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. 

Science has answers - II: God is Not Necessary for the Creation of the Universe - Says Stephen Hawking

This entry is the continuation of an earlier entry on the genesis of the universe, and perspectives on that issue, both from scientific standpoint and theological standpoint. Here, the main focus will be on the "life" aspect of the universe. Read the first part of this topic: Here

ATI one-stop referential page for notes on DNA studies

Reviews on mtDNA studies:

Haplogroups L0, L1, L2 & L3

Mitochondrial DNA M1 haplogroup: A Response To Ana M. Gonzalez et al. 2007

L1, L2 & L3 haplogroups: mtDNA Analysis of Nile River Valley Populations

"Ethno-specific" markers?

Who were the Ancient Israelites? A Multidisciplinary search for Answers

Image Caption: "Parting of the Red Sea", during the alleged emigration of ancestors of Jewish people, made famous by the biblical legend. Click on the image for enlargement

Introduction: 

 

Over the years, this has become an age-old question: Who were the ancient Israelites, really? In what capacity did they actually exist, or what not, and do biblical stories around their eponymous ancestors and rulers reflect actual events?

This is actually a topic that came to attention quite a few years back, and to this day, the topic is controversial as ever. Part of the reason it is controversial, is the religious loyalties of elements both within and outside academia, that said persons want to defend. The other, which like the just-mentioned, probably goes without saying, is apparently longstanding identity/racial politics which certain camps are intent on passionately defending.

On the academic front, say for example—Egyptology, those who do not wish to shake up long held traditional narratives—usually highly romantic portrayals that have become cemented in many minds, with the aid of the likes of Hollywood—of what went down in ancient Egypt (Kmtnwt), and are perhaps in part inspired by biblical narratives, are also very reluctant to look at the subject at different, perhaps refreshing and more sober, angles. Whatever the camp, these ideologues generally share in common, resistance to re-examining their prevailing perceptions/preconceptions in the face of ongoing inflow of strongly substantive material, which challenge said viewpoints.

An Interesting Encounter...

Several months back, in a forum discussion, the present author came across something quite interesting on the website of the owner of the said forum—going by the name of F. W. Sweet, and this is what it says/said:

"It seems that Dr. Shriver’s maternal grandfather moved from Pennsylvania to Iowa, then to California, leaving behind in the process most of his ties with his relatives.23 Dr. Shriver, it turns out, (see photograph above) is one of the 74 million White Americans with significant recent African genetic admixture.

In a coincidentally similar fashion, Dr. Rick Kittles, Shriver’s collaborator from Howard University in Washington, discovered that he carries the FY-null genetic marker at genome position 16q24.3. This marker is found in 998 out of every thousand Europeans but found in only one out of thousand Africans. Many of Dr. Kittles’s other ancestry-informative markers tell the same unexpected story. Dr. Kittles (see photograph above) is one of the many Black Americans with strong European genetic admixture. And yet, and there is no other way to say this, Dr. Shriver “looks White” and Dr. Kittles definitely “looks Black.” Why is there such a discrepancy between measured genetic admixture and physical appearance?" - by F. W. Sweet

At the time, this is what the present author posted in response to the extract:

Yes, I’ve seen both Dr. Shriver’s and Dr. Kittle's appearance, and I must say, it is hard to believe that either have low European or African recent ancestry respectively. If indeed the labeled sample belonged to either party, assuming that the said alternative coincidences did not arise from any probable technicality in the labeling, then I can only come to the conclusion that, the DNA sites examined as such, were made possible because those sites were kept intact in either one of their immediate parents, and if Shriver’s mum’s reaction is any indicator to go by, upon hearing the news, these markers would have been kept intact in her “white-appearing” father. Speaking of father, according to Mr. Shriver, how did he reach the conclusion that it had to be from his mother’s dad’s side, and not necessarily from his mother’s maternal side? Also, could it not have come from his father's side, and if not, why? Were many of the said ‘markers’ deemed to have been sex-biased in their genetic transmission?

I had the result for two or three years before I even looked up the ID number of the person whom we tested. I looked at who it was and it was me! I checked myself and the rest of my relatives and tracked it through my family. I never considered that there were any African people in my family. There’s no real variation in my family. The admixture must have been pretty far back. It just so happens that we can detect it with the markers we have. My mom especially stood out as being surprised, maybe because I told her it was coming through her father. She still doesn’t believe it about her family! The part of Pennsylvania where my mother’s father came from is where the Underground Railroad ended. There are several towns right here in Southern Pennsylvania where there are very light-skinned African-American communities that are the remnants of the Underground Railroad. - by Shriver

So, not only would those markers have to be deemed “invisible” in terms of their impression on phenotype, but they would have had to remain intact to account for their genetic integrity throughout the parent-to-offspring transmissions for at least a few generations. For Dr. Kittles to retain that level of melanin, it occurs to me that he’d had to have been a product of a union between parents from families that had maintained endogamy for at least a few recent generations, likely of families that have had long enough tradition of socially identifying with the “black“ or “colored” community. I suspect, since I cannot say for certain without independent corroboration, that either of these two researchers would likely indirectly clue us in on this possibility through either paternal and/or maternal DNA markers, which by normal account, correspond to Y-chromosome markers and mtDNA respectively. Either that, or else more “AIM” would have been needed to be identified to account, if not *indirectly*, for the genetic component counterparts of their ancestors who were responsible for transmission of their phenotypic appearance - as is the case with skin color and hair texture for example. I realize these traits have their own markers, but I'm referring to the broader hereditary component of the parties who were primarily responsible for transmitting those traits. It is hard to imagine that only those 'visible' markers of those ancestors withstood the test of time, while every other component of their genetic transmission was swamped through the generations, particularly for 'immediate' family households who would swear that the maternal and paternal lines of the said family come predominantly from one ethnic endogamous group [be it "white" or "black"].

With regards to piece about Kittle’s ancestry, this was said:

In a coincidentally similar fashion, Dr. Rick Kittles, Shriver’s collaborator from Howard University in Washington, discovered that he carries the FY-null genetic marker at genome position 16q24.3. This marker is found in 998 out of every thousand Europeans but found in only one out of thousand Africans. - by F.W. Sweet

But in the tables provided, this location should have been associated with MC1R-314*, and not the FY-null marker, which is supposed to have been located at 1q23.2. Was this a typo, or something else is at work here?

And indeed, that was a typo, as the author himself admitted, upon my issuing of the notification above. If indeed the typo was in wrongly naming the loci, which it appears it is/was, then MC1R-314*'s — an allele known to prevalent in folks of recent African ancestry — location in Mr. Kittles' sample should come as no surprise.

Short of some extraordinarily rare situation of these two geneticists — aka Shriver and Kittles — being products of union between a) a parent heterozygous at certain loci linked to outward phenotype traits like skin color, eye color, hair thickness et al., which are generally observed predominantly in one geography than another or in one ethnic group than another, and a parent largely homozygous across said loci, b)OR else, between parents who happen to both be heterozygous at some or the other section of said loci, wherein the offspring [in this case, either Shriver or Kittles] somehow wound up being largely homozygous across said loci, from the look of things, there are very strong indications here that what Shriver was actually looking at as his own, might well have been Rick Kittles' DNA sample, and likewise, Shriver's DNA sample was mistaken for Kittles'. There might have been a technicality at the lab [could be labeling mishap for example, though some other yet-to-be-determined factor(s) could have been the cause] , which somehow escaped both Shriver's and Kittles' attention, and so, they took it for granted, no matter how awkward the results turned out to be, as their own, respectively. This would explain the seemingly reverse results for each candidate, who coincidentally, were partners on research work. Short of specific independent corroboration, obviously this amounts to conjecture on my end; let's just say that I'm throwing out there, a possible scenario for what could have accounted for the results we are told about, aside from considering one of those rare genealogical situations. One thing most of us would agree on, is that those results are certainly interesting!
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*Further reading:

— Skin pigmentation gene alleles

— Skin pigmentation gene alleles — Part 2

Lactose Tolerance Phenotypes in Africa

NY Times [italicized extract below] — On the findings that Sarah Tishkoff and her team found, as have others too, showing that the C−13.9kbT allele which is determined to be a predictor of lactose tolerance in Europe, has not been effective in predicting lactose tolerance in Africa, even though this is a continent where lactose tolerance amongst various groups, particularly those that practice pastoralism, has been well documented. The reason for this phenomenon is 'convergent evolution', wherein several distinct alleles different from the European examples appear to be promoters of lactose tolerance...

Geneticists wondered if the lactose tolerance mutation **in Europeans**, identified in 2002, had arisen among pastoral peoples elsewhere.

But it seemed to be largely absent from Africa, even though pastoral peoples there generally have some degree of tolerance...

After testing for lactose tolerance and genetic makeup among 43 ethnic groups in East Africa, she and her colleagues have found three **new** mutations **all independent of one another** and **of the European mutation**, that keep the lactase gene permanently switched on.

Meanwhile, what needs to be understood when considering lactose tolerance situations in Africa, courtesy Mulcare et al. 2004…

—1) Lactase persistence varies widely in frequency among different human populations, both between and within continents.

Examples of within continents variations...

*E.g. 1 - in Europe itself variation is apparent - Almost all Dutch people and 99 percent of Swedes are lactose tolerant, but the mutation becomes **progressively** less common in Europeans who live at increasing distances from the ancient Funnel Beaker region - NY Times, an article on Sarah Tishkoff's 2004 findings on lactase phenotypes in African samples.

*E.g. 2 - Southern Europeans generally showed lower lactose tolerance phenotypes than regions to their north.

*E.g 3 - After testing for lactose tolerance and genetic makeup among 43 ethnic groups in East Africa, she and her colleagues have found three **new** mutations **all independent of one another

Example of between continents variation:

*E.g. - After testing for lactose tolerance and genetic makeup among 43 ethnic groups in East Africa, she and her colleagues have found three **new** mutations **all independent of one another** and **of the European mutation**, that keep the lactase gene permanently switched on.

—2) To date [as of 2003], there have been no reports of allele frequencies for the C−13.9kbT polymorphism in populations living in Africa.

[as of 2004] The frequency of −13.9kb*T type was low or zero in most of the African groups tested. In relation to this, we have the following examples:

*E.g. 1 - In the African populations, the −13.9kb*T allele was only found in a few individuals; all but one of these individuals were from Cameroon, [and these were in the main, ancestral or paraphyletic R1*-M173 carriers]

*E.g. 2 - It is noteworthy that −13.9kb*T was not found in East Africa at all, even though the data sets included many known pastoralists and groups with a high frequency of lactase persistence.

—3) Previous studies of African populations showed variation in the frequency of lactase persistence among population groups, as well as a complex pattern of distribution (reviewed in Flatz 1987; Holden and Mace 1997; Swallow and Hollox 2000).

African populations display multiple lifestyles, with milk-drinking and non–milk-drinking groups often living in close proximity, and have complex demographic histories. Some examples below:

* E.g. 1 - Pastoralists, such as the Fulbe in Nigeria, typically have higher frequencies of lactase persistence than nonpastoralists in the same country—for example, the Yoruba and Igbo

* E.g. 2 - The lactase-persistence phenotype is usually observed at low frequencies in Bantu- and Khoisan-speaking groups (<20%); Comparisons of the predicted frequencies of lactase persistence, deduced from the frequency of −13.9kb*TT and −13.9kb*CT genotypes, with the reported frequencies obtained from lactose-tolerance testing, showed these were significantly different in all of the African populations except the Fulbe and the Hausa.

—4) Why it is misleading to use reports for African American candidates as representative of lactose tolerance phenotypes amongst Africans:

*Although the −13.9kb*T allele frequency in Americans with African ancestry is consistent with their lactase-persistence frequency (Enattah et al. 2002), there is known to be substantial admixture between African Americans and European Americans (Parra et al. 1998)

So, African American examples of the C-13.9kbT alleles could represent introgression from European Americans, since as already noted above, at the time of Mulcare et al.’s study, “To date, there have been no reports of allele frequencies for the C−13.9kbT polymorphism in populations living in Africa” and Mulcare et al. themselves found that “the frequency of −13.9kb*T is too low to explain the observed frequency of lactase persistence.”

*In relation to point 3 at the top - Though African American gene pool are largely reflective of those of their ancestral African populations, it doesn’t represent the overall gene pool of Africa, and it may well have been subjected to some micro-evolutionary processes, however low, since the time of separation from source African populations, including — as noted above — bidirectional genetic introgression with populations that are otherwise rarely geographically proximate to African populations.

*African American lifestyles may not necessarily parallel those of their respective ancestral populations and other African populations.

And as already noted, but not the least…

—5) While the C−13.9kb*T allele has been proclaimed to be a predictor of lactose tolerance in Europeans [see Enattah and colleagues (2002)], Mulcare et al.’s results show that the −13.9kb*T allele cannot be causal of lactase persistence in most Africans [although it could possibly explain lactase persistence in some Cameroonians].

Other reading:
More on R1*-M173 bearers

P2 Clades: The Arrival of E3a and E3b Haplogroups

The MAJOR PN2 CLADES - E3a and E3b haplogroups: Investigating the backdrop against which they came about.

Recently, it has been proposed that E3b originated in sub-Saharan Africa and expanded into the Near East and northern Africa at the end of the Pleistocene (Underhill et al. 2001). - Cruciani et al. 2004, Phylogeographic analysis of haplogroup E3b...

We hear much about E3b and E3a haplogroup bearing populations in Africa, the major haplogroups on the African landscape today, but when and where did these lineages likely come about?

Here is what the present author of the blog thinks occurred, based on the information available to the author:

Between 23 and 18ky ago—Ogolian period begins, which coincides with and is likely connected to the LGM weather situation.

23,000 BP ~ 21,050 BC: "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 ]

—Much of North Africa and the Sahara are characterized by adverse weather conditions, with much of the region turning arid. The Sahara at this time, extends south beyond its current boundaries to a certain point, possibly a little beyond the Niger bend.

Arid conditions extend all the way to the "horn" coast of the African Horn region, possibly encouraging populations to reside more inwards—away from that horn-shaped coastal region; rather, likely towards the region straddling southern Sudan, Ethiopia, Kenya and Uganda or even further—region straddling Uganda, Kenya, and Tanzania.

—PN2 clade (E3) bearers in the vicinity of the Sudanese-Central African Republic -Ugandan-Kenyan region give rise to E3a ~ between 21 and 18 ky ago [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. At this time, it was likely the M78 derivative that came about ~ between 19 and 15 ky ago. It was also likely during this period, that some E3b-M35 variants spilled over to the "southwest Asia", which would be identified as E-M34. The E-M78* likely arose somewhere in the bidirectional-migration route between Northeast and sub-Saharan East Africa; this location was likely in the region straddling upper Egypt and Sudan of the eastern Sahara, amongst earlier E-M35 migrants from sub-Saharan East Africa. These M78 bearers were increasingly pressured to move further south due to progressive aridity, possibly as far as Uganda-Kenya and/or Tanzanian general region.

—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.

10th millennium BC ~ 12ky ago: At Ounjougou—"It is not until the Holocene and the return of humid climatic conditions, beginning in the 10th millennium BC, that it is possible to again observe evidence of human occupation." — Aziz Ballouche [see: Link ]

"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...

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 ]

It's very probable that this E3a bearing group(s) came into contact with the then wandering earlier-inhabitants of west Africa, who would have been pressured to move southward beyond the then Saharan desert boundaries, due to progressing aridity of the Ogolian period. These groups could have brought their central-Saharan pottery [e.g. found in Niger] traditions with them [developed perhaps sometime during the transitioning period to the wetter phase of the Sahara], just as the E3a bearing group(s) brought the microlithic traditions that they possibly picked up in the vicinity of the Shum Laka region [see above excerpt carbon dating estimations of finds] …and/or else…the new migrants produced their own versions of pottery in their new found location [as it is not noted whether these pottery had affinities with examples found in the aforementioned central Saharan region], at a time when it was trendy to carry stuff in pottery ware in the Saharan-Sahelian zone, with the filling up river systems due to the Monsoon rains.

The 10,000 and 9,000 BC (Phase 1 of the Holocene in Ounjougou): "The first sedimentary sequence of the Holocene can be observed at the Ravin de la Mouche. It's a channel dug into yellow Pleistocene silt and filled with coarse grained sand and pebbles. As a chronological reference for the upper levels of this early Holocene site, we hold ten radiocarbon dates between 9400 and 8400 BC cal. The associated lithic industry evidences predominantly a unidirectional mode of debitage. But also other technologies, such as bipolar on anvil or multidirectional, have been applied by the Early Holocene population. The raw material mainly used was quartz. The typological range consists of small retouched flakes, geometric microliths and perçoirs, but also of continuously retouched bifacial arrowheads and backed points." — Human population and paleoenvironment in West Africa [see: Link]

"By" 11,000 years BP ~ by 9050 BC:

"The age of the sediment in which they were found suggests that the six ceramic fragments discovered between 2002 and 2005 are at least 11,400 years old. Most ancient ceramics from the Middle East and the central and eastern Sahara regions are 10,000 and between 9-10,000 years old, respectively." — Human population and paleoenvironment in West Africa [see: Link]

By the 'beginning' of 8,000 BC: "Outstandingly, there has been evidence of the presence of pottery and seed grinding implements since at least the beginning of the 8th millennium BC. It is therefore the oldest site. The eighth millennium (Phase 2 of the Holocene in Ounjougou) known of this socio-economic type in sub-Saharan Africa...

The pottery and the seed grinding implements of phase 2 of Ounjougou are the oldest artefacts of this type known at present in sub-Saharan Africa. To current knowledge, the pottery of Ounjougou could either have been invented in the actual Sudano-Sahelian zone or been imported from the Central Sahara, where there has been evidence since the ninth millennium BC. Still, the oldest pottery known in the Sahara, from the site of Tagalagal in Niger, is already quite diversified at the moment of its appearance, possibly meaning that the technique has been introduced.

The lithic industry of the phases 1 and 2 on the other hand shows similarities to both more southern and Saharan industries. Quartz microliths, obtained through bipolar debitage on anvil, are a characteristic of the West African techno-complex according to Kevin MacDonald. Bifacially retouched arrowheads, in contrast, are specific for Saharan production." — Human population and paleoenvironment in West Africa [see: Link]

"The eighth millennium (Phase 2 of the Holocene in Ounjougou): The subsequent Holocene sequence is well documented by two principal sites, the Ravin du Hibou and Damatoumou. The archaeological levels can be quite clearly chronologically placed by means of a date obtained through OSL measurements (9420±410 Ka) and seven radiocarbon dates (between 8000 and 7000 BC cal). The lithic industry, exclusively quartz, is characterised by unidirectional, bidirectional and peripheral debitage, as well as by bipolar on anvil. There are essentially microlithic tools: perçoirs, backed points, notched pieces, denticulates, scrapers, retouched flakes and geometric microliths. Some small bifacially retouched arrowheads were also found on those sites. At the Ravin du Hibou, seven sherds have been found during excavation. They are heavily fragmented and thus preventing the reconstruction of the form of the vessel. Quartz has always been used as a temper. In just a single case, grog has been used in addition. Two shards show identifiable decorations. Two different techniques have been used: A rolled impression, possibly made with a peigne fileté souple or with a cordelette, and a simple comb impression. There were also seed grinding implements discovered at the Ravin du Hibou, a fragment of a seed grinding stone and a cylindrical upper grinding stone." — Human population and paleoenvironment in West Africa [see: Link]

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On the DNA side:

If we look at the samplings undertaken thus far, the west African populations on Atlantic-bordering west coasts—like the Senegalese samples, these groups undoubtedly have amongst the highest frequencies of E3a lineages, but there is something to be discerned: These groups largely carry M2, P1, and M180 lineages devoid of the M191 mutation, perhaps indicating the earlier E3a bearers, while many of the Bantu speaking groups of central, east and southern Africa carry those 191 derivatives:

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. — Cruciani et al. 2002

The above suggests that the oldest E3a bearing population(s) ultimately moved to the far west corner of the continent.

From Semino et al. 2004, we have:

It is also of interest, that the Senegalese samples have higher E3* frequency, which attains its highest frequency in Ethiopian populations, than the Bantu speaking groups, where the only group tested positive, was that of the South African Bantu sample:

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 Senegalese sample also bears the E-M.35* 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%

E-M78 in descending order….

Arab Morocco = 42.9%, Oromo = 35.9%, Amhara = 22.9%, Sudan =17.5%, Tunisian = 15.5%, Berber (Southern Morocco) = 12.5%, Arab (Morocco) = 11.4%, Berber (Morocco) = 10.9%, Algerian (32) = 6.3%, Berber (north central Morocco) = 1.6%, North Cameroon = 1.3%, Senegalese =.7%

E-M81 in descending order…

Saharawish (North Africa) = 75.9%, Berber (Morocco) = 68.7%, Berber (north central Morocco) = 65.1%, Berber (southern Morocco) = 65%, Algerian = 53.1%, Arab (Morocco) = 52.3%, Arab (Morocco) = 32.6%, Mali = 29.5%, Tunisian = 27.6%, Sudan = 5%, Senegalese = .7%

E-M33 in descending order…

Mali = 34.1%, North Cameroon = 7.9%, Senegalese = 5%, Burkina Faso = 3.8%, Saharawish (North Africa) = 3.4%, Berber (north‐central Morocco) = 3.2%, Sudan = 2.5%, Berber (Morocco) = 1.6%

E-M75 in descending order…

Bantu (South Africa) = 15.1%, Burkina Faso = 11.3%, Khoisan (South Africa) = 4.6%, Sudan = 5%, North Cameroon = 3.3%, Senegalese = 2.9%, Ethiopian (Oromo) = 1.3%

Looking at this data, among predominantly E3a-bearing Niger-Congo language speakers, Senegalese groups have the highest E3* frequency, as well as E-M35*. It follows the North Cameroon sample in this instance, in the E-M78 frequencies - though I’m not sure if those North Cameroon samples comprise of Niger-Congo speaking groups, Nilo-Saharan or some other language phylum group. In west Africa, it succeeds only Mali [and Niger, which wasn‘t included in this sample]—as one of the areas which have considerable Niger-Congo speakers—to have E-M81 bearing candidates, but then, Mali is also well known for its Saharan Tamazight speakers.

In reference to the above, some might look at a lineage as, say E-M78 and imagine it to be a trace of interaction with Saharan or coastal North African Afrasan speaking groups, but microsatellite inspection would indicate otherwise:

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 [b]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.

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, 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.

http://www.journals.uchicago.edu/na101/home/literatum/publisher/uchicago/journals/production/ajhg/2004/74/5/386295/images/medium/fg3.gif Source: Semino et al., Origin, Diffusion, and Differentiation of Y‐Chromosome Haplogroups E and J, 2004.

Some time during post 11ky ago expansions into the wet Sahara, before its return to aridity, with activity going on across the Saharan expanse, like cattle domestication for example, E3a bearers spread well into central-east Sahara. It was likely during this period that HbS mutations were localized, with the oldest E3a bearing groups nearer to the Atlantic-hugging west coasts bearing the Senegalese haplotype, while the Benin haplotype was able to have a more far-reaching expansion northward and northeast ward, due its situation in Niger River Valley vis-à-vis North Africa and the rest of the Sahara.
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Additional references to those mentioned in the body of the post:

*Semino et al., Origin, Diffusion, and Differentiation of Y‐Chromosome Haplogroups E and J, 2004.

* http://www.esd.ornl.gov/projects/qen/nercAFRICA.html

*Knight et al. 2003 : http://www.bec.ucla.edu/papers/Mountain_3-7-05.pdf

*Cruciani et al. 2004, Phylogeographic analysis of haplogroup E3b.

* Cruciani et al. 2007, Tracing Past Human Male Movements in Northern/Eastern Africa and Western Eurasia: New Clues from Y-chromosomal Haplogroups E-M78 and J-M12.