Of course, so long as one accepts that Berber expansion was male dominated, that data point isn't necessarily very informative when it comes to Berber origins.
3. The Cushitic peoples may have extended farther into the Sahara during its green period prior to the 5.9 kyr event, into areas that are now exclusively Berber or Chadic or Nilo-Saharan. Berber could have extended from a patriarchal clan at the fringe of the Cushitic range around this time. The Iberoaurusian substrate speculations of scenario 2 could apply to this scenario as well.
But, this scenario does not require such a radical remaking of the Coptic language in such short order. On the other hand, new absolute Egyptian chronologies favor unified state formation closer to 3100 BCE, rather than 3500 BCE, and puts the Neolithic to Copper Age transition around 3700 BCE in Egypt, providing more breathing room for this transition to happen while suggesting a Berber expansion technology.
Berber Y-DNA could fit as a subset of the Cushitic Y-DNA mix quite easily - the Berber clade of Y-DNA E likely had its origins in Cushitic territory.
Contrary to the ergative substrate hypothesis advanced above, it appears that there are at least a few Cushitic and Omotic langauges that are not nominative-accusative (the main alternative to ergative), although most languages in both families are nominative-accusative as are all Semitic languages. Thus, an ergative Cushitic language as a source for Berber is not necessarily impossible scenario (an Omotic language source can be ruled out linguistically from lack of lexical similarity).
But, the case for an ergative substrate influence is supported by the geographical diversity of this kind of case marking within the Berber languages. It is fully present in Morocco and Northern Algeria where the Iberomaurusian substrate was present, is only partially present in the deep Saharan Tuareg adjacent to the substrate area (perhaps due to substrate languages in the deep desert derived from the Capsian culture which was in turn derived from Iberomaurusian, but thrived in the deeper desert), and is absent in dialects in Egypt and Libya where there is no such substrate influence (although archaic words indicate that it might once have been present there). The absence of ergative case markings in Berber languages closest to the Cushitic linguistic range, and its presence most strongly in those places most distant from the Cushitic linguistic range, disfavors the hypothesis that proto-Berber was ergative prior to encountering substrate influences.
The case for the existence of a significant non-Cushitic substrate that is a source of a larger share of Berber mtDNA is also supported by the quite modest amounts of mtDNA L clades among some Berbers despite the fact that they are common place in Cushitic populations. In Morocco, for example, African mtDNA is much more common in Moroccan Arabs than in Moroccan Berbers among whom it is almost absent. Also, the immense regional variation in Berber mtDNA disfavors the hypothesis that Berber expansion was gender balanced and instead favors the hypothesis that Berbers during their expansion largely assimilated local women into their society who had deeper local geographic roots.
The scenario in 2 involving Coptic deviation from other Afro-Asiatic languages could still apply, but it could happen much more gradually (perhaps substantially in the early Neolithic as well) if the pressure of being an origin for Berber ca. 3900-3700 BCE were removed.
On balance, scenario 3 is probably more likely than scenario 2, although I can't easily rule out either scenario.
Other interesting discussions of Berber origins are found in a blog post here.
Implications for Bell Beaker ethnogenesis
There is compelling evidence that Y-DNA R1b xV88 arrived in Western Europe with the Bell Beaker people once they came into being in Iberia and expanded dramatically from there in the Copper and Bronze Ages in Western and Northern Europe in parallel to the Corded Ware culture (which was Y-DNA R1a dominated) in the East, after the Y-DNA G2 dominated first farmers of Europe transformed the human geography of the continent and then crashed and burned as their first wave Neolithic societies collapsed. These people had origins to the East of Iberia and did not arrive via NW Africa. Their language was probably Vasconic in character, although it may have been influenced by whatever local Iberian substrate was present when they arrived.
The Andalusian Neolithic which arrived in Southern Iberia in the 6th Millenium BCE, before any other part of Iberia, and was notable for its absence of cattle. Cereals and legumes domesticated in the Fertile Crescent, and olives, where their dietary mainstays. Only pigs and rabbits were used as meat sources, and they may have been wild. This development could have had a NW African source, but the absence of sheep, goats and cattle which were important parts of the NW African Neolithic from the Andalusian Neolithic, argues against this possibility. And, this Southern part of Iberia, where the Bell Beaker people would eventually arrive, was beyond the range of the Cardial Pottery Neolithic that arrived in Eastern Iberia ca. 4700 BCE. Cattle farming arrives in Southern Iberia only with the Bell Beaker people ca. 3000 BCE.
Metalworking also arrived in NW Africa only once Bell Beaker people arrived there, and the oldest NW African mines date only to the Iron Age, long after mining was well established in Nubia, Iberia, Bohemia, the Caucasus, and Anatolia.
At the time the Bell Beaker people arrived, Iberia was already rich in mtDNA H in its female population relative to other first farmer communities, probably partially as a result of pre-Neolithic migrations there ultimately from West Asia via Europe and partially as a result of first wave Neolithic migrations boosted by serial founder effects far along the path of first wave farmers in Europe, although the Bell Beaker people could have brought some mtDNA H females with them as part of a folk migration as well and the exact route by which they arrived is not entirely clear.
These people, Iberian and pre-Bell Beaker alike, gave birth to a new Bell Beaker identity in Southwest Iberia, whose new formed resulting culture would prove dominant relative to the first wave stone age farmers and hunter-gatherer cultures that had preceded them in Europe.
Some of these women's ancestors migrated to NW Africa in Mesolithic times in what was either a gender balanced migration or a bride exchange trade relationship, and probably spoke an ergative language that was not Vasconic. Several hundred years before the Bell Beaker people arrived in Iberia, their European derived language and culture was replaced by pastoralist Berbers who swooped in as their food production faltered in the face of an increasingly arid climate and these Berbers took them as wives and either slaughtered most of their men or excluded them from having children.
Other ancestors of these women repopulated Europe further to the North in the Mesolithic, taking a largely Atlantic and Baltic coastal route, which accounts for the genetic similarities between Berbers and the Saami people.
Bell Beaker expansion into Europe, boosted by newly acquired lactose persistence in NW Europe that then refluxed back to Southern European Basque, caused the gene pool of Western Europe to have the high levels of R1b xV88 and mtDNA H that have characterized Western Europe ever since then. Subsequent Celtic and Germanic Indo-European conquerers, mostly after Bronze Age collapse triggered by a major climate event, had a comparatively minor demic impact on these already metal age people with a dairying component to their food production in most places.
A few Bell Beaker people also went from Iberia to NW Africa, but ultimately had a fairly shallow demic impact compared to their impact on Western Europe, perhaps because the relatively newly arrived Berber men had more impressive economic prospects (and quite possible more effective metal tools and weapons before Bell Beaker expansion was in full swing) than the stone age failed farmers of most of Western Europe.