Update on Investigation into the "Mysterious" EpiPaleolithic Maghrebi Remains!

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Introduction

This entry is supposed to serve as an update and add-on to a blog entry that was first published here back in May 5th, 2010, under the heading, An Investigation into the "Mysterious" Mesolithic Maghrebi populations. The arguments made there—in the main, are still quite sound, but over the years, some DNA-assignment shuffling within the reconstructed human mtDNA phylogenetic network had taken place. This sort of thing happens quite a bit in the field of molecular genetics, usually in the form of either changing the phylogenetic location of a newly identified clade or a preexisting one, and/or renaming entire clades with new naming schemes, since researchers tend to see information about larger phenomena in the form of fragments. As such, sometimes previous information (source material), especially on newly identified clades, becomes obscure or rarer. To address a situation such as this, in the few occasions where they may have occurred, this entry has revisited elements of the aforementioned entry, modify as necessary, or simply add to information previously posted. 

Unwinding the Convoluted Character of the Emergence of Imazighen Groups

The sequence of events involved in the genesis of the diversity that we see today in Imazighen groups is something that not only generates a considerable degree of interest, but also one that continues to challenge even the experts who've spent a good deal of their time in unwinding the archaeological, cultural and biological developments that accompanied the development of the Imazighen.

Amongst the Imazighen, perhaps the tawny-hued coastal northwestern groups draw in the most curiousity, in terms of their seemingly asymmetric sourcing of their gene pool—comprising of Y DNA, predominantly made up of autochthonous African markers, and mtDNA, in most cases made up of largely "Eurasian"-tagged markers—and the question of when they attained their apparent tawny or "light-skin" epidermal phenotype, in a continent dominated largely by 'dark skin' [of varying degrees] autochthonous groups. All sorts of rounds of rationalizing and speculation have taken place over the years, in efforts to explain what appears to be an anomaly of some sort to some, from tying contemporary Imazighens to the so-called Mecthoid (or supposed "Cro-Magnoid") types of the EpiPaleolithic and Neolithic era to being outright descendents of the likes of Vandals, Arabs or "Near Easterners", as opposed to being descendents of autochthonous Africans with genetic influence from groups that spent their evolutionary history outside of mainland Africa. None of these of course, have born out to be based on facts consistent with evidence. To take the "Mechtoid" example for instance, attempts had been taken by Eurocentric scholars to suggest that these were the ancestors of contemporary coastal northwest African Imazighen populations, by arguing for their supposed "caucasoid" cranio-facial phenotype, the supposed morphological link with the European Cro-Magnon specimens, and by typifying them as "Mediterranean caucasiod" types [See: Mechta and Afalou: Do they and the so-called "Mechtoids" constitute a type with the "Cro-Magnon"? and Mechta-Afalou and the so-called Mechtoids: Continued!]

At least one study states this: 

the most ancient, i.e. those from Taforalt in Morocco, Afalou-bou-Rhummel in Algeria and Singa in the Sudan, cannot be considered as being either Negro or San, whereas the later Jebel Sahaba sample (c. 12000 B.P.), the Wadi Halfa (c. 11950 - 6400 B.P.) and the Mechta-el-Arbi individuals (c. 8500 B.P.) and the Jebel Moya sample (c. 2950 - 2350 B.P.) are not significantly removed from the Negro populations. - Santiago Genovés

Bearing in mind those ages provided in that extract above, it should be noted that from DNA analysis, it has been implied that the Imazighen ("Berbers") ancestor emerged ca. 8.2 kya or so [Arredi et al. 2004] in northeast Africa; given this, the northwest African samples here [the Taforalt, Afalou-bou-Rhummel, and the Mechta-el-Arbi] are all too old to be associated with the contemporary Imazighen. The age given to the Mechta-el-Arbi specimens is the only one that comes close to any age associated with contemporary Imazighen speakers; but even here, it is questionable, given that Imazighen expansion in northwest Africa is dated even more recently than the upper end 8 kya time frame—that expansion dates to ca. 2.3 kya or so. The point is, although some find it tempting to associate the contemporary Imazighen with these EpiPaleolithic and Neolithic era northwest African specimens, available data suggest otherwise.

Speaking of DNA, skin pigmentation analysis suggest that "west Eurasian" contribution likely explains the coastal northwest African 'outlier' skin tones; granted, it is quite highly likely that coastal northwest African Imazighen would have still undergone *some* level of skin tone lightening, even if they weren't influenced by "west Eurasians", as they moved to the sub-tropical areas, especially in the Atlas mountain areas. This skin lightening event though, would have likely produced—at most—the level of skin tones seen in the likes of the San "Bushmen" and the KhoiSans. The UV radiation levels in the supra-tropical and sub-tropical regions of Africa are simply not as acute as those found in the even more northerly latitudes of Europe, Asia and elsewhere. Recalling on Norton et al (clickable), we have... 

"The frequency of the SLC24A5 111*A allele outside of Europe is largely accounted for by high frequencies in geographically proximate populations in northern Africa, the Middle East, and Pakistan (ranging from 62% to 100%)."

"The relatively high frequencies of the derived allele in Central Asian, Middle Eastern, and North Africa seem likely to be due to gene flow with European populations."

Which also doesn't rule out the probability of North Africans receiving some of their skin tone variations from so-called "Middle Easterners" as well.

Citing Rando et al. 1998 [mtDNA analysis of Northwest African populations reveals genetic exchanges with European, Near Eastern and sub-Saharan populations] along the way,...

Here is a theory: Shortly after their emergence ca. 8 ky ago or so, nomadic pastoralist Imazighen groups dispersed from where they emerged in eastern Sahara, likely in the region straddling Egypt and Sudan, and moved northward [and also possibly westward in the Sahara]. Here, they would come into contact with arriving Neolithic groups from the so-called Near East, who would have also included E-M78* carriers [along with Hg J carriers], which made its way to the “Near East” at an earlier time frame. Being nomadic, these E-M78* and E-M81 Imazighen carriers would have likely been male-biased; however, their dispersal may have included notably Hg M1 carriers from their point of origin, amongst other common L type mtDNA lineages common in north Africa. The incoming Hg J and returning Hg E carriers would have been accommodated by “Eurasian” tagged mtDNA markers that are generally common to Europeans and “Near Easterners”, along with those more commonly found in the “Near East”. These would have presumably included some, if not somewhat limited, European mtDNA markers radiated from Last Glacial Maximum refugium centers in the so-called Near East, likely radiated from the likes of Anatolia. The following might prove to be insightful, notwithstanding outdated constructs that the authors apply in the course of their analysis... 

A great number of the 99 L3E sequences in our sample from the Berbers and other Moroccans, West-Saharans, and Mauritanians seem to be of European descent in view of the numerous matches (more than one fourth) with European but not Near Eastern sequences. The average transitional distance to the nearest neighbours in the European/Near Eastern mtDNA pool is as low as .4, which would correspond to an age of 8000 years. The same figure is also obtained for the L3 sequences from the Algerian Berbers (Corte-Real et al. 1996)...

Some further Near Eastern mtDNA lineages, more similar to extant European lineages, might have come along from the Near East with the (or some) ancestors of the Iberomaurusians, but the bulk of them probably arrived in North Africa with the posterior Mesolithic and Neolithic waves. There is thus a caveat with the European appearance of North African mtDNAs: the same lineage types that came from the Near East and dispersed along the southern Mediterranean littoral around the Last Glacial Maximum (possibly spreading the Gravettian cultures) or after the Younger Dryas (bringing the Neolithic) may also have taken the northern route along the Mediterranean sea. It is therefore difficult to establish at present a clear cut between European and Near Eastern mitochondrial lineages. Nevertheless, there is strong evidence for some European genetic input into North Africa, as for example testified by Haplogroups U5 (Richards et al. 1998) and V (Vandals, Portuguese and Spanish colonization).

The Neolithic hypothesis above seems like the more plausible scenario. And to exemplify the difficulty grappling researchers in unwinding the very complex history of the north African Imazighen,... 

In summary, the mitochondrial landscape of Northwest Africa appears to be quite complex, and cannot be studied in isolation from the European, Near Eastern or sub-Saharan mitochondrial background. Population affinity diagrams reflect essentially the north-south gradient, which is evident from cluster compositions, whereas sequence comparisons employing the mtDNA database reveal the traces in Northwest Africa of (1) Paleolithic settlement(s) before the Last Glacial Maximum, (2) Neolithic waves, and (3) migrations of northern Europeans (and possibly others, such as Phoenicians, Romans, Arabs, and Iberians) in historical times.

These multiregional influences may explain the partially conflicting interpretations of North African data, which emphasize indigenous development and European/West Asian affinity (Irish, 1197, 1998) and a clear relationship to Iberians in particular (Arnaiz-Villena et al. 1995) or disclaim specific relationships to Iberians (Comas et al. 1998) and significant (Neolithic) demic diffusion from the Near East (Barbujani et al. 1994; Bosch, et al. 1997). 

These same Neolithic groups would have found their way to southeast Europe and onto islands therein, like Crete. However, because the nomadic Imazighen groups now situated in the coastal areas of northeast Africa were male-biased and with small effective population size, their mixing with the females that came along the Neolithic groups would have given the appearance of substantial intermixing. However, these nomadic pastoralist Imazighen groups would have not been the type that would have allowed arriving Neolithic groups to dominate them. So, it would appear that instead, the Neolithic elements who intermixed with them, adopted the languages and other aspects of the nomadic Imazighen groups, while their Neolithic traditions continued to stay with them. Consequently, the nomadic Imazighen groups too would be influenced by those traditions, resulting in settlement moves amongst them, like those near the oasis on the western desert of the Nile Valley. This is where they’d have likely made initial efforts to settle before moving to the far western areas. By the bronze age Holocene period, it would appear that some coastal North Africans had spilled over to southeast European areas, with Crete being an example of that. Other Imazighen nomads spread through the length of the Sahara, likely mixing with other groups therein; and again, being male-biased, they would have picked up mtDNA gene pools of those other groups. This would explain the gradient that authors like Rando et al. observed: 

The mitochondrial data of the Northwest African populations (Berber from Morocco and Algeria, Moroccans, West-Saharans, Mauritanians, Tuareg) show a mosaic composition of mtDNA types, with a pronounced gradient of sub-Saharan lineages from north to south: at the one extreme, the Berbers from Morocco have a predominantly European (Iberian) affinity, while at the other extreme, the Tuareg are closely related to sub-Saharan West Africans as represented by several Senegalese groups in this study, whereas the West-Saharans and Mauritanians are somewhat intermediate. It is remarkable that the Tuareg bear little mitochondrial resemblance to the Berber populations, although they speak a Berber language. 

Hg U6 would have invariably been spread across the Sahara, with relative frequency peaks in the western end of it. At any rate, subsequent intrusions into north Africa, e.g. the likes of Phoenicians, the Greco-Romans or the Vandals, would have likely left a rather limited genetic imprint only in centers of foreign administration. It is quite plausible that much of the European-specific maternal lineages came around the historic periods after those epochs, as perhaps best indicated in one of the extracts above, when the author said: "(3) migrations of northern Europeans (and possibly others, such as Phoenicians, Romans, Arabs, and Iberians) in historical times." On the other hand, when the authors said, "sequence comparisons employing the mtDNA database reveal the traces in Northwest Africa of (1) Paleolithic settlement(s) before the Last Glacial Maximum", they were likely alluding to the likes of the autochthonous north African marker of U6, which at any rate, generally comprise a relatively smaller portion of the Imazighen mtDNA gene pool. It is not clear if much earlier contacts with the likes of Cretans would have contributed to Imazighen gene pool in a substantial way, but it’s certainly possible that some degree of genetic exchange with elements therein had resulted in a portion of mtDNA gene pool spilling into north Africa, perhaps by groups returning with African ancestry. Anyway, this could very well also have contributed to the frequency of seemingly European-specific mtDNA. Contact between Cretan inhabitants and north Africans have been spoken about on many occasions, and even implicated in images of antiquity, like the example below:

The characters with frizzy-looking hair—although with the resolution of the image above, it is rather difficult to ascertain—are said to be north Africans. Other images from the Minoans seem to invoke a considerably heterogenous or "mixed" people; the following are photographs of images on Minoan sarcophagi...

Sarcophagus portion #1:

 
Sarcophagus portion #1 blown up below:




 
Sarcophagus portion #2 blown up below:

In ancient Egyptian artwork:

In ancient Egyptian art, the first group to their western desert—in an area now dominated by Imazighen speaking populations—that *tentatively appears on their records from the predynastic era onwards, are the "Tjehenu/Tehenu"; these people were generally painted in dark hue as the Egyptians themselves were. In the old Dynastic era, one comes across another group of people in the western desert area of the Nile Valley; they were presumably referred to as the "Tjamahu/Tamahu". These latter group of people were generally depicted in the light-skin tone, in a manner not different from the Aamu, generally known by many as "Asiatics". The "Tehenu" were presumably located in the coastal areas on the western desert region, while the "Tamahou" were presumably located in the more southward areas of the western desert. The latter were generally depicted sporting interesting body tattoos, and feather head gear. There are also other groups attested to in the western desert areas; namely the "Meshwesh/Mashawash" and the "Libu/Lebu (Ribu/Rebu)", notably mentioned in the New Kingdom era [see Merneptah stele for example], in the Rameside period. Any group here or any combination of these groups may have been ancestors of the contemporary north African Imazighen. Below, is a repro of a wall relief depicting what appears to be a "Meshwesh" figure under captive, and other figures from the western desert areas, possibly the "Tjamahu" (Tamahu/Tamahou)...

 

A curious feature though about the Minoan art, is the seeming consistent [though not necessarily exclusively] depictions of the male figures in dark hue, with some being even in plain black tone; this seems to be the case in the ancient Egyptian example below, and the Minoan painted counterpart underneath that...

Below, is an occasion showing individuals in plain black hue...


Relaxing on visual aids, and resuming our theory at hand...

With substantial gene flow from European maternal gene pool in the historic period, it’s likely that some of the older Eurasian mtDNA markers may have experienced unfavorable genetic drift, lowering their relative frequency. Likewise, genetic drift may have worked favorably for the more historic European markers from the Iberian peninsula. Though not exclusively, the following examples of historic events must have surely had their own role to play, in contributing to coastal northwest African gene pool,...

 
Trafficking of women from the other side of the Mediterranean sea as slaves surely must have left its own mark. Then there were also sudden waves of migration to the north African coast during the fall of direct northwest African rule in the Iberian peninsula; no doubt families who reached the north African coast had left some genetic imprint therein. And of course, again, genetic drift has its own role to play in all this.

All that aside, a look at samplings so far undertaken in coastal northwest Africa suggests that these have generally relied on sampling small, scattered populations [see Cherni et al. 2005], giving fragmented or incomplete picture of northwest African maternal gene pool structure.
________________________________________________________________
*References:

— As noted in the paragraphs.

'*' corresponds to record that was/is taken into consideration with regards to the Tjehenu/Tehenu. For instance, the "Tehenu" Palette was subsequently discussed here: The So-called Tehenu Palette

An Analysis of "The Dawn of Human Matrilineal Diversity"

The authors of the recent study titled "The Dawn of Human Matrilineal Diversity" suggest that the divergence of the immediate ancestors of contemporary KhoiSan groups from a common ancestral maternal gene pool—shared with "non-KhoiSan" African groups—couldn't have occurred later than 90,000 years bp, and place the upper bound of this 'split' at a time range of 140,000-210,000 years bp. The goal here, would be to put this observation to test.

First, a few things to straighten out:

D. M. Behar et al. 2008 say...

A more recent geographically restricted enrichment of the African maternal gene pool was shown to have occurred during the early Upper Paleolithic, when populations carrying mtDNA clades M1 and U6 arrived to north and northeast Africa from Eurasia, hardly penetrating the sub-Saharan portion of the continent, except Ethiopia.

This goes back to that very questionable proposition about the African lineages of U6 and M1 being of Eurasian origin, when there is very little evidence to support such—the issue was discussed in detail here:

Mitochondrial DNA M1 haplogroup: A Response To Ana M. Gonzalez et al. 2007 [clickable link]

M1 and U6 are far from being Eurasian-derived lineages. Preponderance of evidence suggests otherwise, as briefed in the link above.

The authors are correct in noting that KhoiSan groups are notable for bearing the deepest clades of contemporary human gene pool; they however, make it seem as though—if only subtly—that the KhoiSans hold the distinction of being "unique" in this regard, when in fact, there are several other African groups who share this distinction. To quote them:

Early studies based on mtDNA control region variation have suggested that KhoiSan divergence dates to an early stage in the history of modern human, whereas their anthropological and linguistic features show closer affinities to each other than to those of other populations in Africa. 21,22 Their distinctiveness is also supported by phylogenetic studies of the male-specific Y chromosome that indicate that the most basal branch of the Y phylogeny is now common among the KhoiSan but is rare or absent in other populations.18 — D. M. Behar et al. 2008

It is a matter of fact that the most basal clades of the Y chromosome are variably distributed across the continent, but with the highest frequencies thus far observed in parts of eastern Africa—as the case is in Sudan and Ethiopia for example, central Africa—as noticed in "pygmy" groups, and yes, in Southern Africa—as found in KhoiSans. From the standpoint of Y chromosome markers, the most basal clades constitute haplogroups like A-M91, B-M60, followed by M168 [designated as haplogroup CT elsewhere], which in the main, also hold the distinction of being quite rare or absent outside of continental Africa.

Additionally, from the citation above, the authors make a link between the basal nature of maternal markers in KhoiSan groups and that of Y chromosome markers:

Early studies based on mtDNA control region variation have suggested that KhoiSan divergence dates to an early stage in the history of modern human,...Their distinctiveness is also supported by phylogenetic studies of the male-specific Y chromosome...

...and indeed, many other papers have indicated that male-specific markers that are characterized as being 'aboriginal' to KhoiSan groups, as opposed to reflecting relatively more recent gene flow from non-KhoiSan groups, tend to be of the basal subtypes that feature considerable microsatellite STR cluster diferences from those of other African groups notable for those same 'basal branches' of Y phylogeny—indicating considerable time of separation between Khoisans and non-neighboring extra-KhoiSan groups. For example...

The paragroup E-M35* has been observed at high frequencies in both eastern (10.5%) and southern (15.2%) Africa,...

... extensive interpopulation E-M35* microsatellite diversity (fig. 2A) between Ethiopians and Khoisan indicates that eastern Africans and Khoisan have been separated for a considerable period of time, as has been suggested elsewhere (Scozzari et al. ¹⁹⁹⁹; Cruciani et al. ²⁰⁰²; Semino et al. ²⁰⁰²). — Cruciani et al., 2004 [1]

...and, from Semino et al.:

The present study reveals that (1) only the Ethiopians share with the Khoisan the deepest human Y-chromosome clades (the African-specific Groups I and II) but with a repertoire of very different haplotypes; (2) most of the Ethiopians and virtually all the Senegalese belong to Group III, whose precursor is believed to be involved in the first migration out of Africa; and (3) the Ethiopian Y chromosomes that fall into Groups VI, VIII, and IX may be explained by back migrations from Asia. The first observation confirms the ancestral affinity between the Ethiopians and the Khoisan, which has previously been suggested by both archaeological and genetic findings... — Semino et al. 2002

...and,

The remaining 37 E-M35* Y chromosomes were found mainly in Africa, with a high frequency in the Ethiopians and the Khoisan...The distribution of E-P2* appears limited to eastern African peoples. The E-M35* lineage shows its highest frequency (19.2%) in the Ethiopian Oromo but with a wider distribution range than E-P2*. Indeed, it is also found at high frequency (16.7%) in the Khoisan of South Africa (Underhill et al. ²⁰⁰⁰; Cruciani et al. ²⁰⁰²) (suggesting, once again, their ancient relationship with Ethiopians) and observed in southern Europe (present study). — Semino et al. 2004 [2]

...but Semino et al. 2002 note that:

In a previous study (Passarino et al. ¹⁹⁹⁸), the genetic structure of the Ethiopian population was investigated using mtDNA and some nonrecombinant Y-chromosome (NRY) markers previously studied in the Khoisan (Soodyall and Jenkins ¹⁹⁹²; Spurdle and Jenkins ¹⁹⁹²)... ...Although the mtDNA did not reveal a particular relationship between Ethiopians and the Khoisan, affinities were suggested by Y-chromosome analyses.

This is apparently attributable to 1) considerable time of separation, as noted, and 2) geographical structuring of markers due to localization after divergence. Hence, even though male-specific markers showed affinities between say, KhoiSan and Ethiopian samples, that were not as apparent in the mtDNA analysis mentioned, these markers too showed distribution and frequency patterns of visibly distinct [and hence polarizing] subtypes between the samples in question.

Semino et al. 2002 note:

Groups I and II are essentially restricted to Africans and appear to be the most divergent clades within the tree. They show a patchy distribution, with high frequencies among isolated hunter-gatherer groups and in some peoples of Ethiopia and Sudan...

...In particular, Group I, observed in 43.6% of the Khoisan (usually considered to be descendants of an early African population), is present in all of the Ethiopian samples...However, figure 1 shows that the Ethiopian and Khoisan samples within Group I fall into different haplotypes (haplotypes 1, 2, and 5 in Ethiopians vs. haplotypes 4, 6, and 7 in the Khoisan), in agreement with an ancient divergence from the same ancestral population, as has been suggested by microsatellite data (Scozzari et al. ¹⁹⁹⁹).

Now, bearing in mind, that D. M. Behar et al. suggest that it would not be parsimonious to date the divergence of KhoiSan ancestors from a common ancestral African group later than 90,000 years bp, can a link then be made between mtDNA markers and male-specific markers in KhoiSans, in terms of basal character of phylogeny and temporal character of genealogical divergence?

Behar et al. for the most part paint a picture of a single wave of migration being the source of the 'aboriginal' KhoiSan maternal gene pool—largely of L0d and L0k markers—no later than 90,000 years bp, [and yes, to answer the question above, the authors did make a link between mtDNA markers and male-specific markers—as mentioned several notes ago]. How does one reconcile this with male-specific markers, considered to be 'aboriginal' to KhoiSan groups, assuming that this wasn't a wave of migration exclusively of females?

Well, from the standpoint of basal character of genealogical phylogeny, there seems to be a common theme of basal haplogroups both maternally and paternally, and so, no qualms there; but from a temporal standpoint, questions arise vis-a-vis any correlation between the 'aborignal' maternal gene pool and male-specific gene pool. This is in no small part due to the fact that according to many publications, the "most basal branch of Y phylogeny" thus far identified date later than the 90,000 y bp time frame cap postulated!

National Geographic's site for "The Genegraphic Project", a project which one of the authors of the present Behar et al. study—that is, Spencer Wells—is a part of, for instance dates the MRCA of haplogroup A-M91 to ca. 55,000 years ago, while B-M60 is dated to ca. 50,000-60,000 years ago. From examination of various publications, the 'average' date given to early successful Out of Africa migrations of anatomically modern humans is ca. 60,000 years ago more or less. Naturally, this would imply that the just mentioned basal haplogroups would have to be older than that OOA date, but still, no work to date that comes to mind, has dated them either earlier than or contemporaneous to ca. 90,000 years bp.

Where does this lead us to? Is it possible then, to assume that the "aboriginal" male-specific gene pool—which was supposed to have been a part of the wave of migration that begat mtDNA markers L0d and L0k—was "erased" by a subsequent wave of migration, which would have likely been male-biased [for if it were not, one would expect some noticeable impact of the co-migration maternal gene pool]? If so, the question becomes when and why.

Furthermore, characteristic Khoisan gene pool extends well to the E-M35* Y chromosome marker, as noted before, and to reiterate...

Indeed, it is also found at high frequency (16.7%) in the Khoisan of South Africa (Underhill et al. ²⁰⁰⁰; Cruciani et al. ²⁰⁰²) (suggesting, once again, their ancient relationship with Ethiopians) and observed in southern Europe (present study). — Semino et al. 2004 [2]

In descending order, courtesy Semino et al. 2004…

Ethiopian (Oromo) - E-M35* = 19.2%, KhoiSan (South Africa) - E-M35* = 16.7%, Ethiopian (Amhara) - E-M35* = 10.4%, Berber (North-Central Morocco) - E-M35* = 7.9%, Berber (Southern Morocco) - E-M35* = 7.5%, Senegalese - E-M35* = 5%, Tunisian - E-M35* = 3.4%, Algerian - E-M35* = 3.1%, Arab (Morocco) - E-M35* = 2.3% , Burkina Faso -E-M35* = .9%

...but overall,

Group III is less frequent in the Khoisan (28.2%), who share with Ethiopians only the M35 haplotype 19 (10.3%). Conversely, the M2 component, which occurs at a frequency of 17.9% in the Khoisan, is virtually absent in the Ethiopians. — Semino et al. 2002

Indeed; consider the fact that E3-P2* is notably rare or absent in KhoiSan groups. The significance of this, is obviously the fact that E3* is a precursor to Pn2 derived clades of E3b [including E-M35] and E3a. Additionally, it is an indicator of yet another subsequent wave of migration likely to be dated later than the 90,000 y bp time cap. However, since Bantu-speakers who live near KhoiSan groups have little to rare E-M35 distribution, in contrast to the considerably high KhoiSan frequencies, it is a hard sell to imagine that these were introduced to them by Bantu-speaking groups.

It is of interest, that Semino et al. 2002 note that...

Although intermediary Bantu-speaking populations currently separate these two groups geographically, archaeological findings suggest that the Khoisan territory once extended above the equator, to present-day southern Ethiopia and Sudan (Nurse et al. ¹⁹⁸⁵, p. 105)...

This would make sense, given the distribution of the most basal branches of Y phylogeny in these regions, which is a characteristic feature of KhoiSan gene pool. However, to reiterate; E3* is rare to absent in KhoiSans, and yet, E-M35* is considerably higher amongst them than most other groups outside of sub-Saharan east Africa, including east African Bantu-speaking populations. E3* is notably present, if not in relatively higher frequencies than elsewhere, in those very same regions that carry the most basal branches of Y phylogeny as the KhoiSans do. This is an interesting contrast between east African and south African groups which predominantly carry these basal branches, aside from the fact that the subtypes of the KhoiSan basal branches largely differ from those in east Africa. It would seem to argue against the idea of haplogroups A and B markers arriving in southern Africa in the same wave of migrations as E-M35* markers [such a prospect would also tend to lower the range of the migration time frame], but yet, each wave of migration in question date later than the 90,000 y bp time cap that is supposed to mark the lower bound of the localization process of "aboriginal" KhoiSan mtDNA markers like L0d and L0k. Then again, perhaps a tenuous [and very tenuous at that, since non-E3* (P2) "Group III" markers are rare to absent in KhoiSan groups of southern Africa] assumption can be that small frequencies of E3* may have been available in KhoiSan groups, but have largely since been drifted out by neutral random genetic drift, while the E3*-Pn2 derived clades of E-M35* were subjected to positive random genetic drift, thereby inflating E-M35* frequency. This only goes to show the considerable complexity that underlies demographic events over time across huge chunks of landmass, which cannot be explained away with simple migration theories!

On a side note, can archeology clue us in on the temporal and spatial dispersion of the KhoiSans immediate ancestors?

Whether tenuously or not so tenuously, certain rock art have been attributed to San hunter-gatherer groups of southern African, like the following for instance...

Courtesy www.metmuseum.org: 
Game Pass Shelter
Kwazulu-Natal
South Africa
Courtesy of the Rock Art Research Institute, University of the Witwatersrand, South Africa
RSA GAM 95

Courtesy www.metmuseum.org:
A line drawing illustrating figures as they appear on the so-called Rosetta Stone.

Side note: Essentially a simplified repro of the above rock art. Notice the slender body plan animation of the human figures, but more interestingly perhaps—in so far as it relates to KhoiSans—the human figure following the first one on the far left "herding" the cow; the figure appears to be bending, but it seems to have steatopygia—a fairly common feature amongst KhoiSan groups, particularly more pronounced in the females.

Some undated "San" paintings - Eastern Cape

 Storm Shelter
Eastern Cape

South Africa

Image courtesy of Geoffrey Blundell

If art can be accurately tied to contemporary groups like KhoiSan s, especially those which are very conservative in their lifestyles over a great dea l of time, and if ancient artwork can be accurately dated, perhaps it can aid us—amongs t other disciplines—in reconstructing demographic events with a reasonable level of precision!
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*References:

—D.M. Behar et al. 2008, The Dawn of Human Matrilineal Diversity

—[2], Semino et al. 2004, Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area
—[1], Cruciani et al. 2004, Phylogeographic Analysis of Haplogroup E3b (E-M215) Y Chromosomes Reveals Multiple Migratory Events Within and Out Of Africa

—Semino et al. 2002, Ethiopians and Khoisan Share the Deepest Clades of the Human Y-Chromosome Phylogeny

Correlating mtDNA Markers with The Journey of Contemporary E3a-bearers' Ancestors

mtDNA may paint a somewhat more complex picture than their Y counterparts, in no small part due to the far much deeper root [taking us back to the earliest traceable MRCA] of the maternal line of contemporary human populations, and hence much greater time depths in which complex patterns of demic processes would have taken place than those of the Y chromosome counterpart, leaving room for relatively larger margins of error in dating earlier coalescent ages, and in which case, there is the real possibility that the evidence of earlier distribution pattern of mtDNA clusters under study could well have been erased by subsequent demographic processes [to put it in a language not too different from Salas et al. 2002]. Keeping this in mind, what could be said about the possible markers that the group ancestral to contemporary west African E3a-bearing populations carried from their point of origin?

Examining several possible candidates…

Salas et al. 2002, in The Making of the African mtDNA Landscape, have noted that:

The paragroup L1 includes the MRCA of human mtDNA, which is at least 150,000–170,000 years old (Horai et al. Horai et al., 1995; Ingman et al. Ingman et al., 2000). Haplogroup L1a (Figure 4a) is common (~ 20%–25%) in East, Central, and southeastern Africa, and is almost absent in North, West, and southern Africa. The main subclade, L1a1, is ~ 33,350 (SE 16,600) years old and is quite starlike, with a predominantly East/southeastern African distribution and a root type that is common in East Africa. There has been considerable drift on several derived types in southeastern Africa. The second principal subclade, L1a2, is ~ 8,300 (SE 3,650) years old and is predominantly Central African, occurring in both Biaka and Mbuti, and, again, several types (in particular, the root type) appear at elevated frequency in southeastern Africa.

An East African origin of L1a seems likely, given that Central African types tend to be more derived in the tree…

With regards to the subtype L1c, the authors say this:

Representatives in West Africa are restricted to two derived subclades, suggesting an expansion westwards relatively late in the evolution of the haplogroup. It is notable, however, that the southeastern representatives tend to be most closely related to Central African types and include types in clusters not present in West Africa. — by Salas et al.

The subtype L1b is something of an interesting case, which as put forth by the said authors,…

L1b (Figure 4b) has a completely different geographical distribution within Africa. It is concentrated in West Africa, with some overflow into Central and North Africa (particularly geographically adjacent areas, connected by the West African coastal pathway) but little in East, southeastern, or southern Africa. It is also common in African Americans (~27% of all L1b-types in the database), in agreement with the known importance of the West African coast to the Atlantic slave trade. A simple interpretation would therefore attribute a West African origin to L1b, with significant diffusion into North and Central Africa. However, because the coalescence time of L1b is estimated at only ~30,000 years—whereas its sister clade, L1c, is estimated at ~60,000 years old—a recent bottleneck and re-expansion in West Africa may have shaped the evolution of L1b. Given the likely origin of its sister clade L1c in Central Africa, a Central African origin seems plausible for L1b as well.

It is an interesting case, because it offers two possible explanations for its high concentration in west Africa, and hence in African American candidates as well, which is that:

1)it could well have originated in west Africa, and then spread to north and central Africa, that is—regions nearby west Africa, as well as the Americas via the slave trade.

2)or it could well have originated in central Africa, which seems to be the springboard point from where L1 subtypes made their way into west Africa; after all, central Africa seems to have the distinction of having considerable frequencies of all the sub-haplogroups thus far mentioned, namely L1a, L1b, and L1c.

If sway were given to the second scenario, given the said *distinctive* element of central Africa, along with the reasons given by the authors, with regards to coalescence ages of L1c and L1b with respect to one another, along with their common considerable presence in central Africa, then a case can be made that it could lend some credence put forth here earlier, about the east-to-westward migratory pathway contextualization of the origins of contemporary west African groups predominantly bearing E3a Y-chromosome markers, which was touched on in the following links:

P2 Clades: The Arrival of E3a and E3b Haplogroups

NRY Haplogroup E3a: Proposing its Origins through a Multidisciplinary lens

In making this Ychromosome-mtDNA correlation, it may well be worth taking note of the distribution patterns of the L1 subtypes:

1)L1a is common in east Africa,…

—but rarer, if not “almost absent” in west, north or south Africa.

—and scarce in African American candidates, “in comparison with other African types”, though it is also worth noting that the African American representatives of this subtype largely match southeast African examples, suggesting that region to be the source of the American candidates carrying that clade.

—and has some notable presence in central Africa and southeast Africa.

2)L1b is common in west Africa,…

—but rarer in east Africa, southeast and south Africa.

—and has notable presence in African American candidates.

—and has notable presence in central Africa and north Africa.

3)L1c is common in central Africa,…

—but rarer in west and southeast Africa, with “virtually none” in east or south Africa.

—and has considerable presence in African American candidates. Thus, it is quite likely that the elevated presence in African American candidates is due to drift, particularly when taking into account that west Africa is generally considered to be an important region where a major section of African American populations trace their ancestry, not to mention that:

A West African origin for the African American L1c types is unlikely, because American types do not match with West African ones, this region being the best represented in the database. — Salas et al.

With regards to this subtype, let’s recall that…

Representatives in West Africa are restricted to two derived subclades, suggesting an expansion westwards relatively late in the evolution of the haplogroup. It is notable, however, that the southeastern representatives tend to be most closely related to Central African types and include types in clusters not present in West Africa. — by Salas et al.

…which would appear to lend further credence to the aforementioned “east-to-westward migratory pathway contextualization of the origins of contemporary west African groups predominantly bearing E3a Y-chromosome markers”, wherein ancestors [originating from *general* geography straddling central-Africa and Sudan] would seek refuge in the Shum Laka region, before heading westward into west Africa.

Now add to that earlier excerpt, this:

The geographic distribution of L1c is especially interesting. More than one-third of L1c haplotypes in our database belong to African Americans, and few of them show matches with continental Africans. The great majority of the remainder of L1c comes from Central Africans, with a few in the west and the southeast. There are virtually none in the east or south; of the “Pygmy” groups sampled, only the western group (the Biaka) have L1c.

Noteworthy, is that most Y marker studies tend show that “Pygmy” groups generally carry markers relatively closer to the root of the tree, but mtDNA analysis on the other hand, paint a more complex picture, perhaps indicating influences from neighboring groups or recent arrivals to the scene. As for the subtype L1c itself, we are told that:

This suggests that the origin of L1c can be placed somewhere in Central Africa towards the Atlantic west coast, in the uncharacterized areas of Angola and the Congo delta, to the south of the putative Bantu homeland, on the route of the “western stream” of the Bantu expansion.

4) Haplogroup L1d:

“Haplogroup L1d (Figure 5b) is nonstarlike and characterizes Khoisan groups (Bandelt and Forster Bandelt and Forster, 1997), where it represents about half of the total haplogroup composition for the southern African samples (!Kung and Khwe). L1d is additionally found at ~ 5% in the southeastern African samples (see also Pereira et al. Pereira et al., 2001), and there is a single East African L1d type from Lake Turkana. This distribution strongly implies an origin for L1d amongst the ancestors of the Khoisan, long before the arrival of Bantu speakers in the region.” [Salas et al.]

5) Haplogroup L1e:

“L1e is restricted almost solely to East Africa” [Salas et al.]

With regards to haplogroup L2, we are told:

1)…it appears that the founder ages for L2a are significantly older than for L1a, consistent with the phylogeographical picture, with an earlier West African origin for the L2a lineages of southeastern Africa and a more recent East African origin for the L1a lineages. Indeed, the age of the L2a founders in southeastern Africa is consistent with an origin in the earliest Bantu dispersal from the Cameroon plateau, 3,500 years ago (Phillipson Phillipson, 1993).

Something about this haplogroup that seems to also lend some credence to the “east-to-westward migratory pathway contextualization of the origins of contemporary west African groups” some time in the Ogolian period, which coincides with the LGM (Last Glacial Maximum elsewhere), is this:

It is difficult to trace the origin of L2a with any confidence. The deepest part of L2a, represented by clusters α1-α3, is most common in East Africa. However, the diversity and TMRCA are similar in East (61,250 [SE 13,500] years) and West (54,100 [SE 17,087] years) Africa. The diversity accumulated separately in East and West Africa, estimated from the main shared founder types (and disregarding the possibility of subsequent gene flow), is again similar in the two regions, at ~14,000 years (14,100 years [SE 5,100], and 13,800 years [SE 4,700], respectively), suggesting a separation shortly after the Last Glacial Maximum.

…give or take in the margin of error, the above is displaying slightly older dates for east African bound examples with respect to the west African bound ones, but otherwise, the dates respective to either geography could well be placed within the same general time frame ranges, just as noted above. But going back to the aforementioned hypothesis, let’s recall that it was stated here that…

PN2 clade (E3) bearers in the vicinity of the general expanse straddling Sudanese-Central African Republic -Ugandan-Kenyan region [get a map aid, if necessary] give rise to E3a ~ between 21 and 18 ky ago [see Semino et al. 2004 for TMRCA dates, pending additional or new info]; E3b-M35* would have likely arose relatively earlier than E3a* [as evidenced by its near absence in some the populations that carry this], sometime prior to the Ogolian and the LGM period…

Bearing "rare" lineages predominantly found in east Africa - i.e. the likely point of origin, along with sequential archaeological evidence for [east-to-west and thereafter, in situ west African south-to-north] repopulation events in west Africa, much of which was abandoned in the Ogolian desertification, show that the earliest E3a bearers - which finds expression in Senegalese samples - could not have arose in situ west Africa, but originated in an eastward oriented geography and migrated to west Africa, as the Ogolian aridity relaxed, bringing along with them new microlithic traditions picked up from the Shum Laka region, settled therein and thereafter underwent demic expansion, resulting in the "high diversity and frequency" of the E3a distribution in west Africa.

In one of the other link, it was stated...

—The E3a bearing group would proceed westward, perhaps meeting groups of earlier lineages at the Shum Laka region of Cameroon, whereby quartz micro-lithic culture had already been in place by around 30 ky ago, hence preceding the rise of E3a common recent ancestor. But this group wouldn’t stay put here, at least not every section of it; they’d proceed to the savanna, grassland or vegetation holdouts in West Africa beyond the then boundaries of the Sahara. This probably occurred some time between 15ky and 13ky ago. During this period, as the **Saharan aridity began to gradually slacken**, some E-M78 bearing proto-Afrasan speaking nomads likely made their way into the Levant via the Sinai corridor.

Others taking refuge in the Cameroonian savanna-tropical forest general region probably followed suit, that is—after the aforementioned initial batch of migrants [bearing E3a descendants]; or else, the same group of people [from the initial migrants] shifted locations along the west African vegetation belts, once it became apparent that the far western reaches didn’t have much to offer, but the water system [as part of the Niger River]—however relatively shallow or what not—offered something additional. Finally, when the conditions in the Sahara were turning around for the better, starting between ~ 12ky and 11ky ago, these migrants would proceed northward, leaving the sort of trails that find expression at Ounjougou—Mali.

Links in question:
P2 Clades: The Arrival of E3a and E3b Haplogroups

NRY Haplogroup E3a: Proposing its Origins through a Multidisciplinary lens

Keeping this in mind, the authors add that:

An easterly origin for L2a also faces the following difficulties: that the other subclades of L2 (L2b, L2c, and L2d) have a clear western distribution, and that L2d diverges earlier in the mtDNA phylogeny than L2a (Torroni et al. Torroni et al., 2001). A possible solution would be an origin for L2a somewhere **between east and west**,

..and

followed by dispersals in both directions along the Sahel corridor.

Hence, essentially reiterating what is stated in the recitation above (in red), i.e. positioning central Africa as a likely center of refuge during the Ogolian aridity before ancestors of contemporary west African groups bearing E3a markers moved into west Africa.

2) sub-haplogroups L2b, L2c and L2d:

Haplogroups L2b, L2c, and L2d appear to be largely confined to West and western Central Africa (and African Americans), with only minor occurrences of a few derived types in the southeast. L2b also shows isolated occurrences in the east and as far north as Iberia. Therefore, an origin for all three in West and western Central Africa seems likely.

What does all this observations of L1 and L2 subtypes ultimately mean at this point? Well, one ought to come out of it with an overall image wherein central Africa had played an important role in the corridor for the "east-to-westward" migration of the ancestors of contemporary E3a-bearing groups of west Africa as a refuge center and thus, radiation point for lineages which have become important in west Africa, central Africa, southeast Africa, southern Africa, and in some cases east Africa as well. This especially becomes apparent, when one takes into account the above mentioned point about central Africa attaining the distinction of harboring these lineages in noticeable frequencies, while the case is shown to be otherwise in either west Africa and/or east Africa, or southern Africa.

With respect to haplogroup L3, we’re informed:

The lineages remaining within L3* represent ~20% of all L3A types in Africa. Although they are distributed throughout the continent, they reach the highest frequencies in East Africa, where they account for about half of all types from this region. This frequency profile suggests an origin for L3 in East Africa (Watson et al. Watson et al., 1997).

This is supported by the evidence that the out-of-Africa migration, which took place from a source in East Africa 60,000–80,000 years ago, gave rise only to L3 lineages outside Africa.

1)sub-haplogroups L3f and L3g:

Both L3f (Figure 8a) and L3g (Figure 8b) are rare and also appear to have an East African origin. L3f* and L3g are virtually restricted to East Africa (with some dispersal into Central Africa, southeastern Africa, and the Near East).

The subclade L3f1 appears to have spread at an early date into West Africa and is correspondingly also better represented in African Americans.

2)sub-haplogroup L3b:

By contrast, the commoner haplogroup L3b (Figure 8c) is predominantly West African, with a substantial representation again in African Americans. It has spilled over into North Africa and on into the Near East. There is very little dispersal into either East Africa or even Central Africa, but several derived types are present in southeastern Africa.

3)sub-haplogroup L3d:

Its sister clade, haplogroup L3d (Figure 9a), is also mainly West African and African American. A number of types are found in southeastern Africa, including one type (in L3d1), matching a Fulbe lineage, at considerably elevated frequency. A second type (in L3d3) is not seen in our southeastern African sample but occurs at high frequency in the south, in both Khwe and !Kung, and matches a type apparently found at high frequency in the Herero (Vigilant et al. Vigilant et al., 1991; not included in the network here because of sequence ambiguities).

4)sub-haplogroup L3e:

—L3e (Figure 9b) is the most widespread, frequent, and ancient of the African L3 clades, comprising approximately one-third of all L3 types in sub-Saharan Africa. This haplogroup has recently been dissected in some detail by Bandelt et al. (Bandelt et al., 2001), who suggest an origin for the haplogroup in the Central Africa/Sudan region ~ 45,000 years ago.

—L3e1 is distributed throughout sub-Saharan Africa, but it is especially common in southeastern Africa. This clade appears to have a west Central African origin and is rare among West Africans, although it is well represented among African Americans…The African American types may be the result of direct transportation from Mozambique, given the lack of West African representatives.

—L3e2 is more frequent in Central and West Africa. It is not possible to distinguish L3e2a without HVS-II information (a transition at np 198), and, as this information is not available in most sequences in the database, we have incorporated L3e2a into L3e2* in Figure 9b.

L3e2* appears not to have been transferred to the southeast, with one exception.

—L3e2* is found mainly in Central Africa, and the derived subclade L3e2b is found primarily in West Africa, with a clear founder type within L3e2*. This indicates a range expansion from Central into West Africa (~9,000 years ago). Other instances of such expansions (for example, in haplogroup L2) may be undetectable, at present, because of poor phylogenetic resolution.

Few L3e2b types are found in southeastern Africa, but a great many are present in African Americans.

—L3e3 is primarily West African, but with its root type present at elevated frequency in the southeast and with some southeastern African derivatives.

—L3e4 is present in East, Central, and West Africa, with one individual in the southeast, but is too rare to draw conclusions from.

Well, what can be learned from pieces on macrohaplogroup L3? From the looks of things, L3b expanded considerably in west Africa, likely after ancestors of contemporary groups bearing E3a markers had situated therein, assuming that they were part [in very modest levels perhaps] of the dispersal involving those ancestors from their point of origin to their west African destination—which would explain lower frequencies elsewhere. Possibly the same with L3d, although in either L3b or L3d's case, the extracts above are rather vague about the timeline of the dispersals [that is certainly the case with L3f1; if there is any possible suggestion here, it may be one where one comes out thinking that L3f1 arrived in west Africa before the ancestors of E3a-bearing groups did]. Hence, inference here is made based on distribution pattern.

Of all the subtypes of L3, as presented above, L3e seems to fit in more with the earlier mentioned scenario of the radiation of mtDNA markers from central Africa as a refuge center [during the extreme periods of aridity] near and at the turn of the Ogolian aridity. Thus the likely origin of this lineage in the general region straddling central Africa and Sudan ca. 45ky ago [as proposed by Salas et al. ] would make sense, particularly as the region where ancestors of E3a groups of west Africa would have picked up carriers of that marker; this wouldn't have been far from, if not within the general area where the forebearers of E3a groups of west Africa first arose. As an afterthought, all this seems to play well with the tabulated L3e TMRCA ages given to the subtypes [numbers in brackets are standard error figures]:

L3e > 49,250 (11,750)

L3e1 > 32,150 (11,450)

L3e1a > 26,750 (12,000)

L3e2 > 37,400 (18,350)

L3e2b > 9,150 (3,100)

L3e3 > 14,150 (4,500)

L3e4 > 24,200 (10,400)

Interestingly, amongst these TMRCA figures, the common west African subtypes of L3e2b and L3e3 are also the markers with TMRCA ages that best reflect the timeframes attached to repopulation demographic processes in west Africa near and/or at the turn of the Ogolian aridity, and shortly thereafter, in accordance with archaeological evidence.

And finally, for the purpose of this topic, the following synopsis from Salas et al. may well prove to be instructive, with some special emphasis to the highlighted pieces, as they appear to buttress several the points already outlined above:

An important influence on the subsequent genetic landscape of the continent is likely to have been the LGM. Paleovegetational studies have indicated that, between 30,000 and 11,000 years ago, much of the continent was extremely arid (Adams and Faure Adams and Faure, 1997). The Sahara advanced hundreds of kilometers further south, and the equatorial rainforests were reduced to a small fraction of their present size, leaving open woodland and savanna in much of the Congo basin. This may have formed a refuge area from which modern humans later dispersed: some with haplogroup L2a east and west, with L1b west; perhaps even some with L1a east and L1d southward. The origins of these expansions may lie earlier, at the beginnings of the Later Stone Age, ~40,000 years ago. Archaeological evidence has demonstrated substantial human activity in the equatorial forest area—for example, in Cameroon and Equatorial Guinea, 35,000 years ago (Martí et al. Martí and Mercader-Florín, 2001).

It is worth noting that the mtDNA data do not support the clustering of sub-Saharan Africans into (pre-Holocene) geographical races, as assumed by many authors (Hiernaux Hiernaux, 1975; Newman Newman, 1995), if only because the so-called “Pygmies” clearly do not form a coherent group. The westerly Biaka sample includes only L1a and L1c, and the more easterly Mbuti include only L1a (shared with the Biaka), L1e and L2. Therefore, the Biaka tend to resemble other Central African populations, whereas the Mbuti more closely resemble those from East Africa, although both groups are much reduced in diversity in comparison with neighboring populations. It is also notable that the Tanzania Khoisan-speaking Hadza resemble other East Africans rather than southern African Khoisan speakers. Both results appear to be consistent with the results from classical markers (Cavalli-Sforza et al. Cavalli-Sforza et al., 1994).

The authors proceed to then make their own correlations between mtDNA distribution and Y marker distribution, although not as detailed as that in the posting here, as it particularly pertains to contemporary west African groups who are generally known for high frequencies of PN2-derived Y marker "E3a".
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*References:
Salas et al. 2002, The Making of the African mtDNA Landscape