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

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Introduction

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

Unwinding the Convoluted Character of the Emergence of Imazighen Groups

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

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

At least one study states this: 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Sarcophagus portion #1:

 
Sarcophagus portion #1 blown up below:




 
Sarcophagus portion #2 blown up below:

In ancient Egyptian artwork:

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

 

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

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


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

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

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

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

— As noted in the paragraphs.

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

U6: A standalone clade?

It is a lineage that spans west and east Africa, and spilling over to portions of southern Europe and "southwest Asia".

In looking at the following diagram...


For those with inadequate screen size, view the above image in full with: here

...it is apparent that at the least, U5 and U6 diverge into respective branches independent from that of the rest of U macro-haplogroup. Similar observation has been made about U1, which too, seems to have an independent branch from the rest of the U haplogroup. In other words, these three—either U1, U5 or U6—don't appear to have an ancestral clade within the main haplogroup U branch which is defined by the nucleotide transition at 1811 or vice versa. This is how it goes, courtesy of Maca-Meyer et al. 2003:

U6 is defined by two motifs represented by positions in the coding and HVR respectively: 3348 and 16172.

U5 is defined by the transitions at: 3197, 9477, 13617 and 16270.

And the rest of the U haplgroup [sans U1], defined by the mutation designated by position: 1811.

Maca-Meyer et al. add that:

U presents the following mutations with respect to rCRS: 73, 263, 311i, 750, 1438, 2706, 4769, 7028, 8860, 11467, 11719, 12308, 12372, 14766 and 15326. - Maca-Meyer et al. 2003

N macrohaplogroup is removed from the root of L3 by about 5 mutations, we are told. This is relevant, in that U haplogroup is often posited as having split from R, which derives from Haplogroup N. Speaking of haplogroup U splitting from R, we are told that this is the case via three mutations represented by: 11467, 12308 and 12372

Hence, the family association has been made between U6 [as is for U1 & U5] and the rest of the U haplogroup, primarily thanks to sharing of the above mentioned transition trio; if it weren't for these basic transitions, U6 would have likely just been considered as just another separate sub-branch of haplogroup R. Perhaps, if a clade was located—sharing the same transition trio but devoid of any known downstream coding or HVR mutations in either U6, U1 or U5 and the rest of haplogroup U, it could provide us with a possible candidate as the proto-U ancestor that gave rise to the divergent U branches in question. However, to date, no such lineage has come to light.

In their publication "The mtDNA Legacy of the Levantine Early Upper Palaeolithic in Africa" - 2006, Anna Olivieri et al.'s argument, like that of Gonzalez et al., depends on the idea that U6 entered Africa in a parallel dispersal with M1, which the present author has demonstrated elsewhere to be a weak hypothesis [see: Mitochondrial DNA M1 haplogroup: A Response To Ana M. Gonzalez et al. 2007]. M1 basal coding markers emerge from that of an African background, and the "missing-link" lineage of the M Macrohaplogroup was found in a sub-Saharan sample [specifically in a Senegalese sample].

Furthermore, Olivieri et al. 2006 themselves acknowledge:

An ancient arrival of M1 in Africa (or in its close proximity) is supported by the fact that none of the numerous M haplogroups in Asia (20, 21) harbors any of the distinguishing M1 root mutations, and by the lack of Asian-specific clades within M1 (and U6), as might be expected in the case of a more recent arrival. The arrival of M1 and U6 in Africa 40 to 45 ka would temporally overlap with the event(s) that led to the peopling of Europe by modern humans.

Not to mention...

Indeed, M1 and U6 in Africa are mostly restricted to Afro-Asiatic–speaking areas.

Why is that? Where did the Afrisan super language phylum emerge? Answer: East Africa.

And they say...

The hypothesis of a back-migration from Asia to Africa is also strongly supported by the current phylogeography of the Y chromosome variation, because haplogroup K2 and paragroup R1b*, both belonging to the otherwise Asiatic macrohaplogroup K, have been observed at high frequencies only in Africa (15, 16). However, because of the relatively low molecular resolution of the Y chromosome phylogeny as compared to that of the mtDNA, it was impossible to come to a firm conclusion about the precise timing of this dispersal (15, 16).

To which, elsewhere [see: R1*-M173 bearing chromosomes in Cameroon], I commented:

By the way, previous genetic research work made very enthusiastic attempts to correlate the likes of U6 and possible "Eurasian"-tagged mtDNA with R1*-M173, supposedly as an attempt to buttress a possible back-migration into Africa; all but failed, with results showing considerable African mtDNA gene pool instead, for populations bearing these chromosomes.

Not only is there lack of apparent parallelism between R1* paragroup distribution and those markers, as the authors seem to be so desperately yearning for, but also the paragroup is essentially absent in all Afrasan speaking groups but those in the Northeast African corner. The marker is even rarer in so-called Southwest Asia than it is in Africa.

Thus, the re-examination point:

— U6 with respect to U5 , or U6 with respect to U1, and U6 with respect to the rest of haplogroup U, doesn't share defining motifs, outside of the basic transitions, particularly at the aforementioned position trio.

— In relation to the above, U6 doesn't have a common recent ancestor that is a U5 sub-lineage or vice versa, U6 doesn't have a common recent ancestor that is a U1 sub-lineage or vice versa, nor does U6 have a common recent ancestor that is a U*(xU1, U5) sub-lineage or vice versa.

...brings us to the question of:

Could U6 then be a standalone clade, in that, short of the aforementioned basic mutations by which the U-designated lineages diverge from macro-haplogroup R — particularly at 11467, 12308 and 12372, it is essentially mutually-independent of the other U-designated lineages?

Simply put...

The relationship of U6 with other U haplogroups is only inferred from non-U subclade-specific basal markers.

U6 is a branch on its own, independent from other U groups, and proto-U6 has not been located to date.

Time will tell, as to whether much more improved resolution of mtDNA will bear out the possible candidate of the elusive proto-U6 ancestor, but until then, it would appear that the proto-U6 bearing population was quite small in size, such that proto-U6 itself would eventually be overwhelmed and essentially be erased by expansion of descendant U6 carriers and possibly, incursions from other populations. It is uncertain whether a proto-U6 ancestor would have been the very same ancestor that begot U1, U5 and U*(xU6,U1,U5) respectively elsewhere, or whether it would have been a single step or a few steps genetic-neighbor to those which begot the latter U groups, but it appears that the latter respective ancestors too were modestly represented 'population-wise', such that they too would have been overwhelmed by subsequent demographic expansions that gave rise to descendant populations and incoming groups from elsewhere. Whatever may be said about a proto-U6 ancestor's origin, one thing is clear: U6 itself is an autochthonous African marker, which would eventually spill over to parts of Europe, particularly those hugging the Mediterranean sea, and parts of "southwest Asia". It too, like M1 (clickable), has been implicated in the expansion of proto-Afrasan (aka proto-Afro-Asiatic) and/or Afrasan speakers outside of mainland Africa.
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*References:

— Maca-Meyer et al. 2003, Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography.

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

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

These studies may perhaps be forgiven for their shortcomings, when considering the dates of publication and the extant knowledge [in the field in question] at the time of publication. Nonetheless, for those who might be in the little know, a few things needed to be straightened out:

C. Fox, 1997:

mtDNA analysis in ancient Nubians supports the existence of gene flow between sub-Sahara and North Africa in the Nile valley

Abstract:

The Hpal (np3,592) mitochondrial DNA marker is a selectively neutral mutation that is very common in sub-Saharan Africa and is almost absent in North African and European populations. It has been screened in a Meroitic sample from ancient Nubia through PCR amplification and posterior enzyme digestion, to evaluate the sub-Saharan genetic influences in this population. From 29 individuals analysed, only 15 yield positive amplifications, four of them (26·7%) displaying the sub-Saharan African marker. Hpa I (np3,592) marker is present in the sub-Saharan populations at a frequency of 68·7 on average. Thus, the frequency of genes from this area in the Merotic Nubian population can be estimated at around 39% (with a confidence interval from 22% to 55%). The frequency obtained fits in a south-north decreasing gradient of Hpa I (np3,592) along the African continent. Results suggest that morphological changes observed historically in the Nubian populations are more likely to be due to the existence of south-north gene flow through the Nile Valley than to in-situ evolution.

Krings et al study, 1999:

mtDNA Analysis of Nile River Valley Populations: A Genetic Corridor or aBarrier to Migration?

To assess the extent to which the Nile River Valley has been a corridor for human migrations between Egypt and sub-Saharan Africa, we analyzed mtDNA variation in 224 individuals from various locations along the river. Sequences of the first hypervariable segment (HV1) of the mtDNA control region and a polymorphic HpaI site at position 3592 allowed us to designate each mtDNA as being of "northern" or "southern" affiliation. Proportions of northern and southern mtDNA differed significantly between Egypt, Nubia, and the southern Sudan. At slowly evolving sites within HV1, northern-mtDNA diversity was highest in Egypt and lowest in the southern Sudan, and southern-mtDNA diversity was highest in the southern Sudan and lowest in Egypt, indicating that migrations had occurred bidirectionally along the Nile River Valley. Egypt and Nubia have low and similar amounts of divergence for both mtDNA types, which is consistent with historical evidence for long-term interactions between Egypt and Nubia. Spatial autocorrelation analysis demonstrates a smooth gradient of decreasing genetic similarity of mtDNA types as geographic distance between sampling localities increases, strongly suggesting gene flow along the Nile, with no evident barriers. We conclude that these migrations probably occurred within the past few hundred to few thousand years and that the migration from north to south was either earlier or lesser in the extent of gene flow than the migration from south to north.

A Response to C. Fox and Krings et al.

The authors rely on just the hypervariable region, which as they acknowledge is known to be limited on the very probable potential of harboring "parallel mutations", and the absence or presence of the restriction enzyme identified site of HpaI site. They say:

Utilizing three sites in this manner should minimize incorrect classification of mtDNA types; however, because the two sites in HV1 are subject to repeated mutations (Hasegawa et al. 1993), we were concerned that some incorrect classification might nevertheless occur....

Approximately one-third of the Nile River Valley mtDNA types could be unambiguously classified on the basis of this database comparison; the results were nearly completely concordant with the classification based on the three sites, with the single discrepancy involving an Egyptian mtDNA that, on the basis of the three sites, was classified as northern but, on the basis of the database comparison, was classified as southern because it was identical to sequences found in two Songhai from Mali and two Kikuyu from Kenya (Watson et al. 1996). Because alteration of the classification of this one sequence does not significantly change any of the results that follow, this Egyptian mtDNA was still classified as northern, in accordance with the results from use of the three sites.

But what do we know of L3 based lineages, do they all have what the authors call?...

In addition, it has been proposed that the HpaI site at 3592 has a single origin in sub-Saharan Africa

Would M1 for instance have this site detected as positive?

The present author sees the method used herein, almost akin to using RFLP in Y chromosomes and microsatellite motifs, without having details on binary markers that could clearly define the monophyletic units themselves, thereby pooling otherwise different lineages based on absence or presence of certain restriction sites. We've seen this in the case of Y chromosomes, wherein E-M78, E-M81 and some other yet-to-be identified lineage were pooled together based on certain RFLP sequences, but when binary markers were tested, these related but distinct lineages came to the fore. Exclusively relying on three hypervariable segment sites for analysis, has definitely got to be one of the weakest aspects of this study, for reasons just mentioned.

In relation to the questions just asked above, we have:

The main sub-Saharan African haplotypes, thus, are characterized by a combination of 10394DdeI(+)/10397AluI(-)/3592HpaI(+) markers (haplogroup L, comprising the LI and L2 lineages) (Chen et al. 1995, 2000). A less frequent group of haplotypes lacks the African-specific 3592 HpaI marker [10394DdeI(+)/ 10397AluI(-)/3592HpaI(-)] (Chen et al. 1995, 2000) and has been designated as haplogroup L3 (Watson et al. 1997). A minority of African haplotypes (2.3% of Africans) lack all three of these mutations [10394DdeI(-)/10397AluI(-)/ 3592HpalI(-)]. Some align with the European lineage U (Chen et al. 2000), but a number of the mtDNAs belong to branches of the African haplogroup L3, itself derived from African haplogroup L1 (Watson et al 1997). — Clemencia Rodas et al., Mitochondrial DNA studies show asymmetrical Amerindian admixture in Afro-Colombian and Mestizo populations, 2003.

Note that even in the above piece, even though restriction enzyme markers allow for grouping into superphyletic units [in the case of those which were deemed to belong to the L3 supergroup, it isn't even that clear-cut, as there are those which lack all the restriction markers tested, and then there are those which harbor 10394 DdeI (+). L1 and L2 lineages on the other hand, seemed to have been pooled under that which tested positive for 3592 HpaI—as such, without further information, we are hardly told about which ones specifically fall into Hgs L1 and L2 respectively], these alone don't tell us much about the specific designated haplogroups or else subclades actually involved. *Distinct* subclades would have just been pooled under specific restriction enzyme identified sites, pending more information on subclade-specific characteristic or definitive markers.

At this point, the present author doesn't question the African origin of Hg M1, and by extension, the possibility of such for the *basic* characteristic motifs for the M macro-haplogroup; The present author merely brought Hg M1 up, as an example of one of the notable L3 derived lineages in East Africa, extending from the sub-Saharan region to the Northeast end. Hg M1 happens to occur predominantly in Africa. The present author's motive here is to get the reader to start thinking about the L3 lineage—which is just as African in origin as L1 and L2 lineages, but lack the so-called "African-specific" site. So, the fact that the term "African-specific" was used, might mislead someone to think that the other mtDNA lineages under study couldn't have also been African.

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

Ana M. Gonzalez et al. published a paper on M1 expansions, 9 July 2007, and a few things about it immediately jumped at the present author. The present author lays these out shortly following the abstract below, which is there to put potential viewers of this page on "the same page" so to speak, as far as the synopsis of the paper is concerned:

Abstract:

Mitochondrial lineage M1 traces an early human backflow to Africa

Ana M Gonzalez , Jose M Larruga , Khaled K Abu-Amero , Yufei Shi , Jose Pestano and Vicente M Cabrera

BMC Genomics 2007, 8:223 doi:10.1186/1471-2164-8-223

Published 9 July 2007

Abstract (provisional)

The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.

Background
The out of Africa hypothesis has gained generalized consensus. However, many specific questions remain unsettled. To know whether the two M and N macrohaplogroups that colonized Eurasia were already present in Africa before the exit is puzzling. It has been proposed that the east African clade M1 supports a single origin of haplogroup M in Africa. To test the validity of that hypothesis, the phylogeographic analysis of 13 complete mitochondrial DNA (mtDNA) sequences and 261 partial sequences belonging to haplogroup M1 was carried out.

Results
The coalescence age of the African haplogroup M1 is younger than those for other M Asiatic clades. In contradiction to the hypothesis of an eastern Africa origin for modern human expansions out of Africa, the most ancestral M1 lineages have been found in Northwest Africa and in the Near East, instead of in East Africa. The M1 geographic distribution and the relative ages of its different subclades clearly correlate with those of haplogroup U6, for which an Eurasian ancestor has been demonstrated.

Conclusions
This study provides evidence that M1, or its ancestor, had an Asiatic origin. The earliest M1 expansion into Africa occurred in northwestern instead of eastern areas; this early spread reached the Iberian Peninsula even affecting the Basques. The majority of the M1a lineages found outside and inside Africa had a more recent eastern Africa origin. Both western and eastern M1 lineages participated in the Neolithic colonization of the Sahara. The striking parallelism between subclade ages and geographic distribution of M1 and its North African U6 counterpart strongly reinforces this scenario. Finally, a relevant fraction of M1a lineages present today in the European Continent and nearby islands possibly had a Jewish instead of the commonly proposed Arab/Berber maternal ascendance.

-Abstract ends-

Present Author's Response To Ana M. Gonzalez et al.

*First, a quick synopsis of the samplings, with regards to where the n=261 M1 bearing samples come from, aside from the 588 participants mentioned in one of the tables [table 2] in the study:

From the present author's assessment of the table, it comes from the following numbers:

A total of 50 Europeans detected for M1.
A total of 154 for Africans.
A total of 28 Asians, barring 8 unknown Arabian haplotypes.
And a total of 29 Jews, who were lumped together from the various continents.
The sum of the above totals, amount to 261 "known" M1 lineages.

*With regards to the authors claim about M1 or its ancestor, having “had an Asiatic origin”, the following comes to mind:

The authors of the study at hand, themselves admit that they haven't come across M1 ancestor in either south Asia or southwest Asia. They also take note of its highest diversity in Ethiopia and east Africa. Yet through the shaky premise of their M1c expansion time frame estimations, they build a conclusion around it, by tying it to a dispersal(s) "parallel" to that of U6 - another African marker whose immediate common recent ancestor, namely proto-U6, appears to be elusive thus far.

Well, they wouldn’t be the only ones who have failed to come across any proto-M1 ancestor in southwest and south Asia [Indian Subcontinent mainly]:

Based on the high frequency and diversity of haplogroup M in India and elsewhere in Asia, some authors have suggested (versus [3]) that M may have arisen in Southwest Asia [16,17,31]. Finding M1 or a lineage ancestral to M1 in India, could help to explain the presence of M1 in Africa as a result of a back migration from India. Yet, to date this has not been achieved [15], this study). Therefore, one cannot rule out the still most parsimonious scenario that haplogroup M arose in East Africa [3]. Furthermore, the lack of L3 lineages other than M and N (indeed, L3M and L3N) in India is more consistent with the African launch of haplogroup M. On the other hand, one also observes that: i) M1 is the only variant of haplogroup M found in Africa; ii) M1 has a fairly restricted phylogeography in Africa, barely penetrating into sub-Saharan populations, being found predominantly in association with the Afro-Asiatic linguistic phylum – a finding that appears to be inconsistent with the distribution of sub-clades of haplogroups L3 and L2 that have similar time depths. — Mait Metspalu et al.

So, while they acknowledge the highest "frequencies and diversities" of M1 particularly in Ethiopia, and generally in East Africa [see below for reference], the authors base their claims about ’origins’ on their expansion estimations of M1c derivatives, presumably predominant in northwest Africa rather than east Africa, and its relative sporadic distribution in 'Europe' and 'Southwest' Asia. They attempt to buttress this, by invoking an initial parallel expansion of M1 and U6 "ancestor" lineages into north Africa via the Nile Valley [from "southwest Asia"], then an expansion from northwest Africa this time around, of U6 and M1 derivatives northward into Europe and then eastward into "southwest" Asia via the Nile Valley corridor in the Sinai peninsula, presumably with a few derivatives making their way into sub-Saharan east Africa, where they then underwent some expansion, to give rise to yet another, but later, dispersal from there into "southwest Asia" and hence, accounting for the 'majority' of M1 lineages in "southwest Asia" being east African derivatives than the north African [M1c] counterparts.

In Africa, haplogroup M1 has supra-equatorial distribution (see additional files 1 and 2). As previously reported its highest frequencies and diversities (Table 2) are found in Ethiopia in particular and in East Africa in general. Two appreciable gradients exist. Frequencies significantly diminished from East to West and also going South to sub-Saharan areas. M1 is not uncommon in the Mediterranean basin showing a peak in the Iberian Peninsula. However, it is rare in continental Europe. Although in low frequencies, its presence in the Middle East has been well established from the South of the Arabian Peninsula to Anatolia and from the Levant to Iran. - Gonzalez et al. 2007

*Furthermore,

The authors gather that their observations correlate with that of other researchers, namely Olivieri et al. (2006). To this extent, they put forth that Olivieri et al.’s M1b corresponds to their M1c, the former’s M1a2 corresponds to their M1b, and the former’s M1a1 corresponds to their M1a. They go onto to add that the coalescence ages arrived by the two research group [that of Olivieri et al. and that of the present authors] also correlate. The present authors note that their coalescence time for M1c (25.7 +/- 6.6 ky) overlaps with Olivieri et al.’s coalescence time for M1b (23.4 +/- 5.6). Similarly, they note that their coalescence age for M1a (22.6 +/- 8.1ky) falls within that of Olivieri et al.’s age for M1a1 at 20.6 +/- 3.4ky. However, this makes way for great discrepancy between the said authors and Olivieri et al., whereby their coalescence age for M1b at 13.7 +/- 4.8ky falls quite short of the latter’s age for M1a2 at 24 +/- 5.7ky. Not only are the subgroup nomenclatures distinct, but this latter discrepancy makes an unsubtle difference, so as to no longer render M1c to be older than M1b [in examining from the ongoing juxtapositioning, utilizing Olivieri et al.'s standpoint], but rather, either place M1c (Olivieri et al.'s M1b) at an age a bit younger or on par with the latter, which should be otherwise according to the present study. Though, by their own admission, the present authors favor Olivieri et al.’s methods over their own:


As our calculations are based only on three lineages and that of Olivieri et al on six, we think that their coalescence time estimation should be more accurate than ours. In fact, when time estimation is based on the eight different lineages (AFR-K143 is common to both sets) a coalescence age of 20.6 +/- ky is obtained.

*But if there is any indication about the tenuous nature of the above thesis, without going into other known details about M1, it would be this alternative viewpoint they came up with:

The alternative idea entertained by the authors, is one where M1 could actually be an autochthonous northwest African lineage, which spread northward into Europe and eastward to "Southwest Asia" and east Africa. Again, to be followed by a yet later dispersal from east Africa, likely sub-Saharan east Africa, particularly the Ethiopian populations.

*We've already seen the subjective nature of the present authors' age estimations, naturally attributable to biases underlying sampling procedures to some degree or another, as demonstrated above with the juxtapositioning of the findings of the present authors to those of Olivieri et al. (2006). Furthermore, erratic mutation rates would have undoubtedly affected the age estimation regime applied by the authors, however they may have downplayed the fact, as demonstrated by their observations surrounding the M1a2 subgroup, leading them to omit said subgroup in their lineage coalescence analysis. What makes this interesting, is that both group of authors sought to build their argument around parallel demic diffusion scenarios of U6 and M1, which has little in way of supporting material to stand on, notwithstanding the passionate efforts to push forward with argument; for instance in Olivieri et al.'s case, they say:

The hypothesis of a back-migration from Asia to Africa is also strongly supported by the current phylogeography of the Y chromosome variation, because haplogroup K2 and paragroup R1b*, both belonging to the otherwise Asiatic macrohaplogroup K, have been observed at high frequencies only in Africa (15, 16). However, because of the relatively low molecular resolution of the Y chromosome phylogeny as compared to that of the mtDNA, it was impossible to come to a firm conclusion about the precise timing of this dispersal (15, 16). - Olivieri et al. (2006)

One can almost sense Olivieri et al.'s venting their frustrations from not getting the "desired" results out on the supposed "relatively low molecular resolution of Y DNA", but indeed, as noted here earlier:

Previous genetic research work made very enthusiastic attempts to correlate the likes of U6 and possible "Eurasian"-tagged mtDNA with R1*-M173, supposedly as an attempt to buttress a possible back-migration into Africa; all but failed, with results showing considerable African mtDNA gene pool instead, for populations bearing these chromosomes.

Gonzalez et al. (2008) also fall into that trap; guess where they look towards, to make a connection between an M1 dispersal [supposedly parallel to a U6 one] and a "Middle Eastern" origin part of their argument? Interestingly, it happens to be from the same Dead Sea sample which was implicated in a clear genetic link with sub-Saharan and Eastern African groups. This is the same Dead Sea sample set that shared R1*-M173 with northern Cameroonian sample set, other African groups with these markers. This is also the same Dead Sea sample set with African G6PD-A alleles that were rare to absent in neighboring groups. And Gonzalez et al. (2008) tell us, that this is also the same sample set which is again distinguished from those of neighboring group in its higher "south of the Sahara" mtDNA markers:

Statistical analysis revealed that, whereas the sample from Amman did not significantly differ from their Levantine neighbours, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its outstanding Eurasian haplogroup U3 frequency (39%) and its south-Saharan Africa lineages (19%) are the highest in the Middle East. On the contrary, the lack ((preHV)1) or comparatively low frequency (J and T) of Neolithic lineages is also striking. Although strong drift by geographic isolation could explain the anomalous mtDNA pool of the Dead Sea sample, the fact that its mtDNA lineage composition mirrors, in geographic origin and haplogroup frequencies, its Y-chromosome pool, points to founder effect as the main cause. - Gonzalez et al. (2008)

They acknowledge above that the "anamolous" character of the Dead Sea sample's Y-DNA pool "mirrors" its mtDNA gene pool, which too is replete with markers mostly found in Africa, including the aforementioned rare paraphyletic R1*-M173. However, something interesting happens, with regards to this Dead Sea sample of an "isolated" group:

Ancestral M1 lineages detected in Jordan that have affinities with those recently found in Northwest but not East Africa question the African origin of the M1 haplogroup.

Interesting, because these the same M1c chromosomes being referred to here, and whose specifics have been dealt with. Despite the apparent post-OOA emigration ties between the African groups and the Dead Sea community, reflected in not only both Y-DNA and mtDNA, but also in the X chrosome markers, Gonzalez et al. (2008) still come to the odd conclusion that its presence in the Dead Sea sample set somehow offers some sort of a challenge on the African origin of M1. The notion itself becomes quite comical, when one considers the fact that they just mentioned in the same breath, the presence of these same M1 clusters in Northwestern Africa, which happened to be their alternative hypothetical point of origin [Gonzalez et al. (2007)], as already noted. As they themselves acknowledge, that's where (northwestern Africa) said M1 clusters are widely distributed, and rather rare in the so-called "Middle East", save for this genetically "anamolous" [the authors' own words] and relatively isolated Dead Sea community, notable for its clear "past ties to sub-Saharan and eastern Africa", to put in Flores et al.'s (2005) words, a team that Gonzalez herself was a part of. "Anamolous", because to put it in the authors' own words, the considerably high post-OOA African ties of the Dead Sea sample dataset sets it appart from many other "Middle Eastern" groups, including its neighbours. So, how M1c clusters (which Gonzalez et al. (2007) dub "ancestral" based on their subjective age estimations) — that are very rare even in the "Middle East" (save for the 'anamolous' Dead Sea dataset) in contrast to their wide distribution in northwestern Africa — suddenly puts a question mark on the African origin of M1, is beyond comprehension.

Not only is there lack of apparent parallelism between R1* paragroup distribution and those aforemention markers of U6 and "Eurasian"-tagged mtDNA markers in Africa itself, as the authors (like Olivieri et al. & Gonzalez et al.) seem to be so desperately yearning for, but also the paragroup is essentially absent in all Afrasan speaking groups but those in the Northeast African corner. The marker is even rarer in so-called Southwest Asia than it is in Africa. This naturally contradicts Olivieri et al.'s acknowledgement in the following...

Indeed, M1 and U6 in Africa are mostly restricted to Afro-Asiatic–speaking areas.

Where did this "Afro-Asiatic" phylum originate? Well, look no further than to Gonzalez et al., whom as we've seen, are energetic about this idea of M1 and U6 "parallelism", not unlike Olivieri et al. (2006); they too, clearly in a way that simulteneously soothens or seeks to explain away a bit of disappoint in the course of the study, say:

The anomalous evolution of M1a2 lineages left the coalescence ages of the eastern Africa M1a expansion uncertain, but as suggested for the sister U6a1 radiation; these movements could be correlated in time with an African origin and expansion of Afroasiatic languages.

There you have it, folks, the answer to that simple question. And as if to defy the two groups of aforementioned research teams above, with regards to the proposed M1 and U6 "parallelism" in a demic expansion scenario, a newer study that came along in December 2008, points this out [a finding that appears to have been reproduced in several other studies]:

Our results highlighted a clear genetic differentiation between Berbers from the Maghreb and Egyptian Berbers. The first seems to be more related to European populations as shown by haplogroup H1 and V frequencies, whereas the latter share more affinities with East African and Nile Valley populations as indicated by the high frequency of M1 and the presence of L0a1, L3i, L4∗, and L4b2 lineages. Moreover, haplogroup U6 was not observed in Siwa. Probably, such a maternal diversity between North African Berbers would have been the result of a conjunction of several geographical, prehistoric, and historic factors which guided contacts (and thus exchanges) between local populations and migrating groups. First, in addition to the geographical distance, which certainly increases the genetic distance, the geographical location of Berber populations is very peculiar: the Berbers from the Maghreb are at the end of a long migration route, whereas Berbers from Siwa are rather in a crossroads between the Middle East, East Africa, sub-Saharan areas and the North African corridor. Therefore, meetings and exchanges between local and migrating populations were not identical in North West and North East Africa. - C. Coudray et al., The Complex and Diversified Mitochondrial Gene Pool of Berber Populations

We are told above, that M1 is substantial in the Siwa group, but no U6 was observed! Furthermore, it would make sense for the Siwa group to be a pristine representative of the aforementioned U6/M1 "parallelism" scenario, given that they are even closer to the so-called "Near East" than the northwestern African "Berbers", would it not? Perhaps it wouldn't be as funny, if Anna Olivieri herself was not a participant of this Coudray et al. study! Speaking of the so-called "Near East", the following claim is interesting, when one takes into account that this area was singled out as one of Gonzalez et al.'s proposed areas of M1 origin, because while looking at it from the alternative proposed origin, presumably the northwestern African one, we are told in a passing that...

That M1 is an autochthonous North African clade that had its earliest spread in northwestern areas marginally reaching the Near East and beyond. This would explain the shortage of basic M1 lineages in the Near East but would leave the Asiatic origin of the M1 ancestor undetermined.

...interesting.

*Another thing that hasn't been relayed through the present study, are details that follow:

The coding regions transitions are likely to change relatively slower than those of hypervariable segments, and hence, likely to remain intact within a clade. To assist in determining which clade to place a monophyletic unit, key coding region transitions have to be identified. In the case of M1, we were told:

We found 489C (Table 3) in all Indian and eastern-African haplogroup M mtDNAs analysed, but not in the non-M haplogroup controls, including 20 Africans representing all African main lineages (6 L1, 4 L2, 10 L3) and 11 Asians.


These findings, and the lack of positive evidence (given the RFLP status) that the 10400 C->T transition defining M has happened more than once, suggest that it has a single common origin, but do not resolve its geographic origin. Analysis of position 10873 (the MnlI RFLP) revealed that all the M molecules (eastern African, Asian and those sporadically found in our population surveys) were 10873C (Table 3). As for the non-M mtDNAs, the ancient L1 and the L2 African-specific lineages5, as well as most L3 African mtDNAs, also carry 10873C.

Conversely, all non-M mtDNAs of non-African origin analysed so far carry 10873T. These data indicate that the **transition 10400 C-->T, which defines haplogroup M**, arose on an African background characterized by the ancestral state 10873C, which is also present in four primate (common and pygmy chimps, gorilla and orangutan) mtDNA sequences. — Semino et al.

...which is significant, as other M lineages are devoid of M1 coding region motifs, not to mention the M1 HVS-I package. The above does demonstrate, how M lineages likely arose on an African 'background' by single-event substitutions in the designated African ancestral counterparts. The ancestral transition of 10873C is substituted by 10873T in non-African non-M haplogroups, while the 10400C transition was substituted in M lineages by 10400T; that ancestral state of 10873C remains at large in the M macrohaplogroup, unlike the so-called non-African & non-M haplogroup counterparts.

Furthermore,...

The 489C transition, as noted above and can be seen from the diagram, is peculiar to the M macrohaplogroup, again suggestive of unique event mutations characterizing the family:

The phylogenetic location of the mutations at nt 489 and 10,873 (arrow) was predicted by our analysis. The seemingly shared mutation at nt 16,129 (by G, Z and M1) is very likely an accidental parallelism. The ancestral states 10400C, 10810C and 10873C are fixed in L1 (as analysed so far) and are present in the ape sequences.


The 16129 sharing across the M1 haplogroups, seems to be one of those instances of random parallel mutation, recalling Chang Sun et al.'s observations of random parallel mutations of certain transitions across the M macrohaplogroup.

We also know that "southwest Asian" and "European" M1 lineages are derivatives of African counterparts, and the same is true for southwest Asian non-M1 affiliated M lineages from south Asia:

Compared to India, haplogroup M frequency in Iran is marginally low (5.3%) and there are no distinguished Iranian-specific sub-clades of haplogroup M. All Iranian haplogroup M lineages can be seen as derived from other regional variants of the haplogroup: eleven show affiliation to haplogroup M lineages found in India, twelve in East and Central Asia (D, G, and M8 ) and one in northeast Africa (M1)…

Indian-specific (R5 and Indian-specific M and U2 variants) and East Asian-specific (A, B and East Asian-specific M subgroups) mtDNAs, both, make up less than 4% of the Iranian mtDNA pool. We used Turkey (88.8 ± 4.0%) as the third parental population for evaluating the relative proportions of admixture from India (2.2 ± 1.7%) and China (9.1 ± 4.1%) into Iran. Therefore we can conclude that historic gene flow from India to Iran has been very limited. — Mait Metspalu et al.

With that said, Semino et al.'s older study still remains strong, the way I see it:

haplogroup M originated in eastern Africa approximately 60,000 years ago and was carried toward Asia. This agrees with the proposed date of an out-of-Africa expansion approximately 65,000 years ago10. After its arrival in Asia, the haplogroup M founder group went through a demographic and geographic expansion. The remaining M haplogroup in eastern Africa did not spread, but remained localized up to approximately 10,000-20,000 years ago, after which it started to expand. — Semino et al.

Elsewhere, I've also talked about some 'basal' M-like lineages in Africa; for instance, at least one of such was identified in the Senegalese sample.

Am. J. Hum. Genet., 66:1362-1383, 2000

mtDNA Variation in the South African Kung and Khwe and Their Genetic Relationships to Other African Populations


"The Asian mtDNA phylogeny is subdivided into two macrohaplogroups, one of which is M. M is delineated by a DdeI site at np 10394 and an AluI site of np 10397. The only African mtDNA found to have both of these sites is the Senegalese haplotype AF24. This haplotype branches off African subhaplogroup L3a (figs.2 and3), suggesting that haplogroup M mtDNAs might have been derived from this African mtDNA lineage..."

The relevant representation in this recap diagram:

Image source: Link

In the image above, the 10397 transition is shown in the L3-M linkage, while 10394, which should show up as positive (as exemplified in the above extract) in the M macrohaplogroup, shows up negative in the linkage between L3 and non-M affiliated lineages.

What does all this talk of specific transitions or nucleotide sequences tell us?

Well, to put the above compilation into perspective, and keep it simple, the point is this:

Semino et al.'s demonstration of certain characteristic basic coding transitions of the M super-haplogroup [not including the key coding region motifs unique to the M1 family], springing directly from African ancestral motifs don't require that M1 has to have a proto "non-African" M1, because all the necessary basic nucleotide sequences have been identified in the autochthonous African gene pool [findings which have been buttressed by later studies, of basic motifs in rare "M-characteristic" basic (African L3) clades], enough to explain the proposed African origin for the M lineage in general, including M1; whereas an Asian origin of M1 would necessitate an Asian "proto-M1" lineage that would explain the relatively young expansion ages of M1 and lack of descendancy from pre-existing Asian M lineages. This hasn't been achieved either by the present study or ones prior to it.

Getting to the gist:

Basal M mtDNA ~ between c. 60 - 80 ky ago

And then, M1 ~ between ~ c. 10 - 30 ky ago

The studies the present author posted, suggest that the basal motifs characteristic of the M macrohaplogroup arose in Africa, anywhere between 60 - 80 ky ago [since they would have likely been in the continent by the time of the 60 ky ago or so OOA migrations] . Sometime between 60 ky and 50 ky ago [some sources place it between 75 - 60 ky ago], these L3 offshoots were carried outside of Africa, amongst early successful a.m.h migrations, which resulted in the populations now living in the Indian-subcontinent, Melanesia and Australia who have these lineages. Not all the basal African L3M lineages, as Semino et al. convincingly put it, left the continent, as indicated by the basal L3a-M motif detected in Senegal, M1 diversity in Africa, particularly East Africa, possibly the dectection of M1 and other M lineages in tandem within a Tanzanian sample (Gonder et al. 2006), and the apparent lack of descendancy of M1 from older-coalescent Asian macrohaplogroup. Rather, it appears that the basal L3M lineages which remained in Africa, underwent a relatively limited demographic intra-African expansion until relatively recently, i.e. between 10 - 30 ky ago, compared to the Asian L3M derivatives, which underwent major expansions, naturally within the quantitatively smaller founder immigrant groups, i.e. the founder effect.

M1 is likely the culmination of relatively more recent demographic expansions of basal L3M lineages in the African continent, with M1 derivative being a successful candidate, in what could have possibly involved other derivatives which might not have expanded to the same level intra-continentally, and subsequently, extra-continentally as well.

M1 has strongly been correlated with the upper Paleolithic expansion of proto-Afrasan groups across the Sahara to coastal north Africa, and further eastward via the Sinai peninsula.