Afro-Asiatic Languages and Uniparental Genetic Markers

There are several major groups of languages within the Afro-Asiatic languages: Semitic (e.g. Arabic and Hebrew), Chadic (e.g. Hasua), Berber (e.g. Tuareg), Omotic, Cushitic, and Coptic (i.e. ancient Egyptian). Discerning the pre-history of these languages is not easy. Neither language features, nor genetics offer a comprehensive pan-linguistic family answer. This post looks at Afro-Asiatic uniparental genetic markers (and was mostly written about six months ago, but never posted as it awaited some editing and polishing).

An analysis of autosomal Afroasiatic genetics appears in a recent post at Ethio Helix. In the Principle Component Analysis done for this dataset, "Component 1 separates Berber/Semitic/Egyptian speakers from Chadic speakers, with Ethiopian Semitic/Cushitic speakers plotting somewhere in between, but closer to the former in this separation. Component 2, separates Ethiopians+Egyptians from the rest. Component 3 Separates the Mozabites from the Rest, with Ethiopians again retaining an intermediate position." Looking at an Admixture analysis with K=5 in this data set on a chart the separates clusters in two dimensions whose distance from each other is based on FsT distance, "The biggest separation for both Axis is for the cluster I nicknamed Cushitic, while the Berber, Semitic and Mozabite clusters appear pretty close, with the Mozabites looking a bit isolated." Berber and Egyptian are close; Cushitic and Chadic are roughly as far from each other and the Egyptian-Berber-Mozabite cluster is from the Cushitic cluster.

Honestly, autosomal data, rather than clarifying the relationships, seems mostly just to muddy the waters further. The notion that Egyptians are more closely linked to Ethiopian populations than non-Ethiopian populations does emerge, however. Also, Egyptians do seem to be more genetically diverse than some of the other populations autosomally. They seem to have genetic components that don't overlap with other populations including the main "Egyptian" component, at a fairly high frequency.

Chadic Languages and Y-DNA R1b-V88

Chadic language speaking men have the most distictive genetic profile.

Although human Y chromosomes belonging to haplogroup R1b are quite rare in Africa, being found mainly in Asia and Europe, a group of chromosomes within the paragroup R-P25(*) are found concentrated in the central-western part of the African continent, where they can be detected at frequencies as high as 95%. Phylogenetic evidence and coalescence time estimates suggest that R-P25(*) chromosomes (or their phylogenetic ancestor) may have been carried to Africa by an Asia-to-Africa back migration in prehistoric times. Here, we describe six new mutations that define the relationships among the African R-P25(*) Y chromosomes and between these African chromosomes and earlier reported R-P25 Eurasian sub-lineages. The incorporation of these new mutations into a phylogeny of the R1b haplogroup led to the identification of a new clade (R1b1a or R-V88) encompassing all the African R-P25(*) and about half of the few European/west Asian R-P25(*) chromosomes. A worldwide phylogeographic analysis of the R1b haplogroup provided strong support to the Asia-to-Africa back-migration hypothesis. The analysis of the distribution of the R-V88 haplogroup in >1800 males from 69 African populations revealed a striking genetic contiguity between the Chadic-speaking peoples from the central Sahel and several other Afroasiatic-speaking groups from North Africa. The R-V88 coalescence time was estimated at 9.2-5.6 [corrected] kya, in the early mid Holocene. We suggest that R-V88 is a paternal genetic record of the proposed mid-Holocene migration of proto-Chadic Afroasiatic speakers through the Central Sahara into the Lake Chad Basin, and geomorphological evidence is consistent with this view.

From Cruciani, et al., "Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages." Eur J Hum Genet. 2010 Jul;18(7):800-7. Epub 2010 Jan 6.

I am deeply skeptical of the data suggested (Dienekes' expedent of dividing estimates by three seems more on target and the entire business of dating Y-chromosomes by mutation rates is suspect), but the linguistic-genetic link is clear.

What is notable about this result?

As one of the five major Afro-Asiatic language families, the origins of this language family are important to understanding the origin of the Afro-Asiatic languages generally, a major unresolved issue.

The genetic case is strong that Chadic has its roots in Asia to Africa backmigration. The low levels of admixture between Chadic and non-Chadic speakers until very recently (the Fulani and Hasua are in the process of merging in ethnic identity to some extent right now), suggests that this relatively genetically distinct population is relatively new to the region relative to other languages.

Since language tends to track Y-DNA more than mtDNA, the strong Y-DNA traces suggest an origin for Chadic languages outside of Africa.

This branch of the Y-DNA R haplogroup is quite basal, so dating this split also puts a minimum date on expansion of the rest of the Y-DNA R haplogroup which is predominant in much of West Eurasia. The Y-DNA haplogroup R1b common among Chadic language speakers in the V88 subtype, however, is generally associated with Western Europe and tenatively, with Indo-Europeans, although the break of the African Y-DNA haplogroup V88 from other R1b haplogroups found in Europe would have happened a very long time ago.

Still, how any R1b haplogroup end up in a linguistically Afro-Asiatic population in the Sahel? This is a mystery.

R1b is not commonly found in Egyptians, Ethiopians, or Berbers.

Indo-Europeans are not attested historically anywhere in Mesopotamia, the Levant, or North Africa until the classical Greeks and Romans expand except at the fringes of the Hittite Empire of the Bronze Age.

Indeed, there is a plausible arguement that there weren't even any Indo-Europeans (and quite possibly very few men with Y-DNA R1b haplogroups) in Western European until the early Bronze Age, with Indo-Europeans possibly arising with the Bell Beaker culture. The Central European Neolithic, for example, up the Danube, is associated with Y-DNA haplogroup R1a (which is absent in Chadic populations), not R1b.

Anatolia is associated with Y-DNA haplogroup J2, which is absent in Chadic populations. South Semitic peoples are associated with Y-DNA haplogroup J1, which is absent in Chadic populations. One would think that migrations to Africa from either area would have included J2 or J1 in the Y-DNA mix of the population, although founder effects with a small founding population of related men could account for their absence as well.

R1b is not exclusively Indo-European, as it is found in the linguistically non-Indo-European Basque people (whose high levels of lactose tolerance suggest a pastrolist dairy utilizing economy for their ancestors), and in Central Asia (which was genetically and in phenotype basicallly European as far as the fringes of Mongolia in the early Bronze Age), but no one suggests that the Chadic and Basque languages have any connection whatsoever.

Anatolia and the Dead Sea are plausible sources based on the presence of basal Y-DNA haplogroup R1b types there. But, we don't really know how or when the genetic outlier pocket of population in the Dead Sea area, for example, ended up there. The population of the Dead Sea, for example, could be derived from refuguees from someplace else who finally found a place to settle in the Dead Sea area at some undocumented point of time in ancient times.

Overview of Y-DNA in Afro-Asiatic Linguistic Families

There are population genetic links to Eurasia in many of Afro-Asiatic populations. On the Y-DNA side, Y-DNA haplogroups T (common in Egypt, Ethiopia and Somolia), J1 (associated with Arabia and other Semitic populations including Ethio-Semitic populations), and R1b-V88 (associated with Chadic language populations) all probably have origins outside Africa. On the mtDNA side, haplogroups M1 and U6 are both probably Eurasian in origin. There are mtDNA similarities between Cushitic and Chadic populations, although their Y-DNA profiles are quite distinct. Also associated with Afro-Asiatic languages is Y-DNA haplogroup Eb3 associated strongly with Egypt and probably having an African origin.

As we look at Afro-Asiatic liguistic origins it looks like Chadic is an outlier genetically within the Afro-Asiatic linguistic family, but each of the Afro-Asiatic lingustic families has a pretty distinctive uniparental genetic marker profile. As Wikipedia notes (footnotes omitted):

The migration of Afroasiatic languages from their original homeland is often thought to have also involved the movements of significant numbers of people. Therefore, attempts have been made to associate Afroasiatic language groups with genetic markers.

The most commonly cited genetic marker in recent decades has been the Y chromosome, which is passed from father to son along paternal lines in un-mixed form, and therefore gives a relatively clear definition of one human line of descent from common ancestors.

Several branches of humanity's Y DNA family tree have been proposed as having an association with the spread of Afroasiatic languages.

Frequency of haplogroup E1b1b in select Afro-Asiatic speakers
Language (Region where historically spoken) Frequency
Cushitic 32–81%
Egyptian languages 36–60%
Berber languages 40–91%
Semitic languages 7–29%
Omotic languages 50%

1. Haplogroup E1b1b is thought to have originated in East Africa. In general, Afroasiatic speaking populations have relatively high frequencies of this haplogroup, with the notable exception of Chadic speaking populations. Christopher Ehret and Shomarka Keita have suggested that the geography of the E1b1b lineage coincides with the distribution of Afroasiatic languages.

2. Haplogroup J1c3 (Y-DNA), formally known as "J1e", is actually a more common paternal lineage than E1b1b in most Semitic speaking populations, but this is associated with Middle Eastern origins and has apparently been spread from there after the original dispersion of Afroasiatic.

3. Haplogroup R1b1a (R-V88), and specifically its sub-clade R-V69, has a very strong relationship with Chadic speaking populations. Unlike other Afroasiatic speakers, Chadic language speakers have low frequencies of Haplogroup E1b1b.

Frequency of Sub-Haplogroup R1b1a in select Afro-Asiatic speakers
Chadic languages -- 28.6-95.5%
Berber languages -- 0-26.9%
Semitic languages -- 0-40%
Egyptian languages -- About 14% of Sudanese Copts had R1b although they were not typed for the V88 marker which defines R1b1a

This was announced in 2010 by Cruciani et al. The majority of R-V88 was found in northern and central Africa, in Chadic speaking populations. It is less common in neighbouring populations.

The authors of Cruciani, et al. (2010) also found evidence of high concentration in Western Egypt and evidence that the closest related types of R1b are found in the Middle East, and to a lesser extent southern Europe. They proposed that an Eastern Saharan origin for Chadic R1b would agree with linguistic theories such as those of Christopher Ehret, that Chadic and Berber form a related group within Afroasiatic, which originated in the area of the Sahara.

The genetics make a quite strong case that Semitic languages are Southwest Asian in origin, probably Levantine, and that Chadic peoples have at least patriline genetic origins outside Africa and are relatively recent arrivals in Africa through male dominanted migrations seem quite convincing. But, this doesn't resolve the question of Afro-Asiatic linguistic origins, because the uniparental genetic markers don't point to a single common genetic origin for Afro-Asiatic language speakers across all of the subfamilies that make up the larger grouping.

Y-DNA Haplogroups T in Afro-Asiatic Linguistic Populations

There is also a good case that Y-DNA haplogroup T, found in a somewhat hard to characterize mix of populations including many Afro-Asiatic populations, is a backmigration to Africa from Southwest Asia. The Wikipedia survey of its frequency in Africa shows 26 instances of non-Afro-Asiatic peoples: 15 (of 256) in the Spanish Canary Islands that trace roots to North Africa, 6 (of 34) in the Bantu speaking South African Lemba who claim to have have Jewish roots, and 3 (of 17) of the Niger-Congo speaking Fulbe in Northern Cameroon right on the Afro-Asiatic and Niger-Congo population boundary in Africa, with the remaining seven instances involving three isolated cases in small Bantu populations, and four involving small percentages in Nilotic populations, each in samples mostly on the Eastern Coast of Africa which would have been exposed to Y-DNA T rich Somolians in the sea trade or near the Western boundary of Afro-Asiatic populations that are relatively rich in Y-DNA T. There were 108 from Afro-Asiatic populations.

Wikipedia on Haplogroup T also notes that:

Since haplogroup T is not associated with the R1, G and J lineages that entered Africa from Eurasia relatively recently, Luis et al. (2004) suggest that the presence of the clade on the African continent may, like R1* representatives, point to an older introduction from Asia.

The Levant rather than Southern Arabia appears to have been the main route of entry, as the Egyptian and Turkish haplotypes are considerably older in age (13,700 ybp and 9,000 ybp, respectively) than those found in Oman (only 1,600 ybp).

According to the authors, the spotty modern distribution pattern of haplogroup T within Africa may therefore represent the traces of a more widespread early local presence of the clade. Later expansions of populations carrying the E1b1b, E1b1a, G and J NRY lineages may have overwhelmed the T clade-bearers in certain localities.

Egypt, Ethiopia and Somolia are the dominant African locations of Y-DNA haplogroup T in Africa. The dispersal pattern of Y-DNA haplogroup T is far less clear cut than in Y-DNA R-V88 suggesting a deeper time depth. There are only a handful of instances apart from the Canary Islands, that are West of Egypt. It is not really a characteristic Berber marker (the one Berber population that showed it was in Lower Egypt and it was also found in Bengahzi near the Egyptian border with Libya). Instead, it marks Coptic, Cushitic and Omotic populations.

Y-DNA Haplogroups E1b1b in Afro-Asiatic Linguistic Populations

All of the Y-DNA T rich populations are also rich in Y-DNA E1b1b.

The Berbers, who lack much Y-DNA T, are even more rich in E1b1b.

On the other hand, E1b1b seems to have deep origins in Africa. Y-DNA haplogroup E is the dominant black African haplogroup (excluding Khoisan and Pygmy populations) where E1b1a (particularly associated with West Africa), E1a (particularly in West Africa and Sudan) and E2 (pan African, but especially Eastern and Southern Africa) are particularly common. There have been proposals for Y-DNA haplogroup E as back migrations, but I find them highly implausible.

Specific E1b1b subhaplogroups have associations with different groups. E1b1b1b (E-V257) is associated with Berbers. E1b1b1c1 (E-M34) is mostly Semitic. E1b1b1d (E-V6), E1b1b1f (E-V42), E1b1b1g (E-V92), and E1b1b2 (E-V16/E-M281) are all associated with Ethiopia. E1b1b1e* is found in Southern and Eastern Africa. Roots in Ethiopia or the vicinity seem likely.

Afroasiatic mtDNA Evidence

In contrast to the evidence from paternally inherited Y DNA, where Cushitic and Chadic linguistic populations have very different profiles from each other, a recent study has shown that a branch of mitochondrial haplogroup L3 links the maternal ancestry of Chadic speakers from the Sahel with Cushitic speakers from East Africa.

Other mitochondrial lineages that are associated with Afroasiatic include mitochondrial haplogroups M1 and haplogroup U6. Gonzalez et al. 2007 suggest that Afroasiatic speakers may have dispersed from East Africa carrying the subclades M1a and U6a1.

mtDNA haplogroups M1 and U6, and Y-DNA hapologroup R-V88 and J1 are back migrations from Southwest Asia when found in Africa, and there are also clearly distinctly non-African genetic signatures in Ethiosemitic language speaking populations. Ethiosemitic languages probably all have a common origin very early in the historic era.

Nilo-Saharan Homeland Proposed

There is a firm linguistic based proposal for the place of origin of the Nilo-Saharan languages (with the reasoning behind it explained in the linked material), a language family most prominently represented by the Maasi of Kenya, who are known for a predominantly pastoralist lifestyle, particularly in East Africa.

The proto-Saharo-Sahelian society can therefore also be placed somewhere in the combined regions of northwestern Sudan and northeastern Chad.

From "The Archaeology of Africa" (1993) via the Linear Population Model blog.

The location in question included the Blue Nile basin near where it merges with the White Nile, and Lake Chad's endoheic basin, and probably dates to a time of increasing aridity in that region.

As my post yesterday noted, an expansion from this source may have been as recent as 1000 B.C.E., at the dawn of the Mediterranean basin's Iron Age, or perhaps a couple of centuries earlier, around the time of Bronze Age collapse.

The accomplishment of locating this homeland is somewhat muted by the fact that the Nilo-Saharan languages are probably the youngest of the major African language families, that it is one of the smaller major language families of the world, and that it is mostly fairly compact in its geographic range (with one notable branch of the language family providing an exception that proves the rule). This makes the task of discerning the relationships between the family's languages phylogenetically, and their geographic origins considerably easier than in the case, for example, of the far older and more widely dispersed Afro-Asiatic macro-language family that includes, for example, the Berber, Hebrew and Arabic languages. On the other hand, the Nilo-Saharan languages were not literate languages until very late in history, and that impedes inquiry into its historical origins, so the task was not entirely without its challenges.

The Origins Of Neighboring Language Families In A Nutshell

Much of the overall narrative of African pre-history hinges on how one resolves the places of origin and sequencing of linguistic expansions that gave rise to the current linguistic landscape of Africa.

The general vicinity where the Nilo-Saharan languages arose also probably overlaps or is adjacent to the homeland for the Chadic languages, associated with pastoralists who roam the African Sahel (most notably the Hasua people) within the Afro-Asiatic language family.

Marnie quotes Tishkoff who brings autosomal genetic insight to the potential relationships between the two language families established from other sources:

Our data support the hypothesis based on linguistic, archeological, mtDNA, and Y chromosome data, that the Sahel has been a corridor for bi-directional migration between eastern and western Africa.  

We observe the highest proportion of the "Nilo-Saharan AAC [ed. ancestral autosomal genetic component]” in the southern/central Sudanese populations (Nuer, Dinka, Shilluk, Nyimang), with decreasing frequency from northern Kenya (e.g. Pokot) to northern Tanzania (Datog, Maasai). From K = 5-13 [ed. refering to the number of ancestral components chosen by the analyst into which the autosomal data are arbitrarily resolved by a mathematical algorhythm], all Nilo-Saharan speaking populations from Kenya, Tanzania, southern Sudan, and Chad cluster with west-central Afroasiatic Chadic speaking populations.   

These results are consistent with linguistic and archeological data, suggesting a possible common ancestry of Nilo-Saharan speaking populations from an eastern Sudanese homeland within the past ~10,500 years, with subsequent bi-directional migration westward to Lake Chad and southward into modern day southern Sudan, and more recent migration eastward into Kenya and Tanzania ~3,000 ya (giving rise to Southern Nilotic speakers) and westward into Chad ~2,500 ya (giving rise to Central Sudanic speakers).   

A proposed migration of proto-Chadic Afroasiatic speakers ~7,000 ya [5000 B.C.E.] from the central Sahara into the Lake Chad Basin may have caused many western Nilo-Saharans to shift to Chadic languages. Our data suggest that this shift was not accompanied by large amounts of Afroasiatic gene flow. Analyses of mtDNA provide evidence for divergence ~8,000 ya [6,000 B.C.E.] of a distinct mtDNA lineage present at high frequency in the Chadic populations and suggest an East African origin for most mtDNA lineages in these populations."

Since Tishkoff's dates are heavily driven by mutation rate methodologies that are often too unreliable to the level of accuracy necessary to make them useful in distinguishing alternative narratives of pre-history, they must be taken with a grain of salt although the relative sequence of events suggested by the mutation rate dates, at least, is probably the most probable possibility absent evidence to the contrary.

While Chadic linguistic populations tend to have generally East African mtDNA lineages (but see, in particular, this paper regarding distinctively Chadic mtDNA lineages), their most distinctive and defining Y-DNA haplogroup, R1b-V88 (which is a branching basal to the European branches of Y-DNA haplogroup R1b) has a likely origin somewhere in far Southeast Europe or Western Central Asia near the likely point of the Y-DNA haplogroup R1a v. R1b divide.  This is very far afield from most of the rest of the African genetic legacy for a population with its ethogenesis possibly taking place in the vicinity of Lake Chad, two thousand years or so before the world's first written historical records, and hence, at a time when what we know about the civilizations that existed is pretty much limited to pots and bones dated to that era.

The Chadic mtDNA paper linked above also notes that:

Within the Afro-Asiatic language phylum, the Chadic branch is linguistically close to the East African Cushitic branch although they are separated by ~2,000 km of territory in which different Semitic and Nilo-Saharan peoples live today. We show that only northern Cushitic groups from Ethiopia and Somalia are genetically close to Chadic populations. Thus, the archaeologically and linguistically supported route of proto-Chadic pastoralists via Wadi Howar [the remnant of the ancient Yellow Nile, a tributary of the Nile from about 8000 to 1000 BCE] to the Chad Basin may have genetic support.

Both language families probably expanded sometime after the initial expansions of the Niger-Congo language family, and the Chadic languages probably expanded no earlier than and quite possibly considerably later than the Cushitic language family.

The homeland of the Niger-Congo language family isn't terribly controversial, and was probably more or less smack dab in the midddle of West Africa at a confluence of some its major rivers; it has only a few remote members not attributable to Bantu expansion (the most notable is the Kordofan language family of Nuba Mountain in Sudan). The Niger-Congo language expansion in Africa, could pre-date the Afro-Asiatic language expansion in Africa, but could also plausible have taken place not long after Afro-Asiatic languages started to expand.

The Niger-Congo languages seem to be associated with locally domesticated Sahel crops, while the Afro-Asiatic languages seem to be associated with Fertile Crescent food production packages. A determination of which language family came first is deeply intertwined with the question of whether Sahel agriculture was developed independently of the Fertile Crescent package, or was only made possible because of animal domestications and concepts that had their source in the Fertile Crescent.

Afro-Asiatic Linguistic Origins

But, the Cushitic language family's origins are a much hotter issue. This is because the status of the Cushitic languages as a source or sink within the Afro-Asiatic languages, which in turn goes to the controversial question of whether the Afro-Asiatic languages have an African or West Asian place of origin.

A "First Farmers" paradigm would suggest a probably origin for the language family in the Levant that expanded and diversified with the Fertile Crescent Neolithic, or perhaps a secondary origin somewhere in the Nile Basin as a language of early adopters of the Fertile Crescent Neolithic in Africa who expanded elsewhere in Africa (with Semitic arriving in the Levant via Egyptian cultural influence).

The main argument for the African origin of Afro-Asiatic languages is that five of the six subfamilies of the Afro-Asiatic languages appear to have origins in Africa (Berber, Chadic, Cushitic, Omotic, and Coptic) and are exclusively African, leaving only the Semitic languages, whose origins can be traced quite a distance back in time through historic and linguistic means (the Ethio-Semitic languages arrived in Ethiopia as a single proto-language probably sometime in the Bronze Age from the Levant; the family tree of the West Semitic languages are reasonable well established in both time and place).

The argument for an African origin of the Afro-Asiatic languages is also bolstered by the fact that the speakers of the Afro-Asiatic languages are not united by a genetic signature that can be rooted in Levatine peoples. Some distinctively Semitic genetic ancestry markers are largely absent in other Afro-Asiatic populations, but the phylogeny of the most widely shared genetic ancestry markers of Afro-Asiatic language speakers have roots that are widely, although not universally, believed to have African origins. But, the genetics are not conclusive, because there is no one genetic ancestry marker that is clearly a distinctive component of the gene pool of all six of the constituent language families of the Afro-Asiatic languages.

In a West Asian origin theory, proto-Afro-Asiatic was imposed on Egyptians and perhaps separately upon Berbers by an early Neolithic colonist superstrate from the Levant made up of people who had enough power to induce language shift in the subject peoples despite not having much of a demic impact visibile in the gene pool, a phenomena documented more than once historically.

In an African origin theory, the Semitic languages, whose speakers are genetic outliers relative to the African language families in the Afro-Asiatic macro-language family, has its roots in an Egyptian superstate population that caused a language shift in the Levantine substrate peoples. We know, historically, that the Levant did have an Egyptian superstrate for more than a thousand years.  But, we don't know what kind of influence Egyptians had in the Levant centuries prior to the earliest attested West Semitic languages which is when the proto-Semitic language would have flourished somewhere in West Asia. 

As a footnote, it is also worth observing that, if there was an Egyptian origin, it would have had to have taken place at least 1500 years or so before Hebrew ethnogenesis which is relatively well dated historically and linguistically, since the West Semitic Akkadian languages and related Northwestern Semitic languages are attested long before the Hebrew people came into being as a cultural construct.  The origins of the Semitic languages in West Asia were most definitely not in a Hebrew Exodus from Egypt.

Of course, even though both a sub-Saharan African origin for the Afro-Asiatic languages and an Egyptian origin for the Afro-Asiatic languages would both probably have the same Egyptian mediated origin for the West Semitic languages (since almost all road to West Asia from Africa with any demographic must pass through Egypt), the case for the Cushitic or Coptic languages (or for that matter the Berber or Omotic languages) being the most basal root of the Afro-Asiatic linguistic tree within Africa is not at all settled (and hence the controversy over the location and timing of the Cushitic homeland).

For what it is worth, while I am personally agnostic on the question of whether the Afro-Asiatic languages arose in Egypt or the Levant (most plausibly Jericho, the first Levantine city, given the tendency of languages to snowball into being predominant in a way very sensitive to the initial conditions when the expansion starts), but I believe that there is a very strong case that the Afro-Asiatic languages expanded from Egypt within Africa with the expansions of the Fertile Crescent Neolithic package of crops and animals, rather than from Ethiopia, for example, which is where the Cushitic languages are mostly spoken today, or some other location. And, there is a very solid archaeological and inferential case that the Fertile Crescent Neolithic package first established itself in Africa in the Nile Basin.

In my view, to the extent that the genetic patterns don't unequivocally show this pattern it is a result of Epipaleolithic (or earlier) population migrations that have a well established archaeological basis, and non-demic language shift events. But, the pattern of languages spreading with societies that have adopted food production methods to the detriment of the existing languages of hunter-gatherer populations is too close to universal to make it anything other than the possibility that is by far the most likely. Clearly there were at least one instance, and really there is a good case that there were two or three instances of predominantly non-demic language shift in the origin of the major Afro-Asiatic language families, given the evidence from the population genetics of the modern speakers of these languages, so genetics can't easily resolve the question of the relationship between the main Afro-Asiatic language families and other evidence must be brought to bear to answer it. Given that there is considerable disagreement amongst linguists on this question given purely linguistic evidence, this also isn't conclusive.

Sources Of West Eurasian Ancestry In Eastern and Southern Africans (updated twice)

A new paper by Pickrell (preprint discussed here in 2012) observes that click language speaking, historically hunter-gatherer populations of Southern Africa (the Khoi-San) have West Eurasian admixture (in the extreme case as much as 15% but more often on the order of 5% or less) dated to 900 to 1800 years ago and predating Dutch and English colonists who gave rise to modern South Africa.

He concludes that this is probably derived from the migrations of people from East Africa.  There, in there, there was substantial West Eurasian admixture ca. 2,700 to 3,300 years ago, around the time of the arrival of Ethio-Semitic languages in Ethiopia from Southern Arabia.

I would add a few observations.

1.  Comparability to East African Hunter-Gatherer Percentages.  The levels of West Eurasian admixture seen in the Khoi-san of Southern Africa is similar to that seen in the Hazda and Sandawe who are click language hunter-gatherer populations of East Africa.  Bantu languages in Mozambique, intermediate between these two groups, also have clicks in their Bantu dialects that were presumably inherited from substrate languages that preceded Bantu expansion there.  The lack of much dilution of West Eurasian ancestry relative to hunter-gatherer populations in East Africa is notable.  It indicates a migration rather than mere diffusion of West Eurasian genes over time (something also supported by the lack of similar West Eurasian ancestry in geographically intermediate parts of Africa).

2.  Push Factors.  These hunter-gatherer population migrations were probably more than mere random wanderings.  Hunter-gatherer populations in East Africa may been retreating from Ethio-Semitic peoples, from later waves of Bantu expansion, or even from Nilo-Saharan expansion in East Africa.  Their exiles may have been a pilot wave in advance of the expansions of groups that cast them out of East African homelands.

3.  West Eurasian Ancestry In East Africans Probably Arose In At Least Three Waves.  Pickrell supposes that the nearly 50% West Eurasian ancestry found in Ethiosemetic peoples in the vicinity of the former D'mt Kingdom of Eritrea and Ethiopia happened in a single event on the grounds of maximum parsimony.

Pickrell relies to a great extent in doing so on a 2012 study by Luca Pagani, et al., so criticism of this part of Pickrell's paper really amounts to criticism of Pagani rather than Pickrell who merely relied on Pagani's findings.

In fact, other evidence makes such a simple scenario unlikely.  Instead, West Eurasian ancestry in East Africa probably arrived in at least three waves: an Upper Paleolithic back migration from West Asia, an early Neolithic back migration from West Asia, and an Ethiosemetic migration from Southern Arabic.

Moreover, the ancestry seen in the Khoi-San, is probably derived largely from the first and second waves, rather than the third.  As discussed below, the source population was from the Ethiopian fringe where Ethiosemitic influence was lightest.  These populations may have experienced only two waves of West Eurasian ancestry.

Some of the evidence includes the following:

* Methodology Mutes Impact Of Prior Waves.  The method used to date the East African-West Eurasian admixture event tends to obscure or ignore waves of admixture other than the most recent one.

* Known Upper Paleolithic Back Migration.  We know that sometime in the Upper Paleolithic era that there was a back migration to North Africa and East African that brought with it mtDNA haplogroups M1 and U6.  This may have been on the order of 10%-20% of the populations at the time - U6 has a more North African distribution, while M1 has a more East African distribution (mtDNA charts via Ethiohelix are informative on this point).

* Chadic-Cushitic Links Indirectly Date Cushites And West Eurasian Contact.  Archaeological evidence suggests that the Chadic people made their way to Lake Chad, after a period of depopulation of the region during an arid climate period, around 5,200 BCE as part of the Gobero culture.  These populations show tighter mtDNA similarities to Cushitic peoples with whom they share pottery designs and words for domesticated animals, suggesting a split of Chadic people away from Cushitic people around that time in the vicinity of Sudan.  But, the Chadic people have a distinct R1b-V88 dominanted Y-DNA profile from that of Cushitic people.  Thus, proto-Chadic men may have taken Cushitic women as wives and then migrated West to Lake Chad.  mtDNA distributions in Northeastern, Eastern and Central Africa, however, tend to follow regional patterns except for one mtDNA L3f clade particular to Chadic peoples and derived from a Cushitic clade.  The TMCRA time depth of the Chadic specific Y-DNA clade and Chadic specific mtDNA clade are consistent with this archaeologically supported date.

* Autosomal Genetic Clustering.  Autosomal evidence points mostly to three clusters - a Northern Berber-Egyptian-Semitic cluster, a Southwestern Chadic cluster, and a Southeastern Cushitic cluster, with each almost equidistant from each other.  All of these Afro-Asiatic populations in turn tend to cluster away from more southerly linguistic populations.  Thus, Northern Afro-Asiatic speakers are part of a significantly West Eurasian cluster, while Chadic and Cushitic populations have less West Eurasian ancestry, and the Chadic population having different kinds of West Eurasian ancestry than other Afro-Asiatic populations.

* High West Eurasian Ancestry In Cushitic Ethiopians.  Many Cushitic populations have as much as about 35% West Eurasian admixture.  This is 10%-15% less than that of Ethiosemitic populations closer to South Arabia, but too small a discrepancy to be accounted for by an initial admixture of South Arabians with Ethiosemitic peoples that then spills over to neighboring Cushitic populations.  This level of impact would be on the same order of magnitude as the Turks in Turkey, or the Indo-Aryans in India.  This would be more than the demographic impact of the Uralic population that brought Hungarian to Hungary (almost nil), less than the demographic impact of the Yaoyi who brought Japanese to Japan (on the order of 50%).

A more plausible scenario is that Cushitic populations had roughly 25% to 35% West Eurasian admixture prior to the arrival of the proto-Ethiosemetic peoples, and that Ethiosemitic invaders added a gender biased additional 10%-15%.  Meanwhile, in the pre-Ethiosemitic Cushitic population, there may have been a 5%-20% or so West Eurasian admixture percentage traceable to the Upper Paleolithic, with the balance appearing with the arrival of the Neolithic revolution probably via the Nile Valley into the Blue Nile basin.

The window of time during which the Neolithic flow of West Eurasian ancestry into Cushitic populations is quite narrow.  It had to predate the emergence of the Chadic people around 5200 BCE, and had to post-date the arrival of the Neolithic revolution in Egypt sometime after 8000 BCE.

* Neolithic Source West Eurasian DNA Likely In This Case.  It is this early Neolithic infusion of West Eurasian ancestry, rather than later Ethiosemitic contributions that probably gradually spilled over into neighboring pre-Cushitic hunter-gatherer populations with click languages over a period of more than 3,000 years.  (Niger-Congo languages were probably not spoken in East Africa until Bantu expansion and Nilo-Saharan languages were likewise probably a late arrival, since there is very little evidence of genetic profiles associated with these languages being present in East Africa until very recently.  These genetic profiles are not a background present in most linguistically Afro-Asiatic populations of the region.)

This is consistent with Pagani's finding that the East African source population is closer to Levantine than Arabian populations, but inconsistent with his findings on the timing of admixture and the number of admixture waves involved. Neolithic source populations were probably from the Levant.  Ethiosemitic population sources were almost surely from South Arabia.

Phantom West Eurasian autosomal DNA profiles for Cushitic and Khoi-San populations can help us to reconstruct genetic profiles of first wave African Neolithic migrant populations.

* Y-DNA T related clues.  Y-DNA haplogroup T is common in Somolia and to a lesser extent in adjacent parts of Ethiopia.  But, the age of the Y-DNA haplogroup T subtypes in Arabia such as Oman are too young (ca. 1600 years) to have been the source for Y-DNA hg T in Ethiopia not less than 2700 years ago with the Ethiosemitic languages.  Instead, given the much older ages of Y-DNA haplogroup T clades in Turkey and Egypt, it is fair to assume that Y-DNA hg T made its way to Ethiopia from the Levant via the Sinai and Nile River.  Thus, significant West Eurasian ancestry evidence by Y-DNA hg T must have arrived in Ethiopia considerably earlier than 2700 years ago, and quite likely during the early Neolithic.  Y-DNA hg T bearers appear to have been farmers, and why would farmers settle in the Arabian desert prior to entering Africa from there?

4.  Copitc was probably a parent language to Cushitic from which Chadic diverged.  Increasingly, the genetic, linguistic and archaeological evidence, taken as a whole, point towards the Neolithic expansion of the ancient Egyptians who spoke a Coptic language as the parent language family to the Cushitic, Omotic, Chadic and Berber language families, and quite possibly, of the Semitic language family as well, within the Afro-Asiatic branch of the language this macro-language family.

Ancient Egyptian may in turn have had origins in a Levantine Fertile Crescent language, but that proto-language, if there was one, was probably obliterated by a Semitic derivative of ancient Egyptian's back migration to the Levant from Egypt evidence by the Afro-Asiatic specific Y-DNA E clades found there today and supported by historical evidence of long periods of Egyptian political dominance in much of the Levant.  The indications of Y-DNA E migrations into West Eurasia are rare exceptions of Africa to West Asian gene flow when mostly since the Upper Paleolithic, the direction of the flow has been back to Africa.

Also, notably, the linguistic tree of Semitic doesn't show much sign of diversification or a bushy structure prior the first attested instance of a Semitic language in the form of Akkadian, just a few hundred years after the ancient Egyptian Civilization really started to reach an advanced state ca. 3000-3500 BCE.

On the other hand, a possibly Levantine proto-Afro-Asiatic that may have given rise to Coptic ca. 8000-7000 BCE as part of a first wave Neolithic expansion, may also have survived and been, in a later form, a substrate to the branch of Coptic that became proto-Semitic ca. 3000-3500 BCE.  So early Semitic languages may be as close to proto-Afro-Asiatic as we can discern with historical linguistic methods, since its departures from Coptic might reflect retention of words and structures from a proto-Afro-Asiatic language.

UPDATE 2/04/2014 based on review of supplemental materials:

5.  The single source East African population for West Eurasian ancestry in the Khoi-San had 25% West Eurasian ancestry, consistent with modern Omotic populations on the Ethiopian fringe.  The Khoi san samples very consistently demonstrate that West Eurasian ancestry is 25% of overall East African ancestry.  This is less than is seen in linguistically Semitic or Cushitic populations, is within the range of linguistically Omotic populations, more than the Maasai, but less than another Nilotic population which is near zero, and more than the Hadza, Sandawe, a couple linguistic isolates and a Bantu population.

In other words, a 25% West Eurasian ancestry percentage in the source population for the Khoi-San suggests an East African source population on the Ethiopian linguistic fringe, rather than the Semitic or Cushitic heartland of Ethiopia.  It also strongly suggests that a single source population is responsible for West Eurasian ancestry in all Khoi-San individuals.

Notably, however, the type of West Eurasian ancestry in the Khoi-San matches the phantom ancestry inferred from East African populations more closely than any modern population, strongly confirming this sourcing for that ancestry.  Compared to modern populations that matches are closest to Southern European and Middle Eastern populations.

UPDATE 2/06/14 based on further analysis:

6.  The Ethio-Semitic demographic impact on Ethiopia may have been close in time to a demographic impact on Ethiopia associated with the arrival of domesticated cattle, obscuring the fact that there were actually two separate and parallel migration waves involved.

The notion that most of the West Eurasian admixture in Ethiopia appeared ca. 2700-3300 years ago is supported by a 2012 study by Luca Pagani, et al., but I have criticized it above, arguing for a Neolithic wave before an Ethio-Semitic wave.  But, these two waves may actually have been parallel or close in time to each other.

At least, anyway, cattle herding accompanied by a major demographic impact may have arrived close in time to the Ethio-Semitic languages may have arrived ca. 2000 BCE-1500 BCE.  If admixture between newly arrived cattle herders and existing Ethiopian populations didn't take off until several centuries after these populations started to co-exist, this could help fit the Luca Pagani admixture dates to a historical source of this admixture at around the correct time in linguistically non-Semitic Ethiopians.

How could this be?

First off, the Cushitic-Chadic split may have happened in Sudan, before Cushitic languages had advanced up the Blue Nile into Ethiopia proper.

Second, as summarized in a previous post here, where it was noted that herding arrived to East Africa later than one might naively expect (emphasis in bold added):

In east Africa pastoralism became established late in the third millenium BC, and over the next 1000 years domestic livestock slowly moved towards Tanzania. These cattle were probably humpless, for the earliest evidence for humped cattle comes from ancient Egyptian paintings dated to around 1500 BC. These authors believe that cattle with cervico-thoracic humps (i.e. with humps on their necks) were first introduced into the Horn of Africa. . . .

The quite late arrival of pastoralism in East Africa, which is also some to relict hunter-gatherer populations which are absent in North Africa and in West/Central Africa to the North of the Congo jungle, suggests that herding (and probably farming as well, at least in less arable land) may have come much sooner to North Africa and West Africa than to East Africa (with Southern Africa not experiencing agriculture until the Bantu expansion arrived there after it had swept the rest of the continent). Indeed, the arrival of cattle herding in East Africa could conceivably have predated Bantu expansion by only a thousand years or so.

If one makes the plausible assumptions that the ancestors of Cushitic populations predate Nilo-Saharan populations in East Africa who in turn pre-date Bantu populations in East Africa, and that all of these language families were spread by cultures that employed herding or farming, the late arrival of cattle herding to East Africa (ca. 3000 BCE to 2000 BCE), the fairly well dated arrival of Bantus in East Africa (ca. 1000 BCE-500 BCE), and the known paleoclimatic wet sahara/dry sahara/chad basin size changes quite tightly constrain and compress the timing of Cushitic and Nilo-Saharan expansions in East Africa. It also probably puts the time that the source cultures for these language families arrives in East Africa sometime after the ethnogenesis of the culture that gave rise to the Niger-Congo languages that are dominant in West Africa (which necessarily predated the expansion of its Bantu branch of that language family ca. 1500 BCE-1000 BCE).

Tishkoff argues based on genetic evidence associated with the digestion of cow's milk by adults and archaeological evidence that:

Cushitic-speaking Afro-Asiatic populations . . . are thought to have migrated into Kenya and Tanzania from Ethiopia ~5,000 years ago and practice a mixture of agriculture and pastoralism . . . [while] the Nilotic-speaking Nilo-Saharan populations. . . are thought to have migrated into Kenya and Tanzania from southern Sudan within the past ~3,000 years and are strict pastoralists.

Thus, according to Tishkoff's account, Nilo-Saharan linguistic populations arrived in East Africa proper only a few centuries before the Bantu expansion reached the area, and the Cushitic population was expanding south from Ethiopia only shortly after Egypt and Sumeria developed written languages at about the same time as the high point of the Indus River Valley civilization, although their arrival in or ethnogenesis in Ethiopia clearly must have happened earlier. 

Tishkoff doesn't reach a conclusion about whether a milk digestion gene specific to Africa arose first in Cushitic or Nilotic populations, but another quote from the same article strong suggests that the Cushitic people, rather than the Nilotic population was its source (and hence that the Cushitic people had cattle farming): "The absence of C-14010 in the southern Sudanese Nilo-Saharan–speaking populations suggests that this allele either originated in or was introduced to the Kenyan Nilo-Saharan populations after their migration from southern Sudan."

Tishkoff also recaps the archaeological evidence for cattle domestication in Africa:

Archeological evidence suggests that cattle domestication originated in southern Egypt as early as ~9,000 years ago but no later than ~7,700 years ago and in the Middle East ~7,000-8,000 years ago, consistent with the age estimate of ~8,000-9,000 years (95% c.i. ~2,200-19,200 years) for the T-13910 allele in Europeans. The more recent age estimate of the C-14010 allele in African populations, ~2,700-6,800 years (95% c.i. ~1,200-23,000 years), is consistent with archeological data indicating that pastoralism did not spread south of the Sahara and into northern Kenya until ~4,500 years ago and into southern Kenya and northern Tanzania ~3,300 years ago. . . 

The main crops of the West African Sahel and some of the Ethiopian Highland crops are indigenous African domestications that were not part of the Fertile Crescent agricultural package. Fertile Crescent crops are a poor fit for parts of Africa beyond the Mediterranean fringe and the Nile basin; they are confined to regions further north than the regions where Fertile Crescent livestock can thrive without evolving to adapt to African weather and diseases. The quoted post dealt only with cattle husbandry, and one needs to look at dating for goats and sheep herding and for indigenous African crops to reliably date the West African and East African Neolithic (I've seen some references, that I'll have to track down, that have proposed an early date of arrival for these herd animals than for cattle.) It could be that early African agriculture didn't include cattle until other parts of the agricultural package were better established.

One possibility that could reconcile the various lines of evidence, and also relax some of the tight constraints in timing discussed above, is to envision the Cushitic languages expanding to the herding of sheep and goats, and the Nilo-Saharan expansion as being boosted by the addition of cattle husbandry to the Cushitic food production package (although, as noted above, Tishkoff's sources, at least, doubt that scenario). . . .

Recent East African autosomal genetic data also makes clear that there was not any significant demic impact of West African Niger-Congo populations in East Africa prior to the Bantu expansion into that region, although the domesticated crops of West Africa and East Africa respectively a testaments to the mutual exchange of locally domesticated plants between the regions at some point in time. . . .

Another implication of this narrative, if it is accurate, is that within the Afro-Asiatic language family, the Berber and Coptic language families probably significantly predate the Cushitic and Chadic language families. (These speculations don't resolve one way or the other the relative origins of Berber and Coptic languages on one hand and the Levantine Semitic languages on the other, although Ethio-Semitic languages surely broke off as a branch of the Semitic languages after all of the language families within the Afro-Asiatic macro-language family were established, probably sometime in the Bronze Age).

The Holocene Climate Events That Shaped Prehistory and Ancient History

There is considerable evidence to support environmental determinism as a key lens through which to understand human history and human prehistory.  This is the view that large scale climate events have been major drivers of cultural transitions, technological innovation and cultural change in modern human prehistory.

In the period from ca. 8000 BCE when the first farmers and herders domesticated crops and animals in the Fertile Crescent, an event known as the Fertile Crescent Neolithic Revolution, until ancient Greco-Roman times which are well documented historically, there have been three such events: the 8.2 kiloyear event, the 5.9 kiloyear event and the 4.1 kiloyear event, and possibly a less severe one as well which helped to precipitate the historical events known as Bronze Age Collapse about 3.2 thousand years ago.  This recap can be read together with a post of about a year and a half ago on a similar topic, but with a greater focus on showing connections to a larger number of historical events.

It takes an artists interpretation to really get a grip on the immensity some of the key pre-Neolithic climate events like the Last Glacial Maximum ca. 20,000 years ago.  Similarly notable pre-Neolithic climate events include: the climate impact of the Toba eruption on Africa (a map of Toba ashfall is here), the cause of the Younger Dryas, and the Middle Stone Age Paleoclimate.  I also have a post on Arabic Paleoclimate which is highly relevant to Out of Africa and beyond scenarios and Neanderthal admixture.

The 8.2 kiloyear event, the first wave of the European Neolithic and Chadic ethnogenesis

The Fertile Crescent Neolithic expanded to the Indus River Valley, to Egypt, and to the parts of the Balkans adjacent to Anatolia, about a thousand years after it arose in the core Fertile Crescent region, in each case, before the 8.2 kiloyear event.  But, this event appears to have bottled up further Neolithic expansion until it ended, at which point the first farmers of Europe started to arrive, particularly in Southern Europe and in the Danube River basin.

This first wave of the European Neolithic revolution in which the first farmers and herders expanded into Europe is mostly associated with the LBK culture in Eastern and Central Europe (ca. 5500 BCE to 4900 BCE) and the roughly contemporaneous Cardial Pottery culture in Southern Europe. This took place in the period of restored positive climate conditions immediately following the 8.2 kiloyear event.

The 8.2 kiloyear event is the term that climatologists have adopted for a sudden decrease in global temperatures that occurred approximately 8,200 years before the present, or c. 6,200 BCE, and which lasted for the next two to four centuries. Milder than the Younger Dryas cold spell that preceded it, but more severe than the Little Ice Age that would follow, the 8.2 kiloyear cooling was a significant exception to general trends of the Holocene climatic optimum. . . .

The 8.2 Ka cooling event may have been caused by a large meltwater pulse from the final collapse of the Laurentide ice sheet of northeastern North America—most likely when the glacial lakes Ojibway and Agassiz suddenly drained into the North Atlantic Ocean. . . . causing significant circum-North Atlantic cooling. Estimates of the cooling vary and depend somewhat on the interpretation of the proxy data, but drops of around 1 to 5 deg C (1 to 9 deg F)have been reported. In Greenland, the event started at 8175 Before Present, and the cooling was 3.3 deg C (decadal average) in less than ~20 years, and the coldest period lasted for about 60 years, and the total duration was about 150 years. Further afield, some tropical records report a 3 deg C (5 deg F) cooling from cores drilled into an ancient coral reef in Indonesia. The event also caused a global CO2 decline of ~ 25 ppm over ~ 300 years. However, the dating and interpretation of this and other tropical sites are more ambiguous than the North Atlantic sites.

Drier conditions were notable in North Africa, while East Africa suffered five centuries of general drought. In West Asia and especially Mesopotamia, the 8.2ky event was a three-hundred year aridification and cooling episode, which may have provided the natural force for Mesopotamian irrigation agriculture and surplus production that were essential for the earliest class-formation and urban life. However multi-centennial changes around the same period are difficult to link specifically to the approximately 100-year abrupt event as recorded most clearly in the Greenland ice cores.

The initial meltwater pulse caused between 0.5 and 4 m (1 ft 8 in and 13 ft 1 in) of sea-level rise. Based on estimates of lake volume and decaying ice cap size, values of 0.4–1.2 m (1 ft 4 in–3 ft 11 in) circulate. Based on sea-level data from below modern deltas, 2–4 m (6 ft 7 in–13 ft 1 in) of near-instantaneous rise is estimated, in addition to 'normal' post-glacial sea-level rise. Meltwater pulse sea-level rise was experienced fully at great distance from the release area. Gravity and rebound effects associated with the shifting of water masses meant that the sea-level fingerprint was smaller in areas closer to the Hudson Bay. The Mississippi delta records ~20%, NW Europe records ~70% and Asia records ~105% of the global averaged amount. The cooling of the 8,200 event was a temporary feature; the sea-level rise of the meltwater pulse was permanent.

The archaeological, linguistic and genetic evidence all support the case that the linguistic group that comprises the Chadic people of the African Sahel, who have high frequencies of the genetically distinct (for Africa and for Afro-Asiatic language speakers) Y-DNA haplogroup R1b-V88 which is estimated to have arisen 7200 BCE to 3600 BCE and also have distinctive mtDNA clades with an estimated origin using more accurate, although hardly exact, mtDNA dating, of 6000 B.C.E.  More archaeological data on the African Neolithic can be found here.

The ancestors of the Chadic people probably arrived on the shores of Lake Chad to fill the vacuum created by the 8.1 kiloyear event around 5200 BCE, which is a date consistent with Y-DNA, mtDNA, archaeological dating around lack Chad and the suggestions of climate data.  A few centuries earlier as a result of the 8.1 kiloyear event, ca. 5500 BCE, Lake Chad pretty had much entirely dried up, but it would have started to fill up again by 5200 BCE (in contrast, a maximal Lake Chad is illustrated here).  This strongly supported and archaeologically grounded date is very useful in the larger scheme of historical linguistics and archaeogenetics.

First, it provides a calibration point for the time depth of one of the Afro-Asiatic languages families.  Almost everyone agrees, in part because of the genetic distinctiveness of the Chadic people relative to other Afro-Asiatic populations, that Chadic is a later branching part of the Afro-Asiatic language family.  This implies that proto-Afro-Asiatic dates to a time frame of more than 7000 years ago.

Second, it provides a time frame for one of the more notable long range folk migrations in human history, because R1b-V88 is an outlier Y-DNA clade in Africa that dd not originate there, but also does not have its origins in recent historic migrations (since there are no obvious modern R1b-V88 populations that could have provided a source for this Y-DNA clade in the Islamic era or the European colonial era).

This migration would was almost certainly after the Neolithic revolution reached Egypt (and very likely proceeded down the Nile River Basin, and then either across the southeast corner of the modern Sahara desert or up the White Nile to its source and then over the river basin divide into the Lake Chad basin.  The Chadic people would have appeared close in time to the arrival of pastoralism south of the Sahara desert.  The fact that Chadic autosomal genetics are quite similar to those of other West Africans, however, suggests that the initial Chadic migrants may have been male dominated and patrilocal, and may have absorbed African mtDNA (although one analysis found that Chadic mtDNA was closer to Afro-Asiatic populations than to other Central Africans) and autosomal genetics by taking local brides.

And, third, it provides a calibration point for other R1b clades such as R1b-M269 that can safely be presumed to be younger than the very basil R1b-V88 clade of that Y-DNA haplogroup.  This is consistent with the ancient DNA evidence that Y-DNA R1b was not present at any great frequency in first wave European Neolithic populations.

The 5.9 kiloyear event and Europe's late Neolithic or copper age demographic transition

The 5.9 kiloyear event (ca. 3900 BCE) is a plausible cause of the abrupt population genetic shift that occurred in Europe sometime between first wave Neolithic populations of the LBK and CP Neolithic, and the population genetics of Western Europe which were present at the advent in Indo-European migration into Western Europe.

The 5.9 kiloyear event was one of the most intense aridification events during the Holocene Epoch. It occurred around 3900 BC (5,900 years BP), ending the Neolithic Subpluvial and probably initiated the most recent desiccation of the Sahara desert. Thus, it also triggered worldwide migration to river valleys, such as from central North Africa to the Nile valley, which eventually led to the emergence of the first complex, highly organised, state-level societies in the 4th millennium BC. It is associated with the last round of the Sahara pump theory. . . .In the Middle East the 5.9 kiloyear event contributed to the abrupt end of the Ubaid period.

The demographic transition could be associated either with the Megalithic culture, which was in much of Atlantic Europe, the first wave Neolithic culture to arrive there, or it could be associated with the Bell Beaker culture which appears to have started to expand from a source in Southern Iberia around 2900 BCE.  Bell Beaker populations show continuity in physical anthropology with prior populations only in the Czech Republic and Northern Spain.

The earliest examples in ancient Y-DNA haplogroup R-M269, which is associated with this demographic transition, is found in two Bell Beaker men from Germany ca. 2650 BCE, and Y-DNA R-M269 had probably reached its current predominant frequencies in Western Europe by 1300 BCE.  Another ancient Y-DNA R-M269 clade individual died around 670 CE in Bavaria.

But, without Y-DNA from the Neolithic Atlantic Megalithic culture, we can't rule out the possibility that R-M269's expansion was (1) part of the the Megalithic culture, whose people were the first farmers of much of Western Europe where the Neolithic revolution arrived later than it did in Eastern Europe and Southern Europe, or (2) the Bell Beaker people who were initially physically distinct in most places where their remains have been found, but who were previously not believed to have been a major source of demographic change in the places where their culture took hold.

Climate evidence would tend to favor an Atlantic Neolithic/Megalithic demographic transition took place just in the wake of the 5.9 kiloyear event that would have depleted any earlier Mesolithic or Neolithic populations of Europe, while the Bell Beaker culture's expansion does not coincide neatly with a major climate event of the Holocene era.

Archaeological evidence also tends to favor the Atlantic Neolithic/Megalithic period as the source of this demographic transition.  A charts from Stephen Shennan et al., Regional population collapse followed initial agriculture booms in mid-Holocene Europe. Nature Communications (2013) reproduced and annotated by Maju at his blog show clearly, the volume of archaeological finds in fairly well studies Europe suggests that the Atlantic Neolithic/Megalithic period were aspects of the same historical event and that this event had a much more dramatic and far more universal than the advent of subsequent Bell Beaker and Corded Ware cultures.

On the other hand, the overall data set and most of the subregions studies show that the Atlantic Neolithic was almost universally followed by a fairly severe bust.  For example, in the time period from 3400 BCE to 2200 BCE, the people of Ireland mostly reverted from their initial farming method of subsistence to a hunting and gathering approach as their primary means of food production.  The demographic transition could represent copper age backfilling of new populations into the gap left by the first bust of the Atlantic Neolithic (in some cases all of the way down to abandoning the Neolithic revolution package of farming technologies entirely) after its initial spectacular boom that eventually substantially replaced or profoundly diluted the genetic contributions of Mesolithic forager populations in Europe to the modern gene pool.

But, if the Atlantic Megalithic culture rather than the Bell Beaker culture is the source of this demographic transition it is still necessary to determine why it is that the first farmers of the Atlantic European region were genetically distinct from the early first farmers of Eastern and Southern Europe, who were part of the LBK and CP archaeological cultures.

The absence of a meaningful proportion of Y-DNA in Western Europe ancestral to Y-DNA haplogroup R-M269 in the modern population genetics of Western Europe and in the available ancient Y-DNA of Western Europe, suggests strongly that R-M269 in Western Europe has its origins in a Neolithic or Copper Age culture that migrated to Western Europe (probably first to Iberia from which both the megalithic and Bell Beaker cultures expanded) from someplace else where Y-DNA R1b haplogroups ancestral to R-M269 are present either currently or have been found in ancient DNA.  Another recent study using a different method also discerned that Y-DNA haplogroup R-M269 has experienced an extremely rapid recent expansion.

The Civilization Destroying 4.1 Kiloyear Event

Another candidate cause for this abrupt population genetic shift (which is not mutually exclusive), would be the 4.1 kiloyear event (ca. 2100 BCE) which is the first major climate event whose effects were well documented in written records.

This event led to a temporary collapse of civilization in Old Kingdom Egypt, Mesopotamia's Akkadian Empire, and the Indus River Valley civilization in South Asia. It is likely that the pork taboo of many Semitic cultures arose during this climate event. The natural disasters that brought down Old Kingdom Egypt at this time may have been a historical source for the legendary history story of the plagues of Exodus.

The 4.2 kiloyear climate event appears to have simultaneously transformed and led to the rapid expansion of Indo-European populations from South Asia to Anatolia to Greece to the Paonian Plain to mountainous far western China. The climate event coincides with or precedes (1) the beginning of the Indo-European Hittites conquest of the non-Indo-European populations of Anatolia and the Northern Fertile Crescent including the non-Indo-European Hattic Civilization, (2) the arrival and conquest of pre-existing non-Indo-European peoples of the Aegean Sea region by Indo-European Mycenean Greeks, (3) the arrival of Sanskrit speaking Indo-Aryan peoples in the Indus River Valley, and (4) the arrival of the Indo-European Tocharian peoples in the Tarim Basin of Asia. The Tocharian migration is a few hundred years after the 4.2 kiloyear climate event and has its origins to the north of the Tarim Basin rather than the epicenter of the other Indo-European expansions of around this time, suggesting that climate change may have exiled them from their previous home until they arrived in a largely unpopulated Tarim Basin.

I suspect that much of the diversification of the Indo-European languages (apart from Tocharian) happened rapidly then, primarily as a result of substrate influences as Indo-European populations conquered linguistically diverse non-Indo-European populations in the general vicinity of a Pontic-Caspian plain homeland, which was becoming less habitable as a result of climate change.

The new Indo-European cultures in all of these regions, except the Tarim Basin which seems to have a different geographic source than the other expansions and did not involve contact with a substrate population, are accompanied by a preference for cremation over inhumation as a means of disposing of the dead. Cremation is also first observed on the Paoian Plain at around this time, presumably as part of a shared set of beliefs held by a rapidly expanding Indo-European culture.

Notably, however, consistent with the theory that they were probably not Indo-Europeans, the Bell Beaker people, who first appear in Western Europe in Southern Iberia ca. 2800 BCE, a culture that eventually expand to most of Western Europe, did not adopt cremation at this time. Instead, cremation arrived in Western Europe with the Urnfield people ca. 1300 BCE.

The 4.2 kiloyear BP aridification event was one of the most severe climatic events of the Holocene period in terms of impact on cultural upheaval. Starting in ≈2200 BC, it probably lasted the entire 22nd century BC. It is very likely to have caused the collapse of the Old Kingdom in Egypt as well as the Akkadian Empire in Mesopotamia. The drought may have also initiated southeastward habitat tracking within the Indus Valley Civilization. . . .

A phase of intense aridity in ≈4.2 ka BP is well recorded across North Africa, the Middle East, the Red Sea, the Arabian peninsula, the Indian subcontinent, and midcontinental North America. Glaciers throughout the mountain ranges of western Canada advanced at about this time. Evidence has also been found in an Italian cave flowstone, and in the Kilimanjaro Ice sheet, Andean glacier ice. The onset of the aridification in Mesopotamia near 4100 B.P also coincided with a cooling event in the North Atlantic, known as Bond event 3.

Aftermath

Ancient Egypt

In ca. 2150 BC the Old Kingdom was hit by a series of exceptionally low Nile floods, which was instrumental in the sudden collapse of centralized government in ancient Egypt. Famines, social disorder, and fragmentation during a period of approximately 40 years were followed by a phase of rehabilitation and restoration of order in various provinces. Egypt was eventually reunified within a new paradigm of kingship. The process of recovery depended on capable provincial administrators, the deployment of the idea of justice, irrigation projects, and an administrative reform.

Mesopotamia

The aridification of Mesopotamia may have been related to the onset of cooler sea surface temperatures in the North Atlantic (Bond event 3), as analysis of the modern instrumental record shows that large (50%) interannual reductions in Mesopotamian water supply result when subpolar northwest Atlantic sea surface temperatures are anomalously cool. The headwaters of the Tigris and Euphrates Rivers are fed by elevation-induced capture of winter Mediterranean rainfall.

The Akkadian Empire—which in 2300 B.C. was the second civilization to subsume independent societies into a single state (the first being ancient Egypt at around 3100 BC) —was brought low by a wide-ranging, centuries-long drought. Archaeological evidence documents widespread abandonment of the agricultural plains of northern Mesopotamia and dramatic influxes of refugees into southern Mesopotamia around 2170 BC. A 180-km-long wall, the "Repeller of the Amorites," was built across central Mesopotamia to stem nomadic incursions to the south. Around 2150 BC, the Gutian people, who originally inhabited the Zagros Mountains, defeated the demoralized Akkadian army, took Akkad, and destroyed it around 2115 BC. Widespread agricultural change in the Near East is visible at the end of the third millennium BC.

Resettlement of the northern plains by smaller, sedentary populations occurred near 1900 BC, three centuries after the collapse.

Arabian peninsula

In the Persian Gulf region, there is a sudden change in settlement pattern, style of pottery and tombs at this time. The 22nd century BC drought marks the end of the Umm al-Nar period and the change to the Wadi Suq period.

China

The drought may have caused the collapse of Neolithic Cultures around Central China during the late third millennium BC. At the same time, the middle reaches of the Yellow River saw a series of extraordinary floods. In the Yishu River Basin, the flourishing Longshan culture was hit by a cooling that made the paddies shortfall in output or even no seeds were gathered. The scarcity in natural resource led to substantial decrease in population and subsequent drop in archaeological sites. About 4000 cal. yr BP the Longshan culture was displaced by the Yueshi culture which was relatively underdeveloped, simple and unsophisticated.

In Egypt, the local, linguistically Coptic Dynasty of Pharaohs was replaced not long after the 4.1 kiloyear event with foreign Semitic Hyskos Pharaohs for a brief period, after which an indigenous Egyptian dynasty was restored to power.

Bronze Age Collapse aka the 3.2 ka climate event

The next historical period in which geographically widespread collapses of civilization and cultural shifts appear is Bronze Age Collapse ca. 1200 BCE which is manifest from at least Anatolia and the Eastern Mediterranean to Western Europe.  This too appears to have roots in a climate event, although not as severe a climate event as the 8.2 kiloyear event, 5.9 kiloyear event, and 4.1 kiloyear event.  Still, a 300 year drought of the kind apparently experienced during the Bronze Age collapse, is no small thing.

The Iron Age really takes off a few centuries after Bronze Age collapse.  This appears to be when Celtic, Italic and Germanic Indo-European languages and cultures appear on the scene in Western and Northern Europe.  The Philistines and the Jewish people arrive in the Southern Levant.  The classical Greek city-states emerge in the Aegean and Greek colonies are established in Italy and Iberia.  The city of Rome is founded.  The non-Indo-European Etruscans are simultaneously establishing themselves in Tuscany.  The second intermediary period ends in Egypt, and pagan Persian princes flourish until Alexander of the Great conquers them and Hellenizes them.

But, this late transition arising from what may have been a less severe climate event than the other discussed in this post, does not appear to have produced a dramatic population genetic transition in Western Europe.

Afro-Asiatic Linguistic Origins From Historic and Linguistic Perspectives

The Afro-Asiatic languages are one of the major language families in existence today. Its main subfamilies are Semitic (e.g. Arabic, Hebrew, Aramaic (Levant), Ahmaric (Ethiopia), Maltese), Chadic (most Hausa, the language of a group of Sahel peoples who were traditionally pastoralists), Berber (particularly Tuareg, a group of North African pastoralists), Cushitic (generally in the vicinity of Ethiopia, Eritrea, and Somalia), Omotic (a small language family spoken in a small area on the Western fringe of the Cushitic area), and Coptic (once the language of ancient Egypt, now a liturgical language of Coptic Christians).

This language family includes some of the oldest languages attested in writing.

The ancient Semitic Akkadian language and related dialects just documented in the Assyrian Dictionary completed this year has a rich written record dating back to around 2500 BCE. The Phoenicians who produced the predecessor to the modern Roman alphabet had a Semitic language, as did the Punic peoples spoke Semitic languages.

Coptic is the second oldest attested written language with hieroglyphs using it dating back to before 3000 BCE. Coptic writing is know to have existed at least five hundred years earlier than the earliest Akkadian writing.

Reconstructions of proto-Afro-Asiatic languages suggest origins at least as late as the Neolithic and probably Cacholithic (i.e. copper age).

One of the oldest cities known to the archaeological record, Jerico, is in the heartland of the Semitic linguistic area.

We know that the Egyptian Neolithic started around 6000 BCE, a couple of thousand years after it began in the Fertile Crescent from which the Egyptian Neolithic derived. One of the notable Egyptian specific contributions was the domestication of the donkey. It is plausible to think that languages and food production technology spread together as part of an overall Neolithic culture expansion (with and/or without a demic component) from the Fertile Crescent. Much of the Levant was subject to Egyptian political dominance for centuries during the Bronze Age.

A story of Afro-Asiatic language family expansion linked to food production technology is somewhat complicated by the fact that agriculture was developed independently in the Sahel with a set of crops different from those of the Fertile Crescent. But, there is less than a perfect consensus regarding when this happened. Some sources seem to indicate that it arose roughly contemporaneously with Fertile Crescent agriculture, while some indicate that it happened much later. It is possible that Sahel agriculture was made possible, in part, by the arrival of domesticated animals from the Fertile Crescent Neolithic complex.

At any rate, it is not necessarily the case that Fertile Crescent agriculture was the sole source of food production technology in Africa. Ethiopia was also an innovator with a number of crop domestications of its own (e.g. coffee and certain local grains), but the timing of these domestications is fuzzy, although Ethiopian domestications were probably later than those in the Fertile Crescent and those of the Sahel.

Sahel crop domestication is tempting to associate with the development of the Niger-Congo languages.

Likewise, tropical food production can be associated pretty strongly with the later Bantu expansion (the largest subset of the Niger-Congo languages) and perhaps also with Austonesians who brought foods of Indonesian origin, like the bananna, with them across the Indian Ocean, and provided one of the main source populations of Madagascar.

All of this evidence suggests that linguistically, one theory that makes sense would be one in which the Afro-Asiatic languages have their roots either in Egypt or the Levant and spread with herding and/or farming from there. Egypt's dominion extended roughly to modern day Lebanon when it met its northern most match with the Hittites (the first historically attested linguistically Indo-European polity of any consequence in Anatolia).

Egypt's influence and trade connections also extended as far south as Ethiopia and Uganda. We have only a little information about the origins of non-Semitic, non-Coptic Afro-Asiatic languages. Archaeological cultures based on old pots and bones and tools have been described in the regions where these languages are spoken, although often not with the same level of detail as contemporaneous archaeological cultures of Europe, Asia and the Middle East. We have ancient Egyptian documents. The Egyptians described three kingdoms to the South of them: Cush, Punt and Yam, and described in detail the goods that they acquired from each.

There are Egyptian documents describing official delegations sent at least as far west as Lake Chad. Some historians of religion argue that the geography of the mythical Egyptian land of the dead corresponds to that of the Lake Chad region that this delegation describes, which is to towards the setting sun from the Nile basin, where Egyptian mythology would have expected the land of the dead to be located.

There is very little evidence, however, to suggest that Afro-Asiatic languages were ever spoken in Anatolia or that they were spoken in Mesopotamia prior to the arrival of Akkadian, although there are a handful of apparently Semitic root words in some of the oldest Sumerian documents, and some of the oldest cave wall art of the Caspian Sea region does depict boats that look very much like Egyptian ones in design.

There is likewise no evidence to support the possibility that Afro-Asiatic languages ever spread beyond the Mesopotamian plain. The Elamite language spoken in Persia in the time of Alexander's reign appeared to show no Afro-Asiatic influences.

I am not aware of any really good studies that pin down the strength and depth of the relationship between Coptic and Akkadian, the oldest written versions of two of the main Afro-Asiatic language families, for which there is the most suggestive evidence to support a case that one is the oldest Afro-Asiatic language family.

Even if the Afro-Asiatic languages originated in the Middle East (e.g. in Jerico, the oldest city known to mankind), it is entirely possible that all known Afro-Asiatic languages, including Semitic, are derivative of Coptic and that any earlier Fertile Crescent Afro-Asiatic languages died before they were noted in any historical records.

Tonality

Tonal languages appear in the Omotic, Chadic, and Cushitic branches of Afroasiatic, according to Ehret (1996). As a prior post today noted, there is also an mtDNA L3 subhaplogroup connection between Chadic and Cushitic populations (that study probably didn't have an Omotic sample at all).

The Semitic, Berber, and Egyptian branches do not use tones phonemically.

How much weight to give to this tonality is hard to say. There is a fair amount of circumstantial evidence, when you look at patterns of semantic tone use globally in all sorts of languages, to suggest that tonality is more of an areal feature than it is an indicator of the ancestral source of a language. Neighboring languages that come from different families often share the feature of semantic tonality, while languages within the same language family often differ in their use of semantic tonality.

There have also been suggestions that tonality is part of a total phoneme set for a language and should be looked at as part of an evaluation of points like a languages consonant and vowel and click inventory. There are also been suggestions that the local climate and ecology can make certain phoneme sets better in some places than in others, that the nature of one part of a phoneme set influences the nature of other parts of the phoneme set, and that there are specific non-random factors that favor particular subtypes of phonemes in particular conditions.

Still, ultimately, a point of similarity between two languages is still a point of similarity and tends to indicate some connection between the two of some kind, and points of dissimilarity between two languages still tends to indicate a separation for some reason. Certainly, the fact that Chadic languages and Cushitic languages sometimes both have semantic tone, while Berber and Coptic and Semitic languages do not, does not hurt the argument that Chadic and Cushitic languages might have broken off from each other later than they broke off from other Afro-Asiatic languages.

North Semitic Languages

Akkadian and the related language Eblamite, appear to have their origins in the North Levant before becoming predominant in the formerly Sumerian language speaking Mesopotamian area which retained Sumerian as a liturgical language until about 100 CE, but made its first conversion to Akkadian around 2000 BCE (and later reverted temporarily to a non-Semitic language during a period of Kassite rule).

The Hebrew Bible doesn't really connect with historical accounts until the Iron Age. For example, the Philistines don't arrive in the Levant until around 1180 BCE (they were exiles from Mycenean Greece during Bronze Age collapse and were one of the "Sea Peoples"). The Biblical date for the arrival of the Jewish people in Egypt (using the Biblical estimate of 430 years from Jospeh to Exodus) roughly coincides with the rule of Egypt by Semitic Hyksos foreigners. Some of the oldest stories in the Bible, such as the Garden of Eden, Noah's flood, and the story of Moses, have well documented earlier strong parallels or geographic links to the Sumerian mythology of Mesopotamia. Hebrew is by most linguistic accounts one of the youngest branches of the Semitic language tree and Arabic is one of its closet linguistic relative, among language both living and dead.

Ethio-Semitic Languages

Linguists have pointed to all of the Ethio-Semitic languages within the Semitic language family arising from the introduction of a single proto-Ethio-Semitic language, probably from southern Arabia and have dated its rapid diversification in Ethiopia and Eritrea to around 800 BCE, although linguistic methods for dating the origin of languages is far from an exact science.

The oldest extant Ethiosemitic language is Ge'ez which survives primarily as a liturgical language of Ethiopian Orthodox Christians, Ethiopian Catholics and Beth Israel Jews. As noted in the link to Wikipedia above:

The Ge'ez language is classified as a South Semitic language. It evolved from an earlier proto-Ethio-Semitic ancestor used to write royal inscriptions of the kingdom of Dʿmt in Epigraphic South Arabian. Ge'ez language is no longer thought, as previously assumed, to be an offshoot of Sabaean or Old South Arabian, and there is linguistic evidence of Semitic languages being spoken in Eritrea and Ethiopia since at least 2000 BC.

However, the Ge'ez alphabet later replaced Epigraphic South Arabian in the Kingdom of Aksum (Epigraphic South Arabian letters were used for a few inscriptions into the 8th century, though not any South Arabian language since Dʿmt). Early inscriptions in Ge'ez and Ge'ez alphabet have been dated to as early as the 5th century BC, and in a sort of proto-Ge'ez written in ESA since the 8th century BC. Ge'ez literature properly begins with the Christianization of Ethiopia (and the civilization of Axum) in the 4th century, during the reign of Ezana of Axum.

The oldest surviving Ge'ez manuscript is thought to be the 5th or 6th century Garima Gospels.

Almost all texts from this early "Aksumite" period are religious (Christian) in nature, many of them translations from Greek, Syriac, Coptic, and later also Arabic. The translation of the Christian Bible was undertaken by Syrian monks known as the Nine Saints, who had come to Ethiopia in the 5th century fleeing the Byzantine persecution of the Monophysites. The Ethiopic Bible contains 81 Books; 46 of the Old Testament and 35 of the New. A number of these Books are called "deuterocanonical" (or "apocryphal" according to certain Western theologians), such as the Ascension of Isaiah, Jubilees, Enoch, the Paralipomena of Baruch, Noah, Ezra, Nehemiah, Maccabees, Moses and Tobit. The Book of Enoch in particular is notable since its complete text has survived in no other language.

Also to this early period dates Qerlos, a collection of Christological writings beginning with the treatise of Saint Cyril known as Hamanot Rete’et, or De Recta Fide, the theological foundation of the Ethiopic Church. Another work is Ser'ata Paknemis, a translation of the monastic Rules of Pachomius. Non-religious works translated in this period include Physiologus, a work of natural history also very popular in Europe.

The Kingdom of D'mt from around 700 BCE to 400 BCE in Eritrea and northern Ethiopia had a succession of about four kings (or possibly four dynasties), and was notable for its irrigated farming, plows, millet, and iron age technology. It collapsed into multiple successor states in different regions that were reunited into the Kingdom of Axum starting before 100 CE and lasting until around 960 CE.

One study links Ethio-semitic to Y-DNA haplogroupJ1c3 and there are distinguishable population genetic differences between Ethio-semitic linguistic populations and Cushitic and Omotic linguistic populations that indicate recent Eurasian admixture to a greater degree in Ethio-semitic populations.

The Baysean estimate of 860 BCE for a common Ethio-semitic, which roughly corresponds to proto-Ge'ez, is probably too young.

Cushitic and Omotic Languages

It is tempting to see the trade relationships of Egypt with these regions as the source of the Cushitic and Omotic languages (with Omotic possibly showing a mix of Nilo-Sharan languages such as Maasi, and Cushitic influence on the Cushitic fringe).

Records of trade expeditions to Punt seem to be a reasonable good fit for Somolia or Lake Albert, had a long running and strong trading relationship with Egypt (myhrr was one of its major exports), and trade with it is attested as far back as the 25th century BCE in Egyptian records (and probably dates back centuries earlier). So, Punt was a Kingdom that probably pre-dated the appearance of Ethio-Semitic languages in Africa and may have been a place where early Cushitic languages were spoken.

Yam appears to be a reasonably good fit for Northern Uganda and was a source for many animals and products associated with tropical Africa. Yam may also have been a major source of copper for Egypt, and in one instance was noted a the Kingdom from which a pygmy individual was brought to Memphis in Egypt.

Indeed, all of the presents attributed to the "Wise Men" in the Nativity story (gold, frankincense and myhrr) could reasonably have come from Punt and Yam, which are black African countries.

Cush was probably north of Punt and Yam and while being South of Nubia (in present day Sudan).

Berber languages

It is tempting to associate the Berber languages with the arrival of pastoralism from Egypt to the region. But, Berbers are genetically distinct from Arabs and Egyptians and show considerable genetic continuity with pre-Neolithic North African hunter-gatherers.

Chadic languages

Chadic languages may be appropriate to associate with the appearance of pastrolist, ceramic cultures that appeared in the region where they are now spoken around 4000 BCE.

There are a few references that seem to be to ancient Egyptian expeditions to Lake Chad, but there does not appear to have been regular, robust trade between Egypt and Chadic peoples in the same way that there as to Kingdoms like Punt and Yam. Some linguistics have hypothesized, however, that Chadic and Cushitic are part of the same branch of the Afro-Asiatic languages with a common linguistic origin in a single proto-language.

Paleoclimate

A 2010 paper by Cruciani, et al., has a nice summary of the Paleoclimatic factors in the Sahara against which the historical migrations and expansions would have played out (citations included):

Over the past thousands of years, the Sahara has undergone dramatic climatic oscillations including arid phases, during which it was largely uninhabitable, and humid episodes, which transformed the desert into a fertile landscape.1 After a hyper-arid period about 23–14.5kya, the Saharan region experienced a monsoonal moist climate, characterized by increased rainfall.2, 3 During the Holocene Climatic Optimum (about 10–5kya), a few thousand years after the beginning of the humid period, flora and fauna repopulated the desert, and a mosaic of savannah and woodland became well established throughout much of the Sahara.3 At the same time, the Sahara was home to giant lakes,4 the largest of which, the paleolake Megachad, may have possibly covered an area of at least 400000km2, more than the Caspian Sea, the biggest lake on earth today.5 This greening scenario was interrupted by a number of arid episodes, and at about 5–6kya, the region experienced a rapid onset of dryer conditions. These marked the beginning of a shift towards permanent aridity, with variations in the distribution and timing of these changes between the eastern and central/western Sahara.3 Human–environment interactions in the Sahara have been greatly influenced by these climate fluctuations.1

Close links between climatic variations and prehistoric human occupation of the Sahara during the early mid Holocene (10–5kya) are documented by archeological6, 7, 8 and paleoanthropological9, 10 evidence.

1.Brooks N, Chiapello I, Di Lernia S, et al. The climate-environment-society nexus in the Sahara from prehistoric times to the present day. J North Afr Stud. 2005;10:253–292.
2.Talbot MR. Late Pleistocene rainfall and dune building in the Sahel. Palaeoecol Afr. 1983;16:203–213.
3.Burroughs WJ. Climate Change in Prehistory. The End of the Reign of Chaos. Cambridge University Press: Cambridge; 2005.
4.Damnati B. Holocene lake records in the northern hemisphere of Africa. J Afr Earth Sci. 2000;31:253–262.
5.Drake N, Bristow C. Shorelines in the Sahara: geomorphological evidence for an enhanced monsoon from palaeolake Megachad. Holocene. 2006;16:901–911.
6.Breunig P, Neumann K, Van Neer W. New research on the Holocene settlement and environment of the Chad Basin in Nigeria. Afr Archaeol Rev. 1996;13:111–145.
7.Huysecom E, Ozainne S, Raeli F, Ballouche A, Rasse M, Stokes S. Ounjougou (Mali): a history of Holocene settlement at the southern edge of the Sahara. Antiquity. 2004;78:579–593.
8.Kuper R, Kröpelin S. Climate-controlled Holocene occupation in the Sahara: motor of Africa's evolution. Science. 2006;313:803–807.[PubMed]
9.Tafuri MA, Bentley RA, Manzi G, Di Lernia S. Mobility and kinship in the prehistoric Sahara: strontium isotope analysis of Holocene human skeletons from the Acacus Mts. (southwestern Libya) J Anthropol Archaeol. 2006;25:390–402.
10.Sereno PC, Garcea EAA, Jousse H, et al. Lakeside cemeteries in the Sahara: 5000 years of Holocene population and environmental change. PLoS One. 2008;3:e2995. [PMC free article][PubMed]

Were The Post-Holocene Arid Period Gobero People Chadic?

The abstract of the paper in footnote ten (also free access) provides (headings omitted) that:

Approximately two hundred human burials were discovered on the edge of a paleolake in Niger that provide a uniquely preserved record of human occupation in the Sahara during the Holocene (~8000 B.C.E. to the present). Called Gobero, this suite of closely spaced sites chronicles the rapid pace of biosocial change in the southern Sahara in response to severe climatic fluctuation.

Two main occupational phases are identified that correspond with humid intervals in the early and mid-Holocene, based on 78 direct AMS radiocarbon dates on human remains, fauna and artifacts, as well as 9 OSL dates on paleodune sand.

The older occupants have craniofacial dimensions that demonstrate similarities with mid-Holocene occupants of the southern Sahara and Late Pleistocene to early Holocene inhabitants of the Maghreb. Their hyperflexed burials compose the earliest cemetery in the Sahara dating to ~7500 B.C.E.

These early occupants abandon the area under arid conditions and, when humid conditions return ~4600 B.C.E., are replaced by a more gracile people with elaborated grave goods including animal bone and ivory ornaments.

The principal significance of Gobero lies in its extraordinary human, faunal, and archaeological record, from which we conclude the following:

1.The early Holocene occupants at Gobero (7700–6200 B.C.E.) were largely sedentary hunter-fisher-gatherers with lakeside funerary sites that include the earliest recorded cemetery in the Sahara.
2.Principal components analysis of craniometric variables closely allies the early Holocene occupants at Gobero with a skeletally robust, trans-Saharan assemblage of Late Pleistocene to mid-Holocene human populations from the Maghreb and southern Sahara.
3.Gobero was abandoned during a period of severe aridification possibly as long as one millennium (6200–5200 B.C.E).
4.More gracile humans arrived in the mid-Holocene (5200–2500 B.C.E.) employing a diversified subsistence economy based on clams, fish, and savanna vertebrates as well as some cattle husbandry.
5.Population replacement after a harsh arid hiatus is the most likely explanation for the occupational sequence at Gobero.
6.We are just beginning to understand the anatomical and cultural diversity that existed within the Sahara during the Holocene.

The climate sequence described is suggestive of an association of the Chadic populations with the newcomers ca. ~5200-4600 B.C.E. who repopulated Gobero in Niger after the mid-Holocene arid period in the Sahara abated.

This time frame is particularly attractive because it is the most recent case of clear population replacement in the archaeological record in the Sahel, where the Chadic language speaking people are found, until the recent historic period. Similarly, early time frames are unattractive, because they are not in clear population continuity with modern populations, and because the population genetics of the Chadic people, mentioned in a separate post, are suggestive of a population that was intrusive to the region.

This date is also not too far out of line with the estimated split between Y-DNA haplogroups R1a and R1b, which is the timeframe that one would expect from a basal branching off from European R1b haplogroups.

In contrast, the Sahara's Holocene Climatic Optimum seems more plausible to associate with the emergence of the Niger-Congo language speaking people who would be displaced to the South in order to maintain their lifestyle as the Sahara aridified, and their Sahel agriculture. The current population of the Sahel shouldn't overlap too much with the pre-mid-Holocene arid period population there. The Niger-Congo linguistic community, unlike the Chadic linguistic community, also doesn't show clear signs of Eurasian genetic links.

The Gobero People's Contemporaries In Egypt

The Neolithic revolution appears in Egypt around 6000 B.C.E. and the Egyptian historic record goes back to about 3100 B.C.E., so these dates would be in a pre-historic period in Egypt, after it had adopted farming and herding, but before it had adopted writing.

Specific, the possibly proto-Chadic people at Gobero would be at the tail end of the Faiyum A culture in Egypt (ca. 6000 B.C.E. to 5000 B.C.E.). As Wikipedia explains regarding this culture:

Continued desiccation forced the early ancestors of the Egyptians to settle around the Nile more permanently and adopt a more sedentary lifestyle. The period from 9000 to 6000 BC has left very little in the way of archaeological evidence. Around 6000 BC, Neolithic settlements appear all over Egypt. Studies based on genetic, and archaeological data have attributed these settlements to migrants from the Fertile Crescent returning during the Egyptian and North African Neolithic. However, some morphological and post-cranial data has linked the earliest farming populations at Fayum, Merimde, and El-Badari, to local North African Nile populations.* The archaeological data suggests that Near Eastern domesticates were incorporated into a pre-existing foraging strategy and only slowly developed into a full-blown lifestyle, contrary to what would be expected from settler colonists from the Near East. Finally, the names for the Near Eastern domesticates imported into Egypt were not Sumerian or Proto-Semitic loan words, which further diminishes the likelihood of a mass immigrant colonization of lower Egypt during the transition to agriculture.

Weaving is evidenced for the first time during the Faiyum A Period. People of this period, unlike later Egyptians, buried their dead very close to, and sometimes inside, their settlements.

Although archaeological sites reveal very little about this time, an examination of the many Egyptian words for "city" provide a hypothetical list of reasons why the Egyptians settled. In Upper Egypt, terminology indicates trade, protection of livestock, high ground for flood refuge, and sacred sites for deities.

* The sources cited for this statement are: Smith, P. (2002) The palaeo-biological evidence for admixture between populations in the southern Levant and Egypt in the fourth to third millennia Bce. u: Egypt and the Levant: Interrelations from the 4th through the Early 3rd Millennium BCE, London-New York: Leicester University Press, 118-128; Keita, S.O.Y. (2005) "Early Nile Valley Farmers from El-Badari: Aboriginals or "European" Agro-Nostratic Immigrants? Craniometric Affinities Considered With Other Data". Journal of Black Studies, Vol. 36 No. 2, pp. 191-208; and Kemp, B. 2005 "Ancient Egypt Anatomy of a Civilisation. Routledge. p. 52-60.

Or, it could have coincided with the early part of the Merimde culture of Egypt (ca. 4800 B.C.E. to 4200 B.C.E.) which appears to have been derived from the Faiyum A culture. But, the funerary practices of the Merimde culture seem entirely unlike those described in the post-arid period people at Gobero. The Merimde people did not have cemetaries or have grave goods, both of which were distinctive aspects of the Gobero burials that were unearthed.

Gobero doesn't have metal artifacts, which would suggest that any Egyptian links may have predated the dawn of the copper age in Egypt ca. 4400 B.C.E. Timewise and based on geography, the Tasian culture of Upper Egypt, ca. 4500 B.C.E. coincides pretty closely with the emergence of post-arid period populations at Gobero.

The post-arid period people at Gobero would seem to predate the Badari culture of Egypt (4400 B.C.E. to 4000 B.C.E. and possibly as far back as 5000 B.C.E.) which is the first one in which direct evidence of agriculture is found. Given that the Badari culture showed strong signs of influences from the Western Desert, it isn't impossible that the Chadic people could have been an important source for the Badari culture, rather than visa versa.

The Gobero People's Contemporaries In The South Levant

The contemporaneous archaeological culture of the South Levant is called the Pottery Neolithic (see also here) and conventionally dated from about 5500 B.C.E. to 4500 B.C.E.

The Gobero People's Contemporaries In Europe

The contemporaneous archaeological cultures in Europe are the Linear Pottery Culture and late Cardium Pottery culture. Thus, this would envision the Chadic people as appearing in the African Sahel around the same time that the Fertile Crescent Neolithic spread to Europe, but in an expansion that was much less dominant in Africa than its European counterparts, presumably because the Fertile Crescent package was nearing its geographic extreme of usefulness there and because the Fertile Crescent package had competition from an indigeneous Sahel Neolithic associated with the Niger-Congo language family there.

The Chadic people may have had less local admixture, particularly patriline local admixture, than other Afro-Asiatic peoples, because the mid-Holocene arid period had left them with a largely vacant region of land to repopulate, while Neolithic migrants bearing the Fertile Crescent package elsewhere in the Afro-Asiatic region may have had to compete with proto-Neolithic populations that had sedentary fishing, hunting, pottery, jewelry, and perhaps even the gathering of pre-domesticated plant that were tended to some extent. Thus, an absence of early populations to dilute them could partially account for Chadic genetic distinctiveness.

However, the parallels between the Chadic arrival and the European early Neolithic shouldn't be overstated, because the Chadic mtDNA signature is closer to that of the Cushitic people than it is the early Neolithic populations of Europe.