Is The Extent Of Afro-Asiatic Related To The Holocene Green Sahara?

Razib Khan has identified a fascinating new paper on African historical genetics. He notes:

- Lots of suspicion about this before. Basically, a West Eurasian-related population (admixed) was extant in the Sahara for the first half of the Holocene.

– I don’t think they’ve totally figured out Afro-Asiatic, and these results make me more open to the idea that Afro-Asiatic came from the Sahara, not less

The paper is using new modern whole genomes, together with a medium sized database of modern and ancient DNA. 

A Green Saharan era ethnogenesis for the Fulani, frames this group of nomadic pastoralists with a Moroccan origin entering North Africa from the East contemporaneously with the migration of the proto-Chadic nomadic pastoralists.

The ancestors of the Chadic people make it to Lake Chad's endorheic basin via the Yellow Nile before it was became a mere wadi by crossing the water basin divide from the source of the Yellow Nile to the Lake Chad basin around 5700 BCE (a date that can be fixed fairly precisely with archaeological dating of the appearance of human settlements on the former shores of the now greatly diminished Lake Chad).

The historical roots of the Chadic people push back the origins of Afro-Asiatic to a date no more recent than the entry of herding into North Africa, but Afro-Asiatic languages could be older than that.

Of course, one challenging aspect of this narrative for the Fulani is how the livestock that they herded could make it away from Iberia to Morocco via the Strait of Gibraltar in this early time frame (which, perhaps not coincidentally, coincides with the emergence of Bell Beaker related cultures on both sides of the strait). But given the short distance that needs to be traversed (with only line of sight navigation required), and the existence of some sort of transcontinental contacts in this region, it isn't too incredible.

Connecting the linguistics of Northeast Africa to Green Sahara era populations is challenging, however, because of subsequent language replacement in the region, leaving only substrate traces of the early Holocene linguistic makeup of the region.

The Berber languages probably date to a mostly population replacing (at least for men) expansion in an era when the Sahara was no longer green again, suggestively close in time to the appearance of the domesticate camel in North Africa. As I noted in a previous post at this blog:

The TMRCA of the Berber Y-DNA E . . . 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.

The Berber expansion, which was not confined to Mediterranean coastal areas, was followed by  Phoenician influence from trading posts of this Levantine maritime civilization, followed by African Latin along the North African coast arising from Roman conquest, which in turn was followed by Arabic as the Islamic empire expanded in the 7th to 8th centuries of the common era.

Substrate influences in Western Berber languages, for example, tend to suggest that unlike most modern Afro-Asiatic languages, this substrate language was probably an ergative language. 

This is a feature shared with Sumerian, the Vasconic languages (of which Basque is the sole surviving representative), and the pre-Indo-European, pre-Afro-Asiatic, pre-Turkish languages of the highlands of West Asia. But, it is a language feature does not have its origins in the Indo-European, Afro-Asiatic, Turkish, Nilo-Saharan, Niger-Congo, or Dravidian languages, even though it is found as an apparent substrate influence in a few isolated examples of Afro-Asiatic languages.

We also know, however, that there is no trace of Caucasian/Iranian hunter-gatherer or farmer ancestry in Fulani DNA. So any genetic connection (either from Africa to Europe or from Europe to Africa) between the known European languages and the pre-Berber languages of North Africa, it is probably a link involving the Vasconic languages rather than Sumerian and/or West Asian languages.

The paper and its abstract (along with a key image from the paper) are as follows: 

Background

The Sahelian Fulani are the largest nomadic pastoral ethnic group. Their origins are still largely unknown and their Eurasian genetic component is usually explained by recent admixture events with northern African groups. However, it has also been proposed that Fulani may be the descendants of ancient groups settled in the Sahara during its last Green phase (12000-5000 BP), as also suggested by Y chromosome results.

Results

We produced 23 high-coverage (30 X) whole genomes from Fulani individuals from 8 Sahelian countries, plus 17 samples from other African groups and 3 Europeans as controls, for a total of 43 new whole genome sequences. These data have been compared with 814 published modern whole genomes and analyzed together with relevant published ancient individuals (for a total of > 1800 samples). These analyses showed that the non-sub-Saharan genetic ancestry component of Fulani cannot be only explained by recent admixture events, but it could be shaped at least in part by older events by events more ancient than previously reported, possibly tracing its origin to the last Green Sahara.

Conclusions

According to our results, Fulani may be the descendants of Saharan cattle herders settled in that area during the last Green Sahara. The exact ancestry composition of such ghost Saharan population(s) cannot be completely unveiled from modern genomes only, but the joint analysis with the available African ancient samples suggested a similarity between ancient Saharans and Late Neolithic Moroccans.

Eugenia D’Atanasio, et al., "Echoes from the last Green Sahara: whole genome analysis of Fulani, a key population to unveil the genetic evolutionary history of Africa" (April 6, 2023) https://www.biorxiv.org/content/10.1101/2023.04.06.535569

The introductory part of the body text notes that:

Among the people living in the Sahel, the Fulani, speaking a language belonging to the Niger-Congo linguistic family, represent an interesting case. They are the largest pastoral ethnic group in the world, with an estimated population of 20-40 million people settled in a broad area covering 18 African countries, from the Atlantic coast to the lake Chad basin and further east to the Blue Nile region in Sudan. Fulani are historically nomadic pastoralists, although most of them have now adopted a sedentary lifestyle based on farming. Nowadays, most Fulani live in western Africa, where the first evidence of their presence traces back to the XI century, when they settled on the Fouta Djallon highlands in central Guinea. Later, they moved eastward along the Niger river and they arrived at the lake Chad region in the XV century. Despite their recent history being relatively known, their origins are still a matter of debate. Over time, it has been proposed that their ancestors could be ancient Egyptians, Nubians, Persians, Jews, Arabs, Ethiopians or western Africans; however, the most widely accepted theories trace the Fulani origins back to ancient northern Africans or near eastern populations. 

In this context, it has also been proposed that the Fulani may be the descendants of ancient Saharan populations. Indeed, the Sahara has not always been as harsh as today: between 12,000 and 5,000 before present (BP), it was a lush and fertile environment occupied by savannah, forests and a wide hydrogeographic network of rivers and lakes. This phase, generally known as “Green Sahara”, was just the last of several alternating arid and humid phases that have characterized the geological history of this region. 

This region was inhabited by different human groups with peculiar material cultures during the last Green Sahara period, as suggested by several paleoanthropological and archeological findings, including several Saharan rock paintings as the rock art in the Tassili-n-Ajjer plateau in the Algerian Sahara, dated to 8,000 BP. Interestingly, this painting represents cattle and pastoralism rituals very similar to the ceremonies still practiced by present-day Fulani, suggesting a possible link between these people and the ancient inhabitants of the Sahara.

The ancient Saharan hypothesis about the Fulani origins seems also to be supported by some analyses of the human Y chromosome: Fulani show a high proportion of a Y lineage, i.e. E1b-M2/Z15939, dating back to the last Green Sahara. This lineage is observed at lower frequencies also in western and northern Africa, while it is absent in other sub-Saharan regions, pointing to a Green Saharan origin in the Fulani ancestors. However, other genetic data seem to give contrasting results. Considering the other human uniparental system, i.e. the mitochondrial DNA (mtDNA), Fulani harbor a non negligible proportion of Eurasian U5b and H1cb haplotypes, possibly arrived from a northern African source. As for the autosomal DNA, genome-wide studies have shown that Fulani people display both a western African component and a northern African/Eurasian one, but the estimates of such components differ across different studies and sub-groups. 

In this context, the most striking result has been obtained from the lactase locus: Fulani show a high proportion of the lactase persistence allele T-13910, that is typical of the European populations. This finding has been explained suggesting that the European lactase persistence haplotype was first introduced in northern Africa and then in the Fulani population by recent admixture with a northern African population about 2000 years ago. 

Similarly, the presence of European ancestry components on the autosomal or uniparental portions of the Fulani genome is usually explained by recent admixture between a Western or Central African source and an “Eurasian” source dating back to the last two millennia.

Despite the general agreement about the presence of a “non-western-African” component in the Fulani genome, the origin and the extent of such a component is still a matter of debate. In the last decades, the increasing number of published individuals analyzed by whole genome sequencing (WGS) has allowed to shed light on different dynamics of the populations included in such studies. However, the number of whole genomes from the African continent is disproportionately low compared to the sequences from other continents, with only few African individuals included in the main genome variation projects, despite the importance of Africa for the past and recent human history. Recently, some projects have focused on the African whole genome variability, partially filling this gap; however, only few whole genomes from Fulani individuals have been published and analyzed so far. The results from these researches confirmed the presence of a “non-western-African” component, that has been suggested to be acquired in recent times, possibly from an eastern Afro-Asiatic source; however, the contrast with data from other portions of the genome still remains and the questions about the origin and past history of Fulani people are still open.  . . . 

Later, in the discussion section, the paper lays out a Green Sahara narrative:

By comparing the Fulani genetic diversity with those of the large number of ancient individuals currently available through an admixture analysis (K=6), we observed that their non-sub-Saharan ancestry is characterized by a component observed in extremely high proportions (virtually 100%) also in ancient Morroccans older than 8000 BP, and an azure Levantine component. We could also see a non-negligible fraction of the WHG red component, as in the Late Neolithic Moroccan individuals, possibly arrived from Iberia to the Maghreb. On the other hand, Fulani lacked the Iran Neolithic/CHG blue component, which was observed instead in modern northern Africans, Middle Easterners and Europeans. 

This pattern of ancestry components can be hardly explained solely by recent admixture between western African and northern African groups. Indeed, in this case, we would have expected to observe also the Iran Neolithic/CHG blue component in the Fulani, since this component is present in all the modern northern African, European and Middle Eastern samples. 

So, the admixture event(s) that forged the non-sub-Saharan ancestry in Fulani should have occurred before the arrival of this component in the areas to the north of the Sahara. It is challenging to obtain exact time estimates for such events, considering that they were probably followed by later admixture events involving the same or very similar source populations. However, considering the results of the admixture analysis (K=6), we can try to define broad time windows. Indeed, considering the presence of the azure (Levantine) and red (WHG) components in Fulani, in addition to the orange (Iberomaurusian) one, and the absence of the blue (Iran Neolithic/CHG) component, we can postulate that their non-sub-Saharan component dates back to about 8000-7000 years ago from a source population similar (except for the blue component) to the Late Neolithic Moroccans (dated about 5000 BCE, considering their radiocarbon time estimates). In addition, the qpAdm analysis also points to a period corresponding to 7000 BP considering the radiocarbon time estimates of the two ancient sources that successfully modelled both FulaniA and FulaniB. Intriguingly, this time window corresponds to the period of the last Green Sahara. . . . 

These Saharan people may have actually been the ancestors of present-day Sahelian people, including Fulani. This is also supported by our admixture analysis, showing that also the Neolithic pastoralists from Kenya and the modern central Sahelian groups showed the orange and azure components at non-negligible proportions. Moreover, the absence of the blue component in the modern Nilo-Saharan groups from both central and eastern Sahel further confirms this hypothesis, since it has been proposed that the Nilo-Saharan languages were much more widespread in the Green Sahara region during the last humid phase, to be replaced by Afro-Asiatic languages only in more recent times (about 1500 years ago). In this context, it is also worth noting that a recent whole genome study further confirmed the presence of a shared ancestry between Fulani and Afro-Asiatic speakers from Eastern Africa. Interestingly, it has also been proposed that the Green Sahara area (more precisely the lake Chad basin, occupied by the Megalake Chad at the time) was also the homeland of the Niger-Congo (i.e. the language currently spoken by Fulani) about 7000 years ago, intriguingly corresponding to the possible time estimate of the Fulani non-sub-Saharan components. This language then spread westwards (and eastwards to a lesser extent) replacing the pre-existing languages.

The exact genetic ancestry composition of the “ghost” Saharan populations cannot be assessed without ancient individuals from that area at that time; however, on the basis of the ancient data currently available, we can propose that they were genetically similar to the Late Neolithic Moroccans here analyzed, although this group already shows the Iranian Neolithic/CHG component that was probably more diluted further south, while the yellow western African component was possibly present at higher proportions.

With the end of the Green Sahara and the subsequent gradual desertification of that region, the Saharan groups moved westwards, eastwards, southwards or northwards, as also suggested by the Y chromosome data. This phenomenon was not abrupt and was slightly longer in the central Sahel rather than in the east depending on the local hydrogeological conditions; according to the archaeological evidence, the changing climate conditions led to changes in the socio-economic organization of the different groups. In particular, it has been suggested that cattle pastoralism became the predominant form of subsistence at that time since it was a more reliable source of food, leading to the establishment of a pan-Saharan cattle cult, as testified by rock paintings and rituals that spread westwards with the pastoral groups in search of new pastures. This scenario may also reconcile the apparent contrasting evidence from different genetic systems linking Fulani with sub-Saharan, northern African, European or eastern African groups; indeed, if we assume the past presence of Green Saharan populations with extensive contacts, it is not surprising that these groups could share genetic affinities. With the Sahara desertification and the following different population dynamics, the genetic differentiation between the different groups may have led to the loss or maintenance of different genetic variants because of genetic drift and/or selection.

All this bulk of data seems to point to a Green Sahara origin of the Fulani with regard to their non-sub-Saharan component. Their ancestors were possibly Saharan cattle herders that moved westwards in response to the changing climate and then mixed with local people. Later, the peculiar Fulani lifestyle, historically characterized by nomadism and endogamy, and their population size dramatic decrease could have prevented the dilution of this ancient “Green Saharan” ancestry component that can be still identified.

Finally, both Fulani clusters show the same ancestry components, pointing to a common ancestry of the two groups, although at different proportions, suggesting different population dynamics.

Niger-Congo language speakers in the Lake Chad region around the time of the Green Sahara seem implausible. Language shift to a Niger-Congo language at a later time resulting in genetic shifts for the "Fulani B" subpopulation of the Fulani who have more West African admixture than the "Fulani A" subgroup considered, seems more likely. But the fact that both the sub-Saharan African, North African and European components of Fulani ancestry all seem to be mostly western leaning, despite some similarities with Nilo-Saharan peoples genetically (which could have happened more centrally during a Green Sahara era), does seem significant.

I discussed possible Berber linguistic origins in a 2015 blog post:

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. . . .

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 . . . 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.