Review: Saudi Arabian Y-Chromosome diversity...relationship with nearby regions

It has become fashionable within elements of 'western' academia, to shift traditionally African-ascribed markers unit by unit to overseas origins, while very few are open to the possibilities that markers long taken for granted as "Eurasian" could actually be of direct African origin. The drivers for such moves can be a matter of trying to shift the Out Of Africa conception of human origins overseas, on a piece by piece and gradual basis, especially given preexisting scant substantiation to the contrary, or else a matter of not coming to terms with the prospect of recent African ancestry in "non-African" territories, which is determined to tarnish "racial purity" by racist cliques, and/or implicates Africans—particularly "black Africans"—as agents of certain "important" sociocultural turning points or "technological breakthroughs" in human history. In this respect, as a common example among many, haplogroup E—the predominant contemporary Y-DNA phylogeny on the African continent which has not only gained reputation for spilling over the boundaries of Africa in a substantial way, but also tied to "turning points" in human history, like say, the turn to a farming economy during the Neolithic era—has gained elevated interest over the years. This interest has accompanied the effort to shift the origins of the haplogroup from Africa to "Eurasia" via a "Middle Eastern origin" theory by certain parties. An earlier example of this, by Chandrasekar & co. (2007), had been discussed on this site; the example this time around comes from Abu-Amero et al. (2009), which will be the subject of review of this blog entry.

DE* as "Last Refuge" of Sects so psychologically troubled by African Ancestry?

The purported finding of DE* paraphyletic haplotypes in only 2 Tibetan sample candidates appears to have caused hysterical excitement in certain quarters, specifically amongst sects of individuals who are psychologically and emotionally tormented by the prospect of African ancestry in their "homelands". But this excitement is emotionally driven, and just that. As such, intellectual engagement gives way to religious cultism as the medium of self-expression. But let's just examine how much or what really lies herein that is worth being hysterically excited over:

• DE* is a descendant clade of M168. M168 is undoubtedly African; this fact alone makes it more than probable that this place [Africa] is also likely where DE* emerged.
  

• DE* is more common in Africa than outside of it -

It has been identified in African samples in more than one accasion in separately-conducted studies, having been identified in 5 Nigerian sampling candidates in one study, *1 in an Egyptian sample [see "Miscellaneous notes" below] and 1 Guinean individual in another . On the other hand, it had purportedly been identified in only 2 Tibetan sampling candidates. So we have 6 to 7 African cases vs. 2 Asian cases.

• DE*'s internal phylogeny is more diverse and widely distributed in Africa -
  

Considering the greater internal phylogenetic branching of haplogroup E vs haplogroup D, it can be suggestive of either 1) longer time-depth for haplogroup E explosion/expansion, and hence, implicating DE* being around longer in Africa, as the homeland of haplogroup E ...

Or

2) that the haplogroup E lineage experienced an explosion that the D counterparts did not achieve in more or less the same time depth. The question becomes: What could account for this?

Either way, with fact being that African Hg E internal phylogeny is more elaborate than Hg D, the end result suggests that the intensity of such intra-E phylogenetic explosion seems to have had some level of erasing effect on DE* distribution. Given the greater pressure, due to greater demic explosion brought to bear on preexisting DE* in Africa — mainly by its own sub-phylogeny — than that which would have been the case in Asia by the YAP+ counterpart sub-phylogeny there, it's amazing that DE* is relentlessly visible enough in the African gene pool, as demonstrated by its greater chance detectability here than elsewhere, including Asia. This suggests that DE* would have been more widely distributed in Africa than in Asia, having been able to withstand greater pressure from greater subsequent demic expansion of Hg E phylogeny than that involving Hg D phylogeny, respectively in Africa and Asia.

The distribution and internal branching of Hg D suggests, on the other hand, that it involved lower scale dispersal of Hg D*, which were relatively more controlled in their subsequent expansion. The distribution pattern for instance, shows that the major subclades of D in different territories are highly differentiated and generally sharply geographically-structured, being confined to territorial spheres. At least that is the image reflected, if one goes by what's professed in the ISOGG.org website, whatever may be said of the credibility:

Sub-group D1 (D-M15) is seen in Tibet, Mongolia, Central Asia, and Southeast Asia, and the sub-groups D* (D-M174) and D3 (D-P47) are seen in Central Asia. The sub-group D2 (D-M55) is seen almost exclusively in Japan.

Hg D* is presumably also identified in the Andaman Islands.

• A hypothetical Hg DE* back-to-Africa migration seems to have been elusive in leaving genetic tracks behind, presumably from south Asia to Africa -
  

The supposed back-migrants would seem to have left no genetic tracks behind in a hypothetical destination from southern Asia via the Arabian peninsula, eastern Africa through to African interior, in a hypothetical back-to-Africa migration scenario. If they did, then it had been thoroughly erased by multiple demographic shifts. Hg D's distribution in south Asia, with rare to no presence in territories between that region and Africa, is however explained by founder effect of OOA migrants, already carrying Hg DE* amongst them.

Chandrasekar's speculation is highly questionable for the same reasons just stated above; see:

Some of the YAP insertion chromosomes without the M174 mutation reached the Mediterranean via Central Asia and gave rise to the E lineage with mutations at M40 and M96 (~31 000 years ago; Hammer et al. 1998). This E lineage back-migrated to Africa through the Levant as hypothesized by Hammer et al. (1997) and Altheide and Hammer (1997).

Hg D is rare to absent in the Levant, and conversely, Hg E is virtually rare to absent in populations that do carry Hg D.

Furthermore, Hg E's presence in the so-called Near East, including the Levant and Europe, serves as gene flow from Africa, because Africa is where the entire Hg E phylogeny occurs, not the Levant. All upstream Hg E markers are exclusively found in Africa, and essentially none in the Levant.

The so-called Near East has far much lower frequencies of Hg E than in mainland Africa, and all of these happen to be subclades of African counterparts. Much of these subclades are relegated to the P2 (PN2) phylogeny. Upstream PN2 clades as generally known, only occur in Africa.

Revisiting Chandrasekar's post again,...

Some of the YAP insertion chromosomes without the M174 mutation reached the Mediterranean via Central Asia and gave rise to the E lineage with mutations at M40 and M96 (~31 000 years ago; Hammer et al. 1998).

It is also of note that Chandrasekar conveniently ignores that DE* has been found in Africa as well, but in even greater frequencies than his personal favored region [as noted in the second point above], i.e. Asia, not to mention that it is essentially non-existent in the so-called Mediterranean or the Levant. With DE* being in Africa, it is not necessary for Hg E to have come from the Levant, for reasons just mentioned and the ones immediately above this last Chandrasekar citation. Instead, Chandrasekar relies heavily on outdated studies, when Hg E phylogeny, as with many others, were in their early stages of being resolved.

His statement above, about "some of the YAP insertion chromosomes without the M174 mutation" has also implications that Chandrasekar seems to have overlooked:

• Common sense intimates that any hypothetical DE* back-to-Africa migration — and it would have to have been major enough — would have been pooled from a newly situated migrant group. The keywords here: "newly situated".
  

Recalling Weale et al....

the presence of the DE* haplogroup has the effect of forcing an earlier date for the most recent common ancestor of all African YAP chromosomes. This reduces the possible time window within which a back-migration to Africa could have occurred under the scenario of an Asian origin for YAP. - Weale et al. 2003, Rare Deep-Rooting Y Chromosome Lineages in Humans.

Indeed! The presence of DE* in Africa suggests that this lineage was in place very shortly after its emergence. The OOA migrants had just recently left Africa for a reason; what on earth would these folks, who had just arrived, go back to Africa for, and at such a gruesomely long distance from a south Asian refuge? Pending tangible evidence of a compelling motive, it makes little sense.

And even if one were to take a hypothetical Asian origin of DE* for granted, based on skin pigmentation allele examinations, the original carriers of these markers would have closely resembled contemporary "black Africans", and even then, Hg E would still not be Asian [considering points above].

Let's face it; it's really not all that complicated: It just so happens that Hg D exists in Asia, while Hg E plays a dominating role in Africa, well, because DE* markers were present in both. Simple enough, isn't it?!

Neither territory has the other respective sub-clade lineage, because these emerged after OOA migrations, understandably.

Not sure why finding DE* therefore, surprises anyone. It's the only way D could have arrived in south Asia sans E; thus, DE* chromosomes brought in from Africa would have to have been around, in order for D to emerge, there is no other way around it. It is also the reason one finds DE* in both Africa, the origin point of destination, and Asia, the destination. However, instead of looking at it that way, some complicate things for themselves, and say that in order for DE* to be in Asia, it surely must have emerged there, and that there is no other way around that.

The most parsimonious explanation generally tends to reduce the number of questions for each answer that it provides than the alternative. In this case, an African origin entailing DE* dispersal in a OOA migration event, paving way for a founder effect situation in southern Asia is the most parsimonious. All things considered [from above], there really is little for the aforementioned sects to be cheerful about, at least from the intellectual side of things, as opposed to the religiously-motivated or plainly wishful end!
_________________________________________________________

Miscellaneous notes:

A lost gem?

The following recently grabbed the attention of the present author of this blog; the abstract goes like this:

The geographic location of Egypt, at the interface between North Africa, the Middle East, and southern Europe, prompted us to investigate the genetic diversity of this population and its relationship with neighboring populations. To assess the extent to which the modern Egyptian population reflects this intermediate geographic position, ten Unique Event Polymorphisms (UEPs), mapping to the nonrecombining portion of the Y chromosome, have been typed in 164 Y chromosomes from three North African populations. The analysis of these binary markers, which define 11 Y-chromosome lineages, were used to determine the haplogroup frequencies in Egyptians, Moroccan Arabs, and Moroccan Berbers and thereby define the Y-chromosome background in these regions. Pairwise comparisons with a set of 15 different populations from neighboring European, North African, and Middle Eastern populations and geographic analysis showed the absence of any significant genetic barrier in the eastern part of the Mediterranean area, suggesting that genetic variation and gene flow in this area follow the "isolation-by-distance" model. These results are in sharp contrast with the observation of a strong north-south genetic barrier in the western Mediterranean basin, defined by the Gibraltar Strait. Thus, the Y-chromosome gene pool in the modern Egyptian population reflects a mixture of European, Middle Eastern, and African characteristics, highlighting the importance of ancient and recent migration waves, followed by gene flow, in the region.

Source: Y-chromosome analysis in Egypt suggests a genetic regional continuity in northeastern Africa

by Manni et al. - 2002

For the complete journal, click here

The piece has raised some questions as to whether the YAP+ chromosomes in "some East Asian populations, such as the Japanese and Tibetans" is the same one identified in the Egyptian sample, i.e. essentially "Hg D", since this is largely the only YAP+ type found in said groups. The answer: Not necessarily, since the authors tested for YAP+, which is shared between Hgs D and E. The Egyptian YAP+ was very likely a paraphyletic chromosome that did not test positive for Hg E*, you know, just like how Hg DE* is devoid of the downstream characteristic markers of Hg E*. The 12f2 marker tested here more than likely refers to Hg J, which in this journal is designated as Hg 9. The nomenclature used here is apparently outdated [after all, this is a 2002 study we're dealing with here], but the finding of an upstream YAP+ chromosome that didn't belong to Hg E (as denoted here by SRY8299) is interesting nonetheless, because it adds to that theme of the unparalleled richness of Hg DE and derivatives on the African continent, as well as the distribution of the upstream DE* clade being *predominantly* an African 'thing'. So, in light of this, Egypt can now be added to the list of African territories wherein rare Hg DE* chromosome appears, a list which has no peers anywhere else where Hg DE* is concerned!

"haplogroup CF and DE molecular ancestors first evolved inside Africa and subsequently contributed as Y chromosome founders to pioneering migrations that successfully colonized Asia. While not proof, the DE and CF bifurcation (Figure 8d ) is consistent with independent colonization impulses possibly occurring in a short time interval."

Source: Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations

by Peter A. Underhill , Toomas Kivisild - 2007

A nutshell!...of what has essentially been more elaborately demonstrated about said markers on this site. The present author of this blog has not yet come across a single genetic journal that says differently about haplotype CF origin.

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!
_______________________________________________________________
*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".
___________________________________________________________
*References:
Salas et al. 2002, The Making of the African mtDNA Landscape

NRY Haplogroup E3a: A Multidisciplinary Proposal of Its Origins

Having touched on this matter in an earlier posting but in a broader topic involving more lineages, this post will focus on one lineage—haplogroup E3a.

Geological and geographical evidence

~23 ky ago: Ogolian aridity takes hold, and renders much of north Africa desertified.

The advent of Hg E3a's TMRCA essentially coincides with rise of the Ogolian aridity.

• 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.

Hence, indications are that the initial territory of an ancestral Hg E3a bearing group would have likely started south of the Sahara, at a time when:

• The Ogolian aridity rendered much of North Africa with adverse weather conditions, turning much of that general region into desert. The Sahara at this time, extends south beyond its current boundaries to a certain point, likely as far as a little beyond the Niger bend.

• The above mentioned geological conditions in the aforementioned geography indicate that the population density in those arid regions would have been quite sparse—meaning, that most populations would have then been concentrated south of the broad desert region.

Reference to the geographical extent of this desertification is laid out here in maps: AFRICA DURING THE LAST 150,000 YEARS [clickable]

Archaeological evidence
Archaeology indicates that much of west Africa during the height of the Ogolian aridity was abandoned, with many of the populations living therein in the pre-Ogolian periods seeking refuge in the last vestiges of vegetation beyond the desert, which at the time - as noted above, extended to as far as beyond the Niger River bend, and possibly few moving to the far northwestern coast of Africa, if not crossing over to the Iberian or Southwestern European region [perhaps to this end, possible case can made from findings in Goncalves et al. 2005?], which was then a major refuge center for European groups trying to cope with the side-effects of the LGM in their neck of the woods. Vivid archaeological indicator of this comes from:

• "After a favourable climatic period, characterised by relatively dense and diversified Palaeolithic occupations, the arid Ogolian begins locally around 23000 years BP and is represented at Ounjougou by a significant depositional and archaeological hiatus." — Aziz Ballouche [see: Link ]

Incidentally, when this was going on in west Africa, arid conditions extended all the way to the horn-shaped coast of the African Horn, possibly encouraging populations to reside relatively more inwards—that is, away from that aridified horn-shaped coastal region; rather, populations of that region were likely encouraged to seek refuge in the general region straddling southern Sudan, Ethiopia, Kenya and Uganda or even further—i.e. region straddling Uganda, Kenya, and Tanzania. [See AFRICA DURING THE LAST 150,000 YEARS, for visual aid—geology conditions via geography in the Ogolian period]

It is again, from archaeological evidence, that we get a picture of when repopulation events make their appearance, and in what pattern they occur, i.e. things which are all relevant to understanding the circumstances and nature of how the Hg E3a bearing group makes it appearance in west Africa:

• Consequently, it has to be seen in the context of heavy rainfalls and a resettlement of the vegetation cover, during the 10th millennium BC, that a **new population** arrives on the Plateau of Bandiagara." — Human population and paleoenvironment in West Africa [see: Link ]

...and we see how these repopulation events occur sequentially from archaeological record, showing a movement from an east-to-westward direction, and thereafter a south-to-northward movement in west Africa itself:

• From 30,600 to 10,000 BC: "A cultural flow, from the southeast of Subsaharan Africa and to the Sahara, could explain the diffusion of the microlithic industries all the way through West Africa. We observe them initially in Cameroon at Shum Laka (30.600-29.000 BC), then at the Ivory Coast in Bingerville (14.100-13.400 BC), in Nigeria in Iwo Eleru (11.460-11.050 BC), and finally in Ounjougou (phase 1, 10th millennium BC)." — Human population and paleoenvironment in West Africa [see: Link ]

This east-to-west movement shows that a new group of people moved into west Africa, because the "microlithic traditions" that appear at Shum Laka had been in existence for as long as ~ 30 ky ago, and yet didn't show up in west Africa proper until ~ 14 ky ago, a late date which works well within the confines of the TMRCA age of Hg E3a. So the people originally responsible for that "microlithic tradition" at Shum Laka were not the people who likely brought that tradition to west Africa, but by a new group of people who passed through Shum Laka. These new group of people first appeared in vegetation holdout regions beyond the Niger bend, and gradually moved northward, eventually reaching to regions as far as that of Ounjougou, as evidenced by the above carbon-dated archaeological finds. It should be remembered that the Ounjougou region was abandoned in the intense desertification period.

*Details of the "microlithic traditions" had been provided in a related earlier post: P2 Clades: The Arrival of E3a and E3b Haplogroups [clickable]

Genetic evidence
The east-to-west movement of new groups [the candidates being E3a bearing group] into west Africa observed above, seems to be lent further support from genealogical finds.

Observations of genetic differentiation within contemporary E3a bearing populations, suggests that the earliest Hg E3a bearing groups, carrying mainly M2, P1 and M180 mutations devoid of the M191 mutation, had moved to the far west region of Africa...from an eastern-oriented origin:

Consider for one,

• Although haplotypes 22, 24, and 41 were probably all involved in the Bantu expansion, the processes that determined the current distribution of these haplotypes in the Sudanese belt (a region south of the Sahara extending from western to central Africa) seem to have been more complex and perhaps involved a separate expansion.

• In particular, haplotype 24 and its derivative, haplotype 22, harbor opposite clinal distributions in the region, a finding that is at odds with the hypothesis of a parallel dispersion of these two lineages in the area.

• Haplotype 22 has a frequency of 23% in Cameroon (where it represents 42% of haplotypes carrying the DYS271 mutation), 13% in Burkina Faso (16% of haplotypes carrying the DYS271 mutation) and only 1% in Senegal (Semino et al. 2002), whereas haplotype 24 reaches its highest frequency (81%) in Senegal (Semino et al. 2002).

• A possible explanation might be that haplotype 24 chromosomes were already present across the Sudanese belt when the M191 mutation, which defines haplotype 22, arose in central western Africa. Only then would a later demic expansion have brought haplotype 22 chromosomes from central western to western Africa, giving rise to the opposite clinal distributions of haplotypes 22 and 24.

Source: Cruciani et al. 2002, A Back Migration from Asia to Sub-Saharan Africa

This piece shows that the oldest Hg E3a bearing populations, characterized by high frequencies of haplotype 24 and relatively modest frequencies of haplotype 22, remain localized in West Africa; the contrasting distribution and frequency patterns of these haplotypes suggest that the higher the population with haplotype 22, the less older it is in its genetic composition relative to those bearing less haplotype 22 in a gene pool dominated by the relatively older haplotypes, like haplotype 24. Senegal appears to have the highest concentration of haplotype 24, and interestingly, the lowest concentration of haplotype 22...thus, making it likely the oldest Hg E3a bearing group.

The Senegalese samples also have other peculiarities that further support the aforementioned idea of their being the oldest Hg E3a bearing group:

• Hg E3 (P2 or PN2 clade):
  
  Bantu (South Africa) - E3* = 1.9%, Senegalese - E3* = 2.9%, Ethiopian (Amhara) - E3* = 10.4%, Ethiopian (Oromo) - E3* = 12.8% in the ascending order.
  

...the 'older' groups appear to have relatively wider distribution of E3, as the Senegalese sample in particular seems to indicate vis-a-vis other Niger-Congo speaking groups elsewhere; a lineage which has by far the highest frequencies and distribution in Ethiopia [which is in East Africa fyi]

The Senegalese sample shows considerably more E-M35* than that from other Niger-Congo speaking groups of sub-Saharan West Africa, which are not immediately neighbouring major "ancient" African groups in East Africa or like Khoisans.

Hg E-M35* lineages:

• In descending order…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%
  

The Senegalese group is also the only sub-Saharan 'predominantly-Niger-Congo' speaking group that shares the rare microsatellite motif with Ethiopians on the E-M78 bearing chromosome:

It is interesting that both E-P2* and E-M35* and their derivatives, E-M78 and E-M123, exhibit in Ethiopians the 12-repeat allele at the DYS392 microsatellite locus, an allele scarcely seen (Y-Chromosome STR Database), especially in other haplogroups and other populations (A.S.S.-B., unpublished data).

In addition, the Ethiopian DYS392-12 allele is usually associated with the unusually short DYS19-11 allele, which is typical of this area. These findings are not easily explained. One possible scenario is that an ancient differentiation of the E-P2 haplogroup occurred in loco (East Africa). However, this also implies a low mutability of the associated microsatellite motif (DYS392-12/DYS19-11). Alternatively, the microsatellite motif may be due to homoplasy.The first scenario is more likely, since this unique microsatellite haplotype occurs in E-P2*, E-M35*, and E-M78 but is almost *absent in all other haplogroups and populations*.

In addition, the high stability of the DYS392 locus (Brinkmann et al. 1998; Nebel et al. 2001) and of the shorter alleles of DYS19 (Carvalho-Silva et al. 1999) has been reported elsewhere.

Moreover, the observation that the derivative E-M78 displays the DYS392-12/DYS19-11 haplotype suggests that it also arose in East Africa. This is illustrated by the microsatellite network (fig. 3, shaded area), which reveals that the Ethiopian branch harboring DYS392-12 is not shared with either Near Eastern or European populations. — Semino et al. Origin, Diffusion, and Differentiation of Y‐Chromosome Haplogroups E and J, 2004.

The Ethiopian sample may not share the said allele with those populations mentioned, including the northwest African samples as far as the present author can tell, but it does share the said allele with the Senegalese sample [see fig. below], which would suggest that the Senegalese M78 derivative didn’t come from interaction with its northwest African neighbors; rather, they may well be relics of ancient migrations from east to west.

For larger image, click on this link: Source

So what do all these genetic indicators say?

Senegalese sample has the highest concentration of haplotype 24 and the lowest concentration of haplotype 22 - making it the most likely ancient Hg E3a bearing group, it also has higher Hg E3 vis-a-vis other Niger-Congo speaking group of west Africa, has the higher Hg E-M35* vis-a-vis other Niger-Congo speaking groups not neighbouring major "ancient" populations of east Africa or south Africa [aka KhoiSans], and has the rare Ethiopian/East African 12-repeat allele at the DYS392 locus.

The advent of Hg E3a itself coincides with the rise of the Ogolian aridity, which rendered much of North Africa to as far as beyond the Niger River bend largely inhabitable, inducing populations to be densely populated south of the Sahara, which is therefore the likely region of the rise of TMRCA of Hg E3a bearers.

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 Hg 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 Hg E3a distribution in west Africa.

All this becomes even more apparent, when one realizes that Hg E3 (PN2 clade) is quite rare even in sub-Saharan west Africa, but even rarer in the Sahara. It has the highest frequency in sub-Saharan east Africa [Ethiopia], where it is deemed to have originated— and so, the likelihood of the emergence of Hg E3a in a region with significantly higher frequencies of Hg E3 makes more sense than vice versa.

The above are all the reason the present author found it particularly simplistic in a discussion that he was a part of in the past, a strange question asked by a discussant, as to how one could possibly reconcile 'high diversity and frequency' of Hg E3a in west Africa with the prospect of its origins outside of west Africa; that question was no doubt a mentality born out of lack of familiarity with genetics and how multidisciplinary science works.

Update!

Getting back to the point raised earlier about the rare 12-repeat allele at DYS392 by Semino et al...

It is interesting that both E-P2* and E-M35* and their derivatives, E-M78 and E-M123, exhibit in Ethiopians the 12-repeat allele at the DYS392 microsatellite locus, an allele scarcely seen (Y-Chromosome STR Database), especially in other haplogroups and other populations (A.S.S.-B., unpublished data). 

In addition, the Ethiopian DYS392-12 allele is usually associated with the unusually short DYS19-11 allele, which is typical of this area. These findings are not easily explained. One possible scenario is that an ancient differentiation of the E-P2 haplogroup occurred in loco (East Africa). However, this also implies a low mutability of the associated microsatellite motif (DYS392-12/DYS19-11). Alternatively, the microsatellite motif may be due to homoplasy.The first scenario is more likely, since this unique microsatellite haplotype occurs in E-P2*, E-M35*, and E-M78 but is almost *absent in all other haplogroups and populations*.

In addition, the high stability of the DYS392 locus (Brinkmann et al. 1998; Nebel et al. 2001) and of the shorter alleles of DYS19 (Carvalho-Silva et al. 1999) has been reported elsewhere.
Moreover, the observation that the derivative E-M78 displays the DYS392-12/DYS19-11 haplotype suggests that it also arose in East Africa. This is illustrated by the microsatellite network (fig. 3, shaded area), which reveals that the Ethiopian branch harboring DYS392-12 is not shared with either Near Eastern or European populations. — Semino et al. Origin, Diffusion, and Differentiation of Y‐Chromosome Haplogroups E and J, 2004.

To which the present author responded...

The Ethiopian sample may not share the said allele with those populations mentioned, including the northwest African samples as far as I can tell, but it does share the said allele with the Senegalese sample [see fig. below], which would suggest that the Senegalese M78 derivative didn’t come from interaction with its northwest African neighbors; rather, they may well be relics of ancient migrations from east to west.

Cruciani et al. in their 2007 publication, Tracing human male movements in northern/eastern Africa and western Eurasia: new clues from Y-chromosomal haplogroups E-M78 and J-M12, had this to say about the 12-repeat allele in question:

“An eastern African origin for this haplogroup was hypothesized on the basis of the basis of the exclusive presence in that area of a putative ancestral 12-repeat at the DYS392 micro satellite , found in association with E-M78 chromosomes (Semino et al. 2004). North-eastern African populations were not represented in that study.

In order to test this hypothesis, we analyzed for DYS392 a geographically widespread subset of the E_M78 chromosomes here identified. We observed that the DYS392 12-repeat allele is associated with the majority of the chromosomes belonging to the north-eastern African E-V12* (15 out of 18) and to the eastern African E-V32 (21 out of 23), with about half (9 out of 21) of the E-V22 chromosomes (both in eastern and north-eastern Africa), with a few of the European E-V13 (2 out of 23) and with some north-African E-V65 (3 out of 16) chromosomes.

These findings show that the DYS392 12-repeat allele is common in different regions characterized by high frequencies of E-M78, and suggest that it was most likely generated by multiple mutation events occurring in different UEP-defined sub-haplogroups. Thus, the DYS392 allele distribution is not informative to infer the place of origin of E-M78 chromosomes.”

Cruciani et al. point out that Northeast Africa wasn't represented in the 2004 Semino et al. study, presumably to emphasize the point that its detection therein would have shown that the 12-repeat allele in question wasn't confined to sub-Saharan east Africa, particularly Ethiopia. It is certainly true that northeastern Africa was not represented, but in fact, a close examination of Semino et al.'s 2004 study, shows that the 12-repeat allele wasn't confined to sub-Saharan east Africa; it makes single or very low appearances in the "Near Eastern" and "European" samples, and interestingly none in north African [sans northeast Africa] samples.

Cruciani et al. on the other hand, did detect the 12-repeat allele in north African [sans northeast Africa], but still in relative low frequency (3 out of 16). The same applies to their findings in European samples, where it appears to be yet rarer than that of the north African samples. Considerable frequency is however noted in their northeast African sample, and consistently, in sub-Saharan east African samples. So, even going by Cruciani et al.'s findings, the greater distribution of the 12-repeat allele in eastern Africa in general, would argue for its introduction from eastern Africa.

Cruciani et al. reckon that simply because the 12-repeat allele is not confined to east Africa, it therefore doesn't allow one to infer the place of origin of E-M78 bearing chromosomes. This ignores the point just made about its relatively rare occurrence outside of east Africa. Cruciani et al. reach this conclusion on the understanding that the 12-repeat allele's appearances in distinct sub-clades invokes homoplasy or parallel mutational events, and indeed, Semino et al. 2004 did not rule out that possibility, but unlike Cruciani et al. they took additional material into consideration:

1) "It is interesting that both E-P2* and E-M35* and their derivatives, E-M78 and E-M123, exhibit in Ethiopians the 12-repeat allele at the DYS392 microsatellite locus, an allele scarcely seen..."

So while there is notable presence of 12-repeat allele bearing E-M78 chromosomes in northeast Africa as well, only in sub-Saharan east Africa does one come across not only considerable frequencies of E3-P2 [PN2 clade], but also the more immediate precursor of Hg E-M78, i.e.— Hg E-M35*, which bear this 12-repeat allele. As far as the present author can discern at this point, pending introduction to studies that suggest otherwise, the ensemble of at least three different PN2 macro-clades—including the ancestral ones—bearing the said "12-repeat allele" only occurs in sub-Saharan east Africa. Case in point:

"...first scenario is more likely, since this unique microsatellite haplotype occurs in E-P2*, E-M35*, and E-M78 but is almost *absent in all other haplogroups and populations*."

2) "One possible scenario is that an ancient differentiation of the E-P2 haplogroup occurred in loco (East Africa). However, this also implies a low mutability of the associated microsatellite motif (DYS392-12/DYS19-11)...

In addition, the high stability of the DYS392 locus (Brinkmann et al. 1998; Nebel et al. 2001) and of the shorter alleles of DYS19 (Carvalho-Silva et al. 1999) has been reported elsewhere."

So again, while not ruling out independent parallel microsatellite mutational events across different PN2 clades, the repeat occurrence of the 12-repeat allele across different PN2 clades, including the ancestral ones, coupled with the possibility of "low mutability", which translates into "high stability" of the locus in question, indicates that the 12 repeat could well have also been inherited from a precursor PN2 clade(s). If the latter is the case, certainly sub-Saharan East Africa as the likely place of origin for the allele, can be put forward as a strong argument. And in getting back to the appearance of this allele in sub-Saharan or Sahelian west Africa, in the Senegalese sample for instance, would tend to favor an east African origin at some point in history, rather than as a remnant of interactions with coastal northwest Africans, where the allele is rare, even going by Cruciani et al.'s findings.